CDS 137 - 565
  /gene="1"
  /product="gp1"
  /function="terminase, small subunit"
  /locus tag="ShowerHandel_1"
    /note=Original Glimmer call @bp 137 has strength 6.24; Genemark calls start at 137
    /note=SSC: 137-565 CP: yes SCS: both ST: NI BLAST-Start: [Terminase small subunit [Mycobacterium Phage LunaBlu]],,NCBI, q1:s1 100.0% 8.25626E-98 GAP: 0 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.86, -4.952163809285357, no F: terminase, small subunit SIF-BLAST: ,,[Terminase small subunit [Mycobacterium Phage LunaBlu]],,WNM73981,100.0,8.25626E-98 SIF-HHPRED: Terminase small subunit; genome packaging, bacteriophage, DNA binding, VIRAL PROTEIN; 1.4A {Enterobacteria phage HK97},,,6Z6E_C,55.6338,97.8 SIF-Syn: 
    /note=The main reason we chose position 137 as the start codon was because both the Glimmer and Genemark predictive models predict that the start codon of gene 1 occurs at position 137. In addition, while the Z-score and final score were not the best among gene candidates, they were relatively strong. Furthermore, choosing 137 as the start codon covers all the coding potential. For these reasons, we chose 137 as the start codon for gene 1.

CDS 573 - 2210
  /gene="2"
  /product="gp2"
  /function="terminase, large subunit"
  /locus tag="ShowerHandel_2"
    /note=Original Glimmer call @bp 573 has strength 5.8; Genemark calls start at 654
    /note=SSC: 573-2210 CP: yes SCS: both-gl ST: NI BLAST-Start: [terminase large subunit [Mycobacterium phage ShiLan] ],,NCBI, q1:s1 100.0% 0.0 GAP: 7 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.034, -6.668278635197846, no F: terminase, large subunit SIF-BLAST: ,,[terminase large subunit [Mycobacterium phage ShiLan] ],,YP_009608077,100.0,0.0 SIF-HHPRED: Terminase large subunit; genome packaging, bacteriophage, ATPase, nuclease, VIRAL PROTEIN; HET: BR; 2.2A {Enterobacteria phage HK97},,,6Z6D_A,94.8624,100.0 SIF-Syn: 
    /note=For this annotation, Glimmer and genemark varied in their predictions of what the start codon would be. We decided to choose 573 as the start codon for this gene because it covers all of the coding potential, is in agreement with Glimmers prediction, has several 100% alignments (1:1 matches) in Blastp, and has the longest open reading frame. Altogether, this information makes 573 our choice for the start codon of this gene, despite it not having the most favorable z-score or final score.

CDS 2241 - 3611
  /gene="3"
  /product="gp3"
  /function="portal protein"
  /locus tag="ShowerHandel_3"
    /note=Original Glimmer call @bp 2277 has strength 10.8; Genemark calls start at 2277
    /note=SSC: 2241-3611 CP: yes SCS: both-cs ST: NI BLAST-Start: [gp3 [Mycobacterium phage Pacc40] ],,NCBI, q1:s1 100.0% 0.0 GAP: 30 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.732, -3.2804507689989406, no F: portal protein SIF-BLAST: ,,[gp3 [Mycobacterium phage Pacc40] ],,YP_002241587,99.7807,0.0 SIF-HHPRED: Portal protein; Bacteriophage, SPP1, Portal Protein, Head completion proteins, Connector Complex, DNA Channel, VIRAL PROTEIN; 2.7A {Bacillus subtilis},,,7Z4W_B,94.5175,100.0 SIF-Syn: 
    /note=Since both 2241 and 2277 do not have 1:1 matches we think 2241 is a more likely match since it has the LORF, and the best z-score and final score. However Genemark and Glimmer both predicted 2277 which makes us hesitate. Both starts cover the entire coding potential.

CDS 3598 - 4353
  /gene="4"
  /product="gp4"
  /function="capsid maturation protease"
  /locus tag="ShowerHandel_4"
    /note=Original Glimmer call @bp 3598 has strength 8.42; Genemark calls start at 3598
    /note=SSC: 3598-4353 CP: yes SCS: both ST: NI BLAST-Start: [head maturation protease [Mycobacterium phage GUmbie] ],,NCBI, q1:s1 100.0% 0.0 GAP: -14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.894, -4.109171212198345, yes F: capsid maturation protease SIF-BLAST: ,,[head maturation protease [Mycobacterium phage GUmbie] ],,YP_009018880,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=We chose 3598 as the start codon for this gene because, in every category we used to evaluate the strength of a start codon candidate, it was the most favorable. It covers all of the coding potential, agrees with the Glimmer and Genemark predictions, has 1:1 matches using Blastp, is the longest reading frame, and has the highest z-score and the final score closest to zero among all the candidates.
    /note=
    /note=Function:
    /note=Mu_F because HHPred alignment to gp15 of phage D29

CDS 4437 - 5030
  /gene="5"
  /product="gp5"
  /function="scaffolding protein"
  /locus tag="ShowerHandel_5"
    /note=Original Glimmer call @bp 4437 has strength 9.84; Genemark calls start at 4437
    /note=SSC: 4437-5030 CP: yes SCS: both ST: NI BLAST-Start: [head scaffolding protein [Mycobacterium phage Saal] ],,NCBI, q1:s1 100.0% 2.57314E-137 GAP: 83 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.205, -2.8084998623841946, yes F: scaffolding protein SIF-BLAST: ,,[head scaffolding protein [Mycobacterium phage Saal] ],,YP_009007472,100.0,2.57314E-137 SIF-HHPRED: Scaffold protein; major capsid protein, HK97-like fold, scaffolding protein, procapsid, VIRUS; 3.72A {Staphylococcus phage 80alpha},,,6B0X_b,74.1117,97.5 SIF-Syn: 
    /note=We chose 4437 as the start codon for this gene because, in every category we used to evaluate the strength of a start codon candidate, it was the most favorable. It covers all of the coding potential, agrees with the Glimmer and Genemark predictions, has 1:1 matches using Blastp, is the longest reading frame, and has the highest z-score and the final score closest to zero among all the candidates.

CDS 5049 - 5870
  /gene="6"
  /product="gp6"
  /function="major capsid protein"
  /locus tag="ShowerHandel_6"
    /note=Original Glimmer call @bp 5049 has strength 13.92; Genemark calls start at 5049
    /note=SSC: 5049-5870 CP: yes SCS: both ST: NI BLAST-Start: [major capsid protein [Mycobacterium phage Saal] ],,NCBI, q1:s1 100.0% 0.0 GAP: 18 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.555, -3.5707972674952195, yes F: major capsid protein SIF-BLAST: ,,[major capsid protein [Mycobacterium phage Saal] ],,YP_009007473,100.0,0.0 SIF-HHPRED: Major capsid protein, gp6; HK97-fold, T=9, tailed bacteriophage, VIRUS; 2.5A {Mycobacterium virus Che8},,,8E16_A,99.6337,100.0 SIF-Syn: 
    /note=Position 5049 is an ideal candidate for the star codon of this gene. It covers all of the coding potential, agrees with the predictions by Genemark and Glimmer, has a multitude of 1:1 matches in Blastp, has the longest open reading frame, and has the most favorable RBS scores among candidates.

CDS 5879 - 6448
  /gene="7"
  /product="gp7"
  /function="head-to-tail adaptor"
  /locus tag="ShowerHandel_7"
    /note=Original Glimmer call @bp 5963 has strength 3.11; Genemark calls start at 5879
    /note=SSC: 5879-6448 CP: yes SCS: both-gm ST: NI BLAST-Start: [head-tail adaptor Ad1 [Mycobacterium phage Pacc40] ],,NCBI, q1:s1 100.0% 6.3538E-130 GAP: 8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.307, -6.452925797815746, no F: head-to-tail adaptor SIF-BLAST: ,,[head-tail adaptor Ad1 [Mycobacterium phage Pacc40] ],,YP_002241591,100.0,6.3538E-130 SIF-HHPRED: Head completion protein; Neck, Portal, T5, VIRUS, VIRAL PROTEIN; 3.2A {Escherichia phage DT57C},,,8HQO_S,94.709,99.9 SIF-Syn: 
    /note=Although 5879 does not have good RBS scores, and 5963 has the most favorable RBS scores, we chose 5879 because it covers the entire coding potential, is the longest open reading frame, and because 5963 does not hace 1:1 matches with Blastp hits.
    /note=
    /note=Function:
    /note=7Z4W_l 4th HHPred hit, matches our naming criteria " must have an
    /note=HHPRED alignment to one of the following crystal structures: SPP1 15
    /note=(5A21 chain C or D in the macromolecular complex) OR must have an
    /note=HHPRED alignment to one of the following crystal structures: HK97 gp6
    /note=or or Bacillus protein yqbG"

CDS 6445 - 6774
  /gene="8"
  /product="gp8"
  /function="head-to-tail stopper"
  /locus tag="ShowerHandel_8"
    /note=Original Glimmer call @bp 6445 has strength 7.13; Genemark calls start at 6445
    /note=SSC: 6445-6774 CP: yes SCS: both ST: NI BLAST-Start: [head-tail adaptor [Mycobacterium phage ShiLan] ],,NCBI, q1:s1 100.0% 1.28057E-71 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.784, -5.461711027312092, no F: head-to-tail stopper SIF-BLAST: ,,[head-tail adaptor [Mycobacterium phage ShiLan] ],,YP_009608083,100.0,1.28057E-71 SIF-HHPRED: Head completion protein gp16; Bacteriophage, SPP1, Portal Protein, Head completion proteins, Connector Complex, DNA Channel, VIRAL PROTEIN; 2.7A {Bacillus subtilis},,,7Z4W_5,99.0826,99.5 SIF-Syn: 
    /note=The negatives of this candidate, position 6445, for the start codon of Gene 8 are that it has poor RBS scores and is not the longest open reading frame. While this is the case, we chose it as the start codon for this gene because it has 1:1 matches and agrees with the prediction made by both Genemark and Glimmer.
    /note=
    /note=Function:
    /note=7Z4W_5 is the 5th HHPred hit, is SPP1 gp16, to meet this criteria: "must
    /note=have an HHPRED alignment to one of the following crystal structures:
    /note=SPP1 16 (5A21 chain E or F in the macromolecular complex) or Bacillus
    /note=protein yqbH"

CDS 6811 - 7107
  /gene="9"
  /product="gp9"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_9"
    /note=Original Glimmer call @bp 6811 has strength 9.48; Genemark calls start at 6811
    /note=SSC: 6811-7107 CP: yes SCS: both ST: NI BLAST-Start: [head-tail connector protein [Mycobacterium phage Pacc40] ],,NCBI, q1:s1 100.0% 8.01792E-65 GAP: 36 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.815, -3.0301037898918786, yes F: Hypothetical Protein SIF-BLAST: ,,[head-tail connector protein [Mycobacterium phage Pacc40] ],,YP_002241593,98.9796,8.01792E-65 SIF-HHPRED: HK97-gp10_like ; Bacteriophage HK97-gp10, putative tail-component,,,PF04883.16,60.2041,99.1 SIF-Syn: 
    /note=6811 is predicted by both Genemark and Glimmer, has the most favorable RBS, and covers the entire coding potential. We choose this as the start codon despite the fact that it does not have the longest open reading frame or any 1:1 matches in Blastp.
    /note=
    /note=Function:
    /note=Has HHPred match to HK97 gp10
    /note="Hendrix lab (studiers of HK97 and capsid construction) never ID`d a
    /note=function for this gene"

