CDS 267 - 569
  /gene="1"
  /product="gp1"
  /function="hypothetical protein"
  /locus tag="Saints25_1"
    /note=Original Glimmer call @bp 267 has strength 10.07; Genemark calls start at 267
    /note=SSC: 267-569 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_DOCTORDIDDLES_2 [Mycobacterium phage DoctorDiddles] ],,NCBI, q1:s1 100.0% 8.35567E-56 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.237, -2.0111200136961407, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DOCTORDIDDLES_2 [Mycobacterium phage DoctorDiddles] ],,AXC37383,93.8144,8.35567E-56 SIF-HHPRED:  SIF-Syn: 
    /note=-Best SD score, longest ORF, multiple 1:1 BLAST matches, agrees with genemark and glimmer, no known function (no BLAST or HHPRED hits)

CDS 566 - 751
  /gene="2"
  /product="gp2"
  /function="hypothetical protein"
  /locus tag="Saints25_2"
    /note=Original Glimmer call @bp 566 has strength 9.42; Genemark calls start at 566
    /note=SSC: 566-751 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein Porky_3 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 2.16412E-35 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.149, -4.5818629940675315, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein Porky_3 [Mycobacterium phage Porky] ],,YP_002014324,100.0,2.16412E-35 SIF-HHPRED:  SIF-Syn: 
    /note=4 base pair overlap, captures all coding potential, glimmer and genemark agree, good SD score, SS Starterator, 1:1 BLAST match

CDS 748 - 1029
  /gene="3"
  /product="gp3"
  /function="hypothetical protein"
  /locus tag="Saints25_3"
    /note=Original Glimmer call @bp 748 has strength 4.83; Genemark calls start at 748
    /note=SSC: 748-1029 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein DRDREY_5 [Mycobacterium phage DrDrey] ],,NCBI, q1:s1 100.0% 1.70675E-56 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.607, -3.342129169857323, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein DRDREY_5 [Mycobacterium phage DrDrey] ],,YP_008409398,100.0,1.70675E-56 SIF-HHPRED:  SIF-Syn: 
    /note=Genemark and Glimmer match, Gap -4, Good SD score, longest ORF, 1:1 BLAST match, SS Starterator

CDS 1022 - 1483
  /gene="4"
  /product="gp4"
  /function="terminase, small subunit"
  /locus tag="Saints25_4"
    /note=Original Glimmer call @bp 1022 has strength 6.25; Genemark calls start at 1022
    /note=SSC: 1022-1483 CP: yes SCS: both ST: SS BLAST-Start: [terminase small subunit [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 3.54321E-109 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.289, -3.934452679007171, yes F: terminase, small subunit SIF-BLAST: ,,[terminase small subunit [Mycobacterium phage Cjw1] ],,NP_817455,100.0,3.54321E-109 SIF-HHPRED: Terminase small subunit; genome packaging, bacteriophage, DNA binding, VIRAL PROTEIN; 1.4A {Enterobacteria phage HK97},,,6Z6E_B,64.7059,99.7 SIF-Syn: 
    /note=Gap -8, glimmer and genemark match, longest ORF, best SD score, BLAST 1:1 match, SS starterator, terminase small subnit support HHPRED and NCBI blast

CDS 1476 - 1820
  /gene="5"
  /product="gp5"
  /function="hypothetical protein"
  /locus tag="Saints25_5"
    /note=Original Glimmer call @bp 1476 has strength 4.93; Genemark calls start at 1476
    /note=SSC: 1476-1820 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_NOSLEEP_6 [Mycobacterium phage NoSleep] ],,NCBI, q1:s1 100.0% 2.39322E-76 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.527, -3.4932654573164204, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_NOSLEEP_6 [Mycobacterium phage NoSleep] ],,AKU42444,100.0,2.39322E-76 SIF-HHPRED:  SIF-Syn: 
    /note=Gap -8, Glimmer and Genemark matched, best SD score, 1:1 BLAST match, SS starterator, Membrane protien confirmed by Phagesdb function frequency and TmHmm
    /note=
    /note=Changed to NKF, has one membrane protein hit

CDS complement (1882 - 2121)
  /gene="6"
  /product="gp6"
  /function="hypothetical protein"
  /locus tag="Saints25_6"
    /note=Original Glimmer call @bp 2121 has strength 10.84; Genemark calls start at 2121
    /note=SSC: 2121-1882 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_HOPEY_7 [Mycobacterium phage Hopey] ],,NCBI, q1:s1 100.0% 2.09015E-49 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.665, -3.139452255336754, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_HOPEY_7 [Mycobacterium phage Hopey] ],,AXH65417,100.0,2.09015E-49 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and GeneMark agree, 1 bp overlap, best SD score, captures all coding potential, SS Starterator, 1:1 BLAST match, NKF

CDS complement (2121 - 2429)
  /gene="7"
  /product="gp7"
  /function="hypothetical protein"
  /locus tag="Saints25_7"
    /note=Original Glimmer call @bp 2429 has strength 10.38; Genemark calls start at 2420
    /note=SSC: 2429-2121 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_NIMROD_7 [Mycobacterium phage Nimrod] ],,NCBI, q1:s1 100.0% 6.88051E-68 GAP: 44 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.511, -4.292997112549713, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_NIMROD_7 [Mycobacterium phage Nimrod] ],,QAY16500,96.2264,6.88051E-68 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark Disagree; chose Glimmer over Genemark because of better SD score. Multiple 1:1 BLAST matches. NKF.

CDS 2474 - 4144
  /gene="8"
  /product="gp8"
  /function="terminase, large subunit"
  /locus tag="Saints25_8"
    /note=Original Glimmer call @bp 2474 has strength 8.83; Genemark calls start at 2474
    /note=SSC: 2474-4144 CP: yes SCS: both ST: SS BLAST-Start: [terminase large subunit [Mycobacterium phage Murphy] ],,NCBI, q1:s1 100.0% 0.0 GAP: 44 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.414, -3.8116689268127657, no F: terminase, large subunit SIF-BLAST: ,,[terminase large subunit [Mycobacterium phage Murphy] ],,YP_008051487,100.0,0.0 SIF-HHPRED: Terminase large subunit; genome packaging, bacteriophage, ATPase, nuclease, VIRAL PROTEIN; HET: BR; 2.2A {Enterobacteria phage HK97},,,6Z6D_A,94.964,100.0 SIF-Syn: 
    /note=Glimmer and Genemark agree. 44bp gap, captures all coding potential, longest ORF, best SD score, SS Starterator, 1:1 BLAST match, large terminase subunit

CDS 4156 - 4377
  /gene="9"
  /product="gp9"
  /function="hypothetical protein"
  /locus tag="Saints25_9"
    /note=Original Glimmer call @bp 4156 has strength 8.34; Genemark calls start at 4156
    /note=SSC: 4156-4377 CP: yes SCS: both ST: SS BLAST-Start: [gp9 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 8.09022E-46 GAP: 11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.549, -3.46411222063, yes F: hypothetical protein SIF-BLAST: ,,[gp9 [Mycobacterium phage Cjw1] ],,NP_817459,100.0,8.09022E-46 SIF-HHPRED:  SIF-Syn: 
    /note=Gap 11, Longest ORF, Suggested Start, Matches the Starterator, captures all coding potential
    /note=not enough probability in HHPRED to have a viable function match

CDS 4364 - 5920
  /gene="10"
  /product="gp10"
  /function="portal protein"
  /locus tag="Saints25_10"
    /note=Original Glimmer call @bp 4364 has strength 9.13; Genemark calls start at 4364
    /note=SSC: 4364-5920 CP: yes SCS: both ST: SS BLAST-Start: [portal protein [Mycobacterium phage 244] ],,NCBI, q1:s1 100.0% 0.0 GAP: -14 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.52, -3.525474288708562, yes F: portal protein SIF-BLAST: ,,[portal protein [Mycobacterium phage 244] ],,YP_654766,100.0,0.0 SIF-HHPRED: Phage portal protein, HK97 family; "neck", "portal", "capsid", "tail tube", VIRUS; 3.58A {Rhodobacter capsulatus},,,6TE9_A,67.3745,100.0 SIF-Syn: 
    /note=Smallest gap
    /note=Glimmer and Genemark agree
    /note=Captures all coding potential
    /note=Second longest ORF
    /note=Best SD score
    /note=Blast 1:1 match
    /note=Confirmed SS
    /note=Portal Protien

CDS 5923 - 6924
  /gene="11"
  /product="gp11"
  /function="capsid maturation protease"
  /locus tag="Saints25_11"
    /note=Original Glimmer call @bp 5923 has strength 8.49; Genemark calls start at 5923
    /note=SSC: 5923-6924 CP: yes SCS: both ST: SS BLAST-Start: [head maturation protease [Mycobacterium phage Dumbo] ],,NCBI, q1:s1 100.0% 0.0 GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.517, -3.5925599723783583, no F: capsid maturation protease SIF-BLAST: ,,[head maturation protease [Mycobacterium phage Dumbo] ],,YP_008051636,100.0,0.0 SIF-HHPRED: Peptidase_S78 ; Caudovirus prohead serine protease,,,PF04586.20,41.7417,99.7 SIF-Syn: Preceding gene is portal
    /note=Glimmer and Genemark agree, 2bp gap, captures all coding potential, best SD score, SS Starterator, longest ORF, 1:1 BLAST match, capsid maturation

CDS 7012 - 8505
  /gene="12"
  /product="gp12"
  /function="major capsid protein"
  /locus tag="Saints25_12"
    /note=Original Glimmer call @bp 7012 has strength 10.89; Genemark calls start at 7012
    /note=SSC: 7012-8505 CP: yes SCS: both ST: NI BLAST-Start: [major head protein [Mycobacterium phage NelitzaMV] ],,NCBI, q1:s1 100.0% 0.0 GAP: 87 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.141, -2.1958114445137396, yes F: major capsid protein SIF-BLAST: ,,[major head protein [Mycobacterium phage NelitzaMV] ],,YP_009197681,100.0,0.0 SIF-HHPRED: Major capsid protein; Virus Procapsid particles, VIRUS; 5.2A {Enterobacteria phage HK97},,,3QPR_B,98.994,100.0 SIF-Syn: 
    /note=Genemark and Glimmer agree, 87 bp gap, longest ORF, best SD score, captures all coding potential, SS Starterator, 1:1 Blast match, major capsid protein, skipped scaffolding protein.

CDS 8628 - 8807
  /gene="13"
  /product="gp13"
  /function="hypothetical protein"
  /locus tag="Saints25_13"
    /note=Original Glimmer call @bp 8628 has strength 10.78; Genemark calls start at 8628
    /note=SSC: 8628-8807 CP: yes SCS: both ST: NI BLAST-Start: [head-tail connector protein [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 4.87452E-34 GAP: 122 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.224, -5.173547162831495, yes F: hypothetical protein SIF-BLAST: ,,[head-tail connector protein [Mycobacterium phage Cjw1] ],,NP_817463,100.0,4.87452E-34 SIF-HHPRED:  SIF-Syn: 
    /note=GeneMark and Glimmer agree. Longest ORF Captures all coding potential. Lowest SD score -5.174
    /note=Starterator NI 
    /note=NCBI blast gives 1 to 1
    /note=NKF but head-to-tail connector protein evidence on blast

CDS 8807 - 9373
  /gene="14"
  /product="gp14"
  /function="head-to-tail adaptor"
  /locus tag="Saints25_14"
    /note=Original Glimmer call @bp 8807 has strength 11.95; Genemark calls start at 8807
    /note=SSC: 8807-9373 CP: yes SCS: both ST: SS BLAST-Start: [head-tail adaptor [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 1.75475E-135 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.423, -3.790975366313636, yes F: head-to-tail adaptor SIF-BLAST: ,,[head-tail adaptor [Mycobacterium phage Cjw1] ],,NP_817464,100.0,1.75475E-135 SIF-HHPRED: Adaptor protein Rcc01688; "neck", "portal", "capsid", "tail tube", VIRUS; 3.58A {Rhodobacter capsulatus},,,6TE9_D,94.1489,99.9 SIF-Syn: 
    /note=Glimmer and Genemark Agree, 1bp overlap, captures all coding potential, longest ORF, SS Starterator, 1:1 BLAST match, head-to-tail adaptor.

CDS 9388 - 9723
  /gene="15"
  /product="gp15"
  /function="head-to-tail stopper"
  /locus tag="Saints25_15"
    /note=Original Glimmer call @bp 9388 has strength 9.3; Genemark calls start at 9388
    /note=SSC: 9388-9723 CP: yes SCS: both ST: SS BLAST-Start: [head closure [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 1.23883E-75 GAP: 14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.365, -4.301170562178417, yes F: head-to-tail stopper SIF-BLAST: ,,[head closure [Mycobacterium phage Cjw1] ],,NP_817465,100.0,1.23883E-75 SIF-HHPRED: HEAD COMPLETION PROTEIN GP16; VIRAL PROTEIN, VIRAL INFECTION, TAILED BACTERIOPHAGE, SIPHOVIRIDAE, SPP1, VIRAL ASSEMBLY, HEAD-TO-TAIL INTERFACE, DNA GATEKEEPER, ALLOSTERIC MECHANISM; 7.2A {BACILLUS PHAGE SPP1},,,5A21_F,99.0991,99.6 SIF-Syn: 
    /note=Glimmer and GeneMark agree.
    /note=Longest ORF captures all coding capacity SD score:-4.301
    /note=gap:14 
    /note=Suggested start 10
    /note=Head to Tail stopper supported by HHPRED and Blast

CDS 9720 - 10100
  /gene="16"
  /product="gp16"
  /function="hypothetical protein"
  /locus tag="Saints25_16"
    /note=Original Glimmer call @bp 9720 has strength 4.1; Genemark calls start at 9720
    /note=SSC: 9720-10100 CP: yes SCS: both ST: SS BLAST-Start: [head-to-tail connector complex protein [Mycobacterium phage Lilizi]],,NCBI, q1:s1 100.0% 8.14574E-87 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.645, -3.1816499351312086, yes F: hypothetical protein SIF-BLAST: ,,[head-to-tail connector complex protein [Mycobacterium phage Lilizi]],,QCG77981,100.0,8.14574E-87 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark agree, 4bp overlap, best SD score, not the longest ORF, SS Starterator, captures all coding potential,1:1 BLAST match, got strong HHpred hits for the minor capsid protein and others but it did not meet the criteria for the official function list. NKF.

