CDS 10 - 270
  /gene="1"
  /product="gp1"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_1"
    /note=
    /note=SSC: 10-270 CP: yes SCS: neither ST: NI BLAST-Start: [hypothetical protein SEA_ASRIEL_1 [Mycobacterium phage Asriel] ],,NCBI, q1:s1 100.0% 2.16785E-58 GAP: 0 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.888, -4.9163222688718005, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ASRIEL_1 [Mycobacterium phage Asriel] ],,AVI03251,100.0,2.16785E-58 SIF-HHPRED:  SIF-Syn: 
    /note=Has a 1:1 BlastP match. There was another one that had a better RBS scores however when I looked at the blastp output, the first one wasn`t a 1:1.

CDS 267 - 560
  /gene="2"
  /product="gp2"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_2"
    /note=Original Glimmer call @bp 267 has strength 9.63; Genemark calls start at 267
    /note=SSC: 267-560 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_SOTRICE96_2 [Mycobacterium phage Sotrice96] ],,NCBI, q1:s1 100.0% 2.84497E-64 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.269, -2.0111200136961407, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_SOTRICE96_2 [Mycobacterium phage Sotrice96] ],,AVI04457,100.0,2.84497E-64 SIF-HHPRED:  SIF-Syn: 
    /note=The start at position 267 is hte longest ORF, covers all the coding potential, has a 1:1 match, has a 4 nucleotide overlap and has the best ribosome binding site score.

CDS 557 - 742
  /gene="3"
  /product="gp3"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_3"
    /note=Original Glimmer call @bp 557 has strength 9.4; Genemark calls start at 557
    /note=SSC: 557-742 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein Porky_3 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 2.67755E-35 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.08, -4.784283191845562, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein Porky_3 [Mycobacterium phage Porky] ],,YP_002014324,100.0,2.67755E-35 SIF-HHPRED:  SIF-Syn: 
    /note=The one I chose had an overlap of 4 nucleotides and 1:1 protein matches. It had a better RBS than the second-longest reading frame and the longerst reading frame had a huge overlap of -214 .

CDS 739 - 1032
  /gene="4"
  /product="gp4"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_4"
    /note=Original Glimmer call @bp 739 has strength 6.77; Genemark calls start at 739
    /note=SSC: 739-1032 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_DUMBO_3 [Mycobacterium phage Dumbo] ],,NCBI, q1:s1 100.0% 1.77783E-60 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.636, -3.342129169857323, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_DUMBO_3 [Mycobacterium phage Dumbo] ],,YP_008051628,100.0,1.77783E-60 SIF-HHPRED:  SIF-Syn: 
    /note=It was the longest reading frame. It also has the best RBS scores. It also had 1:1 matches

CDS 1010 - 1138
  /gene="5"
  /product="gp5"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_5"
    /note=Original Glimmer call @bp 1010 has strength 11.05; Genemark calls start at 1022
    /note=SSC: 1010-1138 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein GOKU_5 [Mycobacterium phage Goku] ],,NCBI, q1:s1 100.0% 2.93843E-22 GAP: -23 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.872, -3.2925703904164987, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein GOKU_5 [Mycobacterium phage Goku] ],,YP_008430521,100.0,2.93843E-22 SIF-HHPRED:  SIF-Syn: 
    /note=Compared the rest of the starts it had the best RBS scores, it was the longest reading frame, and it had 1:1 matches. Was predicted by Glimmer. Covers all the coding potential. 23 bp overlap is seen in other phages as well.

CDS 1131 - 1592
  /gene="6"
  /product="gp6"
  /function="terminase, small subunit"
  /locus tag="Balomoji_6"
    /note=Original Glimmer call @bp 1131 has strength 7.33; Genemark calls start at 1131
    /note=SSC: 1131-1592 CP: yes SCS: both ST: NI BLAST-Start: [terminase small subunit [Mycobacterium phage Command613]],,NCBI, q1:s1 100.0% 1.8262E-108 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.462, -3.6907860541164537, yes F: terminase, small subunit SIF-BLAST: ,,[terminase small subunit [Mycobacterium phage Command613]],,QGJ93991,100.0,1.8262E-108 SIF-HHPRED:  SIF-Syn: 
    /note=It was the longest reading frame. 1:1 matches and had the best overall RBS scores. Covers all the coding potential.

CDS complement (1678 - 1989)
  /gene="7"
  /product="gp7"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_7"
    /note=Original Glimmer call @bp 1989 has strength 5.57; Genemark calls start at 2001
    /note=SSC: 1989-1678 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_ICEE_7 [Mycobacterium phage Icee] ],,NCBI, q1:s1 100.0% 1.81137E-68 GAP: 47 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.54, -4.565998384613451, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ICEE_7 [Mycobacterium phage Icee] ],,AXC37723,100.0,1.81137E-68 SIF-HHPRED:  SIF-Syn: 
    /note=Was the longest open reading frame and had multiple 1:1 matches, was predicted by Genemark, and the one predicted by Glimmer did not have 1:1 protein matches so this one was chosen.

CDS 2037 - 4700
  /gene="8"
  /product="gp8"
  /function="terminase, large subunit"
  /locus tag="Balomoji_8"
    /note=Original Glimmer call @bp 2037 has strength 7.42; Genemark calls start at 2037
    /note=SSC: 2037-4700 CP: yes SCS: both ST: NI BLAST-Start: [exonuclease [Mycobacterium phage Kostya] ],,NCBI, q1:s1 100.0% 0.0 GAP: 47 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.363, -3.9166971242758706, no F: terminase, large subunit SIF-BLAST: ,,[exonuclease [Mycobacterium phage Kostya] ],,YP_002014477,100.0,0.0 SIF-HHPRED: Terminase large subunit; genome packaging, bacteriophage, ATPase, nuclease, VIRAL PROTEIN; HET: BR; 2.2A {Enterobacteria phage HK97},,,6Z6D_A,51.6347,100.0 SIF-Syn: 
    /note=It was the longest reading frame, It had 1:1 matches, and had the best final score of -3.917. Predicted by both tools.

CDS 4712 - 4933
  /gene="9"
  /product="gp9"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_9"
    /note=Original Glimmer call @bp 4745 has strength 7.16; Genemark calls start at 4712
    /note=SSC: 4712-4933 CP: yes SCS: both-gm ST: NI BLAST-Start: [gp9 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 1.08355E-45 GAP: 11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.578, -3.46411222063, yes F: Hypothetical Protein SIF-BLAST: ,,[gp9 [Mycobacterium phage Cjw1] ],,NP_817459,100.0,1.08355E-45 SIF-HHPRED:  SIF-Syn: 
    /note=Chose Genemark prediction for longest ORF, many 1:1 blastp matches, smaller gap and best RBS scores.

CDS 4920 - 6476
  /gene="10"
  /product="gp10"
  /function="portal protein"
  /locus tag="Balomoji_10"
    /note=Original Glimmer call @bp 4920 has strength 9.39; Genemark calls start at 4920
    /note=SSC: 4920-6476 CP: yes SCS: both ST: NI BLAST-Start: [portal protein [Mycobacterium phage DrDrey] ],,NCBI, q1:s1 100.0% 0.0 GAP: -14 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.549, -3.525474288708562, yes F: portal protein SIF-BLAST: ,,[portal protein [Mycobacterium phage DrDrey] ],,YP_008409404,100.0,0.0 SIF-HHPRED: Portal protein; Prohead I, icosahedral symmetry, HK97, phage, capsid, VIRUS; 3.6A {Escherichia phage HK97},,,8FQL_L,70.2703,100.0 SIF-Syn: 
    /note=Even though it does not have the longest reading frame, it had 1:1 blastp matches and had the best final score. Covers all the coding potential.

CDS 6479 - 7573
  /gene="11"
  /product="gp11"
  /function="capsid maturation protease"
  /locus tag="Balomoji_11"
    /note=Original Glimmer call @bp 6479 has strength 9.4; Genemark calls start at 6479
    /note=SSC: 6479-7573 CP: yes SCS: both ST: NI BLAST-Start: [head maturation protease [Mycobacterium phage Kostya] ],,NCBI, q1:s1 100.0% 0.0 GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.546, -3.5925599723783583, no F: capsid maturation protease SIF-BLAST: ,,[head maturation protease [Mycobacterium phage Kostya] ],,YP_002014480,100.0,0.0 SIF-HHPRED: Peptidase_S78 ; Caudovirus prohead serine protease,,,PF04586.21,35.4396,99.5 SIF-Syn: 
    /note=It had the best final score and it was the longest reading frame. After using blastp, I saw it had many 1:1 matches. Covers all the coding potential.

CDS 7661 - 9154
  /gene="12"
  /product="gp12"
  /function="major capsid protein"
  /locus tag="Balomoji_12"
    /note=Original Glimmer call @bp 7661 has strength 10.28; Genemark calls start at 7661
    /note=SSC: 7661-9154 CP: yes SCS: both ST: NI BLAST-Start: [major head protein [Mycobacterium phage Phaux] ],,NCBI, q1:s1 100.0% 0.0 GAP: 87 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.173, -2.1958114445137396, yes F: major capsid protein SIF-BLAST: ,,[major head protein [Mycobacterium phage Phaux] ],,YP_008052185,100.0,0.0 SIF-HHPRED: Scaffolding domain delta; Prohead I, icosahedral symmetry, HK97, phage, capsid, VIRUS; 3.5A {Escherichia phage HK97},,,8FQK_G,98.5916,100.0 SIF-Syn: 
    /note=Predicted by both tools, the longest reading frame and had the best overall final score. Covers all the coding potential.

CDS 9221 - 9412
  /gene="13"
  /product="gp13"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_13"
    /note=Original Glimmer call @bp 9221 has strength 8.61; Genemark calls start at 9221
    /note=SSC: 9221-9412 CP: yes SCS: both ST: NI BLAST-Start: [head-tail connector protein [Mycobacterium phage Kostya] ],,NCBI, q1:s1 100.0% 2.66479E-35 GAP: 66 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.752, -3.5466635877785, yes F: Hypothetical Protein SIF-BLAST: ,,[head-tail connector protein [Mycobacterium phage Kostya] ],,YP_002014482,100.0,2.66479E-35 SIF-HHPRED:  SIF-Syn: 
    /note=Predicted by both tools, is the longest reading frame and had the best overall final score. Covers all the coding potential.

CDS 9412 - 9978
  /gene="14"
  /product="gp14"
  /function="head-to-tail adaptor"
  /locus tag="Balomoji_14"
    /note=Original Glimmer call @bp 9412 has strength 11.03; Genemark calls start at 9412
    /note=SSC: 9412-9978 CP: no SCS: both ST: NI BLAST-Start: [head-tail adaptor [Mycobacterium phage NelitzaMV] ],,NCBI, q1:s1 100.0% 2.42289E-135 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.452, -3.790975366313636, yes F: head-to-tail adaptor SIF-BLAST: ,,[head-tail adaptor [Mycobacterium phage NelitzaMV] ],,YP_009197683,100.0,2.42289E-135 SIF-HHPRED: Head completion protein; Neck, Portal, T5, VIRUS, VIRAL PROTEIN; 3.2A {Escherichia phage DT57C},,,8HQO_S,97.8723,99.9 SIF-Syn: 
    /note=The start position that was chosen was 9412, as it was predicted by both tools, it has the longest ORF, has 1:1 match as well as the best RBS. This start position also has a 1 nucleotide overlap.

CDS 9991 - 10326
  /gene="15"
  /product="gp15"
  /function="head-to-tail stopper"
  /locus tag="Balomoji_15"
    /note=Original Glimmer call @bp 9991 has strength 9.09; Genemark calls start at 9991
    /note=SSC: 9991-10326 CP: no SCS: both ST: NI BLAST-Start: [head closure [Mycobacterium phage Kostya] ],,NCBI, q1:s1 100.0% 1.30001E-75 GAP: 12 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.131, -4.4057176022952405, no F: head-to-tail stopper SIF-BLAST: ,,[head closure [Mycobacterium phage Kostya] ],,YP_002014484,100.0,1.30001E-75 SIF-HHPRED:  SIF-Syn: 
    /note=The start position 9991 was chosen as it was predicted by both tools, has the longest ORF that covers all of the coding potential , best RBS, a 12  nucleotide gap and a 1:1 match.

CDS 10323 - 10703
  /gene="16"
  /product="gp16"
  /function="head-to-tail connector"
  /locus tag="Balomoji_16"
    /note=Original Glimmer call @bp 10323 has strength 5.05; Genemark calls start at 10323
    /note=SSC: 10323-10703 CP: no SCS: both ST: NI BLAST-Start: [minor tail protein [Mycobacterium phage Kostya] ],,NCBI, q1:s1 100.0% 7.49312E-87 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.675, -3.1816499351312086, yes F: head-to-tail connector SIF-BLAST: ,,[minor tail protein [Mycobacterium phage Kostya] ],,YP_002014485,100.0,7.49312E-87 SIF-HHPRED: Minor_capsid_2 ; Minor capsid protein,,,PF11114.12,92.0635,99.1 SIF-Syn: 
    /note=The 10203 start position was chosen as it was predicted by both tools, has the longest ORF which covers all of the coding potential as well as having the best RBS Scores.

CDS 10681 - 11085
  /gene="17"
  /product="gp17"
  /function="tail terminator"
  /locus tag="Balomoji_17"
    /note=Original Glimmer call @bp 10681 has strength 5.76; Genemark calls start at 10681
    /note=SSC: 10681-11085 CP: no SCS: both ST: NI BLAST-Start: [head-tail adaptor [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 5.02897E-95 GAP: -23 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.609, -3.8462096892182602, yes F: tail terminator SIF-BLAST: ,,[head-tail adaptor [Mycobacterium phage Cjw1] ],,NP_817467,100.0,5.02897E-95 SIF-HHPRED: TAIL-TO-HEAD JOINING PROTEIN GP17; VIRAL PROTEIN, VIRAL INFECTION, TAILED BACTERIOPHAGE, SIPHOVIRIDAE, SPP1, VIRAL ASSEMBLY, HEAD-TO-TAIL INTERFACE, DNA GATEKEEPER, ALLOSTERIC MECHANISM; 7.2A {BACILLUS PHAGE SPP1},,,5A21_G,94.7761,99.5 SIF-Syn: 
    /note=The chosen start position was 10681, as it was predicted by both tools, it covers all of the coding potential and it contains the second highest RBS scores. It does have a nucleotide overlap of 56 as well.

CDS 11112 - 12083
  /gene="18"
  /product="gp18"
  /function="major tail protein"
  /locus tag="Balomoji_18"
    /note=Original Glimmer call @bp 11112 has strength 14.82; Genemark calls start at 11112
    /note=SSC: 11112-12083 CP: no SCS: both ST: NI BLAST-Start: [major tail protein [Mycobacterium phage Kostya] ],,NCBI, q1:s1 100.0% 0.0 GAP: 26 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.79, -3.080676611399484, yes F: major tail protein SIF-BLAST: ,,[major tail protein [Mycobacterium phage Kostya] ],,YP_002014487,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=The start position that was chosen was 11112, as it was predicted by both tools as well as having the LORF which covered all of the coding potential, has the best RBS Scores and a 26 nucleotide gap.