CDS 7097 - 7501
  /gene="10"
  /product="gp10"
  /function="tail terminator"
  /locus tag="ShowerHandel_10"
    /note=Original Glimmer call @bp 7253 has strength 9.68; Genemark calls start at 7097
    /note=SSC: 7097-7501 CP: yes SCS: both-gm ST: NI BLAST-Start: [head-tail adaptor [Mycobacterium phage Boomer] ],,NCBI, q1:s1 100.0% 2.19429E-89 GAP: -11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.921, -4.825272756372522, no F: tail terminator SIF-BLAST: ,,[head-tail adaptor [Mycobacterium phage Boomer] ],,YP_002014227,100.0,2.19429E-89 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,97.7612,99.4 SIF-Syn: 
    /note=We chose 7097 because it has decent RBS scores, covers the entire coding potential, matches the prediction of Genemark, and has 1:1 matches in Blastp (7253 does not)
    /note=
    /note=Function:
    /note=The second HHPred hit is 5A21_G, SPPT gp 17, matching criteria: "must
    /note=have an HHPRED alignment to one of the following: SPP1 17 (5A21 chain
    /note=G in the macromolecular complex) or Lambda U (3FZ2_chains A through
    /note=F)"

CDS complement (7109 - 7273)
  /gene="11"
  /product="gp11"
  /locus tag="ShowerHandel_11"
    /note=Original Glimmer call @bp 7273 has strength 4.04
    /note=SSC: 7273-7109 CP: no SCS: glimmer ST: NI BLAST-Start:  GAP: 336 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.337, -6.118389669402134, no F:  SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=This gene is going to be deleted because its open reading frame over laps with genes 9 and 10 from Phamerator Image

CDS 7610 - 8419
  /gene="12"
  /product="gp12"
  /function="major tail protein"
  /locus tag="ShowerHandel_12"
    /note=Original Glimmer call @bp 7610 has strength 14.98; Genemark calls start at 7610
    /note=SSC: 7610-8419 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein [Sneathia sanguinegens] ],,NCBI, q1:s1 100.0% 0.0 GAP: 336 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.147, -2.338663114094478, yes F: major tail protein SIF-BLAST: ,,[hypothetical protein [Sneathia sanguinegens] ],,WP_015982045,100.0,0.0 SIF-HHPRED: YSD1_22 major tail protein; Bacteriophage tail, helical assembly, VIRAL PROTEIN; 3.5A {Bacteriophage sp.},,,6XGR_M,56.1338,96.6 SIF-Syn: 
    /note=7610 is the best start codon candidate because it has the most favorable RBS scores, covers all of the coding potential, has 1:1 matches in Blastp, and agrees with the predictions by Genemark and Glimmer. The issues with this start codon are it does not have the longest open reading frameand it has a relatively large gap.

CDS 8538 - 9089
  /gene="13"
  /product="gp13"
  /function="tail assembly chaperone"
  /locus tag="ShowerHandel_13"
    /note=Original Glimmer call @bp 8538 has strength 10.01; Genemark calls start at 8538
    /note=SSC: 8538-9089 CP: yes SCS: both ST: NI BLAST-Start: [tail assembly chaperone [Mycobacterium phage WIVsmall] ],,NCBI, q1:s1 100.0% 8.94648E-130 GAP: 118 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.216, -2.1958114445137396, yes F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Mycobacterium phage WIVsmall] ],,YP_008059973,100.0,8.94648E-130 SIF-HHPRED: GP24_25 ; Mycobacteriophage tail assembly protein,,,PF17388.6,31.694,95.8 SIF-Syn: 
    /note=We chose this start codon for gene #13 because it covers all the coding potential, agrees with the prediction by Genemark and Glimmer, has 1:1 matches in Blastp, and has the best RBS scores. The only downsides of this start codon are that it did not have the longest open reading frame.

CDS 9148 - 9474
  /gene="14"
  /product="gp14"
  /function="tail assembly chaperone"
  /locus tag="ShowerHandel_14"
    /note=Original Glimmer call @bp 9040 has strength 7.88; Genemark calls start at 9148
    /note=SSC: 9148-9474 CP: yes SCS: both-gm ST: NI BLAST-Start: [tail assembly chaperone [Mycobacterium phage LOCARD]],,NCBI, q1:s1 100.0% 9.35255E-68 GAP: 58 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.337, -5.062450304550039, no F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Mycobacterium phage LOCARD]],,WDW19988,98.1481,9.35255E-68 SIF-HHPRED:  SIF-Syn: 
    /note=The start is at position 9148 and is not the longest section of gene but it has a smaller gene overlap than some others on table. Has a 1:1, and the section of the gene doesn`t have the best Z score but it`s better than the Glimmer start.

CDS 9492 - 13019
  /gene="15"
  /product="gp15"
  /function="tape measure protein"
  /locus tag="ShowerHandel_15"
    /note=Original Glimmer call @bp 9492 has strength 7.56; Genemark calls start at 9492
    /note=SSC: 9492-13019 CP: no SCS: both ST: NI BLAST-Start: [tail length tape measure protein [Mycobacterium phage ShiLan] ],,NCBI, q1:s1 100.0% 0.0 GAP: 17 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.477, -3.8116689268127657, no F: tape measure protein SIF-BLAST: ,,[tail length tape measure protein [Mycobacterium phage ShiLan] ],,YP_009608089,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=A very long section of the gene that starts at 9471 to 13019. The start and stop covers the whole coding potential, has more than 10 1:1s, and has a 4 nucleotide overlap(-4)(ideal). This section isn`t at all the best score even of the top 5 other sections but it is the longest section

tRNA 11051 - 11122
  /gene="16"
  /product="tRNA-Thr(ggt)"
  /locus tag="SHOWERHANDEL_16"
    /note=tRNA-Thr(ggt)

CDS 13020 - 14729
  /gene="17"
  /product="gp17"
  /function="minor tail protein"
  /locus tag="ShowerHandel_17"
    /note=Original Glimmer call @bp 13020 has strength 12.3; Genemark calls start at 13020
    /note=SSC: 13020-14729 CP: yes SCS: both ST: NI BLAST-Start: [minor tail subunit [Mycobacterium phage ShiLan] ],,NCBI, q1:s1 100.0% 0.0 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.961, -4.821320819095688, no F: minor tail protein SIF-BLAST: ,,[minor tail subunit [Mycobacterium phage ShiLan] ],,YP_009608090,100.0,0.0 SIF-HHPRED: Dit_N ; Distal tail protein, N-terminal domain,,,PF16774.9,27.5923,99.3 SIF-Syn: 
    /note=Doesn`t have the best RBS score of the bunch, other sections have better ones. This section of the gene that starts at 13020 to 14729. The start and stop covers the whole coding potential, is the longest, has more than 20 1:1s, and has no nucleotide overlap/gap while the others have gaps of 70+.

CDS 14813 - 16522
  /gene="18"
  /product="gp18"
  /function="minor tail protein"
  /locus tag="ShowerHandel_18"
    /note=Original Glimmer call @bp 14813 has strength 13.78; Genemark calls start at 14813
    /note=SSC: 14813-16522 CP: yes SCS: both ST: NI BLAST-Start: [minor tail protein [Mycobacterium phage ShiLan] ],,NCBI, q1:s1 100.0% 0.0 GAP: 83 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.303, -2.606079664606164, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Mycobacterium phage ShiLan] ],,YP_009608091,100.0,0.0 SIF-HHPRED: Sipho_Gp37 ; Siphovirus ReqiPepy6 Gp37-like protein,,,PF14594.10,85.5888,99.9 SIF-Syn: 
    /note=A long section of the gene that starts at 14813 to 16522 and a length of 1,710. It has a 1:1 with 10+ other sequences, and has a 83 nucleotide gap (a lot). It has the best final and Z-score in comparison to the others.

CDS 16579 - 17409
  /gene="19"
  /product="gp19"
  /function="Minor tail Protein"
  /locus tag="ShowerHandel_19"
    /note=Original Glimmer call @bp 16579 has strength 9.64; Genemark calls start at 16579
    /note=SSC: 16579-17409 CP: yes SCS: both ST: NI BLAST-Start: [minor tail protein [Mycobacterium phage Burwell21] ],,NCBI, q1:s1 100.0% 0.0 GAP: 56 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.877, -3.1896562502401133, yes F: Minor tail Protein SIF-BLAST: ,,[minor tail protein [Mycobacterium phage Burwell21] ],,YP_009955129,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=It`s not the longest section of the gene, only shorter by a bit, the longest has a length of 846. This section does have a better Z-and final score than the others, however the gap is a lot.

CDS 17406 - 19958
  /gene="20"
  /product="gp20"
  /function="minor tail protein"
  /locus tag="ShowerHandel_20"
    /note=Original Glimmer call @bp 17406 has strength 7.7; Genemark calls start at 17406
    /note=SSC: 17406-19958 CP: yes SCS: both ST: NI BLAST-Start: [minor tail protein [Mycobacterium phage Cabrinians] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.421, -4.694587342996602, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Mycobacterium phage Cabrinians] ],,YP_009189740,100.0,0.0 SIF-HHPRED: Endoglucanase; Thermogutta terrifontis endoglucanase of HG5 family, Cellulase, apo structure, HYDROLASE; HET: SO4; 1.56A {Thermogutta terrifontis},,,8AG9_A,18.3529,97.6 SIF-Syn: 
    /note=The gene segment chosen has the longest length (2553) and a 4 nucleotide overlap(ideal). It has the third best Final-score and the second best Z-score. The prediction covers the entire coding potential.

CDS 19955 - 21844
  /gene="21"
  /product="gp21"
  /function="minor tail protein"
  /locus tag="ShowerHandel_21"
    /note=Original Glimmer call @bp 19955 has strength 7.2; Genemark calls start at 19955
    /note=SSC: 19955-21844 CP: yes SCS: both ST: NI BLAST-Start: [minor tail protein with lysin activity [Mycobacterium phage ShiLan] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.026, -5.6562426662814325, no F: minor tail protein SIF-BLAST: ,,[minor tail protein with lysin activity [Mycobacterium phage ShiLan] ],,YP_009608094,100.0,0.0 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,53.5771,100.0 SIF-Syn: 
    /note=The start and stop positions are predicated by both Glimmer and Genemark, it has a 1:1 with multiple other sequences. The RBS score wasn`t the best (Zscore and Final score pretty low in comparison), but it does have the ideal overlap of 4 and the spacer is in a good range.

CDS 21844 - 23046
  /gene="22"
  /product="gp22"
  /function="minor tail protein"
  /locus tag="ShowerHandel_22"
    /note=Original Glimmer call @bp 21844 has strength 3.86; Genemark calls start at 21802
    /note=SSC: 21844-23046 CP: yes SCS: both-gl ST: NI BLAST-Start: [minor tail protein [Mycobacterium phage Cabrinians] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.426, -5.916673162539987, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Mycobacterium phage Cabrinians] ],,YP_009189742,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Choosing this gene segment, Genemark over Glimmer start. Overlap is a bit much and it only has one 1:1, but has a better RBS score by a bit and has the longest ORF

CDS 23070 - 23411
  /gene="23"
  /product="gp23"
  /function="minor tail protein"
  /locus tag="ShowerHandel_23"
    /note=Original Glimmer call @bp 23070 has strength 5.24; Genemark calls start at 23070
    /note=SSC: 23070-23411 CP: yes SCS: both ST: NI BLAST-Start: [head protein [Mycobacterium phage Cabrinians] ],,NCBI, q1:s1 100.0% 1.21691E-69 GAP: 23 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.205, -2.297359520375101, yes F: minor tail protein SIF-BLAST: ,,[head protein [Mycobacterium phage Cabrinians] ],,YP_009189743,100.0,1.21691E-69 SIF-HHPRED:  SIF-Syn: 
    /note=The start and stop positions are predicated by both Glimmer and Genemark, has the best RBS and the gap isn`t too bad compared the others, but not ideal(23). Has multiple 1:1 matches but isn`t the longest ORF though.
    /note=This is the 7th minor tail protein in a row, please check.