CDS 10078 - 10482
  /gene="17"
  /product="gp17"
  /function="tail terminator"
  /locus tag="Saints25_17"
    /note=Original Glimmer call @bp 10078 has strength 6.96; Genemark calls start at 10078
    /note=SSC: 10078-10482 CP: yes SCS: both ST: SS BLAST-Start: [head-tail adaptor [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 4.06463E-95 GAP: -23 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.58, -3.8462096892182602, yes F: tail terminator SIF-BLAST: ,,[head-tail adaptor [Mycobacterium phage Cjw1] ],,NP_817467,100.0,4.06463E-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,96.2687,99.4 SIF-Syn: 
    /note=Smallest gap
    /note=Glimmer and Genemark match
    /note=All coding potential captured
    /note=Not the longest ORF
    /note=best SD score
    /note=1:1 NCBI BLAST match
    /note=SS confirmed
    /note=Tail terminator

CDS 10509 - 11483
  /gene="18"
  /product="gp18"
  /function="major tail protein"
  /locus tag="Saints25_18"
    /note=Original Glimmer call @bp 10509 has strength 14.53; Genemark calls start at 10509
    /note=SSC: 10509-11483 CP: yes SCS: both ST: SS BLAST-Start: [major tail protein [Mycobacterium phage DrDrey] ],,NCBI, q1:s1 100.0% 0.0 GAP: 26 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.759, -3.080676611399484, yes F: major tail protein SIF-BLAST: ,,[major tail protein [Mycobacterium phage DrDrey] ],,YP_008409412,100.0,0.0 SIF-HHPRED: YSD1_22 major tail protein; Bacteriophage tail, helical assembly, VIRAL PROTEIN; 3.5A {Bacteriophage sp.},,,6XGR_L,62.037,97.2 SIF-Syn: 
    /note=Glimmer and Genemark agree, 26bp gap, best SD score, longest ORF, captures all coding potential, SS Starterator, 1:1 BLAST Match, major tail protein

CDS 11543 - 12016
  /gene="19"
  /product="gp19"
  /function="head fiber protein"
  /locus tag="Saints25_19"
    /note=Original Glimmer call @bp 11543 has strength 7.97; Genemark calls start at 11543
    /note=SSC: 11543-12016 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_NOSLEEP_20 [Mycobacterium phage NoSleep] ],,NCBI, q1:s1 100.0% 6.6152E-102 GAP: 59 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.919, -2.7423981586358774, yes F: head fiber protein SIF-BLAST: ,,[hypothetical protein SEA_NOSLEEP_20 [Mycobacterium phage NoSleep] ],,AKU42458,100.0,6.6152E-102 SIF-HHPRED: Head fiber protein; supercoiled triple repeating helix-turn-helix, VIRAL PROTEIN; 1.52A {Bacillus phage phi29},,,3QC7_A,73.8854,99.4 SIF-Syn: 
    /note=Best overlap
    /note=Glimmer and Genemark agreed
    /note=Longest ORF
    /note=Captures all coding potential
    /note=Best SD score
    /note=1:1 NCBI BLAST match
    /note=SS confirmed
    /note=head fiber protein

CDS 12137 - 12598
  /gene="20"
  /product="gp20"
  /function="tail assembly chaperone"
  /locus tag="Saints25_20"
    /note=Original Glimmer call @bp 12137 has strength 13.19; Genemark calls start at 12137
    /note=SSC: 12137-12598 CP: yes SCS: both ST: SS BLAST-Start: [tail assembly chaperone [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 5.63173E-108 GAP: 120 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.586, -3.6571726089641587, yes F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Mycobacterium phage Cjw1] ],,NP_817470,100.0,5.63173E-108 SIF-HHPRED: GP24_25 ; Mycobacteriophage tail assembly protein,,,PF17388.5,33.9869,96.2 SIF-Syn: 
    /note=Glimmer and Genemark agree, 120bp gap, not the longest ORF, best SD score, captures all coding potential, SS starterator, 1:1 BLAST match, tail assembly protein

CDS join(12137..12589,12589..13008)
  /gene="21"
  /product="gp21"
  /function="tail assembly chaperone"
  /locus tag="Saints25_21"
    /note=
    /note=SSC: 12137-13008 CP: yes SCS: neither ST: SS BLAST-Start: [tail assembly chaperone [Mycobacterium phage Pharsalus] ],,NCBI, q1:s25 100.0% 0.0 GAP: -462 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.586, -3.6571726089641587, yes F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Mycobacterium phage Pharsalus] ],,AOT23907,92.3567,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Frame shift gene
    /note=No Glimmer or genemark
    /note=Captures all coding potential
    /note=Second longest ORF
    /note=Best SD score
    /note=Starterator SS

CDS 13001 - 17728
  /gene="22"
  /product="gp22"
  /function="tape measure protein"
  /locus tag="Saints25_22"
    /note=Original Glimmer call @bp 13001 has strength 8.04; Genemark calls start at 13001
    /note=SSC: 13001-17728 CP: yes SCS: both ST: SS BLAST-Start: [tape measure protein [Mycobacterium phage Moldemort] ],,NCBI, q1:s1 100.0% 0.0 GAP: -9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.749, -2.9625409806968013, no F: tape measure protein SIF-BLAST: ,,[tape measure protein [Mycobacterium phage Moldemort] ],,QBJ04922,99.9365,0.0 SIF-HHPRED: Tape Measure Protein, gp57; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alpha},,,6V8I_CF,44.8254,98.9 SIF-Syn: 
    /note=Best Gap
    /note=Glimmer and Genemark match
    /note=Captures all coding potential
    /note=longest ORF
    /note=best SD score
    /note=1:1 NCBI BLAST match
    /note=SS confirmed
    /note=Tape measure protein

CDS 17758 - 19419
  /gene="23"
  /product="gp23"
  /function="minor tail protein"
  /locus tag="Saints25_23"
    /note=Original Glimmer call @bp 17758 has strength 8.4; Genemark calls start at 17758
    /note=SSC: 17758-19419 CP: yes SCS: both ST: SS BLAST-Start: [minor tail subunit [Mycobacterium phage Lilac] ],,NCBI, q1:s1 100.0% 0.0 GAP: 29 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.136, -5.358093050197135, no F: minor tail protein SIF-BLAST: ,,[minor tail subunit [Mycobacterium phage Lilac] ],,YP_009011784,100.0,0.0 SIF-HHPRED: HYPOTHETICAL PROTEIN 19.1; VIRAL PROTEIN, DISTAL TAIL PROTEIN; 2.95A {BACILLUS PHAGE SPP1},,,2X8K_C,20.7957,99.4 SIF-Syn: 
    /note=Best overlap
    /note=Glimmer and Genemark agree
    /note=Captures all coding potential
    /note=Longest ORF
    /note=Does not have best SD score
    /note=1:1 NCBI BLAST match
    /note=SS Starterator confirmed
    /note=Minor tail protein

CDS 19407 - 21086
  /gene="24"
  /product="gp24"
  /function="minor tail protein"
  /locus tag="Saints25_24"
    /note=Original Glimmer call @bp 19491 has strength 6.45; Genemark calls start at 19407
    /note=SSC: 19407-21086 CP: yes 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, 1.055, -6.622157809994246, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Mycobacterium phage Kostya] ],,YP_002014492,100.0,0.0 SIF-HHPRED: Tail protein, 43 kDa; tail protein, structural genomics, PSI, MCSG, Protein Structure Initiative, Midwest Center for Structural Genomics, UNKNOWN FUNCTION; 2.1A {Neisseria meningitidis MC58} SCOP: b.106.1.1,,,3D37_A,89.2665,98.8 SIF-Syn: 
    /note=Glimmer and Genemark do not agree but going with Genemark prediction so as to not cleave off coding potential in GenemarkS, 13 bp overlap, not the best SD score, longest ORF, captures all coding potential in GenemarkS, NI Starterator but start at 19407 called more often than start at 19491, 1:1 BLAST match, evidence suggests that it is a minor tail protein of some sorts.

CDS 21095 - 21928
  /gene="25"
  /product="gp25"
  /function="minor tail protein"
  /locus tag="Saints25_25"
    /note=Original Glimmer call @bp 21095 has strength 9.92; Genemark calls start at 21107
    /note=SSC: 21095-21928 CP: yes SCS: both-gl ST: SS 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, 3.141, -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=Glimmer and GeneMark disagree,Glimmer was chosen due to Starterator calling more times, best SD score, longest ORF, SS starterator, captures all coding potential lower gap; 8 bp gap; 1:1 BLAST, evidence suggests that this is a minor tail protein.

CDS 21945 - 24341
  /gene="26"
  /product="gp26"
  /function="hypothetical protein"
  /locus tag="Saints25_26"
    /note=Original Glimmer call @bp 21945 has strength 8.76; Genemark calls start at 21945
    /note=SSC: 21945-24341 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 0.0 GAP: 16 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.742, -3.055523716677687, no F: hypothetical protein SIF-BLAST: ,,[minor tail protein [Mycobacterium phage Porky] ],,YP_002014347,99.8747,0.0 SIF-HHPRED: HYALURONATE LYASE; LYASE, HYALURONAN BINDING CARBOHYDRATE BINDING MODULE, CBM, PL FAMILY 8, PL8, HYL; HET: EDO; 1.2A {STREPTOCOCCUS PNEUMONIAE TIGR4},,,4D0Q_A,20.3008,97.7 SIF-Syn: 
    /note=Best overlap
    /note=Glimmer and Genemark agree
    /note=Captures all coding potential
    /note=Longest ORF
    /note=Best SD score
    /note=1:1 NCBI BLAST match
    /note=SS starterator confirmed
    /note=HHpred hits for hydrolase or lyase, but phages db function calls for minor tail protein. The poor coverage and the lack of consensus make it hard to determine function. In the official function list minor tail proteins are lysine and collagen rich proteins, which do not appear in HHpred

CDS 24338 - 27175
  /gene="27"
  /product="gp27"
  /function="hypothetical protein"
  /locus tag="Saints25_27"
    /note=Original Glimmer call @bp 24338 has strength 7.2; Genemark calls start at 24338
    /note=SSC: 24338-27175 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Mycobacterium phage ChotaBhai]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.994, -3.095100142625534, yes F: hypothetical protein SIF-BLAST: ,,[minor tail protein [Mycobacterium phage ChotaBhai]],,QDF17642,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and GeneMark agree; 4 bp overlap; SS Starterator; best SD score; longest ORF; 1:1 BLAST match. Despite large number of BLAST hits, NKF because no HHpred.

CDS 27176 - 28138
  /gene="28"
  /product="gp28"
  /function="hypothetical protein"
  /locus tag="Saints25_28"
    /note=Original Glimmer call @bp 27176 has strength 3.39; Genemark calls start at 27176
    /note=SSC: 27176-28138 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 0.0 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.679, -3.2495416658190135, yes F: hypothetical protein SIF-BLAST: ,,[minor tail protein [Mycobacterium phage Porky] ],,YP_002014349,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark agree, 0 bp gap, best SD score, longest ORF, captures all coding potential, SS Starterator, 1:1 BLAST match, NKF.

CDS 28208 - 28636
  /gene="29"
  /product="gp29"
  /function="hypothetical protein"
  /locus tag="Saints25_29"
    /note=Original Glimmer call @bp 28208 has strength 14.02; Genemark calls start at 28208
    /note=SSC: 28208-28636 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_MURICA_28 [Mycobacterium phage Murica]],,NCBI, q1:s1 100.0% 2.05671E-89 GAP: 69 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.13, -2.156361006712914, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_MURICA_28 [Mycobacterium phage Murica]],,ATN91063,100.0,2.05671E-89 SIF-HHPRED: AVR-Pia protein; UNKNOWN FUNCTION; NMR {Magnaporthe oryzae},,,2MYW_A,26.0563,46.5 SIF-Syn: 
    /note=GeneMark and Glimmer agree. Best SD score. Longest ORF. All coding capacity covered. Gap 69. Evidence for hypothetical protein in the NCBI Blast. HHpred NKF. Starterator called 108 of 249 of the suggested start at 11.

CDS complement (28623 - 28808)
  /gene="30"
  /product="gp30"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Saints25_30"
    /note=Original Glimmer call @bp 28808 has strength 1.62; Genemark calls start at 28808
    /note=SSC: 28808-28623 CP: yes SCS: both ST: SS BLAST-Start: [HTH DNA binding protein [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 6.35143E-35 GAP: 132 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 0.892, -7.028301864955391, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[HTH DNA binding protein [Mycobacterium phage Cjw1] ],,NP_817480,100.0,6.35143E-35 SIF-HHPRED: Hypothetical protein; alpha-beta, helix-turn-helix, Structural Genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, UNKNOWN FUNCTION; HET: MSE, ACY; 1.83A {Rhodopseudomonas palustris} SCOP: a.35.1.13,,,2O38_A,72.1311,98.0 SIF-Syn: 
    /note=Glimmer and GeneMark agree; longest ORF; 12 bp gap; SS Starterator; 1:1 BLAST match; helix-turn-helix DNA binding domain HHpred.

CDS 28941 - 29225
  /gene="31"
  /product="gp31"
  /function="hypothetical protein"
  /locus tag="Saints25_31"
    /note=Original Glimmer call @bp 28941 has strength 9.83; Genemark calls start at 28941
    /note=SSC: 28941-29225 CP: no SCS: both ST: SS BLAST-Start: [gp31 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 3.63349E-62 GAP: 132 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.151, -2.253377680616507, yes F: hypothetical protein SIF-BLAST: ,,[gp31 [Mycobacterium phage Cjw1] ],,NP_817481,100.0,3.63349E-62 SIF-HHPRED: DUF3551 ; Protein of unknown function (DUF3551),,,PF12071.11,39.3617,89.1 SIF-Syn: 
    /note=Glimmer and Genemark agree, 132 bp gap, best SD score, longest ORF, does not capture all coding potential, SS Starterator, 1:1 BLAST match, Not enough evidence to determine function

CDS 29299 - 30801
  /gene="32"
  /product="gp32"
  /function="lysin A"
  /locus tag="Saints25_32"
    /note=Original Glimmer call @bp 29299 has strength 7.69; Genemark calls start at 29299
    /note=SSC: 29299-30801 CP: yes SCS: both ST: SS BLAST-Start: [endolysin [Mycobacterium phage 244] ],,NCBI, q1:s1 100.0% 0.0 GAP: 73 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.568, -5.538930744277278, no F: lysin A SIF-BLAST: ,,[endolysin [Mycobacterium phage 244] ],,YP_654789,100.0,0.0 SIF-HHPRED:  SIF-Syn: occurs immediately before Holin
    /note=Lysin A was called using synteny. Longest ORF, captures all coding potential. Start codon TTG. 73 bp gap, Starterator SS. Not the best SD score: -5.539. Function Lysin A through synteny. Evidence suggests that it is Lysin A through synteny, but HHpred data does have strong hits for it.

CDS 30805 - 31188
  /gene="33"
  /product="gp33"
  /function="holin"
  /locus tag="Saints25_33"
    /note=Original Glimmer call @bp 30805 has strength 12.31; Genemark calls start at 30805
    /note=SSC: 30805-31188 CP: yes SCS: both ST: SS BLAST-Start: [holin [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 3.4588E-82 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.896, -4.763756451838196, no F: holin SIF-BLAST: ,,[holin [Mycobacterium phage Cjw1] ],,NP_817483,100.0,3.4588E-82 SIF-HHPRED: Phage_holin_7_1 ; Mycobacterial 2 TMS Phage Holin (M2 Hol) Family,,,PF16081.8,93.7008,100.0 SIF-Syn: 
    /note=Glimmer and GeneMark agree; 3 bp gap; second best SD; largest ORF; SS Starterator; 1:1 BLAST match; holin HHpred.