CDS 12203 - 12664
  /gene="19"
  /product="gp19"
  /function="tail assembly chaperone"
  /locus tag="Balomoji_19"
    /note=Original Glimmer call @bp 12203 has strength 12.58; Genemark calls start at 12203
    /note=SSC: 12203-12664 CP: no SCS: both ST: NI BLAST-Start: [tail assembly chaperone [Mycobacterium phage Dusk] ],,NCBI, q1:s25 100.0% 9.04786E-109 GAP: 119 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.615, -3.6571726089641587, yes F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Mycobacterium phage Dusk] ],,YP_009224288,86.4407,9.04786E-109 SIF-HHPRED:  SIF-Syn: 
    /note=The start position that was chosen was at 12203 as it was predicted by both tools, contains the LORF that covers all of the coding potential, has a 47 nucleotide gap, and 9 1:1 matches.

CDS 12796 - 13074
  /gene="20"
  /product="gp20"
  /function="tail assembly chaperone"
  /locus tag="Balomoji_20"
    /note=Original Glimmer call @bp 12796 has strength 4.91; Genemark calls start at 12796
    /note=SSC: 12796-13074 CP: no SCS: both ST: NI BLAST-Start: [tail assembly chaperone [Mycobacterium phage Kostya] ],,NCBI, q1:s1 100.0% 5.81053E-60 GAP: 131 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.458, -6.8421897688016795, no F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Mycobacterium phage Kostya] ],,YP_002014489,100.0,5.81053E-60 SIF-HHPRED:  SIF-Syn: 
    /note=The start position that was chosen was at 12796 as it was predicted by both tools, had the longest ORF and covered all of the coding potential. Contains 2 1:1 matches as well as a 16 nucleotide gap.

CDS 13067 - 17800
  /gene="21"
  /product="gp21"
  /function="tape measure protein"
  /locus tag="Balomoji_21"
    /note=Original Glimmer call @bp 13067 has strength 8.21; Genemark calls start at 13067
    /note=SSC: 13067-17800 CP: no SCS: both ST: NI BLAST-Start: [tape measure protein [Mycobacterium phage Command613]],,NCBI, q1:s1 100.0% 0.0 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.779, -2.9625409806968013, yes F: tape measure protein SIF-BLAST: ,,[tape measure protein [Mycobacterium phage Command613]],,QGJ94008,99.8732,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Start at 13067 was chosen as it was predicted by both tools, covers all of the coding potential, has the LORF, contains the best RBS scores, an 8 nucleotide overlap and over 20+ 1:1 matches.

CDS 17830 - 19491
  /gene="22"
  /product="gp22"
  /function="minor tail protein"
  /locus tag="Balomoji_22"
    /note=Original Glimmer call @bp 17830 has strength 8.08; Genemark calls start at 17830
    /note=SSC: 17830-19491 CP: no SCS: both ST: NI BLAST-Start: [minor tail protein [Mycobacterium phage DrDrey] ],,NCBI, q1:s1 100.0% 0.0 GAP: 29 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.164, -5.358093050197135, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Mycobacterium phage DrDrey] ],,YP_008409417,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=The start at 17830 was chosen as it was predicted by both tools as well has having the longest ORF which covers all of the coding potential. It also has a 29 nucleotide gap.

CDS 19479 - 21158
  /gene="23"
  /product="gp23"
  /function="minor tail protein"
  /locus tag="Balomoji_23"
    /note=Original Glimmer call @bp 19563 has strength 6.41; Genemark calls start at 19479
    /note=SSC: 19479-21158 CP: no SCS: both-gm ST: NI BLAST-Start: [minor tail protein [Mycobacterium phage Kostya] ],,NCBI, q1:s1 100.0% 0.0 GAP: -13 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.077, -6.622157809994246, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Mycobacterium phage Kostya] ],,YP_002014492,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=The start position of 19479 was chosen, it was only predicted by Genemark but it does have the LORF as well as a 13 nucleotide overlap.

CDS 21167 - 22000
  /gene="24"
  /product="gp24"
  /function="minor tail protein"
  /locus tag="Balomoji_24"
    /note=Original Glimmer call @bp 21167 has strength 10.07; Genemark calls start at 21179
    /note=SSC: 21167-22000 CP: no SCS: both-gl ST: NI BLAST-Start: [minor tail protein [Mycobacterium phage Kostya] ],,NCBI, q1:s1 100.0% 0.0 GAP: 8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.173, -2.66069824281639, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Mycobacterium phage Kostya] ],,YP_002014493,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=The start position of 21167 was chosen with only having 1 tool predicting it, being Genemark. It does contain the LORF which covers all of the coding potential, and has a 313 nucleotide overlap.

CDS 22017 - 24413
  /gene="25"
  /product="gp25"
  /function="minor tail protein"
  /locus tag="Balomoji_25"
    /note=Original Glimmer call @bp 22017 has strength 7.96; Genemark calls start at 22017
    /note=SSC: 22017-24413 CP: no SCS: both ST: NI BLAST-Start: [minor tail protein [Mycobacterium phage Bask21] ],,NCBI, q1:s1 100.0% 0.0 GAP: 16 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.773, -3.055523716677687, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Mycobacterium phage Bask21] ],,YP_009591186,99.6241,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=The start position of 22017 was chosen as it was predicted by both tools, with all of the coding potential being covered as it also has the LORF. It contains a 16 nucleotide gap.

CDS 24410 - 27250
  /gene="26"
  /product="gp26"
  /function="minor tail protein"
  /locus tag="Balomoji_26"
    /note=Original Glimmer call @bp 24410 has strength 3.28; Genemark calls start at 24410
    /note=SSC: 24410-27250 CP: no SCS: both ST: NI BLAST-Start: [minor tail protein [Mycobacterium phage Dusk] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.026, -3.095100142625534, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Mycobacterium phage Dusk] ],,YP_009224294,100.0,0.0 SIF-HHPRED: Beta-lactamase; colibactin peptidase, S12 peptidase, HYDROLASE, HYDROLASE-INHIBITOR complex; HET: 2PE, Z9A, Z9G, 97N, AV0; 2.3A {Escherichia coli CFT073},,,7MDF_A,33.5095,100.0 SIF-Syn: 
    /note=The start position of 24410 was chosen as it was predicted by both tools , has the LORF which covers all of the coding potential, contains a 4 nucleotide overlap, as well as having the best RBS scores.

CDS 27251 - 28195
  /gene="27"
  /product="gp27"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_27"
    /note=Original Glimmer call @bp 27251 has strength 4.52; Genemark calls start at 27251
    /note=SSC: 27251-28195 CP: yes SCS: both ST: NI BLAST-Start: [minor tail protein [Mycobacterium phage Dusk] ],,NCBI, q1:s1 100.0% 0.0 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.427, -3.8426483658976065, yes F: Hypothetical Protein SIF-BLAST: ,,[minor tail protein [Mycobacterium phage Dusk] ],,YP_009224295,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=It has the best and longest open frame, it has 0 overlap, the start was predicted by both technologies, it has more than one 1:1 BLASTP match, and it has the best RBS score.

CDS 28275 - 28703
  /gene="28"
  /product="gp28"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_28"
    /note=Original Glimmer call @bp 28275 has strength 15.22; Genemark calls start at 28275
    /note=SSC: 28275-28703 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_RAKIM_30 [Mycobacterium phage Rakim] ],,NCBI, q1:s1 100.0% 9.60017E-89 GAP: 79 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.162, -2.156361006712914, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_RAKIM_30 [Mycobacterium phage Rakim] ],,AEJ92568,100.0,9.60017E-89 SIF-HHPRED:  SIF-Syn: 
    /note=It has the best and longest open reading frame, both technologies predicted the same start, it contains all of the coding potential, it has more than one 1:1 BLASTP match, it has the best RBS scores, and it has the lowest gap.

CDS complement (28700 - 28876)
  /gene="29"
  /product="gp29"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Balomoji_29"
    /note=Original Glimmer call @bp 28876 has strength 1.45; Genemark calls start at 28876
    /note=SSC: 28876-28700 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_RAKIM_31 [Mycobacterium phage Rakim] ],,NCBI, q1:s1 100.0% 1.43975E-32 GAP: 132 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 0.913, -7.028301864955391, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[hypothetical protein SEA_RAKIM_31 [Mycobacterium phage Rakim] ],,AEJ92675,100.0,1.43975E-32 SIF-HHPRED: TrfB transcriptional repressor protein; Helix-turn-helix, complex, transcription; 2.5A {Escherichia coli},,,5CLV_N,77.5862,98.2 SIF-Syn: 
    /note=This gene has the worst RBS scores but is predicted by both technologies, is the longest gene with the longest open reading frame, contains all the coding potential, has a 1:1 BLAST P match, and has the smallest gap.

CDS 29009 - 29293
  /gene="30"
  /product="gp30"
  /function="membrane protein"
  /locus tag="Balomoji_30"
    /note=Original Glimmer call @bp 29009 has strength 8.75; Genemark calls start at 29009
    /note=SSC: 29009-29293 CP: yes SCS: both ST: NI BLAST-Start: [gp31 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 4.49554E-62 GAP: 132 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.183, -2.253377680616507, yes F: membrane protein SIF-BLAST: ,,[gp31 [Mycobacterium phage Cjw1] ],,NP_817481,100.0,4.49554E-62 SIF-HHPRED:  SIF-Syn: 
    /note=This gene has the best RBS score, covers all of the coding potentials, is predicted by both technologies, has the longest reading frame, has a 1:1 Blast P match, and has the smallest gap.

CDS 29367 - 30869
  /gene="31"
  /product="gp31"
  /function="lysin A"
  /locus tag="Balomoji_31"
    /note=Original Glimmer call @bp 29367 has strength 7.15; Genemark calls start at 29367
    /note=SSC: 29367-30869 CP: yes SCS: both ST: NI BLAST-Start: [endolysin [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 0.0 GAP: 73 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.592, -5.538930744277278, no F: lysin A SIF-BLAST: ,,[endolysin [Mycobacterium phage Cjw1] ],,NP_817482,100.0,0.0 SIF-HHPRED: Cortical-lytic enzyme; spore, cortex, peptidoglycan-lysin, hydrolase; HET: MES; 1.8A {Clostridium perfringens},,,5JIP_A,39.8,99.5 SIF-Syn: 
    /note=This gene does not have the best RBS score, covers all of the coding potentials because of the TTG that is not represented,  has the best gap, the technologies both predict it, and has a 1:1 Blast P match.

CDS 30873 - 31256
  /gene="32"
  /product="gp32"
  /function="holin"
  /locus tag="Balomoji_32"
    /note=Original Glimmer call @bp 30873 has strength 12.46; Genemark calls start at 30873
    /note=SSC: 30873-31256 CP: yes SCS: both ST: NI BLAST-Start: [holin [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 4.2794E-82 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.923, -4.763756451838196, no F: holin SIF-BLAST: ,,[holin [Mycobacterium phage Cjw1] ],,NP_817483,100.0,4.2794E-82 SIF-HHPRED: Phage_holin_7_1 ; Mycobacterial 2 TMS Phage Holin (M2 Hol) Family,,,PF16081.9,93.7008,100.0 SIF-Syn: 
    /note=This gene does not have the best RBS score but it does have the best LORF, has a 1:1 Blast P match, the smallest gap, is predicted by both technologies, and covers all of the coding potential.

CDS 31249 - 31587
  /gene="33"
  /product="gp33"
  /function="rtcB-like RNA ligase"
  /locus tag="Balomoji_33"
    /note=Original Glimmer call @bp 31249 has strength 11.4; Genemark calls start at 31249
    /note=SSC: 31249-31587 CP: yes SCS: both ST: NI BLAST-Start: [gp34 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 2.14819E-75 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.453, -6.403886157111313, no F: rtcB-like RNA ligase SIF-BLAST: ,,[gp34 [Mycobacterium phage Cjw1] ],,NP_817484,100.0,2.14819E-75 SIF-HHPRED:  SIF-Syn: 
    /note=includes all coding potential, the longest reading frame, has multiple 1:1 matches, a 51 nucleotide gap, and the best ribosome siting score

CDS 31584 - 32441
  /gene="34"
  /product="gp34"
  /function="lysin B"
  /locus tag="Balomoji_34"
    /note=Original Glimmer call @bp 31584 has strength 8.19; Genemark calls start at 31584
    /note=SSC: 31584-32441 CP: yes SCS: both ST: NI BLAST-Start: [lysin B [Mycobacterium phage Kostya] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.872, -3.8154491356968365, yes F: lysin B SIF-BLAST: ,,[lysin B [Mycobacterium phage Kostya] ],,YP_002014504,100.0,0.0 SIF-HHPRED: Gene 12 protein; alpha/beta sandwich, CELL ADHESION; 2.0A {Mycobacterium phage D29},,,3HC7_A,90.8772,100.0 SIF-Syn: 
    /note=This gene has the best RBS scores, has the longest LORF, covers all the coding potential, has a 1:1 Blast P match, is predicted by both technologies, is the longest gene, and has the preferred -4 nucleotide gap.

CDS 32438 - 32854
  /gene="35"
  /product="gp35"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_35"
    /note=Original Glimmer call @bp 32438 has strength 10.81; Genemark calls start at 32438
    /note=SSC: 32438-32854 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein Porky_36 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 5.10738E-95 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 0.983, -7.2690057605968725, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein Porky_36 [Mycobacterium phage Porky] ],,YP_002014357,100.0,5.10738E-95 SIF-HHPRED:  SIF-Syn: 
    /note=This gene does not have the best RBS scores, but the gap is -4 which is optimal, however, it is also not the best LORF, but it still covers all of the coding potential has a 1:1 Blast P match, and is predicted by both technologies.

CDS 32861 - 33106
  /gene="36"
  /product="gp36"
  /function="NrdH-like glutaredoxin"
  /locus tag="Balomoji_36"
    /note=Original Glimmer call @bp 32861 has strength 10.14; Genemark calls start at 32861
    /note=SSC: 32861-33106 CP: yes SCS: both ST: NI BLAST-Start: [thioredoxin domain [Mycobacterium phage Contagion] ],,NCBI, q1:s1 100.0% 6.52989E-51 GAP: 6 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.035, -5.356325827079472, no F: NrdH-like glutaredoxin SIF-BLAST: ,,[thioredoxin domain [Mycobacterium phage Contagion] ],,YP_008410054,100.0,6.52989E-51 SIF-HHPRED: Adaptive-response sensory-kinase sasA; Alpha/Beta protein, Thioredoxin fold, TRANSFERASE; NMR {Synechococcus elongatus} SCOP: l.1.1.1, c.47.1.15,,,1T4Y_A,96.2963,99.3 SIF-Syn: 
    /note=This gene altogether has the best RBS score, is predicted by both technologies, has the best LORF, has a 1:1 match in Blast P, covers all the coding potential, and has the best gap.