CDS 23554 - 23808
  /gene="24"
  /product="gp24"
  /function="minor tail protein"
  /locus tag="ShowerHandel_24"
    /note=Original Glimmer call @bp 23554 has strength 9.77; Genemark calls start at 23554
    /note=SSC: 23554-23808 CP: yes SCS: both ST: NI BLAST-Start: [minor tail protein [Mycobacterium phage Cabrinians] ],,NCBI, q1:s1 100.0% 1.005E-54 GAP: 142 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.497, -3.6907860541164537, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Mycobacterium phage Cabrinians] ],,YP_009189744,100.0,1.005E-54 SIF-HHPRED:  SIF-Syn: 
    /note=The start and stop positions are predicated by both Glimmer and Genemark, but it has a pretty short gene length so it definitely isn`t the longest ORF. It has the best RBS and multiple 1:1 matches.

CDS 23821 - 24459
  /gene="25"
  /product="gp25"
  /function="minor tail protein"
  /locus tag="ShowerHandel_25"
    /note=Original Glimmer call @bp 23821 has strength 7.37; Genemark calls start at 23821
    /note=SSC: 23821-24459 CP: yes SCS: both ST: NI BLAST-Start: [minor tail protein [Mycobacterium phage Burwell21] ],,NCBI, q1:s1 100.0% 3.0449E-147 GAP: 12 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.652, -3.3060637489568596, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Mycobacterium phage Burwell21] ],,YP_009955135,100.0,3.0449E-147 SIF-HHPRED:  SIF-Syn: 
    /note=The start and stop positions are predicated by both Glimmer and Genemark, it has a 1:1 with multiple other sequences. The RBS score wasn`t the best (Zscore and Final score were only second best), but it does have a better gap distance and the spacer is in a good range compared to the other positions.

CDS 24456 - 25280
  /gene="26"
  /product="gp26"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_26"
    /note=Original Glimmer call @bp 24456 has strength 0.44; Genemark calls start at 24456
    /note=SSC: 24456-25280 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ZIZZLE_24 [Mycobacterium phage Zizzle]],,NCBI, q1:s1 100.0% 2.90192E-176 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.297, -4.123435721190396, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ZIZZLE_24 [Mycobacterium phage Zizzle]],,QYC54810,100.0,2.90192E-176 SIF-HHPRED:  SIF-Syn: 
    /note=The start and stop positions are predicated by both Glimmer and Genemark and this section has the best Z and Final score but its length isn`t the longest. It`s shorter by 60 BP. The overlap is ideal and it has a multiple 1:1 matches. 
    /note=
    /note=This is a hypothetical protein, shouldn`t be minor. Please take a look.

CDS complement (25286 - 25483)
  /gene="27"
  /product="gp27"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="ShowerHandel_27"
    /note=Original Glimmer call @bp 25465 has strength 10.18; Genemark calls start at 25483
    /note=SSC: 25483-25286 CP: yes SCS: both-gm ST: NI BLAST-Start: [HTH DNA binding protein [Mycobacterium phage Pacc40] ],,NCBI, q1:s1 100.0% 1.25448E-38 GAP: 148 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.474, -6.661315563983987, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[HTH DNA binding protein [Mycobacterium phage Pacc40] ],,YP_002241609,100.0,1.25448E-38 SIF-HHPRED:  SIF-Syn: 
    /note=I prefer the GeneMark start, it has a longer length and the gap is wide but not as much as the Glimmer gap. The Final and Z scores are better but the spacer isn`t ideal in comparison. It`s also a bit longer.

CDS 25632 - 25916
  /gene="28"
  /product="gp28"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_28"
    /note=Original Glimmer call @bp 25632 has strength 10.51; Genemark calls start at 25632
    /note=SSC: 25632-25916 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein FDI15_gp026 [Mycobacterium phage ShiLan] ],,NCBI, q1:s1 100.0% 3.35356E-61 GAP: 148 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.226, -2.253377680616507, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDI15_gp026 [Mycobacterium phage ShiLan] ],,YP_009608101,100.0,3.35356E-61 SIF-HHPRED:  SIF-Syn: 
    /note=The start and stop positions are predicated by both Glimmer and Genemark, it has a 1:1 with multiple other sequences. The RBS score were the best and it does have a better gap distance. The spacer is in a good range compared to the other positions and it`s the longest.

CDS 25923 - 26069
  /gene="29"
  /product="gp29"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_29"
    /note=Original Glimmer call @bp 25923 has strength 8.82
    /note=SSC: 25923-26069 CP: no SCS: glimmer ST: NI BLAST-Start: [hypothetical protein FDG57_gp027 [Mycobacterium phage Mutaforma13] ],,NCBI, q1:s1 100.0% 1.37755E-25 GAP: 6 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.13, -4.4536196888290105, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDG57_gp027 [Mycobacterium phage Mutaforma13] ],,YP_009591334,100.0,1.37755E-25 SIF-HHPRED:  SIF-Syn: 
    /note=Positional annotation: The start position 25923 because it was predicted by both tools. This has the highest z score and a spacer of 12. Although the gap is 166 nucleotides, there is a high coding potential. This also has a high gap and  a low final score

CDS 26066 - 26206
  /gene="30"
  /product="gp30"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_30"
    /note=Original Glimmer call @bp 26066 has strength 11.49; Genemark calls start at 26066
    /note=SSC: 26066-26206 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_CHE8_30 [Mycobacterium phage Che8] ],,NCBI, q1:s1 100.0% 1.81316E-23 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.237, -2.0895162839948163, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_CHE8_30 [Mycobacterium phage Che8] ],,NP_817368,100.0,1.81316E-23 SIF-HHPRED:  SIF-Syn: 
    /note=The start position of 26066 was chosen because it was the longest ORF. There is only one other option and that other option has a higher final score, lower z score, and a gap of 71. This on the other hand, has a longer length and higher final score.

CDS 26273 - 26506
  /gene="31"
  /product="gp31"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_31"
    /note=Original Glimmer call @bp 26273 has strength 15.26; Genemark calls start at 26273
    /note=SSC: 26273-26506 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein I5H19_gp029 [Mycobacterium phage Burwell21] ],,NCBI, q1:s1 100.0% 1.59658E-43 GAP: 66 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.817, -3.0248543014571307, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein I5H19_gp029 [Mycobacterium phage Burwell21] ],,YP_009955141,100.0,1.59658E-43 SIF-HHPRED:  SIF-Syn: 
    /note=The start position is 26273 because it was predicted by both tools. This has the highest z score score and high spacer. This has the LORF.

CDS 26503 - 27699
  /gene="32"
  /product="gp32"
  /function="lysin A"
  /locus tag="ShowerHandel_32"
    /note=Original Glimmer call @bp 26503 has strength 11.85; Genemark calls start at 26503
    /note=SSC: 26503-27699 CP: yes SCS: both ST: NI BLAST-Start: [endolysin [Mycobacterium phage ShiLan] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.208, -4.229395370396053, no F: lysin A SIF-BLAST: ,,[endolysin [Mycobacterium phage ShiLan] ],,YP_009608105,100.0,0.0 SIF-HHPRED: N-acetylmuramoyl-L-alanine amidase amiD; ZINC AMIDASE, PGRP, Peptidoglycan Recognizing Protein, AmpD, N-ACETYLMURAMYL-L-ALANINE AMIDASE, Cell wall biogenesis/degradation, Hydrolase, Lipoprotein, Membrane, Metal-binding; HET: GOL, AH0; 1.75A {Escherichia coli},,,3D2Y_A,36.6834,99.4 SIF-Syn: 
    /note=The start position is 26503 because it was predicted by both tools. While the final score is not the highest one, this one has the longest open reading frame and has a spacer of 10. This has a high coding potential consistently throughout.

CDS 27699 - 28700
  /gene="33"
  /product="gp33"
  /function="lysin B"
  /locus tag="ShowerHandel_33"
    /note=Original Glimmer call @bp 27699 has strength 11.86; Genemark calls start at 27699
    /note=SSC: 27699-28700 CP: yes SCS: both ST: NI BLAST-Start: [endolysin [Mycobacterium phage ShiLan] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.167, -4.455662434380964, no F: lysin B SIF-BLAST: ,,[endolysin [Mycobacterium phage ShiLan] ],,YP_009608106,100.0,0.0 SIF-HHPRED: Gene 12 protein; alpha/beta sandwich, CELL ADHESION; 2.0A {Mycobacterium phage D29},,,3HC7_A,72.3724,100.0 SIF-Syn: 
    /note=The start position is 27699 since it was predicted by two tools. This one is the longest coding reading frame, has the LORF, and the smallest gap.

CDS 28709 - 28942
  /gene="34"
  /product="gp34"
  /function="Holin"
  /locus tag="ShowerHandel_34"
    /note=Original Glimmer call @bp 28709 has strength 7.74; Genemark calls start at 28709
    /note=SSC: 28709-28942 CP: yes SCS: both ST: NI BLAST-Start: [holin [Mycobacterium phage Tweety] ],,NCBI, q1:s1 100.0% 5.20843E-44 GAP: 8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.397, -3.9166971242758706, no F: Holin SIF-BLAST: ,,[holin [Mycobacterium phage Tweety] ],,YP_001469265,100.0,5.20843E-44 SIF-HHPRED: Phage_r1t_holin ; Putative lactococcus lactis phage r1t holin,,,PF16945.9,89.6104,99.9 SIF-Syn: 
    /note=The start position is 28709 since it was predicted by both tools. This gene has the shortest gap, the highest final score, and a larger length

CDS 28939 - 29313
  /gene="35"
  /product="gp35"
  /function="Membrane protein"
  /locus tag="ShowerHandel_35"
    /note=Original Glimmer call @bp 28939 has strength 9.16; Genemark calls start at 28939
    /note=SSC: 28939-29313 CP: yes SCS: both ST: NI BLAST-Start: [minor tail protein [Mycobacterium phage Cabrinians] ],,NCBI, q1:s1 100.0% 3.75561E-80 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.671, -5.4858509637772555, no F: Membrane protein SIF-BLAST: ,,[minor tail protein [Mycobacterium phage Cabrinians] ],,YP_009189755,100.0,3.75561E-80 SIF-HHPRED:  SIF-Syn: 
    /note=The start position is 28939 since it was predicted by both tools. This has the highest z score and the smallest gap. There is a 100% query coverage

CDS 29310 - 29570
  /gene="36"
  /product="gp36"
  /function="Hypothetical protein"
  /locus tag="ShowerHandel_36"
    /note=Original Glimmer call @bp 29337 has strength 5.96; Genemark calls start at 29337
    /note=SSC: 29310-29570 CP: yes SCS: both-cs ST: NI BLAST-Start: [hypothetical protein FDI15_gp034 [Mycobacterium phage ShiLan] ],,NCBI, q1:s1 100.0% 7.27306E-56 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.403, -6.042179413656743, no F: Hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI15_gp034 [Mycobacterium phage ShiLan] ],,YP_009608109,100.0,7.27306E-56 SIF-HHPRED:  SIF-Syn: 
    /note=While this wasn`t predicted by either Glimmer or Genemark, we think that the start position for this gene is 29310 since it has the LORF, has a good gap, and a good spacer.