CDS 31181 - 31519
  /gene="34"
  /product="gp34"
  /function="hypothetical protein"
  /locus tag="Saints25_34"
    /note=Original Glimmer call @bp 31181 has strength 12.02; Genemark calls start at 31181
    /note=SSC: 31181-31519 CP: no SCS: both ST: SS BLAST-Start: [gp34 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 1.73626E-75 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.429, -6.403886157111313, no F: hypothetical protein SIF-BLAST: ,,[gp34 [Mycobacterium phage Cjw1] ],,NP_817484,100.0,1.73626E-75 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark agree, 8 bp overlap, not the best SD score, longest ORF, does not capture all coding potential, SS Starterator, 1:1 BLAST match, Not enough evidence to determine function

CDS 31516 - 32373
  /gene="35"
  /product="gp35"
  /function="lysin B"
  /locus tag="Saints25_35"
    /note=Original Glimmer call @bp 31516 has strength 7.4; Genemark calls start at 31516
    /note=SSC: 31516-32373 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, 2.842, -3.8154491356968365, yes F: lysin B SIF-BLAST: ,,[lysin B [Mycobacterium phage Kostya] ],,YP_002014504,100.0,0.0 SIF-HHPRED:  SIF-Syn: lysis cassette and holin
    /note=Good overlap
    /note=Glimmer and Genemark agree
    /note=Captures all coding potential
    /note=Longest ORF
    /note=Best SD score
    /note=Blast 1:1 match
    /note=SS starterator confirmed
    /note=Lysin B but HHpred has high probability and coverage on holin

CDS 32370 - 32786
  /gene="36"
  /product="gp36"
  /function="hypothetical protein"
  /locus tag="Saints25_36"
    /note=Original Glimmer call @bp 32370 has strength 10.75; Genemark calls start at 32370
    /note=SSC: 32370-32786 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein Porky_36 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 4.12801E-95 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 0.961, -7.2690057605968725, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein Porky_36 [Mycobacterium phage Porky] ],,YP_002014357,100.0,4.12801E-95 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and GeneMark agree; not the best SD score, captures all coding potential,14 bp overlap; second longest ORF; 1:1 BLAST match; Phages DB NKF. Strong HHpred hits, but not enough evidence to suggest function.

CDS 32793 - 33038
  /gene="37"
  /product="gp37"
  /function="NrdH-like glutaredoxin"
  /locus tag="Saints25_37"
    /note=Original Glimmer call @bp 32850 has strength 10.18; Genemark calls start at 32793
    /note=SSC: 32793-33038 CP: yes SCS: both-gm ST: NI BLAST-Start: [thioredoxin domain [Mycobacterium phage DrDrey] ],,NCBI, q1:s1 100.0% 4.3901E-51 GAP: 6 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.008, -5.356325827079472, no F: NrdH-like glutaredoxin SIF-BLAST: ,,[thioredoxin domain [Mycobacterium phage DrDrey] ],,YP_008409431,100.0,4.3901E-51 SIF-HHPRED: NrdH-redoxin; NRDH, THIOREDOXIN, GLUTAREDOXIN, REDOX PROTEIN, DOMAIN SWAPPING, ELECTRON TRANSPORT; 2.69A {Corynebacterium ammoniagenes} SCOP: c.47.1.1,,,1R7H_A,95.0617,99.4 SIF-Syn: 
    /note=Glimmer and Genemark disagree, 6 bp gap, not best SD score, longest ORF, captures all coding potential, NI Starterator, 1:1 BLAST match, Function most likely an NrdH-like glutaredoxin because called on both HHpred and  PhagesDB.

CDS complement (33178 - 33324)
  /gene="38"
  /product="gp38"
  /function="hypothetical protein"
  /locus tag="Saints25_38"
    /note=Original Glimmer call @bp 33324 has strength 5.59; Genemark calls start at 33324
    /note=SSC: 33324-33178 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_PAT3_37 [Mycobacterium phage Pat3] ],,NCBI, q1:s1 100.0% 8.65211E-28 GAP: 4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.864, -2.717905214045128, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_PAT3_37 [Mycobacterium phage Pat3] ],,AYR00154,100.0,8.65211E-28 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and GeneMark agree, 4 bp gap, best SD score, longest ORF, captures all coding potential in GeneMarkS, SS Starterator, 1:1 BLAST match, NKF

CDS complement (33329 - 33715)
  /gene="39"
  /product="gp39"
  /function="Lsr2-like DNA bridging protein"
  /locus tag="Saints25_39"
    /note=Original Glimmer call @bp 33715 has strength 8.94; Genemark calls start at 33715
    /note=SSC: 33715-33329 CP: yes SCS: both ST: SS BLAST-Start: [nucloid associated Lsr2-like [Mycobacterium phage Mindy] ],,NCBI, q1:s1 100.0% 3.71105E-88 GAP: 47 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.732, -3.0766426734767767, yes F: Lsr2-like DNA bridging protein SIF-BLAST: ,,[nucloid associated Lsr2-like [Mycobacterium phage Mindy] ],,YP_009225327,100.0,3.71105E-88 SIF-HHPRED: Lsr2 ; Lsr2,,,PF11774.11,83.5938,100.0 SIF-Syn: 
    /note=Glimmer and GeneMark agree, 47 bp gap, best SD score, longest ORF, captures all coding potential in GeneMarkS, SS Starterator, 1:1 BLAST match, strong HHPRED and Phagesdb Function Frequency hits for Lsr2-like DNA bridging protein

CDS complement (33763 - 33954)
  /gene="40"
  /product="gp40"
  /function="hypothetical protein"
  /locus tag="Saints25_40"
    /note=Original Glimmer call @bp 33954 has strength 4.66; Genemark calls start at 33954
    /note=SSC: 33954-33763 CP: yes SCS: both ST: NI BLAST-Start: [gp40 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 1.39339E-39 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.992, -4.641378341780927, no F: hypothetical protein SIF-BLAST: ,,[gp40 [Mycobacterium phage Cjw1] ],,NP_817490,100.0,1.39339E-39 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark agree, 2 bp gap, ATG start codon more likely than GTG, not best SD score, not longest ORF, captures all coding potential, NI Starterator, 1:1 BLAST match, Not enough evidence to determine function

CDS complement (33957 - 34424)
  /gene="41"
  /product="gp41"
  /function="hypothetical protein"
  /locus tag="Saints25_41"
    /note=Original Glimmer call @bp 34424 has strength 4.3; Genemark calls start at 34424
    /note=SSC: 34424-33957 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_SIMPLIPHY_42 [Mycobacterium phage Simpliphy] ],,NCBI, q1:s1 100.0% 3.42151E-109 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.511, -3.5268154277366257, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_SIMPLIPHY_42 [Mycobacterium phage Simpliphy] ],,AXH50578,100.0,3.42151E-109 SIF-HHPRED:  SIF-Syn: 
    /note=Good overlap of 4 bp
    /note=Glimmer and Genemark agree
    /note=Captures all coding potential
    /note=Longest ORF
    /note=Best SD score
    /note=Blast match 1:1
    /note=SS starterator confirmed
    /note=No known function

CDS complement (34421 - 34897)
  /gene="42"
  /product="gp42"
  /function="hypothetical protein"
  /locus tag="Saints25_42"
    /note=Original Glimmer call @bp 34897 has strength 2.75; Genemark calls start at 34897
    /note=SSC: 34897-34421 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein JMN86_gp60 [Mycobacterium phage Petruchio] ],,NCBI, q1:s1 100.0% 2.59315E-58 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.434, -3.708514821076885, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein JMN86_gp60 [Mycobacterium phage Petruchio] ],,YP_009980117,88.2812,2.59315E-58 SIF-HHPRED:  SIF-Syn: 
    /note=Captures all coding potential
    /note=Best overlap
    /note=Genemark and Glimmer agree
    /note=Second longest ORF
    /note=Best SD score
    /note=Blast 1:1 were found but sequence identity was low
    /note=SS starterator confirmed
    /note=NKF

CDS complement (34894 - 35223)
  /gene="43"
  /product="gp43"
  /function="hypothetical protein"
  /locus tag="Saints25_43"
    /note=Original Glimmer call @bp 35223 has strength 0.92; Genemark calls start at 35223
    /note=SSC: 35223-34894 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDG56_gp044 [Mycobacterium phage Bask21] ],,NCBI, q1:s1 99.0826% 4.04972E-70 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.679, -3.1085431521568267, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDG56_gp044 [Mycobacterium phage Bask21] ],,YP_009591204,98.1651,4.04972E-70 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark agree, 8 bp overlap, best SD score, longest ORF, captures all coding potential in self-trained genemark, SS Starterator, 1:1 BLAST match, Not enough evidence to determine function

CDS complement (35216 - 35329)
  /gene="44"
  /product="gp44"
  /function="hypothetical protein"
  /locus tag="Saints25_44"
    /note=Original Glimmer call @bp 35329 has strength 7.59
    /note=SSC: 35329-35216 CP: yes SCS: glimmer ST: NI BLAST-Start: [hypothetical protein P755_gp046 [Mycobacterium phage Quink] ],,NCBI, q1:s1 100.0% 2.17086E-17 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.257, -6.195624325390232, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein P755_gp046 [Mycobacterium phage Quink] ],,YP_008531122,100.0,2.17086E-17 SIF-HHPRED:  SIF-Syn: 
    /note=Genemark did not call it
    /note=Best overlap
    /note=Captures all coding potential (small), more coding potential on genemark S
    /note=Longest ORF
    /note=Best SD score
    /note=SS starterator confirmed
    /note=1:1 BLAST match
    /note=No known function

CDS complement (35326 - 35454)
  /gene="45"
  /product="gp45"
  /function="hypothetical protein"
  /locus tag="Saints25_45"
    /note=Original Glimmer call @bp 35454 has strength 12.3; Genemark calls start at 35454
    /note=SSC: 35454-35326 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_MURPHY_47 [Mycobacterium phage Murphy] ],,NCBI, q1:s1 100.0% 1.09408E-19 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.246, -4.104100924355445, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_MURPHY_47 [Mycobacterium phage Murphy] ],,YP_008051526,100.0,1.09408E-19 SIF-HHPRED:  SIF-Syn: 
    /note=Best overlap
    /note=Genemark and Glimmer agree
    /note=Captures all coding potential
    /note=Third longest ORF
    /note=Not good SD score
    /note=1:1 BLAST match
    /note=SS Starterator confirmed
    /note=No known function as evidenced by HHpred

CDS complement (35454 - 35621)
  /gene="46"
  /product="gp46"
  /function="hypothetical protein"
  /locus tag="Saints25_46"
    /note=Original Glimmer call @bp 35621 has strength 2.6; Genemark calls start at 35621
    /note=SSC: 35621-35454 CP: yes SCS: both ST: SS BLAST-Start: [site-specific recombination directionality factor RDF [Mycobacterium phage Murphy] ],,NCBI, q1:s1 100.0% 1.33848E-29 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.71, -5.238109312333945, no F: hypothetical protein SIF-BLAST: ,,[site-specific recombination directionality factor RDF [Mycobacterium phage Murphy] ],,YP_008051527,100.0,1.33848E-29 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark agree, 4 bp overlap, best SD score, longest ORF, captures all coding potential in genemark S, SS Starterator, 1:1 BLAST match, Not enough evidence to determine function

CDS complement (35618 - 35788)
  /gene="47"
  /product="gp47"
  /function="hypothetical protein"
  /locus tag="Saints25_47"
    /note=Original Glimmer call @bp 35788 has strength 5.87; Genemark calls start at 35788
    /note=SSC: 35788-35618 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_UKULELE_44 [Mycobacterium phage Ukulele] ],,NCBI, q1:s23 100.0% 2.30594E-33 GAP: 58 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.605, -5.380462049242474, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_UKULELE_44 [Mycobacterium phage Ukulele] ],,ALA06276,71.7949,2.30594E-33 SIF-HHPRED:  SIF-Syn: 
    /note=Not good gap
    /note=Genemark and Glimmer agree
    /note=All coding potential captured (Genemark S)
    /note=Not longest ORF
    /note=Not great SD score
    /note=1:1 BLAST match
    /note=SS starterator confirmed
    /note=No known function

CDS complement (35847 - 36062)
  /gene="48"
  /product="gp48"
  /function="hypothetical protein"
  /locus tag="Saints25_48"
    /note=Original Glimmer call @bp 36062 has strength 9.98; Genemark calls start at 36062
    /note=SSC: 36062-35847 CP: no SCS: both ST: SS BLAST-Start: [gp49 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 1.10356E-42 GAP: 18 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.753, -3.303727606004721, yes F: hypothetical protein SIF-BLAST: ,,[gp49 [Mycobacterium phage Cjw1] ],,NP_817498,100.0,1.10356E-42 SIF-HHPRED:  SIF-Syn: 
    /note=GeneMark and Glimmer agree. Not capturing all coding capacity. Lowest SD score 3.304. Longest ORF, Gap of 18. Suggested start at 1. 109 of 109. 1 to 1 in NCBI blast. Not enough coverage or probability in HHPRED.

CDS complement (36081 - 36227)
  /gene="49"
  /product="gp49"
  /function="hypothetical protein"
  /locus tag="Saints25_49"
    /note=Original Glimmer call @bp 36227 has strength 7.62; Genemark calls start at 36227
    /note=SSC: 36227-36081 CP: yes SCS: both ST: SS BLAST-Start: [gp50 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 1.17019E-26 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.741, -5.154811153158988, no F: hypothetical protein SIF-BLAST: ,,[gp50 [Mycobacterium phage Cjw1] ],,NP_817499,100.0,1.17019E-26 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark agree, 1 bp overlap, not the best SD score, not the longest ORF, captures all coding potential, SS Starterator, 1:1 BLAST match, Not enough evidence to determine function due to poor HHpred hits.

CDS complement (36227 - 36622)
  /gene="50"
  /product="gp50"
  /function="hypothetical protein"
  /locus tag="Saints25_50"
    /note=Original Glimmer call @bp 36622 has strength 12.13; Genemark calls start at 36622
    /note=SSC: 36622-36227 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein Porky_48 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 1.52902E-89 GAP: 286 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.899, -3.473611599459246, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein Porky_48 [Mycobacterium phage Porky] ],,YP_002014369,100.0,1.52902E-89 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and GeneMark agree. Longest ORF. Gap of 286. Not the best SD score. 3.474. 103 of 109 start site 1. NCBI blast 1 to 1. Not enough coverage and probability in HHPRED

CDS complement (36909 - 37211)
  /gene="51"
  /product="gp51"
  /function="membrane protein"
  /locus tag="Saints25_51"
    /note=Original Glimmer call @bp 37211 has strength 6.19; Genemark calls start at 37232
    /note=SSC: 37211-36909 CP: yes SCS: both-gl ST: SS BLAST-Start: [gp52 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 4.04961E-62 GAP: 250 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.586, -3.3060637489568596, yes F: membrane protein SIF-BLAST: ,,[gp52 [Mycobacterium phage Cjw1] ],,NP_817501,100.0,4.04961E-62 SIF-HHPRED: Putative drug/sodium antiporter; transporter, TRANSPORT PROTEIN; HET: OLC, CAC; 2.7A {Escherichia coli},,,4Z3N_A,83.0,92.2 SIF-Syn: 
    /note=Glimmer and Genemark do not agree, 250 bp gap, best SD score, not the longest ORF, captures all coding potential, SS Starterator, 1:1 BLAST match,  TMHNM: two trans membrane domain hits so most likely a membrane protein.

