CDS complement (1 - 564)
  /gene="1"
  /product="gp1"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_1"
    /note=Original Glimmer call @bp 564 has strength 7.36; Genemark calls start at 564
    /note=SSC: 564-1 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein HWC34_gp01 [Microbacterium phage Alex44] ],,NCBI, q1:s1 100.0% 6.14383E-134 GAP: 83 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.899, -2.707694805492614, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein HWC34_gp01 [Microbacterium phage Alex44] ],,YP_009847682,100.0,6.14383E-134 SIF-HHPRED:  SIF-Syn: 
    /note=High coding potential and likely a gene
    /note=Start is agreed upon by GeneMark and Glimmer at 564, 43 MAs, gap/overlap of 83
    /note=Various hits on Blastp for hypothetical protein
    /note=Only 1 hit with a probability of 90, but only a 50% coverage for RNA Polymerase 
    /note=No solid evidence to support RNA Polymerase
    /note=No TMR predicted

CDS complement (648 - 1469)
  /gene="2"
  /product="gp2"
  /function="DNA primase/polymerase"
  /locus tag="SwissCheezer_2"
    /note=Original Glimmer call @bp 1469 has strength 15.23; Genemark calls start at 1469
    /note=SSC: 1469-648 CP: no SCS: both ST: NI BLAST-Start: [DNA primase/polymerase [Microbacterium phage LilyLou]],,NCBI, q1:s1 100.0% 0.0 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.502, -3.54831954703195, no F: DNA primase/polymerase SIF-BLAST: ,,[DNA primase/polymerase [Microbacterium phage LilyLou]],,QDF16030,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=High coding potential and likely a gene
    /note=Glimmer and GeneMark agree on the start 1469, 20 MAs, 1 gap/overlap
    /note=Similar nucleotide similarity with two phams, both call a function of DNA primase/polymerase
    /note=HHPred hits for DNA primase/polymerase
    /note=BlastP also showed strong results of DNA primase/polymerase
    /note=0 TMRs

CDS complement (1471 - 2874)
  /gene="3"
  /product="gp3"
  /function="DNA primase"
  /locus tag="SwissCheezer_3"
    /note=Original Glimmer call @bp 2874 has strength 16.98; Genemark calls start at 2766
    /note=SSC: 2874-1471 CP: no SCS: both-gl ST: NI BLAST-Start: [DNA primase [Microbacterium phage ArMaWen] ],,NCBI, q1:s1 100.0% 0.0 GAP: 48 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.977, -3.005970110175159, yes F: DNA primase SIF-BLAST: ,,[DNA primase [Microbacterium phage ArMaWen] ],,AZV01766,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=- on GenMark we declared that this was a gene because of high and consistent coding potential 
    /note=- we agreed the best start site was 2874 because it has been manually annotated 44 times. 
    /note=- We agreen on the function of DNA primase because each function site from, phamerator, hhpred, blast p, and deepTMHMM has data supporting dna primase

CDS complement (2923 - 3093)
  /gene="4"
  /product="gp4"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_4"
    /note=Original Glimmer call @bp 3093 has strength 10.17; Genemark calls start at 3093
    /note=SSC: 3093-2923 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein HWC34_gp04 [Microbacterium phage Alex44] ],,NCBI, q1:s1 100.0% 6.2483E-31 GAP: 54 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.319, -3.9531326986493704, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein HWC34_gp04 [Microbacterium phage Alex44] ],,YP_009847685,100.0,6.2483E-31 SIF-HHPRED:  SIF-Syn: 
    /note=This is likely a gene because although GeneMark lacks consistently high and flat peaks
    /note=There are 23 MA`s, meaning that 23 individuals agreed on the same start choice meaning it would have to be a gene
    /note=The function of this gene is likely a hypothetical protein because the sources we used were unable to give a specific function, particularly HHPred