CDS 29557 - 30378
  /gene="37"
  /product="gp37"
  /function="DnaQ-like (DNA polymerase III subunit)"
  /locus tag="ShowerHandel_37"
    /note=Original Glimmer call @bp 29584 has strength 12.16; Genemark calls start at 29584
    /note=SSC: 29557-30378 CP: no SCS: both-cs ST: NI BLAST-Start: [DnaQ-like DNA polymerase III subunit [Mycobacterium phage Che8] ],,NCBI, q1:s1 100.0% 0.0 GAP: -14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.815, -3.0478325568523097, no F: DnaQ-like (DNA polymerase III subunit) SIF-BLAST: ,,[DnaQ-like DNA polymerase III subunit [Mycobacterium phage Che8] ],,NP_817375,100.0,0.0 SIF-HHPRED: DNA_polB_Kod1_like_exo; DEDDy 3`-5` exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases.,,,cd05780,45.0549,99.3 SIF-Syn: 
    /note=The start position is 29557 since this has the LORF. While the gap is larger the spacer is small. This wasn`t predicted by Genemark or Glimmer but this gene was selected.

CDS 30462 - 30683
  /gene="38"
  /product="gp38"
  /function="Hypothetical protein"
  /locus tag="ShowerHandel_38"
    /note=Original Glimmer call @bp 30465 has strength 6.25; Genemark calls start at 30465
    /note=SSC: 30462-30683 CP: yes SCS: both-cs ST: NI BLAST-Start: [hypothetical protein AU088_gp036 [Mycobacterium phage Cabrinians] ],,NCBI, q1:s1 100.0% 5.03765E-44 GAP: 83 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.048, -5.213475109731446, no F: Hypothetical protein SIF-BLAST: ,,[hypothetical protein AU088_gp036 [Mycobacterium phage Cabrinians] ],,YP_009189758,100.0,5.03765E-44 SIF-HHPRED:  SIF-Syn: 
    /note=The start position is 30462. This has the LORF, the smallest gap, and longest coding potential region

CDS 30691 - 30768
  /gene="39"
  /product="gp39"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_39"
    /note=Genemark calls start at 30676
    /note=SSC: 30691-30768 CP: yes SCS: genemark-cs ST: NI BLAST-Start: [hypothetical protein SEA_KOELLA_31 [Mycobacterium phage Koella] ],,NCBI, q1:s10 100.0% 3.01406E-5 GAP: 7 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.376, -4.980654393880506, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_KOELLA_31 [Mycobacterium phage Koella] ],,AWY03652,73.5294,3.01406E-5 SIF-HHPRED:  SIF-Syn: 
    /note=The start position is 30664. This is the longest reading frame, a small gap, and it has a higher final score. But it doesn`t have the LORF.

CDS complement (30837 - 30983)
  /gene="40"
  /product="gp40"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_40"
    /note=Original Glimmer call @bp 30983 has strength 7.84; Genemark calls start at 30983
    /note=SSC: 30983-30837 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_CHE9D_42 [Mycobacterium phage Che9d] ],,NCBI, q1:s1 100.0% 1.15544E-25 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.129, -4.534089041695007, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_CHE9D_42 [Mycobacterium phage Che9d] ],,NP_818015,100.0,1.15544E-25 SIF-HHPRED:  SIF-Syn: 
    /note=The start position is 30983 since it was predicted by both Glimmer and Genemark. This is the longest reading frame, with the highest final score.

CDS complement (30976 - 31182)
  /gene="41"
  /product="gp41"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_41"
    /note=Original Glimmer call @bp 31182 has strength 11.46; Genemark calls start at 31182
    /note=SSC: 31182-30976 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein N850_gp046 [Mycobacterium phage Jabbawokkie] ],,NCBI, q1:s1 100.0% 1.49389E-41 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.916, -4.897971560974249, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein N850_gp046 [Mycobacterium phage Jabbawokkie] ],,YP_008410718,100.0,1.49389E-41 SIF-HHPRED:  SIF-Syn: 
    /note=The start position 31182 on the reverse strand was chosen because it was predicted by both tools, is the longest ORF, has a small gap, covers all coding potential, has a few 1:1 blastp matches, and has the best RBS scores. 
    /note=*check for membrane protein

CDS complement (31179 - 31301)
  /gene="42"
  /product="gp42"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_42"
    /note=Original Glimmer call @bp 31301 has strength 3.65; Genemark calls start at 31319
    /note=SSC: 31301-31179 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein N850_gp047 [Mycobacterium phage Jabbawokkie] ],,NCBI, q1:s1 100.0% 3.7798E-21 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.561, -5.574346888390875, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein N850_gp047 [Mycobacterium phage Jabbawokkie] ],,YP_008410719,100.0,3.7798E-21 SIF-HHPRED:  SIF-Syn: 
    /note=Covers all coding potential, has a 1:1 sequence match, and there is 1 nucleotide overlap. However, the scores of this sequence are not the best of the ones presented.

CDS complement (31301 - 31423)
  /gene="43"
  /product="gp43"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_43"
    /note=Original Glimmer call @bp 31423 has strength 4.25
    /note=SSC: 31423-31301 CP: no SCS: glimmer ST: NI BLAST-Start: [hypothetical protein AU088_gp041 [Mycobacterium phage Cabrinians] ],,NCBI, q1:s1 100.0% 5.34346E-20 GAP: 7 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.761, -5.220380545373514, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein AU088_gp041 [Mycobacterium phage Cabrinians] ],,YP_009189763,100.0,5.34346E-20 SIF-HHPRED:  SIF-Syn: 
    /note=The final score is small, and the gene is not predicted by Gene Mark. There is a small gap and 1 1:1 match on blastp.

CDS complement (31431 - 32651)
  /gene="44"
  /product="gp44"
  /function="transposase"
  /locus tag="ShowerHandel_44"
    /note=Original Glimmer call @bp 32651 has strength 9.06; Genemark calls start at 32651
    /note=SSC: 32651-31431 CP: no SCS: both ST: NI BLAST-Start: [transposase [Mycobacterium phage Priscilla] ],,NCBI, q1:s1 100.0% 0.0 GAP: 10 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.91, -5.50074291708362, no F: transposase SIF-BLAST: ,,[transposase [Mycobacterium phage Priscilla] ],,YP_009961659,100.0,0.0 SIF-HHPRED: RNA-guided DNA endonuclease TnpB; CRISPR-Cas, Transposon-associated protein, RNA BINDING PROTEIN;{Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539},,,8H1J_A,90.1478,100.0 SIF-Syn: 
    /note=This sequence has a prediction that partly covers the coding potential, is predicted by both Gene Mark and Glimmer, and has one top match from Blastp. However, it is not the longest sequence, nor does it have the best scores compared to the other sequences.

CDS complement (32662 - 32826)
  /gene="45"
  /product="gp45"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_45"
    /note=Original Glimmer call @bp 32826 has strength 2.78
    /note=SSC: 32826-32662 CP: no SCS: glimmer ST: NI BLAST-Start: [hypothetical protein AU088_gp043 [Mycobacterium phage Cabrinians] ],,NCBI, q1:s1 100.0% 1.04337E-31 GAP: 395 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.635, -3.8690725721777643, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein AU088_gp043 [Mycobacterium phage Cabrinians] ],,YP_009189765,100.0,1.04337E-31 SIF-HHPRED:  SIF-Syn: 
    /note=The length and scores are technically the best because there is nothing that results to form a comparison. There is one match that has perfect alignment. It is not predicted by Gene Mark but is by Glimmer.

tRNA complement (33046 - 33125)
  /gene="46"
  /product="tRNA-Lys(ctt)"
  /locus tag="SHOWERHANDEL_46"
    /note=tRNA-Lys(ctt)

CDS 33222 - 34523
  /gene="47"
  /product="gp47"
  /function="tyrosine integrase"
  /locus tag="ShowerHandel_47"
    /note=Original Glimmer call @bp 33222 has strength 11.95; Genemark calls start at 33222
    /note=SSC: 33222-34523 CP: no SCS: both ST: NI BLAST-Start: [endonuclease [Mycobacterium phage Cabrinians] ],,NCBI, q1:s1 100.0% 0.0 GAP: 395 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.399, -4.358093050197135, no F: tyrosine integrase SIF-BLAST: ,,[endonuclease [Mycobacterium phage Cabrinians] ],,YP_009189767,100.0,0.0 SIF-HHPRED: Integrase; PROTEIN-DNA COMPLEX, DNA BINDING PROTEIN-DNA COMPLEX; HET: PTR; 3.8A {Enterobacteria phage lambda} SCOP: d.163.1.1, d.10.1.4,,,1Z1B_B,94.6882,100.0 SIF-Syn: 
    /note=This sequence is the longest, but doesn`t have the best z-score and final scores. There is a 395 nucleotide gap and has a perfect match with the top result.

CDS complement (34600 - 35046)
  /gene="48"
  /product="gp48"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_48"
    /note=Original Glimmer call @bp 35046 has strength 8.37; Genemark calls start at 35046
    /note=SSC: 35046-34600 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein AU088_gp046 [Mycobacterium phage Cabrinians] ],,NCBI, q1:s1 100.0% 3.19744E-101 GAP: 1002 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.978, -6.01284768743864, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein AU088_gp046 [Mycobacterium phage Cabrinians] ],,YP_009189768,100.0,3.19744E-101 SIF-HHPRED:  SIF-Syn: 
    /note=There is a 1002 nucleotide gap, part of the coding potential is covered, and has a perfect match with the top result. This sequence is also the longest but does not have the best scores. The order of the genes are mixed up, so the gaps and the stop codons are mixed up as well.

CDS 36049 - 36282
  /gene="49"
  /product="gp49"
  /function="Cro (control of repressor's operator)"
  /locus tag="ShowerHandel_49"
    /note=Original Glimmer call @bp 36049 has strength 3.59; Genemark calls start at 35971
    /note=SSC: 36049-36282 CP: no SCS: both-gl ST: NI BLAST-Start: [gp39 [Mycobacterium phage Ardmore] ],,NCBI, q1:s43 100.0% 1.63582E-47 GAP: 1002 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.64, -5.490418349731808, no F: Cro (control of repressor`s operator) SIF-BLAST: ,,[gp39 [Mycobacterium phage Ardmore] ],,YP_003495180,64.7059,1.63582E-47 SIF-HHPRED:  SIF-Syn: 
    /note=The start position 36049 was chosen because it was predicted by Glimmer, has multiple matches.
    /note=
    /note=Check start position

CDS complement (35310 - 36050)
  /gene="50"
  /product="gp50"
  /function="immunity repressor"
  /locus tag="ShowerHandel_50"
    /note=Original Glimmer call @bp 36050 has strength 4.78; Genemark calls start at 35882
    /note=SSC: 36050-35310 CP: no SCS: both-gl ST: NI BLAST-Start: [transcriptional repressor [Mycobacterium phage Cabrinians] ],,NCBI, q1:s1 100.0% 8.97302E-179 GAP: 292 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.676, -5.6853845463436965, no F: immunity repressor SIF-BLAST: ,,[transcriptional repressor [Mycobacterium phage Cabrinians] ],,YP_009189769,100.0,8.97302E-179 SIF-HHPRED: a.35.1.2 (C:) P22 C2 repressor, DNA-binding domain {Salmonella bacteriophage P22 [TaxId: 10754]} | CLASS: All alpha proteins, FOLD: lambda repressor-like DNA-binding domains, SUPFAM: lambda repressor-like DNA-binding domains, FAM: Phage repressors,,,SCOP_d3jxbc_,32.5203,97.6 SIF-Syn: 
    /note=Check start

CDS 36343 - 36633
  /gene="51"
  /product="gp51"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_51"
    /note=Original Glimmer call @bp 36343 has strength 5.65; Genemark calls start at 36343
    /note=SSC: 36343-36633 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein AU088_gp049 [Mycobacterium phage Cabrinians] ],,NCBI, q1:s1 100.0% 4.6806E-64 GAP: 292 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.05, -2.5410833118725082, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein AU088_gp049 [Mycobacterium phage Cabrinians] ],,YP_009189771,100.0,4.6806E-64 SIF-HHPRED:  SIF-Syn: 
    /note=Has the best score, predicted by both Genemark and glimmer. Prediction covers all of coding potential.