CDS complement (33268 - 33789)
  /gene="37"
  /product="gp37"
  /function="HNH endonuclease"
  /locus tag="Balomoji_37"
    /note=Original Glimmer call @bp 33789 has strength 4.11; Genemark calls start at 33855
    /note=SSC: 33789-33268 CP: no SCS: both-gl ST: NI BLAST-Start: [HNH endonuclease [Mycobacterium phage Toto] ],,NCBI, q1:s1 100.0% 1.86903E-125 GAP: 188 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.773, -3.0377949497172554, yes F: HNH endonuclease SIF-BLAST: ,,[HNH endonuclease [Mycobacterium phage Toto] ],,YP_009208446,100.0,1.86903E-125 SIF-HHPRED: HNH homing endonuclease; HNH catalytic motif, Helix-turn-helix DNA binding domain, protein-DNA complex, DNA binding protein-DNA COMPLEX; HET: EDO; 2.92A {Bacillus phage SPO1} SCOP: d.285.1.1, d.4.1.3,,,1U3E_M,60.6936,99.8 SIF-Syn: 
    /note=While both technologies do not predict this start position, the gap isn`t the best, and the LORF is not the best, the coding potential is completely covered by the start position, there is a 1:1 Blasp P match, the RBS scores are the best and this start position does not have an abundance of sequence that doesn`t have a high coding potential.

CDS complement (33978 - 34364)
  /gene="38"
  /product="gp38"
  /function="Lsr2-like DNA bridging protein"
  /locus tag="Balomoji_38"
    /note=Original Glimmer call @bp 34364 has strength 10.98; Genemark calls start at 34364
    /note=SSC: 34364-33978 CP: yes SCS: both ST: NI BLAST-Start: [nucloid associated Lsr2-like [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 6.31263E-88 GAP: 47 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.763, -3.0766426734767767, yes F: Lsr2-like DNA bridging protein SIF-BLAST: ,,[nucloid associated Lsr2-like [Mycobacterium phage Cjw1] ],,NP_817489,100.0,6.31263E-88 SIF-HHPRED: Protein lsr2; anti-parallel beta sheet, dimer, DNA BINDING PROTEIN; 1.728A {Mycobacterium tuberculosis},,,4E1P_A,43.75,99.7 SIF-Syn: 
    /note=Both technologies predict this gene, the gap is the best, it has a 1:1 blast p match, it covers all of its coding potential, the RBS scores are the best and the LORF is the best.

CDS complement (34412 - 34609)
  /gene="39"
  /product="gp39"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_39"
    /note=Original Glimmer call @bp 34603 has strength 6.51; Genemark calls start at 34603
    /note=SSC: 34609-34412 CP: yes SCS: both-cs ST: NI BLAST-Start: [hypothetical protein SEA_NELITZAMV_39 [Mycobacterium phage NelitzaMV] ],,NCBI, q1:s1 100.0% 5.10906E-41 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.625, -6.4397615658552345, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_NELITZAMV_39 [Mycobacterium phage NelitzaMV] ],,YP_009197707,100.0,5.10906E-41 SIF-HHPRED:  SIF-Syn: 
    /note=Both technologies did not predict this gene start but the predicted start was only 6  nucleotides away, this start also does not have the best RBS score but the gap is the preferred -4 gap, the LORF is the best, the gene is the longest, the coding potential is covered (in my eyes), and there is a 1:1 Blast P match.

CDS complement (34606 - 35070)
  /gene="40"
  /product="gp40"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_40"
    /note=Original Glimmer call @bp 35046 has strength 5.49; Genemark calls start at 35070
    /note=SSC: 35070-34606 CP: yes SCS: both-gm ST: NI BLAST-Start: [hypothetical protein SEA_GLEXAN_39 [Mycobacterium phage Glexan] ],,NCBI, q1:s1 100.0% 2.27321E-108 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.872, -3.8154491356968365, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_GLEXAN_39 [Mycobacterium phage Glexan] ],,AXH49858,100.0,2.27321E-108 SIF-HHPRED:  SIF-Syn: 
    /note=The start position of 35070 is the longest ORF, covers all the coding potential, has multiple 1:1 match, has a 4 nucleotide overlap, and has the best  ribosome binding site score.

CDS complement (35067 - 35435)
  /gene="41"
  /product="gp41"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_41"
    /note=Original Glimmer call @bp 35435 has strength 4.67; Genemark calls start at 35435
    /note=SSC: 35435-35067 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein N860_gp071 [Mycobacterium phage Redno2] ],,NCBI, q1:s1 100.0% 6.05103E-80 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.605, -3.389881189012514, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein N860_gp071 [Mycobacterium phage Redno2] ],,YP_008410229,100.0,6.05103E-80 SIF-HHPRED:  SIF-Syn: 
    /note=The start position of 35435 is the longest ORF, covers all the coding potential, has multiple 1:1, has a 8 nucleotide overlap, has the best ribosome binding site score.

CDS complement (35428 - 35703)
  /gene="42"
  /product="gp42"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_42"
    /note=Original Glimmer call @bp 35703 has strength 4.71; Genemark calls start at 35703
    /note=SSC: 35703-35428 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_GLEXAN_41 [Mycobacterium phage Glexan] ],,NCBI, q1:s1 100.0% 3.38135E-59 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.54, -3.5268154277366257, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_GLEXAN_41 [Mycobacterium phage Glexan] ],,AXH49860,100.0,3.38135E-59 SIF-HHPRED:  SIF-Syn: 
    /note=The start at position 35703 is the longest ORF, covers all the coding potential, has a 1:1 match, has a 4 nucleotide overlap and has the best ribosome binding site score.

CDS complement (35700 - 35882)
  /gene="43"
  /product="gp43"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_43"
    /note=Original Glimmer call @bp 35882 has strength 2.35; Genemark calls start at 35882
    /note=SSC: 35882-35700 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_GLEXAN_42 [Mycobacterium phage Glexan] ],,NCBI, q1:s1 100.0% 5.0256E-36 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.773, -3.0377949497172554, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_GLEXAN_42 [Mycobacterium phage Glexan] ],,AXH49958,100.0,5.0256E-36 SIF-HHPRED:  SIF-Syn: 
    /note=The start, 35882and stop, 35700  codons include all of the potential coding information. The four nucleotide overlap allows the most efficient translation, has a single 1:1 match, and the 2nd highest Z value meaning it has the most optimal ribosome binding site score.

CDS complement (35879 - 36064)
  /gene="44"
  /product="gp44"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_44"
    /note=Genemark calls start at 36064
    /note=SSC: 36064-35879 CP: yes SCS: genemark ST: NI BLAST-Start: [hypothetical protein SEA_GLEXAN_43 [Mycobacterium phage Glexan] ],,NCBI, q1:s1 100.0% 1.56688E-32 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.773, -3.326590488964225, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_GLEXAN_43 [Mycobacterium phage Glexan] ],,AXH49959,98.3607,1.56688E-32 SIF-HHPRED:  SIF-Syn: 
    /note=This is not the best start/stop codon because there aren`t any 1:1 matches with Blastp, the nucleotide overlap isn`t the most optimal. The main concern was no amino acid matches with blast p.

CDS complement (36057 - 36485)
  /gene="45"
  /product="gp45"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_45"
    /note=Original Glimmer call @bp 36494 has strength 6.1; Genemark calls start at 36494
    /note=SSC: 36485-36057 CP: yes SCS: both-cs ST: NI BLAST-Start: [hypothetical protein N857_gp082 [Mycobacterium phage Wanda] ],,NCBI, q1:s1 100.0% 4.81242E-61 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.279, -4.154841807616074, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein N857_gp082 [Mycobacterium phage Wanda] ],,YP_008410471,85.8156,4.81242E-61 SIF-HHPRED:  SIF-Syn: 
    /note=This is not the best start/stop codon because there aren`t any 1:1 matches with Blastp, the nucleotide overlap isn`t the most optimal. The main concern was no amino acid matches with blast p.

CDS complement (36482 - 36634)
  /gene="46"
  /product="gp46"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_46"
    /note=Original Glimmer call @bp 36634 has strength 4.14; Genemark calls start at 36634
    /note=SSC: 36634-36482 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_GLEXAN_45 [Mycobacterium phage Glexan] ],,NCBI, q1:s1 100.0% 7.37333E-28 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.224, -4.782222827850149, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_GLEXAN_45 [Mycobacterium phage Glexan] ],,AXH49967,100.0,7.37333E-28 SIF-HHPRED:  SIF-Syn: 
    /note=It has 1:1 amino acid matches, one nucleotide, Genemark and Glimmer predicted it as best start, the best Z-score(2.224) and final score(-4.782)

CDS complement (36634 - 36849)
  /gene="47"
  /product="gp47"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_47"
    /note=Original Glimmer call @bp 36849 has strength 10.01; Genemark calls start at 36849
    /note=SSC: 36849-36634 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DOCTORDIDDLES_46 [Mycobacterium phage DoctorDiddles] ],,NCBI, q1:s1 100.0% 1.62772E-42 GAP: 18 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.783, -3.303727606004721, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_DOCTORDIDDLES_46 [Mycobacterium phage DoctorDiddles] ],,AXC37427,100.0,1.62772E-42 SIF-HHPRED:  SIF-Syn: 
    /note=It has the 1:1, 13 nucleotide gap, has the longest reading frame, the highest Z-score(2.783) and final score(-3.304)

CDS complement (36868 - 37014)
  /gene="48"
  /product="gp48"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_48"
    /note=Original Glimmer call @bp 37014 has strength 7.24; Genemark calls start at 37014
    /note=SSC: 37014-36868 CP: yes SCS: both ST: NI BLAST-Start: [gp50 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 1.44782E-26 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.766, -5.154811153158988, no F: Hypothetical Protein SIF-BLAST: ,,[gp50 [Mycobacterium phage Cjw1] ],,NP_817499,100.0,1.44782E-26 SIF-HHPRED:  SIF-Syn: 
    /note=It has two 1:1 matches, best nucleotide gap, best final score, and includes all coding potential

CDS complement (37014 - 37355)
  /gene="49"
  /product="gp49"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_49"
    /note=Original Glimmer call @bp 37355 has strength 13.9; Genemark calls start at 37355
    /note=SSC: 37355-37014 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_GLEXAN_48 [Mycobacterium phage Glexan] ],,NCBI, q1:s1 100.0% 9.47865E-77 GAP: 285 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.929, -3.473611599459246, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_GLEXAN_48 [Mycobacterium phage Glexan] ],,AXH49863,100.0,9.47865E-77 SIF-HHPRED:  SIF-Syn: 
    /note=There are multiple 1:1 matches with blast, nucleotide overlap isn`t the most efficient but it still works, the longest reading frame, and all information is included within the reading frame

CDS complement (37641 - 37943)
  /gene="50"
  /product="gp50"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_50"
    /note=Original Glimmer call @bp 37943 has strength 5.96; Genemark calls start at 37964
    /note=SSC: 37943-37641 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein DRDREY_51 [Mycobacterium phage DrDrey] ],,NCBI, q1:s1 100.0% 2.80833E-61 GAP: 250 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.615, -3.3060637489568596, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein DRDREY_51 [Mycobacterium phage DrDrey] ],,YP_008409444,100.0,2.80833E-61 SIF-HHPRED:  SIF-Syn: 
    /note=It has multiple matches within blast, but it doesn`t have the longest reading frame, or the best nucleotide overlap, but all the information is within the reading frame.

CDS 38194 - 39075
  /gene="51"
  /product="gp51"
  /function="tyrosine integrase"
  /locus tag="Balomoji_51"
    /note=Original Glimmer call @bp 38194 has strength 12.55; Genemark calls start at 38194
    /note=SSC: 38194-39075 CP: yes SCS: both ST: NI BLAST-Start: [tyrosine integrase [Mycobacterium phage Glexan] ],,NCBI, q1:s1 100.0% 0.0 GAP: 250 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.763, -4.096047812582576, yes F: tyrosine integrase SIF-BLAST: ,,[tyrosine integrase [Mycobacterium phage Glexan] ],,AXH49865,100.0,0.0 SIF-HHPRED: Gp33; Bacteriophage, Brujita, DNA-binding, Integrase, DNA BINDING PROTEIN; HET: ACT, GOL; 1.847A {Mycobacterium phage Brujita},,,5VFZ_A,97.9522,100.0 SIF-Syn: 
    /note=Has multiple matches within blastp has the longest reading frame, but not the best nucleotide overlap, but all information is within the reading frame.

CDS 39214 - 39453
  /gene="52"
  /product="gp52"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_52"
    /note=Original Glimmer call @bp 39214 has strength 8.09; Genemark calls start at 39214
    /note=SSC: 39214-39453 CP: yes SCS: both ST: NI BLAST-Start: [gp54 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 4.3498E-48 GAP: 138 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.817, -3.409075959487936, yes F: Hypothetical Protein SIF-BLAST: ,,[gp54 [Mycobacterium phage Cjw1] ],,NP_817503,100.0,4.3498E-48 SIF-HHPRED:  SIF-Syn: 
    /note=There are multiple 1:1 matches with blast p, 8 nucleotide space, and it has the longest reading frame,

CDS complement (39431 - 40204)
  /gene="53"
  /product="gp53"
  /function="membrane protein"
  /locus tag="Balomoji_53"
    /note=Original Glimmer call @bp 40204 has strength 4.25; Genemark calls start at 40204
    /note=SSC: 40204-39431 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_GLEXAN_52 [Mycobacterium phage Glexan] ],,NCBI, q1:s1 100.0% 0.0 GAP: 94 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.598, -3.6929813131220834, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein SEA_GLEXAN_52 [Mycobacterium phage Glexan] ],,AXH49960,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=The start position was because it covered the best coding potential and was predicted by both Genmark and Glimmer. It`s the largest open reading frame, and it has the highest  ribosome binding site scores, and many 1:1 blasp matches
    /note=
    /note="HHpred predicts a membrane protein, it`s not as reliable as it does not meet the ideal conditions as there is a low probability and high e-value"

CDS complement (40299 - 40739)
  /gene="54"
  /product="gp54"
  /function="immunity repressor"
  /locus tag="Balomoji_54"
    /note=Original Glimmer call @bp 40739 has strength 10.75; Genemark calls start at 40598
    /note=SSC: 40739-40299 CP: yes SCS: both-gl ST: NI BLAST-Start: [transcriptional repressor [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 1.43179E-103 GAP: 216 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.589, -4.411286114293053, no F: immunity repressor SIF-BLAST: ,,[transcriptional repressor [Mycobacterium phage Porky] ],,YP_002014375,100.0,1.43179E-103 SIF-HHPRED:  SIF-Syn: 
    /note=Shows that this gene has a high probability and low e-value, it is likely to have HHpred match to the C1 protein
    /note=
    /note=1:1 blasp matches
    /note=
    /note=The start position was chosen because it was predicted by Glimmer. It has the largest open reading frame and has the same ribosome binding site score as another match that has the start codon at 40730.