CDS 37462 - 38343
  /gene="52"
  /product="gp52"
  /function="tyrosine integrase"
  /locus tag="Saints25_52"
    /note=Original Glimmer call @bp 37462 has strength 11.78; Genemark calls start at 37462
    /note=SSC: 37462-38343 CP: yes SCS: both ST: NI BLAST-Start: [gp53 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 0.0 GAP: 250 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.733, -4.096047812582576, yes F: tyrosine integrase SIF-BLAST: ,,[gp53 [Mycobacterium phage Cjw1] ],,NP_817502,100.0,0.0 SIF-HHPRED: Gp33; Bacteriophage, Brujita, DNA-binding, Integrase, DNA BINDING PROTEIN; HET: ACT, GOL; 1.847A {Mycobacterium phage Brujita},,,5VFZ_A,97.6109,100.0 SIF-Syn: 
    /note=Glimmer and GeneMark agree. Longest ORF. All coding potential. NI Starterator, Not the best SD score: 4.096. Gap 250. HHpred hits suggest tyrosine integrase function

CDS 38482 - 38721
  /gene="53"
  /product="gp53"
  /function="hypothetical protein"
  /locus tag="Saints25_53"
    /note=Original Glimmer call @bp 38482 has strength 7.79; Genemark calls start at 38482
    /note=SSC: 38482-38721 CP: yes SCS: both ST: SS BLAST-Start: [gp54 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 3.5157E-48 GAP: 138 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.787, -3.409075959487936, yes F: hypothetical protein SIF-BLAST: ,,[gp54 [Mycobacterium phage Cjw1] ],,NP_817503,100.0,3.5157E-48 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark agree, 138 bp gap, best SD score, longest ORF, captures all coding potential, SS Starterator, 1:1 BLAST match, not enough evidence to suggest a function

CDS complement (38699 - 39472)
  /gene="54"
  /product="gp54"
  /function="membrane protein"
  /locus tag="Saints25_54"
    /note=Original Glimmer call @bp 39310 has strength 5.07; Genemark calls start at 39472
    /note=SSC: 39472-38699 CP: yes SCS: both-gm ST: NI BLAST-Start: [gp55 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 0.0 GAP: 94 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.569, -3.6929813131220834, yes F: membrane protein SIF-BLAST: ,,[gp55 [Mycobacterium phage Cjw1] ],,NP_817504,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Genemark agreed (different from Glimmer)
    /note=Captured all coding potential (Genemark S)
    /note=Big Gap
    /note=Best SD score
    /note=Longest ORF
    /note=NA Starterator

CDS complement (39567 - 39998)
  /gene="55"
  /product="gp55"
  /function="immunity repressor"
  /locus tag="Saints25_55"
    /note=Original Glimmer call @bp 39998 has strength 10.98; Genemark calls start at 39866
    /note=SSC: 39998-39567 CP: yes SCS: both-gl ST: SS BLAST-Start: [transcriptional repressor [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 5.08247E-101 GAP: 225 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.56, -4.268618610724321, no F: immunity repressor SIF-BLAST: ,,[transcriptional repressor [Mycobacterium phage Cjw1] ],,NP_817505,100.0,5.08247E-101 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer agreed
    /note=Didnt choose longest ORF
    /note=Better SD score
    /note=Better start site (ATG)
    /note=Consistant with auto annotation
    /note=NA Starterator
    /note=Blast 1:1 match
    /note=Captures all coding potential
    /note=Immunity repressor

CDS 40224 - 40322
  /gene="56"
  /product="gp56"
  /function="hypothetical protein"
  /locus tag="Saints25_56"
    /note=Genemark calls start at 40224
    /note=SSC: 40224-40322 CP: yes SCS: genemark ST: SS BLAST-Start: [gp57 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 6.1944E-13 GAP: 225 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.994, -2.442961286954254, yes F: hypothetical protein SIF-BLAST: ,,[gp57 [Mycobacterium phage Cjw1] ],,NP_817506,100.0,6.1944E-13 SIF-HHPRED:  SIF-Syn: 
    /note=No Glimmer Start, 225 bp gap, best SD score, longest ORF, captures all coding potential, strong coding potential in GenemarkS, SS Starterator, 1:1 BLAST match, Not enough evidence to suggest function

CDS 40319 - 40456
  /gene="57"
  /product="gp57"
  /function="hypothetical protein"
  /locus tag="Saints25_57"
    /note=Original Glimmer call @bp 40319 has strength 9.16; Genemark calls start at 40319
    /note=SSC: 40319-40456 CP: yes SCS: both ST: SS BLAST-Start: [gp58 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 3.38095E-23 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.821, -5.574333665528913, yes F: hypothetical protein SIF-BLAST: ,,[gp58 [Mycobacterium phage Cjw1] ],,NP_817507,100.0,3.38095E-23 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and GeneMark agree. Not the Longest ORF. All coding potential covered. Best SD score. Gap -4. Starterator all calls it start site 4. 106 of 106. SS. Solid HHPRED match but not enough evidence to call the function.

CDS 40453 - 41292
  /gene="58"
  /product="gp58"
  /function="pentapeptide repeat protein"
  /locus tag="Saints25_58"
    /note=Original Glimmer call @bp 40453 has strength 7.38; Genemark calls start at 40453
    /note=SSC: 40453-41292 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein Porky_57 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.509, -3.531715028714623, yes F: pentapeptide repeat protein SIF-BLAST: ,,[hypothetical protein Porky_57 [Mycobacterium phage Porky] ],,YP_002014378,98.5765,0.0 SIF-HHPRED: Qnr; pentapeptide repeat, antibiotic resistance, DNA topoisomerase II, CELL CYCLE; HET: MLY; 2.0A {Aeromonas hydrophila},,,3PSS_A,33.6918,99.7 SIF-Syn: 
    /note=Glimmer and GeneMark agree; 4 bp overlap; best SD score; longest ORF; pentapeptide repeat protein as evidenced by Phagesdb and HHPRED

CDS 41294 - 41440
  /gene="59"
  /product="gp59"
  /function="hypothetical protein"
  /locus tag="Saints25_59"
    /note=Original Glimmer call @bp 41294 has strength 16.07; Genemark calls start at 41294
    /note=SSC: 41294-41440 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein Porky_58 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 7.49612E-26 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.975, -4.65945827897842, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein Porky_58 [Mycobacterium phage Porky] ],,YP_002014379,100.0,7.49612E-26 SIF-HHPRED:  SIF-Syn: 
    /note=Not the longest ORF. All coding capacity SD score is the best @ -4.659. Gap of 1. 109 of 120 called it start site 9. No HHPRED hits, added NCBI Blast evidence

CDS 41437 - 41715
  /gene="60"
  /product="gp60"
  /function="DNA binding protein"
  /locus tag="Saints25_60"
    /note=Original Glimmer call @bp 41437 has strength 10.0; Genemark calls start at 41437
    /note=SSC: 41437-41715 CP: yes SCS: both ST: SS BLAST-Start: [gp61 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 1.26677E-61 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.695, -5.269767271831238, no F: DNA binding protein SIF-BLAST: ,,[gp61 [Mycobacterium phage Cjw1] ],,NP_817510,100.0,1.26677E-61 SIF-HHPRED: DNA-directed RNA polymerase subunit P; Transcription, DNA-directed RNA polymerase; HET: ZN; 3.5A {Thermococcus kodakarensis},,,4QIW_W,48.913,93.2 SIF-Syn: 
    /note=Glimmer and Genemark agree, 4 base pair overlap, second best SD score, not the longest ORF, captures all coding potential, SS Starterator, 1:1 BLAST match, DNA-Binding protein

CDS 42259 - 42564
  /gene="61"
  /product="gp61"
  /function="hypothetical protein"
  /locus tag="Saints25_61"
    /note=Original Glimmer call @bp 42259 has strength 3.99; Genemark calls start at 42259
    /note=SSC: 42259-42564 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein GOKU_60 [Mycobacterium phage Goku] ],,NCBI, q1:s1 100.0% 1.57221E-65 GAP: 543 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.994, -2.5052746077145835, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein GOKU_60 [Mycobacterium phage Goku] ],,YP_008430576,100.0,1.57221E-65 SIF-HHPRED:  SIF-Syn: 
    /note=Longest ORF. Best SD score, large gap, All coding capacity. Glimmer and GeneMark agree. 109 of 109 in starterator. Suggested start site of 1.

CDS 42698 - 42931
  /gene="62"
  /product="gp62"
  /function="hypothetical protein"
  /locus tag="Saints25_62"
    /note=Original Glimmer call @bp 42698 has strength 4.86; Genemark calls start at 42698
    /note=SSC: 42698-42931 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_NELITZAMV_61 [Mycobacterium phage NelitzaMV] ],,NCBI, q1:s1 100.0% 2.25713E-49 GAP: 133 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.71, -5.220380545373514, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_NELITZAMV_61 [Mycobacterium phage NelitzaMV] ],,YP_009197729,100.0,2.25713E-49 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and GeneMark agree; best SD score; not the longest ORF; wide gap due to insertion of 63 between genes 61 and 62; NKF

CDS 42931 - 43092
  /gene="63"
  /product="gp63"
  /function="hypothetical protein"
  /locus tag="Saints25_63"
    /note=Original Glimmer call @bp 42931 has strength 15.17; Genemark calls start at 42931
    /note=SSC: 42931-43092 CP: yes SCS: both ST: SS BLAST-Start: [gp65 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 2.19015E-31 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.732, -2.996985748252251, yes F: hypothetical protein SIF-BLAST: ,,[gp65 [Mycobacterium phage Cjw1] ],,NP_817514,100.0,2.19015E-31 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark agree, 216 bp gap, best SD score, not longest ORF, SS Starterator, 1:1 BLAST match, Not enough evidence to suggest function

CDS 43241 - 43642
  /gene="64"
  /product="gp64"
  /function="hypothetical protein"
  /locus tag="Saints25_64"
    /note=Original Glimmer call @bp 43241 has strength 9.56; Genemark calls start at 43313
    /note=SSC: 43241-43642 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein PBI_DUMBO_66 [Mycobacterium phage Dumbo] ],,NCBI, q1:s1 100.0% 1.50748E-93 GAP: 148 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.269, -4.884061719576212, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_DUMBO_66 [Mycobacterium phage Dumbo] ],,YP_008051691,100.0,1.50748E-93 SIF-HHPRED: DUF6197 ; Family of unknown function (DUF6197),,,PF19698.2,83.4586,99.8 SIF-Syn: 
    /note=Glimmer and Genemark dont agree, 148 bp overlap, not best SD score, captures all coding potential, SS Starterator, 1:1 BLAST match,

CDS 43639 - 44607
  /gene="65"
  /product="gp65"
  /function="exonuclease"
  /locus tag="Saints25_65"
    /note=Original Glimmer call @bp 43639 has strength 9.51; Genemark calls start at 43639
    /note=SSC: 43639-44607 CP: yes SCS: both ST: SS BLAST-Start: [exonuclease [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.413, -5.927454668325683, no F: exonuclease SIF-BLAST: ,,[exonuclease [Mycobacterium phage Cjw1] ],,NP_817517,100.0,0.0 SIF-HHPRED: Mitochondrial genome maintenance exonuclease 1; human MGME1, DNA complex, DNA exonuclease, DNA BINDING PROTEIN; 2.702A {Homo sapiens},,,5ZYT_C,87.5776,99.9 SIF-Syn: 
    /note=Good overlap of 4; Glimmer and Genemark agree; longest ORF; Decent SD score; 1:1 NCBI matches; SS starterator;

CDS 44604 - 45014
  /gene="66"
  /product="gp66"
  /function="hypothetical protein"
  /locus tag="Saints25_66"
    /note=Original Glimmer call @bp 44604 has strength 6.07; Genemark calls start at 44604
    /note=SSC: 44604-45014 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_MURPHY_68 [Mycobacterium phage Murphy] ],,NCBI, q1:s1 100.0% 3.04559E-95 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.685, -5.290324183593171, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_MURPHY_68 [Mycobacterium phage Murphy] ],,YP_008051547,100.0,3.04559E-95 SIF-HHPRED:  SIF-Syn: 
    /note=Genemark and glimmer agree
    /note=Good overlap (3 bp)
    /note=Longest ORF
    /note=Good SD score
    /note=Captures all coding potential
    /note=Blast 1:1 match
    /note=SS starterator confirmed
    /note=No known function

CDS 45007 - 45729
  /gene="67"
  /product="gp67"
  /function="ERF family DNA pairing protein"
  /locus tag="Saints25_67"
    /note=Original Glimmer call @bp 45007 has strength 9.66; Genemark calls start at 45007
    /note=SSC: 45007-45729 CP: yes SCS: both ST: SS BLAST-Start: [ERF family ssDNA binding protein [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 2.73403E-176 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.04, -4.522979412939132, no F: ERF family DNA pairing protein SIF-BLAST: ,,[ERF family ssDNA binding protein [Mycobacterium phage Porky] ],,YP_002014389,100.0,2.73403E-176 SIF-HHPRED: ERF ; ERF superfamily,,,PF04404.15,57.0833,99.9 SIF-Syn: 
    /note=Best overlap of -8; Glimmer and Genemark agree; longest ORF; Best SD score; 1:1 BLAST match; 
    /note=matched function with Cwj1

CDS 45722 - 46033
  /gene="68"
  /product="gp68"
  /function="hypothetical protein"
  /locus tag="Saints25_68"
    /note=Original Glimmer call @bp 45722 has strength 7.1; Genemark calls start at 45722
    /note=SSC: 45722-46033 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein Porky_69 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 2.79221E-72 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.992, -5.86668762350679, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein Porky_69 [Mycobacterium phage Porky] ],,YP_002014390,100.0,2.79221E-72 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and genemark agree
    /note=Longest ORF
    /note=Okay SD score
    /note=Captures all coding potential
    /note=1:1 BLAST match
    /note=Good overlap
    /note=SS starterator confirmed
    /note=No known function

CDS 46033 - 46503
  /gene="69"
  /product="gp69"
  /function="hypothetical protein"
  /locus tag="Saints25_69"
    /note=Original Glimmer call @bp 46033 has strength 8.21; Genemark calls start at 46033
    /note=SSC: 46033-46503 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_DUMBO_71 [Mycobacterium phage Dumbo] ],,NCBI, q1:s1 100.0% 2.59185E-110 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.899, -2.6453814847322845, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_DUMBO_71 [Mycobacterium phage Dumbo] ],,YP_008051696,100.0,2.59185E-110 SIF-HHPRED:  SIF-Syn: 
    /note=best overlap of -1; Glimmer and Genemark agree; longest ORF; Best SD score; 1:1 BLAST matches; SS starterator; no HHPRED matches

CDS 46503 - 46871
  /gene="70"
  /product="gp70"
  /function="hypothetical protein"
  /locus tag="Saints25_70"
    /note=Original Glimmer call @bp 46503 has strength 11.04; Genemark calls start at 46503
    /note=SSC: 46503-46871 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein Kostya_72 [Mycobacterium phage Kostya] ],,NCBI, q1:s1 100.0% 9.3999E-82 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.917, -5.2484617369160205, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein Kostya_72 [Mycobacterium phage Kostya] ],,YP_002014540,100.0,9.3999E-82 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and genemark agree
    /note=Second longest ORF
    /note=Good SD score
    /note=Captures all coding potential
    /note=No gap or overlap
    /note=1:1 BLAST match
    /note=SS starterator confirmed
    /note=No known function found

CDS 46874 - 47242
  /gene="71"
  /product="gp71"
  /function="hypothetical protein"
  /locus tag="Saints25_71"
    /note=Original Glimmer call @bp 46874 has strength 9.3; Genemark calls start at 46874
    /note=SSC: 46874-47242 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein Porky_72 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 1.23652E-85 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.994, -2.442961286954254, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein Porky_72 [Mycobacterium phage Porky] ],,YP_002014393,100.0,1.23652E-85 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and GeneMark agree. Not quite the longest ORF. Best SD score -2.443. Gap of 2. starterator is not informative. a 1 to 1 match in Phages db blast. Not enough coverage and probability to use HHPRED as evidence.