CDS 36630 - 36722
  /gene="52"
  /product="gp52"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_52"
    /note=Genemark calls start at 36630
    /note=SSC: 36630-36722 CP: no SCS: genemark ST: NI BLAST-Start: [hypothetical protein PBI_BUZZLYSEYEAR_54 [Mycobacterium phage BuzzLyseyear] ],,NCBI, q1:s1 100.0% 8.96616E-11 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.646, -3.31900957015528, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_BUZZLYSEYEAR_54 [Mycobacterium phage BuzzLyseyear] ],,YP_009125047,100.0,8.96616E-11 SIF-HHPRED:  SIF-Syn: 
    /note=Has the best score and an overlap instead of a gap. Predicted by only genemark, and it is the longest ORF.

CDS 36719 - 36916
  /gene="53"
  /product="gp53"
  /function="transposase"
  /locus tag="ShowerHandel_53"
    /note=Original Glimmer call @bp 36719 has strength 3.48; Genemark calls start at 36719
    /note=SSC: 36719-36916 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein VC69_gp045 [Mycobacterium phage Inventum] ],,NCBI, q1:s31 100.0% 1.99763E-39 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.765, -3.1513923047253267, yes F: transposase SIF-BLAST: ,,[hypothetical protein VC69_gp045 [Mycobacterium phage Inventum] ],,YP_009125326,68.4211,1.99763E-39 SIF-HHPRED: a.6.1.5 (B:1-69) automated matches {Escherichia phage [TaxId: 10710]} | CLASS: All alpha proteins, FOLD: Putative DNA-binding domain, SUPFAM: Putative DNA-binding domain, FAM: Terminase gpNU1 subunit domain,,,SCOP_d6hn7b1,81.5385,99.1 SIF-Syn: 
    /note=check start 
    /note=Predicted by both Glimmer and Gene Mark, has 9 perfect matches, is the longest, and has the best scores. It also has a 4 nucleotide gap.

CDS 36957 - 37151
  /gene="54"
  /product="gp54"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_54"
    /note=Original Glimmer call @bp 36957 has strength 5.98; Genemark calls start at 36957
    /note=SSC: 36957-37151 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein AU088_gp052 [Mycobacterium phage Cabrinians] ],,NCBI, q1:s1 100.0% 2.50862E-37 GAP: 40 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.497, -5.84799742031764, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein AU088_gp052 [Mycobacterium phage Cabrinians] ],,YP_009189774,100.0,2.50862E-37 SIF-HHPRED:  SIF-Syn: 
    /note=Predicted by both Genemark and Glimmer. While longest ORF, it is not the best score. Has one match only

CDS 37148 - 37432
  /gene="55"
  /product="gp55"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_55"
    /note=Original Glimmer call @bp 37148 has strength 5.32; Genemark calls start at 37148
    /note=SSC: 37148-37432 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein CL77_gp049 [Mycobacterium phage GUmbie] ],,NCBI, q1:s1 100.0% 6.79982E-63 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.495, -4.73460372112482, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein CL77_gp049 [Mycobacterium phage GUmbie] ],,YP_009018925,100.0,6.79982E-63 SIF-HHPRED:  SIF-Syn: 
    /note=Position 37148 was chosen by both tools as well as had the longest ORF with few gaps and many 1:1 matches.

CDS 37429 - 37617
  /gene="56"
  /product="gp56"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_56"
    /note=Original Glimmer call @bp 37459 has strength 2.95; Genemark calls start at 37429
    /note=SSC: 37429-37617 CP: yes SCS: both-gm ST: NI BLAST-Start: [hypothetical protein AU088_gp054 [Mycobacterium phage Cabrinians] ],,NCBI, q1:s1 100.0% 1.78965E-35 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.012, -4.717114992838803, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein AU088_gp054 [Mycobacterium phage Cabrinians] ],,YP_009189776,100.0,1.78965E-35 SIF-HHPRED:  SIF-Syn: 
    /note=Position 37429 was chosen by Genemark but not Glimmer but does have few gaps and many other matches.

CDS 37614 - 38261
  /gene="57"
  /product="gp57"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_57"
    /note=Original Glimmer call @bp 37614 has strength 8.61; Genemark calls start at 37614
    /note=SSC: 37614-38261 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein AU088_gp055 [Mycobacterium phage Cabrinians] ],,NCBI, q1:s1 100.0% 3.66916E-154 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.118, -4.496270967456145, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein AU088_gp055 [Mycobacterium phage Cabrinians] ],,YP_009189777,100.0,3.66916E-154 SIF-HHPRED:  SIF-Syn: 
    /note=Position 37614 was chosen by both Genemark and Glimmer while containing few gaps with many 1:1 matches.

CDS 38341 - 38619
  /gene="58"
  /product="gp58"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_58"
    /note=Original Glimmer call @bp 38341 has strength 5.99; Genemark calls start at 38341
    /note=SSC: 38341-38619 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_SAAL_57 [Mycobacterium phage Saal] ],,NCBI, q1:s1 100.0% 6.92662E-60 GAP: 79 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.186, -4.274735973818826, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_SAAL_57 [Mycobacterium phage Saal] ],,YP_009007524,100.0,6.92662E-60 SIF-HHPRED:  SIF-Syn: 
    /note=Position 38341 was predicted by both Genemark and Glimmer with the longest ORF as well as many 1:1 matches.

CDS 38616 - 38963
  /gene="59"
  /product="gp59"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_59"
    /note=Original Glimmer call @bp 38616 has strength 10.38; Genemark calls start at 38616
    /note=SSC: 38616-38963 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_SAAL_58 [Mycobacterium phage Saal] ],,NCBI, q1:s1 100.0% 1.14208E-78 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.226, -2.17469248771465, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_SAAL_58 [Mycobacterium phage Saal] ],,YP_009007525,100.0,1.14208E-78 SIF-HHPRED:  SIF-Syn: 
    /note=Position 38616 was predicted by both Genemark and Glimmer, and has the longest ORF and few gaps with many 1:1 matches.

CDS 38960 - 39457
  /gene="60"
  /product="gp60"
  /function="WhiB family transcription factor"
  /locus tag="ShowerHandel_60"
    /note=Original Glimmer call @bp 38963 has strength 6.49; Genemark calls start at 38954
    /note=SSC: 38960-39457 CP: yes SCS: both-cs ST: NI BLAST-Start: [WhiB family transcription factor [Mycobacterium phage Jarcob]],,NCBI, q1:s1 100.0% 7.02785E-119 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.495, -4.285511190005401, no F: WhiB family transcription factor SIF-BLAST: ,,[WhiB family transcription factor [Mycobacterium phage Jarcob]],,UVK58524,100.0,7.02785E-119 SIF-HHPRED: Redox- and pH-responsive transcriptional regulator WhiB3; redox sensor, transcriptional factor, protein-DNA complex, TRANSCRIPTION, TRANSCRIPTION-DNA-Transferase complex; 2.44A {Mycobacterium tuberculosis},,,8CYF_A,52.1212,99.8 SIF-Syn: 
    /note=Position 38963 was predicted by Glimmer but not Genemark, although the stop was about 10 nucleotides different with at least  2 1:1 matches.

CDS 39454 - 39939
  /gene="61"
  /product="gp61"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_61"
    /note=Original Glimmer call @bp 39454 has strength 4.16; Genemark calls start at 39445
    /note=SSC: 39454-39939 CP: no SCS: both-gl ST: NI BLAST-Start: [hypothetical protein M040_gp56 [Mycobacterium phage SiSi] ],,NCBI, q1:s1 100.0% 8.62553E-112 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.712, -3.1816499351312086, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein M040_gp56 [Mycobacterium phage SiSi] ],,YP_008051182,100.0,8.62553E-112 SIF-HHPRED:  SIF-Syn: 
    /note=Position 39427 was selected by Glimmer but not Genemark. This position was listed as having the longest ORF with many 1:1 matches.

CDS 39936 - 40217
  /gene="62"
  /product="gp62"
  /function="WhiB family transcription factor"
  /locus tag="ShowerHandel_62"
    /note=Original Glimmer call @bp 39936 has strength 6.66; Genemark calls start at 39936
    /note=SSC: 39936-40217 CP: no SCS: both ST: NI BLAST-Start: [WhiB [Mycobacterium phage Saal] ],,NCBI, q1:s1 100.0% 1.58374E-60 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.801, -3.1379842619144376, no F: WhiB family transcription factor SIF-BLAST: ,,[WhiB [Mycobacterium phage Saal] ],,YP_009007528,100.0,1.58374E-60 SIF-HHPRED: Transcriptional regulator WhiB; RNA polymerase, Transcription factor, Iron cluster, TRANSCRIPTION-TRANSFERASE-DNA complex;{Streptomyces venezuelae},,,8DY7_H,86.0215,99.9 SIF-Syn: 
    /note=Position 39936 was selected by Glimmer but not Genemark and has many 1:1 matches and few gaps.

CDS 40214 - 40579
  /gene="63"
  /product="gp63"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="ShowerHandel_63"
    /note=Original Glimmer call @bp 40214 has strength 3.75; Genemark calls start at 40214
    /note=SSC: 40214-40579 CP: yes SCS: both ST: NI BLAST-Start: [DNA binding protein [Mycobacterium phage Saal] ],,NCBI, q1:s1 100.0% 2.75148E-84 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.856, -3.0228743540871426, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[DNA binding protein [Mycobacterium phage Saal] ],,YP_009007529,100.0,2.75148E-84 SIF-HHPRED: Putative uncharacterized protein; DNA BINDING PROTEIN; NMR {Hyperthermus butylicus},,,2LVS_A,78.5124,99.4 SIF-Syn: 
    /note=Position 40214 was chosen by both Genemark and Glimmer as well as containing few gaps and the longest ORF with many 1:1 matches.

CDS 40579 - 40731
  /gene="64"
  /product="gp64"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_64"
    /note=Original Glimmer call @bp 40579 has strength 8.15; Genemark calls start at 40579
    /note=SSC: 40579-40731 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein M609_gp063 [Mycobacterium phage Job42] ],,NCBI, q1:s2 100.0% 2.10979E-28 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.736, -5.351280609534597, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein M609_gp063 [Mycobacterium phage Job42] ],,YP_008126653,98.0392,2.10979E-28 SIF-HHPRED:  SIF-Syn: 
    /note=Position 40579 was selected by both Glimmer and Genemark, with few gaps, at least 2 1:1 matches.