CDS 40956 - 41054
  /gene="55"
  /product="gp55"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_55"
    /note=Genemark calls start at 40956
    /note=SSC: 40956-41054 CP: yes SCS: genemark ST: NI BLAST-Start: [gp57 [Mycobacterium phage 244] ],,NCBI, q1:s1 100.0% 5.51151E-13 GAP: 216 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.026, -2.442961286954254, yes F: Hypothetical Protein SIF-BLAST: ,,[gp57 [Mycobacterium phage 244] ],,YP_654812,100.0,5.51151E-13 SIF-HHPRED:  SIF-Syn: 
    /note="May not be reliable as it doesn`t meet the conditions of high probability and low e-value
    /note=
    /note=Not 1:1 match
    /note=
    /note=The start position was chosen because it was predicted by Genmark. It has the largest open frame, and it has the highest ribosome binding site scores.

CDS 41051 - 41188
  /gene="56"
  /product="gp56"
  /function="membrane protein"
  /locus tag="Balomoji_56"
    /note=Original Glimmer call @bp 41051 has strength 8.12; Genemark calls start at 41051
    /note=SSC: 41051-41188 CP: yes SCS: both ST: NI BLAST-Start: [gp58 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 4.18308E-23 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.847, -5.574333665528913, yes F: membrane protein SIF-BLAST: ,,[gp58 [Mycobacterium phage Cjw1] ],,NP_817507,100.0,4.18308E-23 SIF-HHPRED:  SIF-Syn: 
    /note=As it has a low probability and high e-value, it doesn`t meet ideal conditions.
    /note=
    /note=Not 1:1 match
    /note=
    /note=The start position was chosen because both Glimmer and Genemark predicted it. It covered the best coding potential, it did not have the most longest reading frame, and it had the highest ribosome binding site scores.

CDS 41185 - 42030
  /gene="57"
  /product="gp57"
  /function="pentapeptide repeat protein"
  /locus tag="Balomoji_57"
    /note=Original Glimmer call @bp 41185 has strength 7.13; Genemark calls start at 41185
    /note=SSC: 41185-42030 CP: yes SCS: both ST: NI BLAST-Start: [pentapeptide repeat protein [Mycobacterium phage Glexan] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.538, -3.531715028714623, yes F: pentapeptide repeat protein SIF-BLAST: ,,[pentapeptide repeat protein [Mycobacterium phage Glexan] ],,AXH49869,100.0,0.0 SIF-HHPRED: NP275-NP276; NOSTOC PUNCTIFORME, PENTAPEPTIDE REPEAT PROTEIN, PRP, RIGHT HANDED QUADRILATERAL BETA HELIX, RHQBH, TOXIN; HET: MES; 1.5A {NOSTOC PUNCTIFORME} SCOP: b.80.8.1, l.1.1.1,,,2J8K_A,0.0,99.8 SIF-Syn: 
    /note=HHpred predicts a pentapeptide repeat protein, it may be reliable as it does meet ideal conditions as the low e-value and high probability.
    /note=
    /note=1:1 match
    /note=
    /note=The Start Position was chosen because it was predicted by both Glimmer and Genmark, it covered the best coding potential, it had the longest reading frame, and it had the highest ribosome binding site scores

CDS 42032 - 42178
  /gene="58"
  /product="gp58"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_58"
    /note=Original Glimmer call @bp 42032 has strength 10.96; Genemark calls start at 42032
    /note=SSC: 42032-42178 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein FDG56_gp060 [Mycobacterium phage Bask21] ],,NCBI, q1:s1 100.0% 1.40817E-25 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.002, -4.65945827897842, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDG56_gp060 [Mycobacterium phage Bask21] ],,YP_009591220,100.0,1.40817E-25 SIF-HHPRED:  SIF-Syn: 
    /note=May not be reliable as it doesn`t meet the conditions of high probability and low e-value
    /note=
    /note=Not 1:1 match
    /note=
    /note=Start Position was chosen because both Genmark and Glimmer predicted it, It covered the best coding potential, It does not have the longest reading frame, and it had the highest ribosome binding site scores

CDS 42175 - 42453
  /gene="59"
  /product="gp59"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_59"
    /note=Original Glimmer call @bp 42175 has strength 9.72; Genemark calls start at 42175
    /note=SSC: 42175-42453 CP: yes SCS: both ST: NI BLAST-Start: [gp61 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 1.56731E-61 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.72, -5.269767271831238, no F: Hypothetical Protein SIF-BLAST: ,,[gp61 [Mycobacterium phage Cjw1] ],,NP_817510,100.0,1.56731E-61 SIF-HHPRED:  SIF-Syn: 
    /note=May not be reliable as it doesn`t meet the conditions of high probability and low e-value
    /note=
    /note=Not 1:1 match
    /note=
    /note=Start Position was chosen because it was predicted by both GenMark and Glimmer. It does not have the longest reading frame

CDS 42997 - 43302
  /gene="60"
  /product="gp60"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_60"
    /note=Original Glimmer call @bp 42997 has strength 2.64; Genemark calls start at 42997
    /note=SSC: 42997-43302 CP: yes SCS: both ST: NI BLAST-Start: [gp62 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 2.29348E-65 GAP: 543 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.026, -2.5052746077145835, yes F: Hypothetical Protein SIF-BLAST: ,,[gp62 [Mycobacterium phage Cjw1] ],,NP_817511,100.0,2.29348E-65 SIF-HHPRED:  SIF-Syn: 
    /note=May not be reliable as it doesn`t meet the conditions of high probability and low e-value
    /note=
    /note=1:1 match
    /note=
    /note=The start position was chosen because it was both Glimmer and Genemark predicted it, it has both the largest open frame and it has the highest ribosome binding site scores

CDS 43316 - 43423
  /gene="61"
  /product="gp61"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_61"
    /note=Genemark calls start at 43316
    /note=SSC: 43316-43423 CP: no SCS: genemark ST: NI BLAST-Start: [hypothetical protein FDI14_gp061 [Mycobacterium phage SirDuracell] ],,NCBI, q1:s1 100.0% 2.77052E-15 GAP: 13 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.258, -1.953940808934884, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDI14_gp061 [Mycobacterium phage SirDuracell] ],,YP_009607991,100.0,2.77052E-15 SIF-HHPRED:  SIF-Syn: 
    /note=HHpred predicts there is a hypothetical protein, but it may not be reliable as it does not meet the ideal conditions as the low probability and the high e-value
    /note=
    /note=Not 1:1 match
    /note=
    /note=The start position was chosen because only Genemark predicted it, it doesn`t have the largest open frame and it has the highest ribosome binding site scores

CDS 43431 - 43664
  /gene="62"
  /product="gp62"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_62"
    /note=Genemark calls start at 43431
    /note=SSC: 43431-43664 CP: no SCS: genemark ST: NI BLAST-Start: [hypothetical protein SEA_NELITZAMV_61 [Mycobacterium phage NelitzaMV] ],,NCBI, q1:s1 100.0% 2.79263E-49 GAP: 7 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.735, -5.220380545373514, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_NELITZAMV_61 [Mycobacterium phage NelitzaMV] ],,YP_009197729,100.0,2.79263E-49 SIF-HHPRED:  SIF-Syn: 
    /note=May not be reliable as it doesn`t meet the conditions of high probability and low e-value
    /note=
    /note=Not 1:1 match
    /note=
    /note=The start position was chosen because it was predicted by only Genemark, it doesn`t have the largest open frame, and it has the highest ribosome binding site scores.

CDS complement (43322 - 43531)
  /gene="63"
  /product="gp63"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_63"
    /note=Original Glimmer call @bp 43531 has strength 2.68
    /note=SSC: 43531-43322 CP: yes SCS: glimmer ST: NI BLAST-Start:  GAP: 132 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.657, -5.321989567155565, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note="May not be reliable as it doesn`t meet the conditions of high probability and low e-value, since it has a low probabilty and low value"
    /note=
    /note=It does not have 1:1
    /note=
    /note=The start position was chosen because it predicted by only Glimmer, it doesn`t have the largest open frame, and it doesn`t have the highest ribosome binding site scores

CDS 43664 - 43825
  /gene="64"
  /product="gp64"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_64"
    /note=Original Glimmer call @bp 43664 has strength 10.09; Genemark calls start at 43664
    /note=SSC: 43664-43825 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_NELITZAMV_62 [Mycobacterium phage NelitzaMV] ],,NCBI, q1:s1 100.0% 2.12785E-31 GAP: 132 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.762, -2.996985748252251, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_NELITZAMV_62 [Mycobacterium phage NelitzaMV] ],,YP_009197730,100.0,2.12785E-31 SIF-HHPRED:  SIF-Syn: 
    /note="May not be reliable as it doesn`t meet the conditions of high probability and low e-value"
    /note=
    /note=Not the 1:1 
    /note=
    /note=The start position was chosen because only Glimmer and Genbank predicted it, it does not have the largest open frame, and it has the highest ribosome binding site scores.

CDS 44015 - 44347
  /gene="65"
  /product="gp65"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_65"
    /note=Original Glimmer call @bp 44015 has strength 13.66; Genemark calls start at 44015
    /note=SSC: 44015-44347 CP: yes SCS: both ST: NI BLAST-Start: [secreted protein [Mycobacterium phage Phaux] ],,NCBI, q1:s1 100.0% 3.32506E-74 GAP: 189 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.026, -2.583959800616441, yes F: Hypothetical Protein SIF-BLAST: ,,[secreted protein [Mycobacterium phage Phaux] ],,YP_008052241,100.0,3.32506E-74 SIF-HHPRED:  SIF-Syn: 
    /note="May not be reliable as it doesn`t meet the conditions of high probability and low e-value"
    /note=
    /note= 1:1 match
    /note=
    /note=The start position was chosen because it was predicted by only Glimmer and Genmark, it had the largest open frame, and has the highest ribosome binding site scores

CDS 44344 - 44673
  /gene="66"
  /product="gp66"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_66"
    /note=Original Glimmer call @bp 44344 has strength 8.91; Genemark calls start at 44344
    /note=SSC: 44344-44673 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_NELITZAMV_64 [Mycobacterium phage NelitzaMV] ],,NCBI, q1:s1 100.0% 4.27918E-75 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.116, -4.497860114175419, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_NELITZAMV_64 [Mycobacterium phage NelitzaMV] ],,YP_009197732,100.0,4.27918E-75 SIF-HHPRED: DUF6197 ; Family of unknown function (DUF6197),,,PF19698.3,98.1651,99.9 SIF-Syn: 
    /note=The start position 44344 was chosen because it was predicted by both tools, has an idea start codon overlap of 4 nucleotides, covers all the coding potential, has many 1:1 overlaps, and has the best RBS scores.

CDS 44670 - 45638
  /gene="67"
  /product="gp67"
  /function="exonuclease"
  /locus tag="Balomoji_67"
    /note=Original Glimmer call @bp 44670 has strength 8.97; Genemark calls start at 44670
    /note=SSC: 44670-45638 CP: yes SCS: both ST: NI BLAST-Start: [exonuclease [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.677, -3.527651923078076, yes F: exonuclease SIF-BLAST: ,,[exonuclease [Mycobacterium phage Porky] ],,YP_002014387,100.0,0.0 SIF-HHPRED: Mitochondrial genome maintenance exonuclease 1; human MGME1, DNA complex, DNA exonuclease, DNA BINDING PROTEIN; 2.702A {Homo sapiens},,,5ZYT_C,80.1242,99.8 SIF-Syn: 
    /note=The start position at 44670 is the LORF, has the best scores for ribosome binding sites, many 1:1 matches, a 4 nucleotide overlap, it was predicted by both tools, and covers all the coding potential.

CDS 45635 - 46045
  /gene="68"
  /product="gp68"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_68"
    /note=Original Glimmer call @bp 45635 has strength 10.92; Genemark calls start at 45635
    /note=SSC: 45635-46045 CP: yes SCS: both ST: NI BLAST-Start: [gp69 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 3.68633E-95 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.71, -5.290324183593171, no F: Hypothetical Protein SIF-BLAST: ,,[gp69 [Mycobacterium phage Cjw1] ],,NP_817518,100.0,3.68633E-95 SIF-HHPRED:  SIF-Syn: 
    /note=The start position 45635 was chosen because it was predicted by both tools, is the longest ORF, has a ideal 4 nucleotide overlap, covers all the coding potential, has many 1:1 blastp matches.

CDS 46038 - 46760
  /gene="69"
  /product="gp69"
  /function="ERF family ssdna binding protein"
  /locus tag="Balomoji_69"
    /note=Original Glimmer call @bp 46038 has strength 9.56; Genemark calls start at 46038
    /note=SSC: 46038-46760 CP: yes SCS: both ST: NI BLAST-Start: [ERF family ssDNA binding protein [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 3.38267E-176 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.067, -4.522979412939132, no F: ERF family ssdna binding protein SIF-BLAST: ,,[ERF family ssDNA binding protein [Mycobacterium phage Porky] ],,YP_002014389,100.0,3.38267E-176 SIF-HHPRED: ERF ; ERF superfamily,,,PF04404.16,56.6667,99.9 SIF-Syn: 
    /note=Even though this sequence isn`t the LORF, it is only off by a few nucleotides and has the best RBS scores. There is only a 8 nucleotide overlap compared to 14, was predicted by both tools, and it covers all the coding potential.

CDS 46753 - 47064
  /gene="70"
  /product="gp70"
  /function="Hypothetical protein"
  /locus tag="Balomoji_70"
    /note=Original Glimmer call @bp 46753 has strength 7.19; Genemark calls start at 46753
    /note=SSC: 46753-47064 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein Porky_69 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 3.45466E-72 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.019, -5.86668762350679, no F: Hypothetical protein SIF-BLAST: ,,[hypothetical protein Porky_69 [Mycobacterium phage Porky] ],,YP_002014390,100.0,3.45466E-72 SIF-HHPRED:  SIF-Syn: 
    /note=The starting position of 46753 was chosen. Genemark and blastp both predict the same gene and the gene contains many 1:1 matches. Additionally, it has the longest ORF, covers the coding potential, and has a short overlap.

CDS 47064 - 47534
  /gene="71"
  /product="gp71"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_71"
    /note=Original Glimmer call @bp 47064 has strength 9.11; Genemark calls start at 47064
    /note=SSC: 47064-47534 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_PHARSALUS_68 [Mycobacterium phage Pharsalus] ],,NCBI, q1:s1 100.0% 3.41703E-111 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.929, -2.6453814847322845, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_PHARSALUS_68 [Mycobacterium phage Pharsalus] ],,AOT23951,100.0,3.41703E-111 SIF-HHPRED:  SIF-Syn: 
    /note=This starting sequence has many 1:1 matches, was predicted by both tools, covers all the coding potential, has a 1 nucleotide overlap, is the LORF and has the best RBS scores.