CDS 47242 - 47415
  /gene="72"
  /product="gp72"
  /function="hypothetical protein"
  /locus tag="Saints25_72"
    /note=Original Glimmer call @bp 47242 has strength 10.09; Genemark calls start at 47242
    /note=SSC: 47242-47415 CP: yes SCS: both ST: SS BLAST-Start: [gp75 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 1.01757E-32 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.59, -5.5524625202905655, no F: hypothetical protein SIF-BLAST: ,,[gp75 [Mycobacterium phage Cjw1] ],,NP_817524,100.0,1.01757E-32 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark agreed
    /note=Captures all coding potential
    /note=Longest ORF
    /note=Best SD score
    /note=BLAST 1:1 match
    /note=SS starterator confirmed
    /note=No known function

CDS 47418 - 47651
  /gene="73"
  /product="gp73"
  /function="hypothetical protein"
  /locus tag="Saints25_73"
    /note=Original Glimmer call @bp 47418 has strength 11.85; Genemark calls start at 47418
    /note=SSC: 47418-47651 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Gardnerella vaginalis] ],,NCBI, q1:s1 100.0% 1.1816E-46 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.605, -3.2669815101762634, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein [Gardnerella vaginalis] ],,WP_015969694,100.0,1.1816E-46 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark agree, 2 bp gap, best SD score, not the longest ORF, does capture all coding potential, SS Starterator, 1:1 BLAST match, Not enough evidence to suggest function

CDS 47648 - 48061
  /gene="74"
  /product="gp74"
  /function="DprA-like DNA processing chain A"
  /locus tag="Saints25_74"
    /note=Original Glimmer call @bp 47648 has strength 9.16; Genemark calls start at 47648
    /note=SSC: 47648-48061 CP: yes SCS: both ST: NI BLAST-Start: [gp77 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 4.02394E-97 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.462, -5.82369656923664, no F: DprA-like DNA processing chain A SIF-BLAST: ,,[gp77 [Mycobacterium phage Cjw1] ],,NP_817526,100.0,4.02394E-97 SIF-HHPRED: DNA processing protein DprA; SAM and Rossmann Fold, DNA processing protein A, DNA BINDING PROTEIN; HET: MSE, SO4; 2.7A {Streptococcus pneumoniae} SCOP: a.60.17.1, c.129.1.4,,,3UQZ_C,98.5401,99.7 SIF-Syn: 
    /note=Glimmer and genemark agree
    /note=Longest ORF
    /note=Best SD score
    /note=Good overlap (3 bp)
    /note=Captures all coding potential
    /note=BLAST 1:1 match
    /note=Not informative
    /note=DprA-like DNA processing chain A

CDS 48058 - 48375
  /gene="75"
  /product="gp75"
  /function="HNH endonuclease"
  /locus tag="Saints25_75"
    /note=Original Glimmer call @bp 48058 has strength 5.39; Genemark calls start at 48058
    /note=SSC: 48058-48375 CP: yes SCS: both ST: SS BLAST-Start: [HNH endonuclease [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 2.13225E-72 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 0.578, -7.69171440769759, no F: HNH endonuclease SIF-BLAST: ,,[HNH endonuclease [Mycobacterium phage Cjw1] ],,NP_817527,100.0,2.13225E-72 SIF-HHPRED: d.4.1.8 (A:513-673) CRISPR-associated endonuclease Cas9/Csn1, HNH domain {Actinomyces naeslundii [TaxId: 1115803]} | CLASS: Alpha and beta proteins (a+b), FOLD: His-Me finger endonucleases, SUPFAM: His-Me finger endonucleases, FAM: HNH domain from CRISPR-associated protein Cas9,,,SCOP_d4ogca2,64.7619,95.6 SIF-Syn: 
    /note=Glimmer and GeneMark agree; 4 bp gap; second longest ORF; Not the best SD score, captures all coding potential, SS Starterator, 1:1 BLAST match,HNH endonuclease as evidenced on BLAST and HHPRED.

CDS 48365 - 48601
  /gene="76"
  /product="gp76"
  /function="hypothetical protein"
  /locus tag="Saints25_76"
    /note=Original Glimmer call @bp 48365 has strength 13.53; Genemark calls start at 48365
    /note=SSC: 48365-48601 CP: yes SCS: both ST: SS BLAST-Start: [gp79 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 1.64513E-47 GAP: -11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.842, -4.0707216408001425, yes F: hypothetical protein SIF-BLAST: ,,[gp79 [Mycobacterium phage Cjw1] ],,NP_817528,100.0,1.64513E-47 SIF-HHPRED:  SIF-Syn: 
    /note=All coding capacity. 11 bp overlap. SD score best at -4.071. Suggested start at 16 108 of 152 say suggested start. 1 to 1 in NCBI blast. Not enough coverage or probability to name a function.

CDS 48598 - 49248
  /gene="77"
  /product="gp77"
  /function="hypothetical protein"
  /locus tag="Saints25_77"
    /note=Original Glimmer call @bp 48598 has strength 8.47; Genemark calls start at 48598
    /note=SSC: 48598-49248 CP: yes SCS: both ST: SS BLAST-Start: [gp80 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 9.90039E-155 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 0.882, -6.988038999513095, no F: hypothetical protein SIF-BLAST: ,,[gp80 [Mycobacterium phage Cjw1] ],,NP_817529,99.0741,9.90039E-155 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark agree, 4 bp overlap, not best SD score, longest ORF, captures all coding potential, SS Starterator, 1:1 BLAST match,

CDS 49245 - 49580
  /gene="78"
  /product="gp78"
  /function="hypothetical protein"
  /locus tag="Saints25_78"
    /note=Original Glimmer call @bp 49230 has strength 8.48; Genemark calls start at 49245
    /note=SSC: 49245-49580 CP: yes SCS: both-gm ST: SS BLAST-Start: [hypothetical protein PHATBACTER_84 [Mycobacterium phage PhatBacter] ],,NCBI, q1:s1 100.0% 2.3007E-75 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.055, -3.3648782290756687, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PHATBACTER_84 [Mycobacterium phage PhatBacter] ],,YP_008857571,100.0,2.3007E-75 SIF-HHPRED:  SIF-Syn: 
    /note=Glimme and GeneMark disagree but GeneMark chosen given 4bp overlap; not the longest ORF;  best SD score, SS Starterator, 1:1 BLAST match NKF given low coverage and probability on BLAST.

CDS 49573 - 50835
  /gene="79"
  /product="gp79"
  /function="DnaB-like dsDNA helicase"
  /locus tag="Saints25_79"
    /note=Original Glimmer call @bp 49573 has strength 9.67; Genemark calls start at 49573
    /note=SSC: 49573-50835 CP: yes SCS: both ST: SS BLAST-Start: [DnaB-like replicative helicase [Mycobacterium phage Phaux] ],,NCBI, q1:s1 100.0% 0.0 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.523, -5.615966648652074, no F: DnaB-like dsDNA helicase SIF-BLAST: ,,[DnaB-like replicative helicase [Mycobacterium phage Phaux] ],,YP_008052257,100.0,0.0 SIF-HHPRED: DNAB-Like Replicative Helicase; ATPase, REPLICATION; 3.91A {Bacillus phage SPP1},,,3BGW_A,99.7619,100.0 SIF-Syn: 
    /note=Not the best SD score. 8 bp overlap. all coding capacity covered. Not the best SD score. Longest ORF. 105 of 198 have the same suggested start at 15. 1 to 1 match on NCBI blast. Enough coverage and probability to call the function.

CDS 50832 - 51020
  /gene="80"
  /product="gp80"
  /function="hypothetical protein"
  /locus tag="Saints25_80"
    /note=Original Glimmer call @bp 50832 has strength 8.27; Genemark calls start at 50832
    /note=SSC: 50832-51020 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein Porky_81 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 1.23399E-36 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.136, -5.085091778133397, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein Porky_81 [Mycobacterium phage Porky] ],,YP_002014402,100.0,1.23399E-36 SIF-HHPRED:  SIF-Syn: 
    /note=Genemark and Glimmer agree
    /note=Smallest overlap
    /note=Captures all coding potential
    /note=3rd longest ORF
    /note=Not best SD score
    /note=BLAST match 1:1
    /note=SS starterator confirmed, 174 of 305 called start site 37
    /note=No known function

CDS 51017 - 51277
  /gene="81"
  /product="gp81"
  /function="WhiB family transcription factor"
  /locus tag="Saints25_81"
    /note=Original Glimmer call @bp 51002 has strength 4.11; Genemark calls start at 51017
    /note=SSC: 51017-51277 CP: yes SCS: both-gm ST: NI BLAST-Start: [WhiB family transcription factor [Mycobacterium phage IHOP]],,NCBI, q1:s1 100.0% 3.7183E-57 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.749, -5.425965548198356, no F: WhiB family transcription factor SIF-BLAST: ,,[WhiB family transcription factor [Mycobacterium phage IHOP]],,AXH47626,100.0,3.7183E-57 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,80.2326,99.8 SIF-Syn: 
    /note=Position 51002 and 51017; Starterator not informative; GeneMark chosen given 4 bp overlap; second best SD score; 1:1 BLAST match; NI Starterator, evidence suggests that it is a WHiB family transcription factor,

CDS 51252 - 51473
  /gene="82"
  /product="gp82"
  /function="hypothetical protein"
  /locus tag="Saints25_82"
    /note=Original Glimmer call @bp 51252 has strength 9.61; Genemark calls start at 51252
    /note=SSC: 51252-51473 CP: yes SCS: both ST: SS BLAST-Start: [gp85 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 5.47027E-45 GAP: -26 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.899, -3.1725816037952645, yes F: hypothetical protein SIF-BLAST: ,,[gp85 [Mycobacterium phage Cjw1] ],,NP_817534,100.0,5.47027E-45 SIF-HHPRED: RraB ; Regulator of ribonuclease activity B,,,PF06877.14,20.5479,64.0 SIF-Syn: 
    /note=Glimmer and Genemark agree, 26 bp overlap,  best SD score, longest ORF, captures all coding potential, SS Starterator, 1:1 BLAST match, not enough evidence suggest a function

CDS 51466 - 51831
  /gene="83"
  /product="gp83"
  /function="hypothetical protein"
  /locus tag="Saints25_83"
    /note=Original Glimmer call @bp 51466 has strength 6.46; Genemark calls start at 51466
    /note=SSC: 51466-51831 CP: yes SCS: both ST: SS BLAST-Start: [gp86 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 2.87093E-83 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.358, -4.314376101284997, yes F: hypothetical protein SIF-BLAST: ,,[gp86 [Mycobacterium phage Cjw1] ],,NP_817535,100.0,2.87093E-83 SIF-HHPRED:  SIF-Syn: 
    /note=Genemark and Glimmer agree
    /note=ATG start codon
    /note=Captures all coding potential
    /note=4th longest ORF
    /note=Best SD score
    /note=BLAST 1:1 match
    /note=SS starterator confirmed
    /note=No known function

CDS 51828 - 52190
  /gene="84"
  /product="gp84"
  /function="Holliday junction resolvase"
  /locus tag="Saints25_84"
    /note=Original Glimmer call @bp 51828 has strength 13.0; Genemark calls start at 51828
    /note=SSC: 51828-52190 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein Porky_85 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 2.59306E-81 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.69, -3.6128803882603027, yes F: Holliday junction resolvase SIF-BLAST: ,,[hypothetical protein Porky_85 [Mycobacterium phage Porky] ],,YP_002014406,100.0,2.59306E-81 SIF-HHPRED: Holliday junction resolvase; archeal holliday junction resolvase helicase DNA binding enzyme phage 15-6 thermus thermophilus, RECOMBINATION; HET: MSE, SO4; 2.5A {Thermus thermophilus phage 15-6},,,7BGS_A,95.8333,99.7 SIF-Syn: 
    /note=Glimmer and GeneMark agree, 4 bp overlap, best SD score, second longest ORF, SS starterator, covers all coding potential, 1:1 BLAST match, HHpred Holliday junction resolvase function.

CDS 52187 - 52381
  /gene="85"
  /product="gp85"
  /function="hypothetical protein"
  /locus tag="Saints25_85"
    /note=Original Glimmer call @bp 52187 has strength 8.87; Genemark calls start at 52187
    /note=SSC: 52187-52381 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein Porky_86 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 9.29462E-38 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.605, -3.329294830936593, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein Porky_86 [Mycobacterium phage Porky] ],,YP_002014407,100.0,9.29462E-38 SIF-HHPRED: Monovalent cation/H+ antiporter subunit B; respiratory, hydrogenase, ion translocation, MEMBRANE PROTEIN; HET: SF4; 3.7A {Pyrococcus furiosus COM1},,,PF04039.16,68.75,86.2 SIF-Syn: 
    /note=Glimmer and Genemark agree, 4 bp overlap,  best SD score, not the longest ORF, captures all coding potential, SS Starterator, 1:1 BLAST match, evidence suggests that its a terminal phage replisome organizer, not enough evidence to suggest function

CDS 52536 - 53477
  /gene="86"
  /product="gp86"
  /function="polynucleotide kinase"
  /locus tag="Saints25_86"
    /note=Original Glimmer call @bp 52536 has strength 11.66; Genemark calls start at 52536
    /note=SSC: 52536-53477 CP: yes SCS: both ST: NI BLAST-Start: [polynucleotide kinase [Mycobacterium phage Murphy] ],,NCBI, q1:s1 100.0% 0.0 GAP: 154 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.732, -3.058913906516345, yes F: polynucleotide kinase SIF-BLAST: ,,[polynucleotide kinase [Mycobacterium phage Murphy] ],,YP_008051567,100.0,0.0 SIF-HHPRED: POLYNUCLEOTIDE KINASE; KINASE, PHOSPHATASE, ALPHA/BETA, P-LOOP, TRANSFERASE; HET: ADP, MSE; 2.33A {Enterobacteria phage T4} SCOP: c.108.1.9, c.37.1.1,,,1LTQ_A,99.6805,100.0 SIF-Syn: 
    /note=Smallest gap
    /note=Genemark and Glimmer agree
    /note=Captures all coding potential
    /note=Longest ORF
    /note=Best SD score
    /note=BLAST 1:1 match
    /note=SS starterator confirmed, called in 126 of 313 start site 41
    /note=Polynucleotide kinase

CDS 53584 - 53952
  /gene="87"
  /product="gp87"
  /function="hypothetical protein"
  /locus tag="Saints25_87"
    /note=Original Glimmer call @bp 53584 has strength 11.5; Genemark calls start at 53584
    /note=SSC: 53584-53952 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_MURPHY_89 [Mycobacterium phage Murphy] ],,NCBI, q1:s1 100.0% 2.72579E-85 GAP: 106 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.977, -2.6197685047743655, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_MURPHY_89 [Mycobacterium phage Murphy] ],,YP_008051568,100.0,2.72579E-85 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and GeneMark agree, best SD score, longest ORF, SS starterator, covers all coding potential, 1:1 BLAST match, PhagesDB Blast NKF.