CDS 40731 - 40964
  /gene="65"
  /product="gp65"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_65"
    /note=Original Glimmer call @bp 40731 has strength 6.68; Genemark calls start at 40731
    /note=SSC: 40731-40964 CP: no SCS: both ST: NI BLAST-Start: [gp56 [Mycobacterium phage Pacc40] ],,NCBI, q1:s1 100.0% 1.83485E-44 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.582, -3.5925599723783583, no F: Hypothetical Protein SIF-BLAST: ,,[gp56 [Mycobacterium phage Pacc40] ],,YP_002241640,100.0,1.83485E-44 SIF-HHPRED:  SIF-Syn: 
    /note=Position 40731 was chosen by both Genemark and Glimmer with many matches and few gaps.

CDS 40961 - 41425
  /gene="66"
  /product="gp66"
  /function="Hypothetical protein"
  /locus tag="ShowerHandel_66"
    /note=Original Glimmer call @bp 40961 has strength 11.75; Genemark calls start at 40961
    /note=SSC: 40961-41425 CP: no SCS: both ST: NI BLAST-Start: [gp57 [Mycobacterium phage Pacc40] ],,NCBI, q1:s1 100.0% 1.90218E-104 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.791, -3.36878816875868, yes F: Hypothetical protein SIF-BLAST: ,,[gp57 [Mycobacterium phage Pacc40] ],,YP_002241641,100.0,1.90218E-104 SIF-HHPRED: Phage_Mu_Gam ; Bacteriophage Mu Gam like protein,,,PF07352.16,53.2468,98.6 SIF-Syn: 
    /note=Position 40961 was chosen by both Genemark and Glimmer with many matches and few gaps.
    /note=
    /note=AJ reset function to hypothetical, needs more investigation. 
    /note=https://seaphages.org/forums/topic/5657/?page=2#post-10856

CDS 41422 - 42399
  /gene="67"
  /product="gp67"
  /function="RecA-like DNA recombinase"
  /locus tag="ShowerHandel_67"
    /note=Original Glimmer call @bp 41422 has strength 12.94; Genemark calls start at 41422
    /note=SSC: 41422-42399 CP: yes SCS: both ST: NI BLAST-Start: [RecA-like DNA recombinase [Mycobacterium phage Brocalys] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.067, -2.583959800616441, no F: RecA-like DNA recombinase SIF-BLAST: ,,[RecA-like DNA recombinase [Mycobacterium phage Brocalys] ],,YP_009303898,99.6923,0.0 SIF-HHPRED: Protein recA; Alpha and beta proteins (a/b, a+b), ATP-binding, Cytoplasm, DNA damage, DNA recombination, DNA repair, DNA-binding, Nucleotide-binding; 1.95A {Thermotoga maritima},,,3HR8_A,61.8462,99.4 SIF-Syn: 
    /note=Position 41422 was chosen by both Genemark and Glimmer and contains many matches to the database and has the longest ORF with few gaps.

CDS 42396 - 42758
  /gene="68"
  /product="gp68"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_68"
    /note=Original Glimmer call @bp 42396 has strength 2.0
    /note=SSC: 42396-42758 CP: yes SCS: glimmer ST: NI BLAST-Start: [HNH endonuclease [Mycobacterium phage BobaPhett] ],,NCBI, q1:s1 100.0% 2.16583E-84 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.972, -4.860773125741789, no F: Hypothetical Protein SIF-BLAST: ,,[HNH endonuclease [Mycobacterium phage BobaPhett] ],,YP_009954857,100.0,2.16583E-84 SIF-HHPRED: d.4.1.5 (A:1-103) Recombination endonuclease VII, N-terminal domain {Bacteriophage T4 [TaxId: 10665]} | CLASS: Alpha and beta proteins (a+b), FOLD: His-Me finger endonucleases, SUPFAM: His-Me finger endonucleases, FAM: Recombination endonuclease VII, N-terminal domain,,,SCOP_d1e7la2,57.5,97.3 SIF-Syn: 
    /note=We chose this start position because it has the highest Z-score, the ideal 4 nucleotide overlap, many 1:1 blastp matches, and has the longest open reading frame,

CDS 42755 - 44062
  /gene="69"
  /product="gp69"
  /function="DNA helicase"
  /locus tag="ShowerHandel_69"
    /note=Original Glimmer call @bp 42755 has strength 8.76; Genemark calls start at 42755
    /note=SSC: 42755-44062 CP: no SCS: both ST: NI BLAST-Start: [DNA helicase [Mycobacterium phage BobaPhett] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.733, -3.2790920053347614, yes F: DNA helicase SIF-BLAST: ,,[DNA helicase [Mycobacterium phage BobaPhett] ],,YP_009954858,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=We chose this start position because GeneMark and Glimmer both predicted the same number. Along with this, it also has the longest ORF.

CDS 44059 - 45009
  /gene="70"
  /product="gp70"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_70"
    /note=Original Glimmer call @bp 44059 has strength 9.95; Genemark calls start at 44059
    /note=SSC: 44059-45009 CP: yes SCS: both ST: NI BLAST-Start: [site-specific DNA-methyltransferase [Mycobacterium phage BobaPhett] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.614, -3.4463834536695686, no F: Hypothetical Protein SIF-BLAST: ,,[site-specific DNA-methyltransferase [Mycobacterium phage BobaPhett] ],,YP_009954859,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=We chose this start position because GeneMark and Glimmer both predicted the same number.

CDS 44996 - 45229
  /gene="71"
  /product="gp71"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_71"
    /note=Original Glimmer call @bp 44996 has strength 8.83; Genemark calls start at 45026
    /note=SSC: 44996-45229 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_BYCHANCE_61 [Mycobacterium phage ByChance] ],,NCBI, q1:s1 100.0% 4.01263E-49 GAP: -14 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.497, -5.769312227415782, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BYCHANCE_61 [Mycobacterium phage ByChance] ],,AXC37242,100.0,4.01263E-49 SIF-HHPRED:  SIF-Syn: 
    /note=This is not the ideal starting position for this gene, as the Nucleotide is above -4, does not have the longest ORF, and was only predicted by Glimmer.

CDS 45223 - 45375
  /gene="72"
  /product="gp72"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_72"
    /note=Original Glimmer call @bp 45223 has strength 10.06; Genemark calls start at 45223
    /note=SSC: 45223-45375 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein VC69_gp063 [Mycobacterium phage Inventum] ],,NCBI, q2:s5 98.0% 7.33104E-28 GAP: -7 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.555, -3.649482460397077, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein VC69_gp063 [Mycobacterium phage Inventum] ],,YP_009125344,92.4528,7.33104E-28 SIF-HHPRED:  SIF-Syn: 
    /note=We chose this start position because it has a 1:1 blastp match, and has the ideal nucleotide overlap of 4, and has the best final score of -4.416.

CDS 45372 - 45995
  /gene="73"
  /product="gp73"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_73"
    /note=Original Glimmer call @bp 45372 has strength 2.51; Genemark calls start at 45372
    /note=SSC: 45372-45995 CP: yes SCS: both ST: NI BLAST-Start: [DNA methylase [Mycobacterium phage ByChance]],,NCBI, q1:s1 100.0% 3.9387E-144 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.684, -5.317780913136193, no F: Hypothetical Protein SIF-BLAST: ,,[DNA methylase [Mycobacterium phage ByChance]],,AXC37244,100.0,3.9387E-144 SIF-HHPRED:  SIF-Syn: 
    /note=We chose this start position because it has a 1:1 blastp match alignment, and has the ideal nucleotide overlap of 4

CDS 46069 - 46452
  /gene="74"
  /product="gp74"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_74"
    /note=Original Glimmer call @bp 46069 has strength 5.48; Genemark calls start at 46069
    /note=SSC: 46069-46452 CP: yes SCS: both ST: NI BLAST-Start: [DNA methylase [Mycobacterium phage ByChance]],,NCBI, q1:s1 100.0% 1.1504E-85 GAP: 73 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.449, -6.856880255498881, no F: Hypothetical Protein SIF-BLAST: ,,[DNA methylase [Mycobacterium phage ByChance]],,AXC37245,100.0,1.1504E-85 SIF-HHPRED:  SIF-Syn: 
    /note=We chose this start position because although this gene does not have the best scores, it has 2 1:1 blastp match alignments, and was predicted by both Glimmer and GeneMark

CDS 46449 - 46610
  /gene="75"
  /product="gp75"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_75"
    /note=Original Glimmer call @bp 46449 has strength 8.68
    /note=SSC: 46449-46610 CP: yes SCS: glimmer ST: NI BLAST-Start: [hypothetical protein SEA_BYCHANCE_65 [Mycobacterium phage ByChance]],,NCBI, q1:s1 100.0% 1.99008E-29 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.712, -3.2616920228519697, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BYCHANCE_65 [Mycobacterium phage ByChance]],,AXC37246,100.0,1.99008E-29 SIF-HHPRED: DUF1922 ; Domain of unknown function (DUF1922),,,PF09082.14,56.6038,89.5 SIF-Syn: 
    /note=We chose this start position because this gene has an ideal -4 Nucleotide Overlap, and has 9 1:1 blastp match alignments. Although it did not have the best scores, it was the best gene candidate.

CDS 46591 - 46740
  /gene="76"
  /product="gp76"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_76"
    /note=Original Glimmer call @bp 46591 has strength 0.15
    /note=SSC: 46591-46740 CP: yes SCS: glimmer ST: NI BLAST-Start: [hypothetical protein SEA_BYCHANCE_66 [Mycobacterium phage ByChance]],,NCBI, q1:s1 100.0% 8.92922E-27 GAP: -20 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.815, -3.494990588194529, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BYCHANCE_66 [Mycobacterium phage ByChance]],,AXC37274,100.0,8.92922E-27 SIF-HHPRED:  SIF-Syn: 
    /note=We chose this start position because it has the highest z score and has a good spacer, as the best binding sites are 4-14 nucleotides from the start codon.

CDS 46737 - 47684
  /gene="77"
  /product="gp77"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_77"
    /note=Original Glimmer call @bp 46737 has strength 9.9; Genemark calls start at 46737
    /note=SSC: 46737-47684 CP: yes SCS: both ST: NI BLAST-Start: [helix-turn-helix DNA-binding domain protein [Mycobacterium phage ByChance]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.147, -2.356391881054909, yes F: Hypothetical Protein SIF-BLAST: ,,[helix-turn-helix DNA-binding domain protein [Mycobacterium phage ByChance]],,AXC37247,100.0,0.0 SIF-HHPRED: Replication initiator A family protein; replication initiation, multidrug resistance, PROTEIN BINDING; HET: SO4; 2.35A {Staphylococcus aureus CA-347},,,4PT7_C,26.0317,97.3 SIF-Syn: 
    /note=We chose this start position because it was predicted by both GeneMark and Glimmer. In addition it has the ideal 4 nucleotide overlap, and has many 1:1 blastp match alignments, and has the best scores such as Z-Score, Spacer, and Final Score.