CDS 47534 - 47902
  /gene="72"
  /product="gp72"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_72"
    /note=Original Glimmer call @bp 47534 has strength 9.93; Genemark calls start at 47534
    /note=SSC: 47534-47902 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ICEE_73 [Mycobacterium phage Icee] ],,NCBI, q1:s1 100.0% 9.97323E-82 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.943, -5.2484617369160205, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ICEE_73 [Mycobacterium phage Icee] ],,AXC37789,100.0,9.97323E-82 SIF-HHPRED:  SIF-Syn: 
    /note=Yes, this starting gene of 47534 is the most ideal since it is a long gene that covers the entire coding potential and was the predicated start by both Genemark and blastp. In addition, there is an overlap of 8 nucleotides to undergo translation and has the best final score.

CDS 47905 - 48276
  /gene="73"
  /product="gp73"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_73"
    /note=Original Glimmer call @bp 47905 has strength 9.34; Genemark calls start at 47905
    /note=SSC: 47905-48276 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ICEE_74 [Mycobacterium phage Icee] ],,NCBI, q1:s1 100.0% 7.23641E-86 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.026, -2.442961286954254, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ICEE_74 [Mycobacterium phage Icee] ],,AXC37790,100.0,7.23641E-86 SIF-HHPRED:  SIF-Syn: 
    /note=This sequence isn`t the LORF (372 vs 378), but it has the best RBS scores and a 2 nucleotide gap. This sequence also has many 1:1 matches, was predicted by both tools, covers all the coding potential.

CDS 48276 - 48449
  /gene="74"
  /product="gp74"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_74"
    /note=Original Glimmer call @bp 48276 has strength 8.95; Genemark calls start at 48276
    /note=SSC: 48276-48449 CP: yes SCS: both ST: NI BLAST-Start: [gp75 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 1.25899E-32 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.615, -5.5524625202905655, no F: Hypothetical Protein SIF-BLAST: ,,[gp75 [Mycobacterium phage Cjw1] ],,NP_817524,100.0,1.25899E-32 SIF-HHPRED: BRCA1-A complex subunit RAP80; Deubiquitinase complex, DUB, Lysine-63 linkage specific, BRCC36-containing, BRCA1A binding, SIGNALING PROTEIN; 3.75A {Mus musculus},,,6GVW_E,29.8246,36.5 SIF-Syn: 
    /note=Yes, the starting position of 48276 was chosen because it was predicated by both Glimmer and Genemark, covers all the coding potential, and is the longest. Additionally, the scores are the both ideal compared to the other gene candidates and has multiple 1:1 matches.

CDS 48452 - 48685
  /gene="75"
  /product="gp75"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_75"
    /note=Original Glimmer call @bp 48452 has strength 11.38; Genemark calls start at 48452
    /note=SSC: 48452-48685 CP: yes SCS: both ST: NI BLAST-Start: [gp76 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 1.46194E-46 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.634, -3.2669815101762634, yes F: Hypothetical Protein SIF-BLAST: ,,[gp76 [Mycobacterium phage Cjw1] ],,NP_817525,100.0,1.46194E-46 SIF-HHPRED:  SIF-Syn: 
    /note=Although this sequence is half the length of the LORF, it was predicted by both tools, has the best RBS scores and only a 2 nucleotide gap rather than a 343 overlap. This sequence starting at 48452 also has many 1:1 matches and covers all the coding potential.

CDS 48682 - 49095
  /gene="76"
  /product="gp76"
  /function="DprA-like DNA processing chain A"
  /locus tag="Balomoji_76"
    /note=Original Glimmer call @bp 48682 has strength 7.49; Genemark calls start at 48682
    /note=SSC: 48682-49095 CP: yes SCS: both ST: NI BLAST-Start: [gp77 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 4.97861E-97 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.486, -5.82369656923664, no F: DprA-like DNA processing chain A SIF-BLAST: ,,[gp77 [Mycobacterium phage Cjw1] ],,NP_817526,100.0,4.97861E-97 SIF-HHPRED: DNA processing protein DprA; SAM and Rossmann Fold, DNA processing protein A, DNA BINDING PROTEIN; HET: SO4, MSE; 2.7A {Streptococcus pneumoniae} SCOP: c.129.1.4, a.60.17.1,,,3UQZ_C,98.5401,99.7 SIF-Syn: 
    /note=This starting position of 48682 was chosen because it has an ideal 4 nucleotide overlap, multiple 1:1 matches, was predicated by both Glimmer and Genemark, and covers the entire coding potential. Finally, it has the best z score and is the longest ORF.
    /note=
    /note=For: Professor Jonhson. It was a DNA processing protein so I`m not sure if it`s able to be classified as a DNA binding protein.

CDS 49092 - 49409
  /gene="77"
  /product="gp77"
  /function="HNH endonuclease"
  /locus tag="Balomoji_77"
    /note=Original Glimmer call @bp 49092 has strength 4.95; Genemark calls start at 49092
    /note=SSC: 49092-49409 CP: yes SCS: both ST: NI BLAST-Start: [HNH endonuclease [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 3.21464E-72 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 0.598, -7.69171440769759, no F: HNH endonuclease SIF-BLAST: ,,[HNH endonuclease [Mycobacterium phage Porky] ],,YP_002014397,100.0,3.21464E-72 SIF-HHPRED:  SIF-Syn: 
    /note=Although the RBS scores are technically not the best and it is not the LORF, this sequence only has a 4 nucleotide overlap vs a 187 overlap with the LORF sequence. This sequence also covers coding potential, was predicted by both tools, and has many 1:1 matches.

CDS 49399 - 49635
  /gene="78"
  /product="gp78"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_78"
    /note=Original Glimmer call @bp 49399 has strength 13.38; Genemark calls start at 49399
    /note=SSC: 49399-49635 CP: yes SCS: both ST: NI BLAST-Start: [gp79 [Mycobacterium phage 244] ],,NCBI, q1:s58 100.0% 4.65648E-48 GAP: -11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.872, -4.0707216408001425, yes F: Hypothetical Protein SIF-BLAST: ,,[gp79 [Mycobacterium phage 244] ],,YP_654834,57.7778,4.65648E-48 SIF-HHPRED:  SIF-Syn: 
    /note=The starting position of 49399 was chosen. Although it has an overlap of 11 nucleotides, the other possible starting positions have overlaps of at least over 100 nucleotides. Additionally, it has multiple 1:1 blastp matches. covers the coding potential, and was predicted by both tools.

CDS 49632 - 50282
  /gene="79"
  /product="gp79"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_79"
    /note=Original Glimmer call @bp 49632 has strength 7.12; Genemark calls start at 49632
    /note=SSC: 49632-50282 CP: yes SCS: both ST: NI BLAST-Start: [gp80 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 3.35824E-156 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 0.904, -6.988038999513095, no F: Hypothetical Protein SIF-BLAST: ,,[gp80 [Mycobacterium phage Cjw1] ],,NP_817529,100.0,3.35824E-156 SIF-HHPRED:  SIF-Syn: 

CDS 50279 - 50614
  /gene="80"
  /product="gp80"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_80"
    /note=Original Glimmer call @bp 50264 has strength 8.52; Genemark calls start at 50279
    /note=SSC: 50279-50614 CP: yes SCS: both-gm ST: NI BLAST-Start: [hypothetical protein PHATBACTER_84 [Mycobacterium phage PhatBacter] ],,NCBI, q1:s1 100.0% 3.06242E-75 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.087, -3.3648782290756687, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PHATBACTER_84 [Mycobacterium phage PhatBacter] ],,YP_008857571,100.0,3.06242E-75 SIF-HHPRED:  SIF-Syn: 

CDS 50607 - 51869
  /gene="81"
  /product="gp81"
  /function="DnaB-like dsDNA helicase"
  /locus tag="Balomoji_81"
    /note=Original Glimmer call @bp 50607 has strength 10.09; Genemark calls start at 50607
    /note=SSC: 50607-51869 CP: no SCS: both ST: NI BLAST-Start: [DnaB-like replicative helicase [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 0.0 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.547, -5.615966648652074, no F: DnaB-like dsDNA helicase SIF-BLAST: ,,[DnaB-like replicative helicase [Mycobacterium phage Cjw1] ],,NP_817531,100.0,0.0 SIF-HHPRED: DNAB-Like Replicative Helicase; ATPase, REPLICATION; 3.91A {Bacillus phage SPP1},,,3BGW_C,99.7619,100.0 SIF-Syn: 
    /note=HHPred predicts this to be a DNAB-like dsDNA helicase, and this may be reliable due to the e-value and probability meeting ideal conditions.

CDS 51866 - 52054
  /gene="82"
  /product="gp82"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_82"
    /note=Original Glimmer call @bp 51866 has strength 11.53; Genemark calls start at 51866
    /note=SSC: 51866-52054 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein FDG56_gp082 [Mycobacterium phage Bask21] ],,NCBI, q1:s1 100.0% 3.88443E-36 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.164, -5.085091778133397, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDG56_gp082 [Mycobacterium phage Bask21] ],,YP_009591242,100.0,3.88443E-36 SIF-HHPRED:  SIF-Syn: 

CDS 52036 - 52311
  /gene="83"
  /product="gp83"
  /function="WhiB family transcription factor"
  /locus tag="Balomoji_83"
    /note=Original Glimmer call @bp 52036 has strength 3.45; Genemark calls start at 52051
    /note=SSC: 52036-52311 CP: yes SCS: both-gl ST: NI BLAST-Start: [transcriptional regulator WhiB-like [Mycobacterium phage SirDuracell] ],,NCBI, q1:s1 100.0% 9.32282E-61 GAP: -19 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.383, -7.20474810947704, no F: WhiB family transcription factor SIF-BLAST: ,,[transcriptional regulator WhiB-like [Mycobacterium phage SirDuracell] ],,YP_009608012,100.0,9.32282E-61 SIF-HHPRED: Probable transcriptional regulator WhiB7; Redox-sensitive, Iron-sulfur cluster, transcription, activator; HET: SF4, MSE; 1.55A {Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)},,,7KUG_C,71.4286,99.6 SIF-Syn: 
    /note=HHPred predicts this be a transcriptional regulator WhiB7, and this may be reliable due to the e-value and probability meeting ideal conditions.
    /note=
    /note=The start position at 52036 is the LORF. It has a 1:1 match and a 19 nucleotide overlap. Although this start does not have the best RBS scores, it covers the most CP and is the LORF.

CDS 52286 - 52504
  /gene="84"
  /product="gp84"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_84"
    /note=Original Glimmer call @bp 52286 has strength 8.72; Genemark calls start at 52286
    /note=SSC: 52286-52504 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein FDG56_gp084 [Mycobacterium phage Bask21] ],,NCBI, q1:s1 100.0% 3.24003E-44 GAP: -26 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.929, -3.1725816037952645, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDG56_gp084 [Mycobacterium phage Bask21] ],,YP_009591244,100.0,3.24003E-44 SIF-HHPRED:  SIF-Syn: 
    /note=The start position at 52286 is the LORF. It has a 1:1 match and a 26 nucleotide overlap. This start has the best RBS scores, covers the most CP, and is the LORF.

CDS 52501 - 52728
  /gene="85"
  /product="gp85"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_85"
    /note=Original Glimmer call @bp 52501 has strength 6.35; Genemark calls start at 52501
    /note=SSC: 52501-52728 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein FDG56_gp085 [Mycobacterium phage Bask21] ],,NCBI, q1:s1 100.0% 1.48932E-47 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.387, -3.867218069942777, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDG56_gp085 [Mycobacterium phage Bask21] ],,YP_009591245,100.0,1.48932E-47 SIF-HHPRED:  SIF-Syn: 
    /note=The start position at 52501 is the LORF. It has a 1:1 match and a 4 nucleotide overlap. This start has the best RBS scores, covers the most CP, and is the LORF.

CDS 52725 - 53087
  /gene="86"
  /product="gp86"
  /function="Holliday junction resolvase"
  /locus tag="Balomoji_86"
    /note=Original Glimmer call @bp 52725 has strength 13.57; Genemark calls start at 52725
    /note=SSC: 52725-53087 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein FDI14_gp086 [Mycobacterium phage SirDuracell] ],,NCBI, q1:s1 100.0% 2.25149E-82 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.376, -4.860117729524838, yes F: Holliday junction resolvase SIF-BLAST: ,,[hypothetical protein FDI14_gp086 [Mycobacterium phage SirDuracell] ],,YP_009608016,100.0,2.25149E-82 SIF-HHPRED: Holliday junction resolvase; archeal holliday junction resolvase helicase DNA binding enzyme phage 15-6 thermus thermophilus, RECOMBINATION; HET: SO4, MSE; 2.5A {Thermus thermophilus phage 15-6},,,7BGS_A,95.8333,99.6 SIF-Syn: 
    /note=HHPred predicts this to be a Holliday junction resolvase, and this may be reliable due to the e-value and probability and meeting ideal conditions
    /note=
    /note=The start position at 52725 is not the LORF. It has a 1:1 match and a 4 nucleotide overlap. This start has the best RBS scores, covers the most CP, but is not the LORF.

CDS 53084 - 53278
  /gene="87"
  /product="gp87"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_87"
    /note=Original Glimmer call @bp 53084 has strength 7.95; Genemark calls start at 53084
    /note=SSC: 53084-53278 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein M039_gp089 [Mycobacterium phage Phaux] ],,NCBI, q1:s1 100.0% 1.85644E-38 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.634, -3.329294830936593, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein M039_gp089 [Mycobacterium phage Phaux] ],,YP_008052263,100.0,1.85644E-38 SIF-HHPRED:  SIF-Syn: 
    /note=The start position at 53084 is not the LORF. It has a 1:1 match and a 4 nucleotide overlap. This start has the best RBS scores, covers the most CP, but is not the LORF.

CDS 53433 - 54374
  /gene="88"
  /product="gp88"
  /function="polynucleotide kinase"
  /locus tag="Balomoji_88"
    /note=Original Glimmer call @bp 53433 has strength 11.26; Genemark calls start at 53433
    /note=SSC: 53433-54374 CP: no SCS: both ST: NI BLAST-Start: [polynucleotide kinase [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 0.0 GAP: 154 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.763, -3.058913906516345, yes F: polynucleotide kinase SIF-BLAST: ,,[polynucleotide kinase [Mycobacterium phage Porky] ],,YP_002014408,100.0,0.0 SIF-HHPRED: Pnkp1; RNA repair, kinase, phosphatase, methyltransferase, ligase, PROTEIN BINDING; HET: SO4, GOL, PO4; 3.3A {Capnocytophaga gingivalis},,,4XRP_A,99.6805,100.0 SIF-Syn: 
    /note=HHPred predicts this to be a polynucleotide kinase, and this may be reliable due to the e-value and probability.
    /note=The start position at 53433 is the LORF. It has a 1:1 match and a 154 nucleotide gap. This start has the best RBS scores, covers the most CP, and is the LORF.

CDS 54374 - 54571
  /gene="89"
  /product="gp89"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_89"
    /note=Original Glimmer call @bp 54374 has strength 5.89; Genemark calls start at 54374
    /note=SSC: 54374-54571 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein Porky_88 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 2.88442E-41 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.499, -3.6129949472896743, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein Porky_88 [Mycobacterium phage Porky] ],,YP_002014409,100.0,2.88442E-41 SIF-HHPRED:  SIF-Syn: 
    /note=The start position at 54374 is the LORF. It has a 1:1 match and a 1 nucleotide overlap. This start has the best RBS scores, covers the most CP, and is the LORF.