CDS 53949 - 54047
  /gene="88"
  /product="gp88"
  /function="hypothetical protein"
  /locus tag="Saints25_88"
    /note=Original Glimmer call @bp 53925 has strength 1.55; Genemark calls start at 53949
    /note=SSC: 53949-54047 CP: yes SCS: both-gm ST: SS BLAST-Start: [hypothetical protein PBI_MURPHY_90 [Mycobacterium phage Murphy] ],,NCBI, q1:s1 100.0% 9.39103E-12 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.998, -4.548361544625773, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_MURPHY_90 [Mycobacterium phage Murphy] ],,YP_008051569,100.0,9.39103E-12 SIF-HHPRED: PetL ; Cytochrome B6-F complex subunit VI (PetL),,,PF05115.17,78.125,90.1 SIF-Syn: 
    /note=Glimmer and Genemark do not agree, 4 bp overlap, not best SD score, not the longest ORF, captures all coding potential, SS Starterator, 1:1 BLAST match? hits from TmHmm and Topcon for Cytochrome complex

CDS 54044 - 55369
  /gene="89"
  /product="gp89"
  /function="RNA ligase"
  /locus tag="Saints25_89"
    /note=Original Glimmer call @bp 54044 has strength 11.12; Genemark calls start at 54044
    /note=SSC: 54044-55369 CP: yes SCS: both ST: SS BLAST-Start: [RNA ligase [Mycobacterium phage Goldilocks] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.324, -4.2111970702621555, no F: RNA ligase SIF-BLAST: ,,[RNA ligase [Mycobacterium phage Goldilocks] ],,AOY11945,99.7732,0.0 SIF-HHPRED: RNA ligase; RNA repair, adenylyltransferase, LIGASE; HET: ATP; 1.547A {Naegleria gruberi},,,6VTB_A,95.6916,100.0 SIF-Syn: 
    /note=Glimmer and genemark agree; longest ORF; best SD score; 1:1 BLAST match; 4 bp overlap; RNA ligase; SS suggested start

CDS 55406 - 56227
  /gene="90"
  /product="gp90"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Saints25_90"
    /note=Original Glimmer call @bp 55406 has strength 5.53; Genemark calls start at 55406
    /note=SSC: 55406-56227 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_DUMBO_92 [Mycobacterium phage Dumbo] ],,NCBI, q1:s1 100.0% 0.0 GAP: 36 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.824, -3.15492870275902, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[hypothetical protein PBI_DUMBO_92 [Mycobacterium phage Dumbo] ],,YP_008051717,100.0,0.0 SIF-HHPRED: Hypothetical protein; alpha-beta, helix-turn-helix, Structural Genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, UNKNOWN FUNCTION; HET: MSE, ACY; 1.83A {Rhodopseudomonas palustris} SCOP: a.35.1.13,,,2O38_A,18.315,96.9 SIF-Syn: 
    /note=Glimmer and GeneMark agree, best SD score, longest ORF, SS starterator, covers all coding potential, 1:1 BLAST match, Phages DB Blast helix-turn-helix DNA binding domain

CDS 56224 - 56484
  /gene="91"
  /product="gp91"
  /function="WhiB family transcription factor"
  /locus tag="Saints25_91"
    /note=Original Glimmer call @bp 56224 has strength 5.14; Genemark calls start at 56224
    /note=SSC: 56224-56484 CP: yes SCS: both ST: SS BLAST-Start: [gp95 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 9.11232E-57 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.746, -3.108788982793736, yes F: WhiB family transcription factor SIF-BLAST: ,,[gp95 [Mycobacterium phage Cjw1] ],,NP_817544,100.0,9.11232E-57 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=Glimmer and Genemark agree, 4 bp overlap, best SD score, longest ORF, captures all coding potential, SS Starterator, 1:1 BLAST match, evidence suggests that its a terminal phage replisome organizer.

CDS 56501 - 56659
  /gene="92"
  /product="gp92"
  /function="hypothetical protein"
  /locus tag="Saints25_92"
    /note=Original Glimmer call @bp 56501 has strength 12.82; Genemark calls start at 56501
    /note=SSC: 56501-56659 CP: yes SCS: both ST: SS BLAST-Start: [gp96 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 3.03853E-29 GAP: 16 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.665, -3.490561115344053, yes F: hypothetical protein SIF-BLAST: ,,[gp96 [Mycobacterium phage Cjw1] ],,NP_817545,100.0,3.03853E-29 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark agree, 16 bp gap, best SD score, not the longest ORF, captures all coding potential, SS Starterator, 1:1 BLAST match, NKF

CDS 56656 - 57126
  /gene="93"
  /product="gp93"
  /function="hypothetical protein"
  /locus tag="Saints25_93"
    /note=Original Glimmer call @bp 56656 has strength 8.75; Genemark calls start at 56656
    /note=SSC: 56656-57126 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_PHRUX_93 [Mycobacterium phage Phrux] ],,NCBI, q1:s1 100.0% 1.49718E-110 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.615, -5.437750947756905, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_PHRUX_93 [Mycobacterium phage Phrux] ],,YP_008052029,100.0,1.49718E-110 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark agree, 4 bp overlap, second best SD score, not the longest ORF, captures all coding potential, SS Starterator, 1:1 BLAST match, not enough evidence to suggest function

CDS 57128 - 57463
  /gene="94"
  /product="gp94"
  /function="hypothetical protein"
  /locus tag="Saints25_94"
    /note=Original Glimmer call @bp 57128 has strength 9.65; Genemark calls start at 57128
    /note=SSC: 57128-57463 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_THRESHER_99 [Mycobacterium phage Thresher]],,NCBI, q1:s1 100.0% 2.45442E-74 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.647, -4.085313187509542, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_THRESHER_99 [Mycobacterium phage Thresher]],,QZD96940,98.1982,2.45442E-74 SIF-HHPRED: CRM1_repeat_2 ; CRM1 / Exportin repeat 2,,,PF18784.4,40.5405,80.6 SIF-Syn: 
    /note=Glimmer and Genemark agree, 1 bp gap, not the best SD score, not the longest ORF, captures all coding potential, SS Starterator, 1:1 BLAST match, not enough evidence to suggest function.

CDS 57460 - 58005
  /gene="95"
  /product="gp95"
  /function="hypothetical protein"
  /locus tag="Saints25_95"
    /note=Original Glimmer call @bp 57496 has strength 3.21; Genemark calls start at 57496
    /note=SSC: 57460-58005 CP: yes SCS: both-cs ST: SS BLAST-Start: [DNA binding protein [Mycobacterium phage Murphy] ],,NCBI, q1:s1 98.3425% 1.59186E-128 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.405, -4.595837784824238, yes F: hypothetical protein SIF-BLAST: ,,[DNA binding protein [Mycobacterium phage Murphy] ],,YP_008051577,98.8889,1.59186E-128 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark agree, but start site 57460 chosen because of 4 bp gap, longest ORF, and evidence on SS Starterator., not the best SD score,  1:1 BLAST match, evidence suggests that it may be some type of enzyme but in HHPred there doesn`t seem to be a common consensus so NKF

CDS 58002 - 58442
  /gene="96"
  /product="gp96"
  /function="SSB protein"
  /locus tag="Saints25_96"
    /note=Original Glimmer call @bp 58002 has strength 8.34; Genemark calls start at 58002
    /note=SSC: 58002-58442 CP: yes SCS: both ST: SS BLAST-Start: [SSB protein [Mycobacterium phage Kostya] ],,NCBI, q1:s1 100.0% 1.38284E-102 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.787, -2.881875840424956, yes F: SSB protein SIF-BLAST: ,,[SSB protein [Mycobacterium phage Kostya] ],,YP_002014568,100.0,1.38284E-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_A,78.0822,100.0 SIF-Syn: 
    /note=Glimmer and Genemark agree, 4 bp overlap, best SD score, not the longest ORF, captures all coding potential, SS Starterator, 1:1 BLAST match, evidence suggests that it is an SSB protein

CDS 58558 - 59337
  /gene="97"
  /product="gp97"
  /function="ClpP-like protease"
  /locus tag="Saints25_97"
    /note=Original Glimmer call @bp 58558 has strength 10.58; Genemark calls start at 58576
    /note=SSC: 58558-59337 CP: yes SCS: both-gl ST: SS BLAST-Start: [head maturation protease [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 0.0 GAP: 115 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.899, -2.7254235724530456, yes F: ClpP-like protease SIF-BLAST: ,,[head maturation protease [Mycobacterium phage Porky] ],,YP_002014421,100.0,0.0 SIF-HHPRED: Putative ATP-dependent Clp protease proteolytic subunit; mitochondrial ClpP, Clp/Hsp 100, ATP-dependent protease, HYDROLASE; HET: GOL, FME, DIO, EDO; 2.1A {Homo sapiens} SCOP: c.14.1.1,,,1TG6_F,68.3398,99.9 SIF-Syn: 
    /note=Glimmer and GeneMark disagree. Glimmner chosen due to better SD. Large gap of 115; Best SD score; SS Starterator; 1:1 BLAST match.

CDS 59334 - 59690
  /gene="98"
  /product="gp98"
  /function="hypothetical protein"
  /locus tag="Saints25_98"
    /note=Original Glimmer call @bp 59418 has strength 8.4; Genemark calls start at 59334
    /note=SSC: 59334-59690 CP: yes SCS: both-gm ST: NA BLAST-Start: [hypothetical protein Porky_101 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 7.8356E-78 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.126, -4.4193642963639475, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein Porky_101 [Mycobacterium phage Porky] ],,YP_002014422,100.0,7.8356E-78 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and genemark did not agree
    /note=Changed start site from glimmer to genemark start site (Glimmer start site would cut off coding potential)
    /note=Captures all coding potential
    /note=4th longest ORF
    /note=Bad SD score
    /note=1:1 BLAST match
    /note=Starterator NA
    /note=No known function

CDS 59691 - 59981
  /gene="99"
  /product="gp99"
  /function="hypothetical protein"
  /locus tag="Saints25_99"
    /note=Original Glimmer call @bp 59691 has strength 10.73; Genemark calls start at 59691
    /note=SSC: 59691-59981 CP: yes SCS: both ST: SS BLAST-Start: [gp105 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 3.94902E-61 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.015, -4.513079314654054, yes F: hypothetical protein SIF-BLAST: ,,[gp105 [Mycobacterium phage Cjw1] ],,NP_817554,100.0,3.94902E-61 SIF-HHPRED: Tail needle protein gp26; Viral protein, P22, Tail Needle, Membrane penetration; 2.75A {Enterobacteria phage P22},,,4ZXQ_D,60.4167,96.1 SIF-Syn: 
    /note=Glimmer and Genemark agree, Gap of 0; Best SD score; longest ORF; captures all coding potential. SS starterator; 1:1 BLAST match; 
    /note=very good HHPRED hit but did not have enough evidence to call it a tail needle protein,

CDS 59986 - 60297
  /gene="100"
  /product="gp100"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Saints25_100"
    /note=Original Glimmer call @bp 59962 has strength 3.36; Genemark calls start at 59986
    /note=SSC: 59986-60297 CP: yes SCS: both-gm ST: SS BLAST-Start: [gp106 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 9.73574E-71 GAP: 4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 0.978, -6.768399669413642, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[gp106 [Mycobacterium phage Cjw1] ],,NP_817555,100.0,9.73574E-71 SIF-HHPRED: Regulatory protein cox; helix-turn-helix, DNA binding, VIRAL PROTEIN; 2.401A {Enterobacteria phage P2},,,4LHF_A,49.5146,98.8 SIF-Syn: 
    /note=Glimmer and genemark do not agree
    /note=Changed to genemark start site (better gap and SD score)
    /note=Captures all coding potential
    /note=Good gap
    /note=4th longest ORF
    /note=BLAST 1:1
    /note=SS starterator confirmed
    /note=helix-turn-helix DNA binding domain

CDS 60479 - 60640
  /gene="101"
  /product="gp101"
  /function="HNH endonuclease"
  /locus tag="Saints25_101"
    /note=Original Glimmer call @bp 60479 has strength 10.35; Genemark calls start at 60479
    /note=SSC: 60479-60640 CP: yes SCS: both ST: SS BLAST-Start: [HNH endonuclease [Mycobacterium phage Quallification]],,NCBI, q1:s1 100.0% 3.63078E-31 GAP: 181 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.399, -3.8426483658976065, no F: HNH endonuclease SIF-BLAST: ,,[HNH endonuclease [Mycobacterium phage Quallification]],,UVK62215,100.0,3.63078E-31 SIF-HHPRED: HNH_3 ; HNH endonuclease,,,PF13392.9,83.0189,99.6 SIF-Syn: 
    /note=Glimmer and GeneMark agree; not shortest gap or best SD score; uncertainty with start site, as pham as many drafts; HNH nuclease as evidenced by NCBI Blast; 1:1 blast match

tRNA 60741 - 60824
  /gene="102"
  /product="tRNA-Arg(cct)"
  /locus tag="SAINTS25_102"
    /note=tRNA-Arg(cct)

tRNA 60827 - 60899
  /gene="103"
  /product="tRNA-Gly(tcc)"
  /locus tag="SAINTS25_103"
    /note=tRNA-Gly(tcc)

CDS 61094 - 61318
  /gene="104"
  /product="gp104"
  /function="hypothetical protein"
  /locus tag="Saints25_104"
    /note=Original Glimmer call @bp 61094 has strength 8.73; Genemark calls start at 61094
    /note=SSC: 61094-61318 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein Porky_107 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 4.34089E-49 GAP: 453 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.434, -3.769471247018311, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein Porky_107 [Mycobacterium phage Porky] ],,YP_002014426,100.0,4.34089E-49 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark agree, 453 bp gap, huge gap may indicate unincluded gene, best SD score, not the longest ORF, captures all coding potential, SS Starterator, 1:1 BLAST match, not enough evidence to suggest function

CDS 61315 - 61578
  /gene="105"
  /product="gp105"
  /function="hypothetical protein"
  /locus tag="Saints25_105"
    /note=Original Glimmer call @bp 61345 has strength 11.09; Genemark calls start at 61345
    /note=SSC: 61315-61578 CP: yes SCS: both-cs ST: SS BLAST-Start: [gp112 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 4.68737E-57 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.352, -4.901215214744926, yes F: hypothetical protein SIF-BLAST: ,,[gp112 [Mycobacterium phage Cjw1] ],,NP_817559,100.0,4.68737E-57 SIF-HHPRED: TcpQ ; Toxin co-regulated pilus biosynthesis protein Q,,,PF10671.12,16.092,50.4 SIF-Syn: 
    /note=Glimmer and GeneMark agree on 61345 suggested start but 61315 start chosen because of longer ORF and bp overlap of 4; 1:1 BLAST; NKF chosen due to low coverage and probability on HHPRED.