CDS 47681 - 48040
  /gene="78"
  /product="gp78"
  /function="helicase loader"
  /locus tag="ShowerHandel_78"
    /note=Original Glimmer call @bp 47681 has strength 7.84; Genemark calls start at 47681
    /note=SSC: 47681-48040 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_BYCHANCE_68 [Mycobacterium phage ByChance]],,NCBI, q1:s1 100.0% 1.16183E-80 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.798, -5.2219144614649, no F: helicase loader SIF-BLAST: ,,[hypothetical protein SEA_BYCHANCE_68 [Mycobacterium phage ByChance]],,AXC37248,100.0,1.16183E-80 SIF-HHPRED: a.179.1.1 (A:2-67) Replisome organizer (g39p helicase loader/inhibitor protein) {Bacteriophage Spp1 [TaxId: 10724]} | CLASS: All alpha proteins, FOLD: Replisome organizer (g39p helicase loader/inhibitor protein), SUPFAM: Replisome organizer (g39p helicase loader/inhibitor protein), FAM: Replisome organizer (g39p helicase loader/inhibitor protein),,,SCOP_d1no1a1,55.4622,99.1 SIF-Syn: 
    /note=We chose this start position because it was predicted by Glimmer and GeneMark, has 5 1:1 blastp match alignments, has the longest open reading frame and the ideal -4 nucleotide overlap.

CDS 48033 - 48257
  /gene="79"
  /product="gp79"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_79"
    /note=Original Glimmer call @bp 48033 has strength 3.05; Genemark calls start at 48027
    /note=SSC: 48033-48257 CP: yes SCS: both-gl ST: NI BLAST-Start: [gp79 [Mycobacterium phage Ramsey] ],,NCBI, q1:s1 100.0% 4.14888E-45 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.899, -5.7788783051464305, no F: Hypothetical Protein SIF-BLAST: ,,[gp79 [Mycobacterium phage Ramsey] ],,YP_002241866,100.0,4.14888E-45 SIF-HHPRED:  SIF-Syn: 
    /note=We chose this start position because, it was predicted by Glimmer, and had many 1:1 blastp match alignments, and has the longest open reading frame.

CDS 48336 - 48536
  /gene="80"
  /product="gp80"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_80"
    /note=Original Glimmer call @bp 48336 has strength 8.2; Genemark calls start at 48336
    /note=SSC: 48336-48536 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein I5H29_gp77 [Mycobacterium phage Doug] ],,NCBI, q1:s1 100.0% 2.29427E-39 GAP: 78 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.991, -2.66371296573402, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein I5H29_gp77 [Mycobacterium phage Doug] ],,YP_009956216,100.0,2.29427E-39 SIF-HHPRED:  SIF-Syn: 
    /note=We chose this start position because it was predicted by both Glimmer and GeneMark, has the best Z-Score and Final Score, and had 2 blastp 1:1 match alignments.

CDS 48533 - 48733
  /gene="81"
  /product="gp81"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_81"
    /note=Original Glimmer call @bp 48521 has strength 4.16; Genemark calls start at 48533
    /note=SSC: 48533-48733 CP: yes SCS: both-gm ST: NI BLAST-Start: [hypothetical protein SEA_BYCHANCE_72 [Mycobacterium phage ByChance]],,NCBI, q1:s1 100.0% 3.46959E-40 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.984, -4.694645446479451, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BYCHANCE_72 [Mycobacterium phage ByChance]],,AXC37251,100.0,3.46959E-40 SIF-HHPRED:  SIF-Syn: 
    /note=The start position 48533 was chosen because it was predicted by both tools, is the longest ORF, has a small gap, covers all the coding potential, has many 1:1 blastp matches, has the best RBS scores.

CDS 48717 - 48983
  /gene="82"
  /product="gp82"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_82"
    /note=Original Glimmer call @bp 48717 has strength 3.93; Genemark calls start at 48717
    /note=SSC: 48717-48983 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_BYCHANCE_73 [Mycobacterium phage ByChance]],,NCBI, q1:s1 100.0% 2.3664E-58 GAP: -17 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.067, -2.5052746077145835, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BYCHANCE_73 [Mycobacterium phage ByChance]],,AXC37252,100.0,2.3664E-58 SIF-HHPRED:  SIF-Syn: 
    /note=The start position 48717 was chosen because it was predicted by both tools, is the longest ORF, has a small gap, covers all the coding potential, has many 1:1 blastp matches, has the best RBS scores.

CDS 48976 - 49359
  /gene="83"
  /product="gp83"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_83"
    /note=Original Glimmer call @bp 48976 has strength 8.69; Genemark calls start at 48976
    /note=SSC: 48976-49359 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_BYCHANCE_74 [Mycobacterium phage ByChance]],,NCBI, q1:s1 100.0% 1.64826E-86 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.642, -3.389881189012514, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BYCHANCE_74 [Mycobacterium phage ByChance]],,AXC37253,100.0,1.64826E-86 SIF-HHPRED:  SIF-Syn: 
    /note=The start position 48976 was chosen because it was predicted by both tools, is the longest ORF, has a small gap, covers all the coding potential, has many 1:1 blastp matches, has the best RBS scores.

CDS 49356 - 49619
  /gene="84"
  /product="gp84"
  /function="membrane protein"
  /locus tag="ShowerHandel_84"
    /note=Original Glimmer call @bp 49407 has strength 2.82; Genemark calls start at 49356
    /note=SSC: 49356-49619 CP: yes SCS: both-gm ST: NI BLAST-Start: [hypothetical protein SEA_BYCHANCE_75 [Mycobacterium phage ByChance] ],,NCBI, q1:s1 100.0% 1.21251E-56 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.497, -3.708514821076885, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein SEA_BYCHANCE_75 [Mycobacterium phage ByChance] ],,AXC37254,100.0,1.21251E-56 SIF-HHPRED:  SIF-Syn: 
    /note=The start position 49356 was chosen because it was predicted by both tools, is the longest ORF, has a small gap, covers all the coding potential, has many 1:1 blastp matches, has the best RBS scores.

CDS 49616 - 49795
  /gene="85"
  /product="gp85"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_85"
    /note=Original Glimmer call @bp 49616 has strength 5.13; Genemark calls start at 49616
    /note=SSC: 49616-49795 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_BYCHANCE_76 [Mycobacterium phage ByChance] ],,NCBI, q1:s1 100.0% 1.8209E-34 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.815, -4.0178693334748665, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BYCHANCE_76 [Mycobacterium phage ByChance] ],,AXC37255,100.0,1.8209E-34 SIF-HHPRED:  SIF-Syn: 
    /note=The start position 49616 was chosen because it was predicted by both tools, is the longest ORF, has a small gap, covers all the coding potential, has many 1:1 blastp matches, has the best RBS scores.

CDS 49792 - 49932
  /gene="86"
  /product="gp86"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_86"
    /note=Original Glimmer call @bp 49792 has strength 1.95; Genemark calls start at 49810
    /note=SSC: 49792-49932 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein PBI_ESTAVE1_97 [Mycobacterium phage Estave1] ],,NCBI, q1:s1 100.0% 1.10576E-23 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.665, -5.708817720043443, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_ESTAVE1_97 [Mycobacterium phage Estave1] ],,YP_009124288,100.0,1.10576E-23 SIF-HHPRED:  SIF-Syn: 
    /note=The start position 49792 was chosen because it was predicted by both tools, is the longest ORF, has a small gap, covers all the coding potential, has many 1:1 blastp matches, has the best RBS scores.

CDS 49932 - 50105
  /gene="87"
  /product="gp87"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_87"
    /note=Original Glimmer call @bp 49932 has strength 15.69; Genemark calls start at 49932
    /note=SSC: 49932-50105 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_BYCHANCE_78 [Mycobacterium phage ByChance] ],,NCBI, q1:s1 100.0% 1.7809E-33 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.817, -3.103539494358988, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_BYCHANCE_78 [Mycobacterium phage ByChance] ],,AXC37257,100.0,1.7809E-33 SIF-HHPRED:  SIF-Syn: 
    /note=The start position 49932 was chosen because it was predicted by both tools, is the longest ORF, has a small gap, covers all the coding potential, has many 1:1 blastp matches, has the best RBS scores.

CDS 50218 - 50547
  /gene="88"
  /product="gp88"
  /function="head-to-tail adaptor"
  /locus tag="ShowerHandel_88"
    /note=Genemark calls start at 50218
    /note=SSC: 50218-50547 CP: yes SCS: genemark ST: NI BLAST-Start: [hypothetical protein SEA_BYCHANCE_79 [Mycobacterium phage ByChance]],,NCBI, q1:s21 100.0% 6.15624E-73 GAP: 112 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.817, -3.0248543014571307, yes F: head-to-tail adaptor SIF-BLAST: ,,[hypothetical protein SEA_BYCHANCE_79 [Mycobacterium phage ByChance]],,AXC37258,84.4961,6.15624E-73 SIF-HHPRED: RNA_pol_Rpb1_1 ; RNA polymerase Rpb1, domain 1,,,PF04997.16,24.7706,95.1 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 50644 - 51183
  /gene="89"
  /product="gp89"
  /function="G-I-Y Y-I-G endonuclease"
  /locus tag="ShowerHandel_89"
    /note=Original Glimmer call @bp 50656 has strength 5.36; Genemark calls start at 50656
    /note=SSC: 50644-51183 CP: yes SCS: both-cs ST: NI BLAST-Start: [endonuclease [Mycobacterium phage Saal] ],,NCBI, q1:s1 100.0% 2.67693E-131 GAP: 96 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.534, -4.458092987303931, yes F: G-I-Y Y-I-G endonuclease SIF-BLAST: ,,[endonuclease [Mycobacterium phage Saal] ],,YP_009007556,100.0,2.67693E-131 SIF-HHPRED:  SIF-Syn: 
    /note=The start position 50644 was chosen because it was predicted by both tools, is the longest ORF, has a small gap, covers all the coding potential, has many 1:1 blastp matches, has the best RBS scores.

CDS complement (50065 - 50673)
  /gene="90"
  /product="gp90"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_90"
    /note=Original Glimmer call @bp 50673 has strength 3.5
    /note=SSC: 50673-50065 CP: yes SCS: glimmer ST: NI BLAST-Start:  GAP: 506 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.059, -4.538672476131182, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=The start position 50673 was chosen because it was predicted by both tools, is the longest ORF, has a small gap, covers all the coding potential, has many 1:1 blastp matches, has the best RBS scores.
    /note=
    /note=AJ switched from membrane protein to hypothetical protein because only TMHMM shows 1 TMH, TopCons didn`t support.

CDS 51180 - 51851
  /gene="91"
  /product="gp91"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_91"
    /note=Original Glimmer call @bp 51180 has strength 10.15; Genemark calls start at 51180
    /note=SSC: 51180-51851 CP: yes SCS: both ST: NI BLAST-Start: [gp90 [Mycobacterium phage Pacc40] ],,NCBI, q1:s1 100.0% 2.66789E-162 GAP: 506 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.14, -2.3719785694936077, yes F: Hypothetical Protein SIF-BLAST: ,,[gp90 [Mycobacterium phage Pacc40] ],,YP_002241674,100.0,2.66789E-162 SIF-HHPRED:  SIF-Syn: 
    /note=The start position 51180 was chosen because it was predicted by both tools, is the longest ORF, has a small gap, covers all the coding potential, has many 1:1 blastp matches, has the best RBS scores.