CDS 54568 - 54666
  /gene="90"
  /product="gp90"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_90"
    /note=Genemark calls start at 54568
    /note=SSC: 54568-54666 CP: yes SCS: genemark ST: NI BLAST-Start: [hypothetical protein Porky_89 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 1.0832E-11 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.792, -6.343429807438574, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein Porky_89 [Mycobacterium phage Porky] ],,YP_002014410,100.0,1.0832E-11 SIF-HHPRED:  SIF-Syn: 
    /note=(Question to self: What does no glimmer start and no glimmer score mean??) The start at 54568 is the LORF. It has a 1:1 match and a 4 nucleotide overlap. This start does not have the best RBS scores but covers the most CP and is the LORF.

CDS 54714 - 56000
  /gene="91"
  /product="gp91"
  /function="RNA ligase"
  /locus tag="Balomoji_91"
    /note=Original Glimmer call @bp 54663 has strength 11.84; Genemark calls start at 54663
    /note=SSC: 54714-56000 CP: no SCS: both-cs ST: NI BLAST-Start: [RNA ligase [Mycobacterium phage Hoonter]],,NCBI, q1:s18 100.0% 0.0 GAP: 47 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.041, -4.515299958532669, no F: RNA ligase SIF-BLAST: ,,[RNA ligase [Mycobacterium phage Hoonter]],,QGJ94267,95.7303,0.0 SIF-HHPRED: RNA ligase; RNA repair, adenylyltransferase, LIGASE; HET: ATP; 1.547A {Naegleria gruberi},,,6VTB_A,96.729,100.0 SIF-Syn: 
    /note=HHPred predicts this to be a RNA ligase, and this may be reliable due to the e-value and probability meeting ideal conditions.
    /note=
    /note=The start at 54663 is the LORF. It has a 1:1 match and a 4 nucleotide overlap. This start does have the best RBS scores, covers the most CP, and is the LORF.

CDS 56037 - 56858
  /gene="92"
  /product="gp92"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_92"
    /note=Original Glimmer call @bp 56037 has strength 5.4; Genemark calls start at 56037
    /note=SSC: 56037-56858 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_COOKIES_89 [Mycobacterium phage Cookies]],,NCBI, q1:s1 100.0% 0.0 GAP: 36 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.717, -5.547625656018686, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_COOKIES_89 [Mycobacterium phage Cookies]],,QAY06619,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=This is the best start since it is the longest with the least amount of Gap.

CDS 56855 - 57115
  /gene="93"
  /product="gp93"
  /function="WhiB family transcription factor"
  /locus tag="Balomoji_93"
    /note=Original Glimmer call @bp 56855 has strength 4.3; Genemark calls start at 56855
    /note=SSC: 56855-57115 CP: yes SCS: both ST: NI BLAST-Start: [WhiB transcriptional factor [Mycobacterium phage Bask21] ],,NCBI, q1:s1 100.0% 1.74933E-56 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.776, -3.108788982793736, yes F: WhiB family transcription factor SIF-BLAST: ,,[WhiB transcriptional factor [Mycobacterium phage Bask21] ],,YP_009591253,100.0,1.74933E-56 SIF-HHPRED: Transcriptional regulator WhiB1; nitric oxide, sigmaA, iron-sulfur, tuberculosis, Wbl protein, SIGNALING PROTEIN; HET: SF4; NMR {Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)},,,5OAY_A,95.3488,99.9 SIF-Syn: 
    /note=This start is recognized by both Genemark and Glimmer and there are a few matches. There is a minimal overlap and the coding potential is completely covered.

CDS 57133 - 57291
  /gene="94"
  /product="gp94"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_94"
    /note=Original Glimmer call @bp 57133 has strength 12.29; Genemark calls start at 57133
    /note=SSC: 57133-57291 CP: yes SCS: both ST: NI BLAST-Start: [gp96 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 3.75942E-29 GAP: 17 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.695, -3.490561115344053, yes F: Hypothetical Protein SIF-BLAST: ,,[gp96 [Mycobacterium phage Cjw1] ],,NP_817545,100.0,3.75942E-29 SIF-HHPRED:  SIF-Syn: 
    /note=The start position at 57113 is the best start position since it has the best z-score of 2.695, the lowest gap with a score of 17, and there were many 1:1 matches.

CDS 57288 - 57740
  /gene="95"
  /product="gp95"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_95"
    /note=Original Glimmer call @bp 57288 has strength 11.2; Genemark calls start at 57288
    /note=SSC: 57288-57740 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_COOKIES_92 [Mycobacterium phage Cookies] ],,NCBI, q1:s1 100.0% 9.04156E-106 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.64, -5.437750947756905, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_COOKIES_92 [Mycobacterium phage Cookies] ],,QAY06622,100.0,9.04156E-106 SIF-HHPRED:  SIF-Syn: 
    /note=There is a minimal overlap and the coding potential is completely covered. The start is recognized by both Genemark and Glimmer.

CDS 57744 - 58187
  /gene="96"
  /product="gp96"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_96"
    /note=Original Glimmer call @bp 57744 has strength 10.96; Genemark calls start at 57744
    /note=SSC: 57744-58187 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_COOKIES_93 [Mycobacterium phage Cookies] ],,NCBI, q1:s1 100.0% 1.47425E-104 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.53, -3.54831954703195, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_COOKIES_93 [Mycobacterium phage Cookies] ],,QAY06623,100.0,1.47425E-104 SIF-HHPRED:  SIF-Syn: 
    /note=The position at 57,744 was predicted by both tools, has the longest ORF, and covers all the coding potential. Unfortunately, there is no overlap, however, there is a 1:1 match and the Z score and final scores are the largest and closest to zero, respectively.

CDS 58189 - 58524
  /gene="97"
  /product="gp97"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_97"
    /note=Original Glimmer call @bp 58189 has strength 8.61; Genemark calls start at 58189
    /note=SSC: 58189-58524 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein FDI14_gp097 [Mycobacterium phage SirDuracell] ],,NCBI, q1:s1 100.0% 2.13067E-75 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.676, -4.085313187509542, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDI14_gp097 [Mycobacterium phage SirDuracell] ],,YP_009608027,100.0,2.13067E-75 SIF-HHPRED:  SIF-Syn: 
    /note=It has the best coding potential and it is recognized by both programs.  However, it does not have a good set of RBS scores, nor does it have a overlap.

CDS 58557 - 59057
  /gene="98"
  /product="gp98"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_98"
    /note=Original Glimmer call @bp 58557 has strength 3.19; Genemark calls start at 58557
    /note=SSC: 58557-59057 CP: yes SCS: both ST: NI BLAST-Start: [DNA binding protein [Mycobacterium phage Kostya] ],,NCBI, q1:s1 100.0% 9.317E-120 GAP: 32 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.235, -4.2482196028815515, no F: Hypothetical Protein SIF-BLAST: ,,[DNA binding protein [Mycobacterium phage Kostya] ],,YP_002014566,100.0,9.317E-120 SIF-HHPRED:  SIF-Syn: 
    /note=The start position at 58557 is the best start position since it has the longest overlap, 1:1 matches, and the best z-score of 1.766.

CDS complement (59176 - 59313)
  /gene="99"
  /product="gp99"
  /locus tag="Balomoji_99"
    /note=Original Glimmer call @bp 59313 has strength 2.76
    /note=SSC: 59313-59176 CP: no SCS: glimmer ST: NI BLAST-Start:  GAP: 340 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.099, -7.598634427877706, no F:  SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=This gene should be deleted because we are adding a gene on the forward strand, and annotate the new gene to the best of our ability.

CDS 59654 - 60094
  /gene="100"
  /product="gp100"
  /function="ssdna binding protein"
  /locus tag="Balomoji_100"
    /note=Original Glimmer call @bp 59654 has strength 8.35; Genemark calls start at 59654
    /note=SSC: 59654-60094 CP: yes SCS: both ST: NI BLAST-Start: [SSB protein [Mycobacterium phage Kostya] ],,NCBI, q1:s1 100.0% 1.71092E-102 GAP: 340 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.025, -4.611371280732909, no F: ssdna binding protein SIF-BLAST: ,,[SSB protein [Mycobacterium phage Kostya] ],,YP_002014568,100.0,1.71092E-102 SIF-HHPRED: Single-stranded DNA-binding protein; DNA binding, quaternary structure, plasticity, inhibitor development, DNA BINDING PROTEIN; HET: FMT; 1.92A {Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)},,,7F5Y_B,75.3425,100.0 SIF-Syn: 
    /note=The start is recognized by both Genemark and Glimmer and the coding potential is completely covered.

CDS 60075 - 60989
  /gene="101"
  /product="gp101"
  /function="clpp-like protease"
  /locus tag="Balomoji_101"
    /note=Original Glimmer call @bp 60210 has strength 10.86; Genemark calls start at 60228
    /note=SSC: 60075-60989 CP: yes SCS: both-cs ST: NI BLAST-Start: [ClpP-like protease [Mycobacterium phage Tomaszewski]],,NCBI, q1:s1 100.0% 0.0 GAP: -20 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.274, -5.074137700978002, no F: clpp-like protease SIF-BLAST: ,,[ClpP-like protease [Mycobacterium phage Tomaszewski]],,QDK02207,100.0,0.0 SIF-HHPRED: Protease 4; protease, bacterial, Hydrolase, Inner membrane, Membrane, Transmembrane, SER/LYS Protease; 2.55A {Escherichia coli},,,3BF0_A,97.3684,100.0 SIF-Syn: 
    /note=The start position at 60075 is the best start position since it has the ORF, longest overlap, 1:1 matches, and the best z-score of 2.274.

CDS 60991 - 61188
  /gene="102"
  /product="gp102"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_102"
    /note=Original Glimmer call @bp 61036 has strength 9.85; Genemark calls start at 60991
    /note=SSC: 60991-61188 CP: yes SCS: both-gm ST: NI BLAST-Start: [hypothetical protein Kostya_102 [Mycobacterium phage Kostya] ],,NCBI, q1:s1 100.0% 1.82737E-38 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.397, -5.07183379116951, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein Kostya_102 [Mycobacterium phage Kostya] ],,YP_002014570,100.0,1.82737E-38 SIF-HHPRED:  SIF-Syn: 
    /note=There is a minimal gap and several matches on BLASTp. The coding potential is completely covered. Suspected Function is as anti-CBASS protein 2.

CDS 61185 - 61541
  /gene="103"
  /product="gp103"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_103"
    /note=Original Glimmer call @bp 61185 has strength 8.11; Genemark calls start at 61185
    /note=SSC: 61185-61541 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein Porky_101 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 9.63907E-78 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.963, -5.507500699639458, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein Porky_101 [Mycobacterium phage Porky] ],,YP_002014422,100.0,9.63907E-78 SIF-HHPRED:  SIF-Syn: 
    /note=There is a minimal gap and several matches on BLASTp. The coding potential is also completely covered.

CDS 61542 - 61832
  /gene="104"
  /product="gp104"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_104"
    /note=Original Glimmer call @bp 61542 has strength 8.52; Genemark calls start at 61542
    /note=SSC: 61542-61832 CP: yes SCS: both ST: NI BLAST-Start: [gp105 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 4.88592E-61 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.042, -4.513079314654054, yes F: Hypothetical Protein SIF-BLAST: ,,[gp105 [Mycobacterium phage Cjw1] ],,NP_817554,100.0,4.88592E-61 SIF-HHPRED:  SIF-Syn: 
    /note=It is recognized by genemark and glimmer and it has many matches. There are also no gaps and it has the longest open reading frame. The coding potential is also covered.

CDS 61837 - 62148
  /gene="105"
  /product="gp105"
  /function="excisionase"
  /locus tag="Balomoji_105"
    /note=Original Glimmer call @bp 61837 has strength 3.48; Genemark calls start at 61813
    /note=SSC: 61837-62148 CP: yes SCS: both-gl ST: NI BLAST-Start: [gp106 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 1.19879E-70 GAP: 4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 0.999, -6.768399669413642, no F: excisionase SIF-BLAST: ,,[gp106 [Mycobacterium phage Cjw1] ],,NP_817555,100.0,1.19879E-70 SIF-HHPRED: Recombination Directionality Factor RdfS; Excisionase, Recombination Directionality Factor, winged helix-turn-helix, superhelix, DNA BINDING PROTEIN; HET: GOL; 2.45A {Mesorhizobium japonicum R7A},,,8DGL_A,49.5146,98.7 SIF-Syn: 
    /note=Was predicted by Glimmer: between this one and the following, this one has a 1:1 match a overlap of 4 nucleotides, and a slightly shorter open reading frame that still covers the whole sequence. overall thi is better
    /note=
    /note=(name did not autofill)

CDS 62201 - 62491
  /gene="106"
  /product="gp106"
  /function="HNH endonuclease"
  /locus tag="Balomoji_106"
    /note=Original Glimmer call @bp 62330 has strength 10.22; Genemark calls start at 62330
    /note=SSC: 62201-62491 CP: no SCS: both-cs ST: NI BLAST-Start: [HNH endonuclease [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 4.93965E-65 GAP: 52 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.828, -4.164592320178568, no F: HNH endonuclease SIF-BLAST: ,,[HNH endonuclease [Mycobacterium phage Cjw1] ],,NP_817556,100.0,4.93965E-65 SIF-HHPRED: d.4.1.3 (M:1-105) Intron-encoded homing endonuclease I-HmuI {Bacteriophage SPO1 [TaxId: 10685]} | CLASS: Alpha and beta proteins (a+b), FOLD: His-Me finger endonucleases, SUPFAM: His-Me finger endonucleases, FAM: Intron-encoded homing endonucleases,,,SCOP_d1u3em1,93.75,99.9 SIF-Syn: 
    /note=This start position has a smaller gap which is more efficient for translation, and gained more 1:1 blastp matches which show that others annotated this particular start position, the ribosome binding site is not the best.

tRNA 62592 - 62675
  /gene="107"
  /product="tRNA-Arg(cct)"
  /locus tag="BALOMOJI_107"
    /note=tRNA-Arg(cct)

tRNA 62678 - 62750
  /gene="108"
  /product="tRNA-Gly(tcc)"
  /locus tag="BALOMOJI_108"
    /note=tRNA-Gly(tcc)

CDS 63065 - 63289
  /gene="109"
  /product="gp109"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_109"
    /note=Original Glimmer call @bp 63065 has strength 7.48; Genemark calls start at 63065
    /note=SSC: 63065-63289 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein Porky_107 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 5.37076E-49 GAP: 573 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.462, -3.769471247018311, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein Porky_107 [Mycobacterium phage Porky] ],,YP_002014426,100.0,5.37076E-49 SIF-HHPRED:  SIF-Syn: 
    /note=This one has a 1:25 match gap of 573 nucleotides, it is not the longest open reading frame, but it still covers the whole sequence.