CDS 61589 - 61963
  /gene="106"
  /product="gp106"
  /function="hydrolase"
  /locus tag="Saints25_106"
    /note=Original Glimmer call @bp 61589 has strength 8.85; Genemark calls start at 61589
    /note=SSC: 61589-61963 CP: yes SCS: both ST: SS BLAST-Start: [hydrolase [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 1.04434E-85 GAP: 10 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.965, -4.698691165234176, no F: hydrolase SIF-BLAST: ,,[hydrolase [Mycobacterium phage Cjw1] ],,NP_817560,100.0,1.04434E-85 SIF-HHPRED: CMP/hydroxymethyl CMP hydrolase; hydrolase; 1.8A {Streptomyces rimofaciens},,,4OHR_A,97.5806,99.5 SIF-Syn: 
    /note=Glimmer and Genemark agree, 10 bp gap, best SD score, not the longest ORF, captures all coding potential, SS Starterator, 1:1 BLAST match, strong evidence to suggest hydrolase as the function, but there is also strong evidence to suggest that it could be a deoxycytidylate deaminase or nucleoside deoxyribosyltransferase.

CDS 61966 - 62445
  /gene="107"
  /product="gp107"
  /function="hypothetical protein"
  /locus tag="Saints25_107"
    /note=Original Glimmer call @bp 61966 has strength 11.4; Genemark calls start at 61966
    /note=SSC: 61966-62445 CP: yes SCS: both ST: SS BLAST-Start: [endolysin; inhibits RNA polymerase [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 6.3134E-113 GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.434, -6.648369742785566, no F: hypothetical protein SIF-BLAST: ,,[endolysin; inhibits RNA polymerase [Mycobacterium phage Cjw1] ],,NP_817561,100.0,6.3134E-113 SIF-HHPRED: dGTP_diPhyd_N ; dATP/dGTP diphosphohydrolase, N-terminal,,,PF18909.3,62.2642,100.0 SIF-Syn: 
    /note=Glimmer and GeneMark agree; smallest gap 2bp; longest ORF; not best SD score; captures all coding potential, starterator suggested start; good probability and coverage on NCBI for endolysin protein but does not show up on HHPRED and has not been called on PhagesDB

CDS 62456 - 63241
  /gene="108"
  /product="gp108"
  /function="DnaQ-like (DNA polymerase III subunit)"
  /locus tag="Saints25_108"
    /note=Original Glimmer call @bp 62456 has strength 11.66; Genemark calls start at 62456
    /note=SSC: 62456-63241 CP: yes SCS: both ST: SS BLAST-Start: [DNA polymerase exonuclease subunit [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 0.0 GAP: 10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.828, -2.794180387977985, yes F: DnaQ-like (DNA polymerase III subunit) SIF-BLAST: ,,[DNA polymerase exonuclease subunit [Mycobacterium phage Cjw1] ],,NP_817562,100.0,0.0 SIF-HHPRED: DNA_polB_Kod1_like_exo; DEDDy 3`-5` exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases.,,,cd05780,71.6475,99.5 SIF-Syn: 
    /note=Glimmer and Genemark agree, 10 bp gap, best SD score, longest ORF, captures all coding potential, SS Starterator, 1:1 BLAST match, evidence suggests that it is a DNA polymerase III subunit.

CDS 63238 - 63480
  /gene="109"
  /product="gp109"
  /function="hypothetical protein"
  /locus tag="Saints25_109"
    /note=Original Glimmer call @bp 63238 has strength 7.62; Genemark calls start at 63238
    /note=SSC: 63238-63480 CP: yes SCS: both ST: SS BLAST-Start: [gp116 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 1.52762E-52 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.352, -4.707395188728813, yes F: hypothetical protein SIF-BLAST: ,,[gp116 [Mycobacterium phage Cjw1] ],,NP_817563,100.0,1.52762E-52 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and GeneMark agree, best SD score, -4 bp overlap, SS Starterator, covers all coding potential, 1:1 BLAST match. PhagesDB NKF

CDS 63488 - 64450
  /gene="110"
  /product="gp110"
  /function="RecA-like DNA recombinase"
  /locus tag="Saints25_110"
    /note=Original Glimmer call @bp 63488 has strength 10.31; Genemark calls start at 63488
    /note=SSC: 63488-64450 CP: yes SCS: both ST: SS 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, 2.828, -3.622410502704947, yes F: RecA-like DNA recombinase SIF-BLAST: ,,[UvsX-like recombinase [Mycobacterium phage Cjw1] ],,NP_817564,100.0,0.0 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,99.0625,100.0 SIF-Syn: 
    /note=Glimmer and Genemark agree, 7 bp gap, best SD score, longest ORF, captures all coding potential, SS Starterator, 1:1 BLAST match, Evidence suggests that it is a RecA-like recombinase

CDS 64447 - 64584
  /gene="111"
  /product="gp111"
  /function="hypothetical protein"
  /locus tag="Saints25_111"
    /note=Original Glimmer call @bp 64447 has strength 5.86
    /note=SSC: 64447-64584 CP: yes SCS: glimmer ST: SS BLAST-Start: [hypothetical protein Porky_115 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 2.47131E-22 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.753, -2.952618745997422, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein Porky_115 [Mycobacterium phage Porky] ],,YP_002014434,100.0,2.47131E-22 SIF-HHPRED: TraV ; Type IV conjugative transfer system lipoprotein (TraV),,,PF09676.13,37.7778,37.2 SIF-Syn: 
    /note=Start called on Glimmer but nothing for GeneMark; 4 bp overlap; not longest ORF; best SD score; no hits on HHPRED but NCBI has full coverage, probability, and 1:1 match for hypothetical protein.

CDS 64571 - 64744
  /gene="112"
  /product="gp112"
  /function="hypothetical protein"
  /locus tag="Saints25_112"
    /note=Original Glimmer call @bp 64571 has strength 10.19; Genemark calls start at 64571
    /note=SSC: 64571-64744 CP: yes SCS: both ST: SS BLAST-Start: [gp119 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 8.34972E-33 GAP: -14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.59, -6.513391808765885, no F: hypothetical protein SIF-BLAST: ,,[gp119 [Mycobacterium phage Cjw1] ],,NP_817566,100.0,8.34972E-33 SIF-HHPRED: GP63 ; Gene product 63,,,PF17471.5,63.1579,92.5 SIF-Syn: 
    /note=overlap of -14; glimmer and genemark agree; longest ORF; decent SD score; good 1:1 BLAST matches; SS starterator. Not enough evidence to suggest function.

CDS complement (64734 - 64844)
  /gene="113"
  /product="gp113"
  /function="hypothetical protein"
  /locus tag="Saints25_113"
    /note=Genemark calls start at 64844
    /note=SSC: 64844-64734 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein SEA_BUCK_119 [Mycobacterium phage Buck] ],,NCBI, q1:s1 100.0% 1.27232E-15 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.289, -4.9845315433504895, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_BUCK_119 [Mycobacterium phage Buck] ],,QGJ95425,100.0,1.27232E-15 SIF-HHPRED:  SIF-Syn: 
    /note=No suggested start from Glimmer, using GeneMark suggested start. SS starterator, better SD score, longest ORF, covers all coding potential via GeneMarkS, 1:1 BLAST match. PhagesDB NKF.

CDS complement (64845 - 65117)
  /gene="114"
  /product="gp114"
  /function="hypothetical protein"
  /locus tag="Saints25_114"
    /note=Original Glimmer call @bp 65069 has strength 6.1; Genemark calls start at 65117
    /note=SSC: 65117-64845 CP: yes SCS: both-gm ST: SS BLAST-Start: [hypothetical protein SEA_BUCK_120 [Mycobacterium phage Buck]],,NCBI, q1:s1 100.0% 1.07788E-58 GAP: 15 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.96, -4.629584883725491, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_BUCK_120 [Mycobacterium phage Buck]],,QGJ95426,100.0,1.07788E-58 SIF-HHPRED: Der f 23 allergen; Allergen; 1.7A {Dermatophagoides farinae},,,5ZJL_A,22.2222,39.4 SIF-Syn: 
    /note=Glimmer and Genemark do not agree but GeneMarrk start chosen, 15 bp gap, not the best SD score, not the longest ORF, captures all coding potential in GenemarkS, SS Starterator, 1:1 BLAST match, not enough evidence to suggest function

CDS 65133 - 65594
  /gene="115"
  /product="gp115"
  /function="kinase"
  /locus tag="Saints25_115"
    /note=Original Glimmer call @bp 65133 has strength 6.6; Genemark calls start at 65133
    /note=SSC: 65133-65594 CP: yes SCS: both ST: SS BLAST-Start: [gp122 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 2.65899E-105 GAP: 15 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.988, -2.5969056218148614, yes F: kinase SIF-BLAST: ,,[gp122 [Mycobacterium phage Cjw1] ],,NP_817569,99.3464,2.65899E-105 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and GeneMark agree, best SD score, longest ORF, SS starterator, covers all coding potential, 1:1 BLAST match, HHPRED sensor kinase protein.

CDS 65591 - 65758
  /gene="116"
  /product="gp116"
  /function="hypothetical protein"
  /locus tag="Saints25_116"
    /note=Original Glimmer call @bp 65591 has strength 8.9; Genemark calls start at 65591
    /note=SSC: 65591-65758 CP: yes SCS: both ST: SS BLAST-Start: [gp123 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 1.41592E-31 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.527, -3.5719506502182776, yes F: hypothetical protein SIF-BLAST: ,,[gp123 [Mycobacterium phage Cjw1] ],,NP_817570,98.1818,1.41592E-31 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark agree, 4 bp overlap, best SD score, not the longest ORF, captures all coding potential, SS Starterator, 1:1 BLAST match, not enough evidence to suggest function

CDS 65742 - 65942
  /gene="117"
  /product="gp117"
  /function="hypothetical protein"
  /locus tag="Saints25_117"
    /note=Original Glimmer call @bp 65742 has strength 10.67; Genemark calls start at 65742
    /note=SSC: 65742-65942 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein Porky_122 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 9.11937E-39 GAP: -17 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.994, -2.970161406017234, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein Porky_122 [Mycobacterium phage Porky] ],,YP_002014441,100.0,9.11937E-39 SIF-HHPRED: DUF2840 ; Protein of unknown function (DUF2840),,,PF11000.11,36.3636,43.4 SIF-Syn: 
    /note=Glimmer and GeneMark agree; longest ORF; captures all coding potential; 17 bp overlap; best SD score; PhagesDB and HHPRED indicate NKF, but NCBI has full coverage and probability; 1:1 BLAST.

CDS 65939 - 66076
  /gene="118"
  /product="gp118"
  /function="hypothetical protein"
  /locus tag="Saints25_118"
    /note=Original Glimmer call @bp 65939 has strength 2.73
    /note=SSC: 65939-66076 CP: yes SCS: glimmer ST: SS BLAST-Start: [gp125 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 3.43775E-24 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.055, -3.222210725506937, yes F: hypothetical protein SIF-BLAST: ,,[gp125 [Mycobacterium phage Cjw1] ],,NP_817572,100.0,3.43775E-24 SIF-HHPRED:  SIF-Syn: 
    /note=No Genemark score, 4 bp overlap, best SD score, longest ORF, captures all coding potential on GenemarkS, SS Starterator, 1:1 BLAST match, not enough evidence to suggest function

CDS 66073 - 66252
  /gene="119"
  /product="gp119"
  /function="hypothetical protein"
  /locus tag="Saints25_119"
    /note=Original Glimmer call @bp 66073 has strength 7.63; Genemark calls start at 66073
    /note=SSC: 66073-66252 CP: yes SCS: both ST: SS BLAST-Start: [gp126 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 5.59661E-35 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.829, -5.046247871416941, no F: hypothetical protein SIF-BLAST: ,,[gp126 [Mycobacterium phage Cjw1] ],,NP_817573,100.0,5.59661E-35 SIF-HHPRED: d.198.1.0 (A:) automated matches {Salmonella typhimurium [TaxId: 90371]} | CLASS: Alpha and beta proteins (a+b), FOLD: Secretion chaperone-like, SUPFAM: Type III secretory system chaperone-like, FAM: automated matches,,,SCOP_d3epua_,96.6102,91.7 SIF-Syn: 
    /note=Glimmer and Genemark agree, Not the Longest ORF because there would be overlap. Gap -4. SS 106 of 106 at start site 7. Captures all coding potential, SS Starterator Good matches on HHPRED but functions not on the official function list.

CDS 66252 - 66383
  /gene="120"
  /product="gp120"
  /function="hypothetical protein"
  /locus tag="Saints25_120"
    /note=Original Glimmer call @bp 66252 has strength 13.57; Genemark calls start at 66252
    /note=SSC: 66252-66383 CP: yes SCS: both ST: SS BLAST-Start: [gp127 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 9.11087E-21 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.69, -5.261583822777037, no F: hypothetical protein SIF-BLAST: ,,[gp127 [Mycobacterium phage Cjw1] ],,NP_817574,100.0,9.11087E-21 SIF-HHPRED: CPSase_sm_chain ; Carbamoyl-phosphate synthase small chain, CPSase domain,,,PF00988.25,72.093,89.8 SIF-Syn: 
    /note=Glimmer and Genemark agree, 1 bp overlap, not the best SD score,  longest ORF, captures all coding potential, SS Starterator, 1:1 BLAST match, not enough evidence to suggest function

CDS 66394 - 66528
  /gene="121"
  /product="gp121"
  /function="hypothetical protein"
  /locus tag="Saints25_121"
    /note=Genemark calls start at 66394
    /note=SSC: 66394-66528 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein DRDREY_130 [Mycobacterium phage DrDrey] ],,NCBI, q1:s1 100.0% 9.45854E-24 GAP: 10 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.767, -5.69021729366323, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein DRDREY_130 [Mycobacterium phage DrDrey] ],,YP_008409521,100.0,9.45854E-24 SIF-HHPRED:  SIF-Syn: 
    /note=Not the Longest ORF. 10bp gap. Start site 2 67 of 106. Called by GeneMark not Glimmer. Not the longest ORF, not the best SD score, 1:1 BLAST match, Captures all coding potential, NKF because there are no HHPRED hits or PhagesDB BLAST.