CDS 51978 - 52310
  /gene="92"
  /product="gp92"
  /function="mycobacteriophage mobile element 2 (MPME 2)"
  /locus tag="ShowerHandel_92"
    /note=Original Glimmer call @bp 51978 has strength 1.24; Genemark calls start at 51978
    /note=SSC: 51978-52310 CP: yes SCS: both ST: NI BLAST-Start: [mobile element MPME [Mycobacterium phage Babsiella] ],,NCBI, q1:s23 100.0% 2.48098E-76 GAP: 126 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.399, -3.8308929311341546, no F: mycobacteriophage mobile element 2 (MPME 2) SIF-BLAST: ,,[mobile element MPME [Mycobacterium phage Babsiella] ],,YP_009013086,83.3333,2.48098E-76 SIF-HHPRED:  SIF-Syn: 
    /note=The start position 51978 was chosen because it was predicted by both tools, is the longest ORF, has a small gap, covers all the coding potential, has many 1:1 blastp matches, has the best RBS scores.

CDS 52440 - 52586
  /gene="93"
  /product="gp93"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_93"
    /note=Original Glimmer call @bp 52440 has strength 6.82; Genemark calls start at 52440
    /note=SSC: 52440-52586 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_LATRETIUM_96 [Mycobacterium phage Latretium]],,NCBI, q1:s24 100.0% 3.20325E-25 GAP: 129 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.883, -4.967562678515084, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_LATRETIUM_96 [Mycobacterium phage Latretium]],,QXO12907,67.6056,3.20325E-25 SIF-HHPRED:  SIF-Syn: 
    /note=The start position 52440 was chosen because it was predicted by both tools, is the longest ORF, has a small gap, covers all the coding potential, has many 1:1 blastp matches, has the best RBS scores.

CDS 52583 - 52885
  /gene="94"
  /product="gp94"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_94"
    /note=Original Glimmer call @bp 52583 has strength 8.4; Genemark calls start at 52583
    /note=SSC: 52583-52885 CP: yes SCS: both ST: NI BLAST-Start: [membrane protein [Mycobacterium phage Saal] ],,NCBI, q1:s1 100.0% 1.40333E-63 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.991, -2.9525085049809894, yes F: Hypothetical Protein SIF-BLAST: ,,[membrane protein [Mycobacterium phage Saal] ],,YP_009007559,100.0,1.40333E-63 SIF-HHPRED:  SIF-Syn: 
    /note=The start position 52583 was chosen because it was predicted by both tools, it is the longest ORF, has a small gap, covers all the coding potential, has many 1:1 blastp matches, has the best RBS scores.

CDS 52867 - 53004
  /gene="95"
  /product="gp95"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_95"
    /note=Original Glimmer call @bp 52882 has strength 8.29; Genemark calls start at 52867
    /note=SSC: 52867-53004 CP: yes SCS: both-gm ST: NI BLAST-Start: [hypothetical protein I5H44_gp094 [Mycobacterium phage Gorge] ],,NCBI, q1:s1 100.0% 1.56484E-22 GAP: -19 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.02, -5.271243305869519, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein I5H44_gp094 [Mycobacterium phage Gorge] ],,YP_009957812,100.0,1.56484E-22 SIF-HHPRED:  SIF-Syn: 
    /note=The start position 52882 was only predicted by Glimmer but chosen because the gap is ideal and there are more 1:1 matches, also the final RBS scores are slightly better than the position predicted by Genemark.

CDS 53013 - 53294
  /gene="96"
  /product="gp96"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_96"
    /note=Original Glimmer call @bp 53013 has strength 10.27; Genemark calls start at 53013
    /note=SSC: 53013-53294 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_SAAL_94 [Mycobacterium phage Saal] ],,NCBI, q1:s1 100.0% 2.21053E-62 GAP: 8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.067, -3.3503726477288405, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_SAAL_94 [Mycobacterium phage Saal] ],,YP_009007561,100.0,2.21053E-62 SIF-HHPRED:  SIF-Syn: 
    /note=The start position 53012 was chosen because it was predicted by both tools, has a positive gap, covers all the coding potential, has many 1:1 blastp matches, has the best RBS scores.

CDS 53294 - 53494
  /gene="97"
  /product="gp97"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_97"
    /note=Original Glimmer call @bp 53294 has strength 6.1; Genemark calls start at 53294
    /note=SSC: 53294-53494 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_SAAL_95 [Mycobacterium phage Saal] ],,NCBI, q1:s1 100.0% 9.69612E-41 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.893, -5.024743752121617, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_SAAL_95 [Mycobacterium phage Saal] ],,YP_009007562,100.0,9.69612E-41 SIF-HHPRED:  SIF-Syn: 
    /note=The start position 53294 was chosen because it was predicted by both tools, has a decent gap, has many 1:1 blastp matches, has the best RBS scores.

CDS 53491 - 53904
  /gene="98"
  /product="gp98"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_98"
    /note=Original Glimmer call @bp 53491 has strength 6.81; Genemark calls start at 53491
    /note=SSC: 53491-53904 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein I5H48_gp096 [Mycobacterium phage Hlubikazi] ],,NCBI, q1:s1 100.0% 5.38493E-92 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.972, -5.371913467750883, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein I5H48_gp096 [Mycobacterium phage Hlubikazi] ],,YP_009958231,99.2701,5.38493E-92 SIF-HHPRED:  SIF-Syn: 
    /note=The start position 53491 was chosen because it was predicted by both tools, it is the longest ORF, has an ideal gap, covers all the coding potential, has the best RBS scores.

CDS 53901 - 54143
  /gene="99"
  /product="gp99"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_99"
    /note=Original Glimmer call @bp 53901 has strength 7.05; Genemark calls start at 53901
    /note=SSC: 53901-54143 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_WEE_102 [Mycobacterium phage Wee] ],,NCBI, q1:s1 100.0% 8.45054E-51 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.506, -4.7117408381653165, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_WEE_102 [Mycobacterium phage Wee] ],,YP_004123924,100.0,8.45054E-51 SIF-HHPRED:  SIF-Syn: 
    /note=The start position 53901 was chosen because it was predicted by both tools, it is the longest ORF, has an ideal gap, covers all the coding potential, has many 1:1 blastp matches, has the best RBS scores.

CDS 54136 - 54297
  /gene="100"
  /product="gp100"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_100"
    /note=Original Glimmer call @bp 54136 has strength 6.38; Genemark calls start at 54136
    /note=SSC: 54136-54297 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_TWEETY_101 [Mycobacterium phage Tweety] ],,NCBI, q1:s1 100.0% 2.33504E-30 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.156, -4.398481360774431, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_TWEETY_101 [Mycobacterium phage Tweety] ],,YP_001469334,100.0,2.33504E-30 SIF-HHPRED:  SIF-Syn: 
    /note=The start position 52583 was chosen because it was predicted by both tools, it is the longest ORF, has a decent gap, has many 1:1 blastp matches, has the best RBS scores.

CDS 54603 - 56039
  /gene="101"
  /product="gp101"
  /function="glycosyltransferase"
  /locus tag="ShowerHandel_101"
    /note=Original Glimmer call @bp 54603 has strength 13.29; Genemark calls start at 54603
    /note=SSC: 54603-56039 CP: yes SCS: both ST: NI BLAST-Start: [glycosyltransferase [Mycobacterium phage James]],,NCBI, q1:s1 100.0% 0.0 GAP: 305 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.195, -4.6079705234137345, no F: glycosyltransferase SIF-BLAST: ,,[glycosyltransferase [Mycobacterium phage James]],,QBI98959,100.0,0.0 SIF-HHPRED: pp-GalNAc-T; pp-GalNAc-T initiates the formation of mucin-type O-linked glycans. UDP-GalNAc: polypeptide alpha-N-acetylgalactosaminyltransferases (pp-GalNAc-T) initiate the formation of mucin-type, O-linked glycans by catalyzing the transfer of alpha-N-acetylgalactosamine (GalNAc) from UDP-GalNAc to hydroxyl groups of Ser or Thr residues of core proteins to form the Tn antigen (GalNAc-a-1-O-Ser/Thr).,,,cd02510,45.8159,99.8 SIF-Syn: 
    /note=The start position 54603 was chosen because it was predicted by both tools, it is the longest ORF, covers all the coding potential, has many 1:1 blastp matches, has the best RBS scores.

CDS 56049 - 56264
  /gene="102"
  /product="gp102"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_102"
    /note=Original Glimmer call @bp 56049 has strength 7.83; Genemark calls start at 56049
    /note=SSC: 56049-56264 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein M609_gp104 [Mycobacterium phage Job42] ],,NCBI, q1:s1 100.0% 2.71641E-43 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.916, -5.186767100221219, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein M609_gp104 [Mycobacterium phage Job42] ],,YP_008126694,100.0,2.71641E-43 SIF-HHPRED:  SIF-Syn: 
    /note=The start position 56049 was chosen because it was predicted by both tools, it is the longest ORF, has a positive gap, has 1:1 blastp matches, has the best RBS scores.

CDS 56267 - 56473
  /gene="103"
  /product="gp103"
  /function="Hypothetical Protein"
  /locus tag="ShowerHandel_103"
    /note=Original Glimmer call @bp 56267 has strength 10.53; Genemark calls start at 56267
    /note=SSC: 56267-56473 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein I5H67_gp105 [Mycobacterium phage Moonbeam] ],,NCBI, q1:s1 100.0% 1.11787E-42 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.841, -5.643396235448333, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein I5H67_gp105 [Mycobacterium phage Moonbeam] ],,YP_009960171,100.0,1.11787E-42 SIF-HHPRED:  SIF-Syn: 
    /note=The start position 56267 was chosen because it was predicted by both tools, has a small gap, covers all the coding potential, has many 1:1 blastp matches, has the best RBS scores.

CDS 56470 - 57093
  /gene="104"
  /product="gp104"
  /function="glycosyltransferase"
  /locus tag="ShowerHandel_104"
    /note=Original Glimmer call @bp 56470 has strength 7.1; Genemark calls start at 56470
    /note=SSC: 56470-57093 CP: yes SCS: both ST: NI BLAST-Start: [glucosyltransferase [Mycobacterium phage Saal] ],,NCBI, q1:s1 100.0% 1.51714E-150 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.809, -5.88628317957017, no F: glycosyltransferase SIF-BLAST: ,,[glucosyltransferase [Mycobacterium phage Saal] ],,YP_009007568,100.0,1.51714E-150 SIF-HHPRED: Glyco_transf_25 ; Glycosyltransferase family 25 (LPS biosynthesis protein),,,PF01755.21,69.5652,99.7 SIF-Syn: 
    /note=The start position 56470 was chosen because it was predicted by both tools, has an ideal gap, covers all the coding potential, has many 1:1 blastp matches, has the best RBS scores.

CDS 57093 - 57419
  /gene="105"
  /product="gp105"
  /function="HNH endonuclease"
  /locus tag="ShowerHandel_105"
    /note=Original Glimmer call @bp 57093 has strength 1.77
    /note=SSC: 57093-57419 CP: no SCS: glimmer ST: NI BLAST-Start: [HNH endonuclease [Mycobacterium phage Cabrinians] ],,NCBI, q1:s1 100.0% 1.92236E-72 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.293, -6.957859150193765, no F: HNH endonuclease SIF-BLAST: ,,[HNH endonuclease [Mycobacterium phage Cabrinians] ],,YP_009189823,100.0,1.92236E-72 SIF-HHPRED: HNH endonuclease; Thermophilic bacteriophage, HNH Endonuclease, DNA nicking, HYDROLASE; 1.52A {Geobacillus virus E2},,,5H0M_A,97.2222,98.7 SIF-Syn: 
    /note=The start position 57093 was chosen because it was predicted by only Glimmer. The GeneMark start was not predicted. This is not the longest ORF and does not cover all the coding potential, but there are a 
    /note=couple 1:1 blastp matches and it has the best RBS scores.