CDS 63286 - 63549
  /gene="110"
  /product="gp110"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_110"
    /note=Original Glimmer call @bp 63316 has strength 10.01; Genemark calls start at 63316
    /note=SSC: 63286-63549 CP: yes SCS: both-cs ST: NI BLAST-Start: [gp112 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 6.13732E-57 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.381, -4.901215214744926, yes F: Hypothetical Protein SIF-BLAST: ,,[gp112 [Mycobacterium phage Cjw1] ],,NP_817559,100.0,6.13732E-57 SIF-HHPRED:  SIF-Syn: 
    /note=this is a 1:1 with 109 other matching titles, it has an optimal gap of -4 it is the longest open reading frame and covers the entire sequence.
    /note=
    /note=the predicted start did not cover all of the coding potential has a worse gap and less title matches.
    /note=
    /note=(Hypothetical Protein)

CDS 63560 - 63934
  /gene="111"
  /product="gp111"
  /function="hydrolase"
  /locus tag="Balomoji_111"
    /note=Original Glimmer call @bp 63560 has strength 13.81; Genemark calls start at 63560
    /note=SSC: 63560-63934 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ASRIEL_109 [Mycobacterium phage Asriel] ],,NCBI, q1:s1 100.0% 2.23708E-85 GAP: 10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.992, -4.698691165234176, no F: hydrolase SIF-BLAST: ,,[hypothetical protein SEA_ASRIEL_109 [Mycobacterium phage Asriel] ],,AVI03345,100.0,2.23708E-85 SIF-HHPRED: purine trans deoxyribosylase; PTD, native, 2`-purine deoxyribosyltansferase, TRANSFERASE; 2.1A {Lactobacillus helveticus} SCOP: c.23.14.1,,,1S2L_A,85.4839,99.6 SIF-Syn: 
    /note=this is a 1:1 with 124 other matching titles, it has a gap of 10 it is the longest open reading frame and covers the entire sequence.

CDS 63934 - 64251
  /gene="112"
  /product="gp112"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_112"
    /note=Original Glimmer call @bp 63934 has strength 7.73; Genemark calls start at 63934
    /note=SSC: 63934-64251 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein Kostya_112 [Mycobacterium phage Kostya] ],,NCBI, q1:s1 100.0% 1.69803E-69 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.64, -5.437750947756905, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein Kostya_112 [Mycobacterium phage Kostya] ],,YP_002014578,100.0,1.69803E-69 SIF-HHPRED: dATP-dGTP_PPHyd ; dATP/dGTP pyrophosphohydrolase,,,PF04447.16,84.7619,99.3 SIF-Syn: 
    /note=this is a 1:1 with 27 other matching titles, it has a gap of -1 it is the longest open reading frame and covers the entire sequence.

CDS 64241 - 64834
  /gene="113"
  /product="gp113"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_113"
    /note=Original Glimmer call @bp 64241 has strength 8.72; Genemark calls start at 64241
    /note=SSC: 64241-64834 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein Porky_111 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 9.81518E-143 GAP: -11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.019, -5.213475109731446, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein Porky_111 [Mycobacterium phage Porky] ],,YP_002014430,100.0,9.81518E-143 SIF-HHPRED: dGTP_diPhyd_N ; dATP/dGTP diphosphohydrolase, N-terminal,,,PF18909.4,48.731,100.0 SIF-Syn: 
    /note=this this a 1:1 match with 197 other matches, the gap is -11 with an overlap, this gene is not the longest open reading frame, covering the entire reading frame

CDS 64845 - 65630
  /gene="114"
  /product="gp114"
  /function="DnaQ-like (DNA polymerase III subunit)"
  /locus tag="Balomoji_114"
    /note=Original Glimmer call @bp 64845 has strength 11.17; Genemark calls start at 64845
    /note=SSC: 64845-65630 CP: yes SCS: both ST: NI BLAST-Start: [DnaQ-like DNA polymerase III subunit [Mycobacterium phage Asriel] ],,NCBI, q1:s1 100.0% 0.0 GAP: 10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.848, -2.8970853586582503, yes F: DnaQ-like (DNA polymerase III subunit) SIF-BLAST: ,,[DnaQ-like DNA polymerase III subunit [Mycobacterium phage Asriel] ],,AVI03348,100.0,0.0 SIF-HHPRED: Cas2-DEDDh; CRISPR, integrase, CRISPR adaptation module, PAM, prespacer, exonuclease, DNA binding protein-DNA complex, enzyme, ribonucleoprotein;{Megasphaera},,,8FYD_D,72.7969,99.2 SIF-Syn: 
    /note=This covers the entire coding potential, has many 1:1 matches, has a gap of 10 that is not ideal for translation, this is the longest open reading, RBS is pretty good

CDS 65627 - 65869
  /gene="115"
  /product="gp115"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_115"
    /note=Original Glimmer call @bp 65627 has strength 9.59; Genemark calls start at 65627
    /note=SSC: 65627-65869 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ASRIEL_113 [Mycobacterium phage Asriel] ],,NCBI, q1:s1 100.0% 1.71215E-52 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.381, -4.707395188728813, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ASRIEL_113 [Mycobacterium phage Asriel] ],,AVI03349,100.0,1.71215E-52 SIF-HHPRED:  SIF-Syn: 
    /note=this is a 1:1 with 3 other matching titles, it has a gap of -4 it is not the longest open reading frame, but has a preferable gap and covers the entire sequence.

CDS 65877 - 66839
  /gene="116"
  /product="gp116"
  /function="RecA-like DNA recombinase"
  /locus tag="Balomoji_116"
    /note=Original Glimmer call @bp 65877 has strength 10.16; Genemark calls start at 65877
    /note=SSC: 65877-66839 CP: yes SCS: both ST: NI BLAST-Start: [UvsX-like recombinase [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 0.0 GAP: 7 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.859, -3.622410502704947, yes F: RecA-like DNA recombinase SIF-BLAST: ,,[UvsX-like recombinase [Mycobacterium phage Cjw1] ],,NP_817564,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=This covers the entire coding potential, with many 1:1 matches, has a gap of 7, longest open reading frame, and the RBS are pretty good.

CDS 66836 - 66973
  /gene="117"
  /product="gp117"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_117"
    /note=Original Glimmer call @bp 66836 has strength 2.87
    /note=SSC: 66836-66973 CP: yes SCS: glimmer ST: NI BLAST-Start: [hypothetical protein Porky_115 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 3.05762E-22 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.783, -2.952618745997422, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein Porky_115 [Mycobacterium phage Porky] ],,YP_002014434,100.0,3.05762E-22 SIF-HHPRED:  SIF-Syn: 
    /note=Covers the entire coding potential. great and many 1;1 blastp matches, ideal gap that is -4, and the ribosome binding site is ideal as well.

CDS 66960 - 67133
  /gene="118"
  /product="gp118"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_118"
    /note=Original Glimmer call @bp 66960 has strength 10.75; Genemark calls start at 66960
    /note=SSC: 66960-67133 CP: yes SCS: both ST: NI BLAST-Start: [gp119 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 1.03307E-32 GAP: -14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.614, -6.513391808765885, no F: Hypothetical Protein SIF-BLAST: ,,[gp119 [Mycobacterium phage Cjw1] ],,NP_817566,100.0,1.03307E-32 SIF-HHPRED:  SIF-Syn: 
    /note=this is a 1:1 with 57 other matching titles, it has a gap of -14 it is the longest open reading frame, and has the most preferable gap of the options and covers the entire sequence.

CDS complement (67123 - 67233)
  /gene="119"
  /product="gp119"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_119"
    /note=Genemark calls start at 67233
    /note=SSC: 67233-67123 CP: yes SCS: genemark ST: NI BLAST-Start: [hypothetical protein SEA_CZYSZCZON1_118 [Mycobacterium phage Czyszczon1] ],,NCBI, q1:s1 100.0% 8.98706E-16 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.317, -4.9845315433504895, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_CZYSZCZON1_118 [Mycobacterium phage Czyszczon1] ],,QAY05302,100.0,8.98706E-16 SIF-HHPRED:  SIF-Syn: 
    /note=This covers the entire coding potential, many 1:1 matches, with a gap of 0, longest open reading frame, and the RBS are pretty good.

CDS complement (67234 - 67506)
  /gene="120"
  /product="gp120"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_120"
    /note=Original Glimmer call @bp 67359 has strength 10.83; Genemark calls start at 67506
    /note=SSC: 67506-67234 CP: yes SCS: both-gm ST: NI BLAST-Start: [hypothetical protein SEA_TRAAWW1_116 [Mycobacterium phage Traaww1] ],,NCBI, q1:s1 100.0% 3.32386E-59 GAP: 15 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.986, -4.629584883725491, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_TRAAWW1_116 [Mycobacterium phage Traaww1] ],,QGJ91929,100.0,3.32386E-59 SIF-HHPRED:  SIF-Syn: 
    /note=It`s the Best gene chosen by Genemark, has 2 1:1 matches, has a 15 nucleotide gap, and has the best ribosome binding site score without having a very large gene overlap problem. Genemark has an advantage over Glimmer because Glimmer had a 162 nucleotide gap while Genemark had only 15 nucleotide gap.

CDS 67522 - 67983
  /gene="121"
  /product="gp121"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_121"
    /note=Original Glimmer call @bp 67522 has strength 6.46; Genemark calls start at 67522
    /note=SSC: 67522-67983 CP: yes SCS: both ST: NI BLAST-Start: [gp122 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 5.13622E-107 GAP: 15 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.02, -2.5969056218148614, yes F: Hypothetical Protein SIF-BLAST: ,,[gp122 [Mycobacterium phage Cjw1] ],,NP_817569,100.0,5.13622E-107 SIF-HHPRED:  SIF-Syn: 
    /note=It`s the best gene chosen by Genemark and Glimmer and has a 1:1 match, a 15 nucleotide gap, the best ribosome binding site, and a smaller gap compared to the other Gene candidates.

CDS 67980 - 68147
  /gene="122"
  /product="gp122"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_122"
    /note=Original Glimmer call @bp 67980 has strength 8.37; Genemark calls start at 67980
    /note=SSC: 67980-68147 CP: yes SCS: both ST: NI BLAST-Start: [gp123 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 1.14822E-32 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.556, -3.5719506502182776, yes F: Hypothetical Protein SIF-BLAST: ,,[gp123 [Mycobacterium phage Cjw1] ],,NP_817570,100.0,1.14822E-32 SIF-HHPRED:  SIF-Syn: 
    /note=it`s the best gene chosen by Genemark and Glimmer, has a 1:1 match, a 4 nucleus overlap, and has the best final and z scores compared to other gene candidates, but does not have the longest open reading frame.

CDS 68131 - 68331
  /gene="123"
  /product="gp123"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_123"
    /note=Original Glimmer call @bp 68131 has strength 10.79; Genemark calls start at 68131
    /note=SSC: 68131-68331 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein Porky_122 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 1.12829E-38 GAP: -17 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.026, -2.970161406017234, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein Porky_122 [Mycobacterium phage Porky] ],,YP_002014441,100.0,1.12829E-38 SIF-HHPRED:  SIF-Syn: 
    /note=it`s the best gene chosen by Genemark and Glimmer, has a 1:1 match, a 4-nucleotide overlap, and has the best final and z-scores compared to the other gene candidates.

CDS 68328 - 68465
  /gene="124"
  /product="gp124"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_124"
    /note=Original Glimmer call @bp 68328 has strength 5.35; Genemark calls start at 68340
    /note=SSC: 68328-68465 CP: yes SCS: both-gl ST: NI BLAST-Start: [gp125 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 4.25336E-24 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.087, -3.222210725506937, yes F: Hypothetical Protein SIF-BLAST: ,,[gp125 [Mycobacterium phage Cjw1] ],,NP_817572,100.0,4.25336E-24 SIF-HHPRED:  SIF-Syn: 
    /note=it`s the best gene chosen by Glimmer, has multiple 1:1 matches, a 4 nucleotide overlap, and has the best final and z-score compared to the other gene candidates.

CDS 68462 - 68641
  /gene="125"
  /product="gp125"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_125"
    /note=Genemark calls start at 68462
    /note=SSC: 68462-68641 CP: yes SCS: genemark ST: NI BLAST-Start: [gp126 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 6.9244E-35 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.855, -5.046247871416941, no F: Hypothetical Protein SIF-BLAST: ,,[gp126 [Mycobacterium phage Cjw1] ],,NP_817573,100.0,6.9244E-35 SIF-HHPRED:  SIF-Syn: 
    /note=it`s the best gene chosen by Genemark, has multiple 1:1 matches, a 4 nucleotide overlap, and has the best final score. Although it doesn`t have the best z-score, it`s other traits make it a better gene candidate than the others.

CDS 68641 - 68772
  /gene="126"
  /product="gp126"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_126"
    /note=Genemark calls start at 68641
    /note=SSC: 68641-68772 CP: yes SCS: genemark ST: NI BLAST-Start: [gp127 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 1.12724E-20 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.716, -5.261583822777037, no F: Hypothetical Protein SIF-BLAST: ,,[gp127 [Mycobacterium phage Cjw1] ],,NP_817574,100.0,1.12724E-20 SIF-HHPRED:  SIF-Syn: 
    /note=it`s the best gene chosen by Genemark, has multiple 1:1 matches, and has the LORF, but as it has multiple 1:1 matches, making it more likely to be a good choice compared to the other gene candidates competitors.

CDS 68783 - 68917
  /gene="127"
  /product="gp127"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_127"
    /note=Genemark calls start at 68783
    /note=SSC: 68783-68917 CP: yes SCS: genemark ST: NI BLAST-Start: [hypothetical protein DRDREY_130 [Mycobacterium phage DrDrey] ],,NCBI, q1:s1 100.0% 1.17026E-23 GAP: 10 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.792, -5.69021729366323, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein DRDREY_130 [Mycobacterium phage DrDrey] ],,YP_008409521,100.0,1.17026E-23 SIF-HHPRED:  SIF-Syn: 
    /note=it was the best gene chosen by genemark, it doesn`t have the best z-scores or final scores, but its other traits make it more desirable than other competitors.

CDS complement (68512 - 68913)
  /gene="128"
  /product="gp128"
  /locus tag="Balomoji_128"
    /note=Original Glimmer call @bp 68913 has strength 8.1
    /note=SSC: 68913-68512 CP: no SCS: glimmer ST: NI BLAST-Start:  GAP: 382 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.147, -7.446192415156777, no F:  SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=deletion/error

CDS complement (69296 - 69559)
  /gene="129"
  /product="gp129"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_129"
    /note=Original Glimmer call @bp 69559 has strength 1.99; Genemark calls start at 69490
    /note=SSC: 69559-69296 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein Kostya_129 [Mycobacterium phage Kostya] ],,NCBI, q1:s1 100.0% 2.58577E-56 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.366, -3.9718914447963414, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein Kostya_129 [Mycobacterium phage Kostya] ],,YP_002014595,100.0,2.58577E-56 SIF-HHPRED: HTH_58 ; Helix-turn-helix domain,,,PF19575.3,42.5287,98.2 SIF-Syn: 
    /note=it was the best gene chosen by Genemark, it doesn`t have the best z-scores or final score, but it matches up with the "Host-Trained Genemark" data better than the other 2 competitors.