CDS complement (66908 - 67171)
  /gene="122"
  /product="gp122"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Saints25_122"
    /note=Original Glimmer call @bp 67171 has strength 2.63; Genemark calls start at 67102
    /note=SSC: 67171-66908 CP: yes SCS: both-gl ST: SS BLAST-Start: [HTH binding domain protein [Mycobacterium phage Goku] ],,NCBI, q1:s1 100.0% 9.83139E-56 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.109, -4.376977241479107, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[HTH binding domain protein [Mycobacterium phage Goku] ],,YP_008430640,98.8506,9.83139E-56 SIF-HHPRED: HTH_58 ; Helix-turn-helix domain,,,PF19575.2,48.2759,97.6 SIF-Syn: 
    /note=Glimmer and Genemark do not agree, 4 bp overlap, not the best SD score, longest ORF, captures all coding potential, SS Starterator, 1:1 BLAST match, evidence suggests that it is a helix-turn-helix DNA binding domain

CDS complement (67168 - 67557)
  /gene="123"
  /product="gp123"
  /function="hypothetical protein"
  /locus tag="Saints25_123"
    /note=Original Glimmer call @bp 67422 has strength 4.08; Genemark calls start at 67557
    /note=SSC: 67557-67168 CP: yes SCS: both-gm ST: SS BLAST-Start: [ParB C-terminal domain [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 9.74365E-87 GAP: 118 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.545, -4.443838065747148, no F: hypothetical protein SIF-BLAST: ,,[ParB C-terminal domain [Mycobacterium phage Porky] ],,YP_002014448,99.2248,9.74365E-87 SIF-HHPRED: b.40.14.1 (A:1-76) Hydrogenase expression/formation protein HypC {Shewanella oneidensis [TaxId: 70863]} | CLASS: All beta proteins, FOLD: OB-fold, SUPFAM: HupF/HypC-like, FAM: HupF/HypC-like,,,SCOP_d3d3ra1,10.8527,36.9 SIF-Syn: 
    /note=Glimmer and Genemark do not agree, 118 bp gap, not the best SD score, longest ORF, captures all coding potential, NI Starterator, 1:1 BLAST match, not enough evidence to suggest function

CDS complement (67676 - 67930)
  /gene="124"
  /product="gp124"
  /function="hypothetical protein"
  /locus tag="Saints25_124"
    /note=Original Glimmer call @bp 67846 has strength 3.59; Genemark calls start at 67846
    /note=SSC: 67930-67676 CP: yes SCS: both-cs ST: NI BLAST-Start: [hypothetical protein Porky_130 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 2.99813E-53 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.732, -3.1379842619144376, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein Porky_130 [Mycobacterium phage Porky] ],,YP_002014449,100.0,2.99813E-53 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark agree, start site was changed to avoid cutting off coding potential, 4 bp overlap, best SD score, not the longest ORF, captures all coding potential in GenemarkS, NI Starterator, 1:1 BLAST match, not enough evidence to suggest function

CDS complement (67927 - 68145)
  /gene="125"
  /product="gp125"
  /function="hypothetical protein"
  /locus tag="Saints25_125"
    /note=Original Glimmer call @bp 68145 has strength 5.05; Genemark calls start at 68145
    /note=SSC: 68145-67927 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein Porky_131 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 6.18502E-46 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.379, -3.8238896197506356, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein Porky_131 [Mycobacterium phage Porky] ],,YP_002014450,100.0,6.18502E-46 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark agree Longest ORF, Gap -4. Best SD score. Captures all coding potential, SS Starterator, 1:1 BLAST match, Not enough evidence to suggest function

CDS complement (68142 - 68594)
  /gene="126"
  /product="gp126"
  /function="hypothetical protein"
  /locus tag="Saints25_126"
    /note=Original Glimmer call @bp 68594 has strength 8.4; Genemark calls start at 68594
    /note=SSC: 68594-68142 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein Porky_132 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 9.46366E-108 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.584, -4.616314719381481, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein Porky_132 [Mycobacterium phage Porky] ],,YP_002014451,100.0,9.46366E-108 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark agree, 4 bp overlap, not the best SD score, longest ORF, captures almost all coding potential but cuts off a little bit in GeneMarkS, SS Starterator, 1:1 BLAST match, not enough evidence to suggest function

CDS complement (68591 - 69055)
  /gene="127"
  /product="gp127"
  /function="hypothetical protein"
  /locus tag="Saints25_127"
    /note=Original Glimmer call @bp 69055 has strength 8.96; Genemark calls start at 69055
    /note=SSC: 69055-68591 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_HOONTER_135 [Mycobacterium phage Hoonter]],,NCBI, q1:s1 100.0% 2.29248E-107 GAP: 14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.055, -3.3648782290756687, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_HOONTER_135 [Mycobacterium phage Hoonter]],,QGJ94301,100.0,2.29248E-107 SIF-HHPRED: 5,10-methenyltetrahydrofolate synthetase; Structural Genomics, PSI, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, Ligase; NMR {Aquifex aeolicus} SCOP: c.124.1.6, l.1.1.1,,,1SOU_A,6.49351,35.0 SIF-Syn: 
    /note=Glimmer and GeneMark agree. Longest ORF. All coding potential. Gap 14. Suggested Start Site 47. 1:1 BLAST.

CDS complement (69070 - 69399)
  /gene="128"
  /product="gp128"
  /function="hypothetical protein"
  /locus tag="Saints25_128"
    /note=Original Glimmer call @bp 69399 has strength 13.49; Genemark calls start at 69399
    /note=SSC: 69399-69070 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_MURPHY_132 [Mycobacterium phage Murphy] ],,NCBI, q1:s1 100.0% 1.80098E-73 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.615, -5.357708860036144, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_MURPHY_132 [Mycobacterium phage Murphy] ],,YP_008051609,100.0,1.80098E-73 SIF-HHPRED: hypothetical protein; Metagenomics target, structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, unknown function; HET: MSE; 1.7A {uncultured marine organism} SCOP: d.58.4.20,,,2OD4_B,64.2202,91.6 SIF-Syn: 
    /note=Glimmer and Genemark agree, 1 bp gap, not best SD score, longest ORF, captures all coding potential in GeneMarkS, SS Starterator, 1:1 BLAST match, not enough evidence to suggest function

CDS complement (69401 - 69718)
  /gene="129"
  /product="gp129"
  /function="hypothetical protein"
  /locus tag="Saints25_129"
    /note=Original Glimmer call @bp 69718 has strength 11.01; Genemark calls start at 69718
    /note=SSC: 69718-69401 CP: yes SCS: both ST: SS BLAST-Start: [gp134 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 1.82584E-69 GAP: 5 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.607, -3.4030855957987485, yes F: hypothetical protein SIF-BLAST: ,,[gp134 [Mycobacterium phage Cjw1] ],,NP_817581,100.0,1.82584E-69 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and GeneMark agree. Longest ORF. Best SD score. 81 of 81 @ start site 2. Not enough coverage or probability to call a function.

CDS complement (69724 - 69849)
  /gene="130"
  /product="gp130"
  /function="hypothetical protein"
  /locus tag="Saints25_130"
    /note=Original Glimmer call @bp 69849 has strength 3.27
    /note=SSC: 69849-69724 CP: no SCS: glimmer ST: SS BLAST-Start: [hypothetical protein PBI_PHRUX_131 [Mycobacterium phage Phrux] ],,NCBI, q1:s1 100.0% 4.30831E-22 GAP: -11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.637, -4.504757315476905, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_PHRUX_131 [Mycobacterium phage Phrux] ],,YP_008052065,100.0,4.30831E-22 SIF-HHPRED: DUF3795 ; Protein of unknown function (DUF3795),,,PF12675.10,29.2683,77.2 SIF-Syn: 
    /note=No Genemark output, 11bp overlap, not best SD score, not the longest ORF, cuts off tail end of coding potential in GenemarkS, SS Starterator, 1:1 BLAST match, not enough evidence to suggest function

CDS complement (69839 - 70045)
  /gene="131"
  /product="gp131"
  /function="hypothetical protein"
  /locus tag="Saints25_131"
    /note=Original Glimmer call @bp 70045 has strength 6.25; Genemark calls start at 70045
    /note=SSC: 70045-69839 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein Porky_138 [Mycobacterium phage Porky] ],,NCBI, q1:s1 100.0% 5.35575E-42 GAP: 45 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.712, -3.0387982655504704, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein Porky_138 [Mycobacterium phage Porky] ],,YP_002014457,100.0,5.35575E-42 SIF-HHPRED: DUF6316 ; Domain of unknown function (DUF6316),,,PF19837.2,70.5882,96.3 SIF-Syn: 
    /note=Glimmer and GeneMark agree, SS starterator, best SD score, covers all coding potential via GeneMarkS. Not the longest ORF, 1:1 BLAST match PhagesDB. Evidence suggests a protein of unknown function.

CDS complement (70091 - 70630)
  /gene="132"
  /product="gp132"
  /function="hypothetical protein"
  /locus tag="Saints25_132"
    /note=Original Glimmer call @bp 70630 has strength 8.87; Genemark calls start at 70630
    /note=SSC: 70630-70091 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_CHOSENONE_138 [Mycobacterium phage ChosenOne] ],,NCBI, q1:s1 100.0% 4.40013E-118 GAP: 39 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.808, -2.8363780677724404, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_CHOSENONE_138 [Mycobacterium phage ChosenOne] ],,QGJ94450,98.2558,4.40013E-118 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and Genemark agree, 39bp gap, best SD score, not the longest ORF, cuts off coding potential in GenemarkS, NI Starterator but leans towards SS, 1:1 BLAST match, not enough evidence to suggest function. about half have suggested start site.

CDS complement (70670 - 71053)
  /gene="133"
  /product="gp133"
  /function="hypothetical protein"
  /locus tag="Saints25_133"
    /note=Original Glimmer call @bp 71053 has strength 4.19; Genemark calls start at 71053
    /note=SSC: 71053-70670 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein GOKU_137 [Mycobacterium phage Goku] ],,NCBI, q1:s1 100.0% 5.2835E-88 GAP: 4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.365, -3.8362837638757656, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein GOKU_137 [Mycobacterium phage Goku] ],,YP_008430651,100.0,5.2835E-88 SIF-HHPRED: Tudor_Agenet_FMR1_rpt2; second Tudor-like Agenet domain found in synaptic functional regulator FMR1 and similar proteins.,,,cd20474,23.622,95.1 SIF-Syn: 
    /note=Glimmer and GeneMark Agree. 4 bp gap. Longest ORF. Not the best SD score but close. Not enough coverage to call a function. 1:1 BLAST.

CDS complement (71058 - 71231)
  /gene="134"
  /product="gp134"
  /function="hypothetical protein"
  /locus tag="Saints25_134"
    /note=Original Glimmer call @bp 71216 has strength 4.95
    /note=SSC: 71231-71058 CP: yes SCS: glimmer-cs ST: SS BLAST-Start: [hypothetical protein PBI_CONTAGION_135 [Mycobacterium phage Contagion] ],,NCBI, q1:s1 100.0% 1.31659E-33 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.072, -4.45567931753621, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_CONTAGION_135 [Mycobacterium phage Contagion] ],,YP_008410151,100.0,1.31659E-33 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer but no GeneMark.  4bp gap, Best SD score. longest ORF. SS Starterator. Captures all coding potential in GenemarkS, 1:1 BLAST match, Evidence suggests that it is a protein of unknown function

CDS complement (71228 - 71473)
  /gene="135"
  /product="gp135"
  /function="hypothetical protein"
  /locus tag="Saints25_135"
    /note=Original Glimmer call @bp 71464 has strength 3.23; Genemark calls start at 71473
    /note=SSC: 71473-71228 CP: yes SCS: both-gm ST: SS BLAST-Start: [hypothetical protein GOKU_140 [Mycobacterium phage Goku] ],,NCBI, q1:s1 100.0% 7.60185E-50 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.448, -4.6476424945195145, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein GOKU_140 [Mycobacterium phage Goku] ],,YP_008430654,100.0,7.60185E-50 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and GeneMark disagree; called less times on Starterator than 71473 start (68 versus 37 times); GeneMark suggested start chosen because of 4 bp overlap. GeneMark start is second longest ORF; not best SD score. NKF due to poor coverage and probability on HHPRED. Cuts off atypical coding potential.

CDS complement (71470 - 71667)
  /gene="136"
  /product="gp136"
  /function="hypothetical protein"
  /locus tag="Saints25_136"
    /note=Original Glimmer call @bp 71667 has strength 7.6; Genemark calls start at 71667
    /note=SSC: 71667-71470 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_MURPHY_142 [Mycobacterium phage Murphy] ],,NCBI, q1:s1 100.0% 5.89302E-40 GAP: 277 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.607, -3.324400402896891, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_MURPHY_142 [Mycobacterium phage Murphy] ],,YP_008051619,100.0,5.89302E-40 SIF-HHPRED: NADPH dehydrogenase 1; CIRCULAR PERMUTATION, CATALYSIS, OLD YELLOW ENZYME, FLAVIN COFACTOR, OXIDOREDUCTASE; HET: FMN, EPE, EDO; 1.552A {Saccharomyces pastorianus},,,4RNW_A,78.4615,89.9 SIF-Syn: 
    /note=Glimmer and Genemark agree. Best SD score. Not the longest ORF. Suggested start site. Some evidence on HHPRED for old yellow enzyme but function not been previously called on BLAST. 1:1 BLAST match.

CDS complement (71945 - 72136)
  /gene="137"
  /product="gp137"
  /function="hypothetical protein"
  /locus tag="Saints25_137"
    /note=Original Glimmer call @bp 72136 has strength 6.65; Genemark calls start at 72136
    /note=SSC: 72136-71945 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_MURPHY_144 [Mycobacterium phage Murphy] ],,NCBI, q1:s1 100.0% 8.97875E-40 GAP: 64 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.511, -3.464766997822752, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_MURPHY_144 [Mycobacterium phage Murphy] ],,YP_008051621,100.0,8.97875E-40 SIF-HHPRED: zf-HC3 ; zinc-finger,,,PF16827.8,68.254,95.6 SIF-Syn: 
    /note=Glimmer and GeneMark agree; not longest ORF; not best SD; SS suggested start; 1:1 BLAST match, HHPRED has solid coverage and probability for zinc-finger but not enough evidence to call it.

CDS 72201 - 72548
  /gene="138"
  /product="gp138"
  /function="hypothetical protein"
  /locus tag="Saints25_138"
    /note=Original Glimmer call @bp 72201 has strength 10.93; Genemark calls start at 72201
    /note=SSC: 72201-72548 CP: yes SCS: both ST: SS BLAST-Start: [gp143 [Mycobacterium phage Cjw1] ],,NCBI, q1:s1 100.0% 9.08311E-77 GAP: 64 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.224, -5.121035876719934, no F: hypothetical protein SIF-BLAST: ,,[gp143 [Mycobacterium phage Cjw1] ],,NP_817590,100.0,9.08311E-77 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and GeneMark agree. Not the best SD score. Longest ORF. Suggested start site. gap 64. 1 to 1 match. not enough evidence

CDS 72623 - 72844
  /gene="139"
  /product="gp139"
  /function="hypothetical protein"
  /locus tag="Saints25_139"
    /note=Original Glimmer call @bp 72683 has strength 2.4; Genemark calls start at 72686
    /note=SSC: 72623-72844 CP: yes SCS: both-cs ST: SS BLAST-Start: [hypothetical protein Kostya_145 [Mycobacterium phage Kostya] ],,NCBI, q1:s1 100.0% 1.78915E-44 GAP: 74 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.437, -6.3867082620457305, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein Kostya_145 [Mycobacterium phage Kostya] ],,YP_002014611,100.0,1.78915E-44 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer and GeneMark disagree; chose different start than what was called from either program (72623) because contains smallest gap and called significant more times on Starterator. 74bp gap, not the longest ORF, SD score is poor, SS starterator, not the longest ORF, PhagesDB, 1:1 BLAST match, Not enough evidence to suggest function.