CDS complement (69556 - 69945)
  /gene="130"
  /product="gp130"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_130"
    /note=Original Glimmer call @bp 69945 has strength 6.64; Genemark calls start at 69945
    /note=SSC: 69945-69556 CP: yes SCS: both ST: NI BLAST-Start: [ParB C-terminal domain [Mycobacterium phage Mindy] ],,NCBI, q1:s1 100.0% 1.48317E-87 GAP: 118 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.574, -4.443838065747148, no F: Hypothetical Protein SIF-BLAST: ,,[ParB C-terminal domain [Mycobacterium phage Mindy] ],,YP_009225416,100.0,1.48317E-87 SIF-HHPRED:  SIF-Syn: 
    /note=it was the best gene chosen by both Glimmer and Genemark, it has the best z-score and has multiple 1-to-1 matches, making up for its final score not being the best.
    /note=
    /note=Check for ParB nuclease annotation?

CDS complement (70064 - 70318)
  /gene="131"
  /product="gp131"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_131"
    /note=Original Glimmer call @bp 70318 has strength 1.33; Genemark calls start at 70234
    /note=SSC: 70318-70064 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_MINDY_132 [Mycobacterium phage Mindy] ],,NCBI, q1:s1 100.0% 4.90464E-53 GAP: 67 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.762, -3.1379842619144376, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_MINDY_132 [Mycobacterium phage Mindy] ],,YP_009225417,100.0,4.90464E-53 SIF-HHPRED:  SIF-Syn: 
    /note=It was the best gene chosen by Glimmer, it has the best z-score, final score, and multiple 1-to-1 matches, it has a problem with its large gene gap, which its competitors also share.

CDS complement (70386 - 70754)
  /gene="132"
  /product="gp132"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_132"
    /note=Original Glimmer call @bp 70754 has strength 3.81
    /note=SSC: 70754-70386 CP: yes SCS: glimmer ST: NI BLAST-Start: [hypothetical protein SEA_NELITZAMV_129 [Mycobacterium phage NelitzaMV] ],,NCBI, q1:s1 100.0% 4.29382E-85 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.297, -4.327759218808925, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_NELITZAMV_129 [Mycobacterium phage NelitzaMV] ],,YP_009197795,100.0,4.29382E-85 SIF-HHPRED:  SIF-Syn: 
    /note=It was the best gene chosen by Glimmer, it has the best z-score and multiple 1-to-1 matches. it also has the the 4 nucleotide overlap, which overall makes it the best competitor.

CDS complement (70751 - 71215)
  /gene="133"
  /product="gp133"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_133"
    /note=Original Glimmer call @bp 71215 has strength 5.11; Genemark calls start at 71215
    /note=SSC: 71215-70751 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_NELITZAMV_130 [Mycobacterium phage NelitzaMV] ],,NCBI, q1:s1 100.0% 5.36073E-107 GAP: 14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.087, -3.3648782290756687, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_NELITZAMV_130 [Mycobacterium phage NelitzaMV] ],,YP_009197796,100.0,5.36073E-107 SIF-HHPRED:  SIF-Syn: 
    /note=The start at the position 71215 is the optimal start position because it`s the longest gene, has the highest Z-score and final score. It also has a 1:1 blastp match, and was predicted by both Genemark and Glimmer to be the best start choice.

CDS complement (71230 - 71559)
  /gene="134"
  /product="gp134"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_134"
    /note=Original Glimmer call @bp 71559 has strength 8.33; Genemark calls start at 71559
    /note=SSC: 71559-71230 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_CRYSTALP_133 [Mycobacterium phage CrystalP] ],,NCBI, q1:s1 100.0% 5.34674E-74 GAP: 5 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.741, -3.392076448018144, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_CRYSTALP_133 [Mycobacterium phage CrystalP] ],,APU02938,100.0,5.34674E-74 SIF-HHPRED:  SIF-Syn: 
    /note=The start at the position 71559 is the optimal start position, as it has the highest RBS, even if it doesn`t have the highest final score or the longest gene. It also has a 1:1 blastp match, and was predicted by both Genemark and Glimmer to be the best start choice. The longest LORF has a Z-score of 2.538, which is lower than the second LORF.

CDS complement (71565 - 72080)
  /gene="135"
  /product="gp135"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_135"
    /note=Original Glimmer call @bp 72080 has strength 12.57; Genemark calls start at 72080
    /note=SSC: 72080-71565 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein FDI14_gp117 [Mycobacterium phage SirDuracell] ],,NCBI, q1:s1 100.0% 3.20949E-119 GAP: 20 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.968, -5.497276861320775, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDI14_gp117 [Mycobacterium phage SirDuracell] ],,YP_009608065,100.0,3.20949E-119 SIF-HHPRED:  SIF-Syn: 
    /note=The start at the position 72080 is the optimal start position, as it is the longest gene, has the highest Z-score and final score. It also has a 1:1 blastp match, and was predicted by both Genemark and Glimmer to be the best start choice.

CDS complement (72101 - 72412)
  /gene="136"
  /product="gp136"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_136"
    /note=Original Glimmer call @bp 72412 has strength 2.9; Genemark calls start at 72427
    /note=SSC: 72412-72101 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_MINDY_138 [Mycobacterium phage Mindy] ],,NCBI, q1:s6 100.0% 4.10804E-68 GAP: 4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.636, -3.324400402896891, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_MINDY_138 [Mycobacterium phage Mindy] ],,YP_009225423,95.3704,4.10804E-68 SIF-HHPRED:  SIF-Syn: 
    /note=The start at the position 72412 is the optimal start position , even though it is not the longest gene, because it has the best RBS. It also has a 1:1 blastp match, and was predicted by Glimmer to be the best start choice.

CDS complement (72417 - 72542)
  /gene="137"
  /product="gp137"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_137"
    /note=Original Glimmer call @bp 72542 has strength 4.65
    /note=SSC: 72542-72417 CP: yes SCS: glimmer ST: NI BLAST-Start: [hypothetical protein SEA_MINDY_139 [Mycobacterium phage Mindy] ],,NCBI, q1:s1 100.0% 7.33141E-22 GAP: -11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.666, -4.504757315476905, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_MINDY_139 [Mycobacterium phage Mindy] ],,YP_009225424,100.0,7.33141E-22 SIF-HHPRED:  SIF-Syn: 
    /note=The start at the position 72611 is the optimal start position, even though it is not the longest gene, because it has the best RBS without cutting off around 3/4 th of the gene. It also has a 1:1 blastp match, even though it was not predicted by either Glimmer or GeneMark to be the best start position.

CDS complement (72532 - 72738)
  /gene="138"
  /product="gp138"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_138"
    /note=Original Glimmer call @bp 72738 has strength 5.62; Genemark calls start at 72738
    /note=SSC: 72738-72532 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein Porky_138 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 6.6264E-42 GAP: 45 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.742, -3.0387982655504704, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein Porky_138 [Mycobacterium phage Porky] ],,YP_002014457,100.0,6.6264E-42 SIF-HHPRED:  SIF-Syn: 
    /note=The start at the position 72738 is the optimal start position, even though it is not the longest gene, because it has the best RBS. It also has a 1:1 blastp match, and was predicted by both Genemark and Glimmer to be the best start choice.

CDS complement (72784 - 73344)
  /gene="139"
  /product="gp139"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_139"
    /note=Original Glimmer call @bp 73344 has strength 8.34; Genemark calls start at 73344
    /note=SSC: 73344-72784 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_COMMAND613_140 [Mycobacterium phage Command613] ],,NCBI, q1:s1 100.0% 1.99547E-118 GAP: 39 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.839, -2.8363780677724404, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_COMMAND613_140 [Mycobacterium phage Command613] ],,QGJ94113,100.0,1.99547E-118 SIF-HHPRED:  SIF-Syn: 
    /note=The start at the position 73344 is the optimal start position, although it is not the longest gene, because it has the best RBS. Although it does not have any 1:1 blastp matches, it was predicted by both Genemark and Glimmer to be the best start choice.

CDS complement (73384 - 73779)
  /gene="140"
  /product="gp140"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_140"
    /note=Original Glimmer call @bp 73779 has strength 3.1; Genemark calls start at 73779
    /note=SSC: 73779-73384 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ASRIEL_135 [Mycobacterium phage Asriel] ],,NCBI, q1:s1 100.0% 5.2233E-91 GAP: 27 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.609, -4.226420930929867, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ASRIEL_135 [Mycobacterium phage Asriel] ],,AVI03366,100.0,5.2233E-91 SIF-HHPRED:  SIF-Syn: 
    /note=Has the longest reading frame, the best RBS score, covers all coding potential, and is predicted by both Glimmer and Gene Mark

CDS complement (73807 - 74016)
  /gene="141"
  /product="gp141"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_141"
    /note=Original Glimmer call @bp 74016 has strength 6.86; Genemark calls start at 74016
    /note=SSC: 74016-73807 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_MINDY_143 [Mycobacterium phage Mindy] ],,NCBI, q1:s1 100.0% 1.61588E-39 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.393, -3.914968956777623, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_MINDY_143 [Mycobacterium phage Mindy] ],,YP_009225428,100.0,1.61588E-39 SIF-HHPRED:  SIF-Syn: 
    /note=Has LORF, the best RBS score, covers all coding potential, 2 1:1 matches, and is predicted by both Glimmer and Gene Mark

CDS 74016 - 74276
  /gene="142"
  /product="gp142"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_142"
    /note=Original Glimmer call @bp 74016 has strength 4.08
    /note=SSC: 74016-74276 CP: yes SCS: glimmer ST: NI BLAST-Start:  GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.157, -6.37541999031433, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Has the LORF, one of the best RBS scores that covers all coding potential

CDS complement (74434 - 74631)
  /gene="143"
  /product="gp143"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_143"
    /note=Original Glimmer call @bp 74631 has strength 6.6; Genemark calls start at 74631
    /note=SSC: 74631-74434 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ASRIEL_139 [Mycobacterium phage Asriel] ],,NCBI, q1:s1 100.0% 2.44128E-39 GAP: 247 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.776, -3.875201829906135, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ASRIEL_139 [Mycobacterium phage Asriel] ],,AVI03368,100.0,2.44128E-39 SIF-HHPRED:  SIF-Syn: 
    /note=The start at the position 74631 is the optimal start position because it`s the longest gene, has the highest RBS and final score. It also has a 1:1 blastp match, and was predicted by both Genemark and Glimmer to be the best start choice.

CDS 74879 - 75556
  /gene="144"
  /product="gp144"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_144"
    /note=Original Glimmer call @bp 75194 has strength 9.39; Genemark calls start at 75194
    /note=SSC: 74879-75556 CP: yes SCS: both-cs ST: NI BLAST-Start: [hypothetical protein SEA_ASRIEL_142 [Mycobacterium phage Asriel] ],,NCBI, q106:s1 53.3333% 1.40211E-79 GAP: 247 bp gap LO: no RBS: Kibler 6, Karlin Medium, 0.966, -7.128060851526577, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ASRIEL_142 [Mycobacterium phage Asriel] ],,AVI03371,100.0,1.40211E-79 SIF-HHPRED:  SIF-Syn: 
    /note=The start at the position 74879 is the optimal start position, even though it is not the longest gene, because it has a higher RBS and final score, without cutting down most of the gene. It also has a 1:1 blastp match, even though it was not predicted by Genemark or Glimmer to be the best start choice.
    /note=
    /note=AJ note check this start for 50bp space compared to 143

CDS complement (74710 - 74934)
  /gene="145"
  /product="gp145"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_145"
    /note=Original Glimmer call @bp 74934 has strength 6.39; Genemark calls start at 74934
    /note=SSC: 74934-74710 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ASRIEL_140 [Mycobacterium phage Asriel] ],,NCBI, q1:s1 100.0% 2.93966E-46 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.519, -3.649482460397077, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ASRIEL_140 [Mycobacterium phage Asriel] ],,AVI03369,100.0,2.93966E-46 SIF-HHPRED:  SIF-Syn: 
    /note=The start at the position 74934 is the optimal start position because it`s the longest gene, has the highest RBS and final score. It also has a 1:1 blastp match, and was predicted by both Genemark and Glimmer to be the best start choice.

CDS complement (74931 - 75122)
  /gene="146"
  /product="gp146"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_146"
    /note=Original Glimmer call @bp 75122 has strength 6.13; Genemark calls start at 75122
    /note=SSC: 75122-74931 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ASRIEL_141 [Mycobacterium phage Asriel] ],,NCBI, q1:s1 100.0% 1.98865E-39 GAP: 564 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.403, -5.857463951082417, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ASRIEL_141 [Mycobacterium phage Asriel] ],,AVI03370,100.0,1.98865E-39 SIF-HHPRED:  SIF-Syn: 
    /note=The start at the position 75122 is the optimal start position, even though it is not the longest gene, because it has the higher RBS and final score. It also has a 1:1 blastp match, and was predicted by both Genemark and Glimmer to be the best start choice.

CDS 75687 - 75848
  /gene="147"
  /product="gp147"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_147"
    /note=Original Glimmer call @bp 75630 has strength 4.08; Genemark calls start at 75630
    /note=SSC: 75687-75848 CP: yes SCS: both-cs ST: NI BLAST-Start: [hypothetical protein SEA_ASRIEL_143 [Mycobacterium phage Asriel] ],,NCBI, q1:s20 100.0% 1.50758E-28 GAP: 564 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.056, -4.833322097261781, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ASRIEL_143 [Mycobacterium phage Asriel] ],,AVI03379,73.6111,1.50758E-28 SIF-HHPRED:  SIF-Syn: 
    /note=The start at the position 75687 is the optimal start position, even though it is not the longest gene, because it has a higher RBS and final score,. It also has a 1:1 blastp match, even though it was not predicted by Genemark or Glimmer to be the best start choice.

CDS join(76414. .76419;1. .270)
  /gene="148"
  /product="gp148"
  /function="Hypothetical Protein"
  /locus tag="Balomoji_148"
    /note=Original Glimmer call @bp 34 has strength 1.72
    /note=SSC: 76414-270 CP: yes SCS: glimmer-cs ST: NI BLAST-Start: [hypothetical protein SEA_ASRIEL_1 [Mycobacterium phage Asriel] ],,NCBI, q6:s1 94.5055% 8.64097E-58 GAP: 565 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.766, -5.172539920119419, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ASRIEL_1 [Mycobacterium phage Asriel] ],,AVI03251,100.0,8.64097E-58 SIF-HHPRED:  SIF-Syn: 
    /note=The start at the position 76414 is the optimal start position, because it is the longest gene and has a higher RBS and final score. Although it does not have any 1:1 blastp matches, it was predicted by Glimmer to be the best start choice.