CDS complement (3148 - 4410)
  /gene="5"
  /product="gp5"
  /function="DNA helicase"
  /locus tag="SwissCheezer_5"
    /note=Original Glimmer call @bp 4410 has strength 9.2; Genemark calls start at 4410
    /note=SSC: 4410-3148 CP: no SCS: both ST: NI BLAST-Start: [DNA helicase [Microbacterium phage DumpQuist]],,NCBI, q1:s1 100.0% 0.0 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.366, -4.301170562178417, no F: DNA helicase SIF-BLAST: ,,[DNA helicase [Microbacterium phage DumpQuist]],,WNM73216,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Determined this was a gene because of high and consistent coding potential within the ORF
    /note=Start site called is 4410, Glimmer and GeneMark agree, Starterator 34 MAs, gap within range of consideration (-8)
    /note=DNA helicase function most supported by both phams on Phamerator in addition to evidence on HHPred and BLASTp
    /note=0 TMRs

CDS complement (4403 - 5200)
  /gene="6"
  /product="gp6"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_6"
    /note=Original Glimmer call @bp 5200 has strength 13.73; Genemark calls start at 5200
    /note=SSC: 5200-4403 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein HWC34_gp06 [Microbacterium phage Alex44] ],,NCBI, q1:s1 100.0% 0.0 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.899, -2.707694805492614, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein HWC34_gp06 [Microbacterium phage Alex44] ],,YP_009847687,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=It has high coding potential, so it is likely a gene. 
    /note=The start call at 5,200 is strongly supported by GeneMark, Glimmer, Starterator (3 MAs)
    /note=Phamerator has no function called for the gene
    /note=When the gene is blasted, no function is called for, so it is a hypothetical protein
    /note=0 TMRs

CDS complement (5193 - 5525)
  /gene="7"
  /product="gp7"
  /function="WhiB family transcription factor"
  /locus tag="SwissCheezer_7"
    /note=Original Glimmer call @bp 5525 has strength 8.51; Genemark calls start at 5525
    /note=SSC: 5525-5193 CP: no SCS: both ST: NI BLAST-Start: [WhiB family transcription factor [Microbacterium phage ArMaWen] ],,NCBI, q1:s1 100.0% 4.00785E-76 GAP: -31 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.435, -3.708514821076885, no F: WhiB family transcription factor SIF-BLAST: ,,[WhiB family transcription factor [Microbacterium phage ArMaWen] ],,AZV01770,100.0,4.00785E-76 SIF-HHPRED:  SIF-Syn: 
    /note=Determined it was a gene due to having high coding potential in the ORF.
    /note=Confirmed by multiple sources to begin at 5525, including Starterator (29 MAs), Glimmer, Gap/Overlap of -31
    /note=Confirmed by Phamerator, Blastp, HHPred, and DeepTMHMM that it has the function of a WhiB family transcription factor.

CDS complement (5495 - 6043)
  /gene="8"
  /product="gp8"
  /function="RuvC-like resolvase"
  /locus tag="SwissCheezer_8"
    /note=Original Glimmer call @bp 6043 has strength 11.27; Genemark calls start at 6043
    /note=SSC: 6043-5495 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_PHOGO_8 [Microbacterium phage Phogo] ],,NCBI, q1:s1 100.0% 1.62921E-129 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.437, -6.268158501073961, no F: RuvC-like resolvase SIF-BLAST: ,,[hypothetical protein SEA_PHOGO_8 [Microbacterium phage Phogo] ],,QJD52806,100.0,1.62921E-129 SIF-HHPRED:  SIF-Syn: 
    /note=* Likely a gene and has coding potential start and stop codons are consident 
    /note=* Glimmer, GeneMark and Starterator (40 MAs), -8 gap/overlap all agree with start choice of 6043 and is the final start call
    /note=*The function is RuvC-like resolvase - supported by Blast and Phamerator similarity between swisscheezer and Dashyla
    /note=*0 TMRs

CDS complement (6036 - 6356)
  /gene="9"
  /product="gp9"
  /function="NrdH-like glutaredoxin"
  /locus tag="SwissCheezer_9"
    /note=Original Glimmer call @bp 6356 has strength 17.12; Genemark calls start at 6356
    /note=SSC: 6356-6036 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein HWC34_gp09 [Microbacterium phage Alex44] ],,NCBI, q1:s1 100.0% 4.09315E-73 GAP: 52 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.994, -2.523003374675015, yes F: NrdH-like glutaredoxin SIF-BLAST: ,,[hypothetical protein HWC34_gp09 [Microbacterium phage Alex44] ],,YP_009847690,100.0,4.09315E-73 SIF-HHPRED:  SIF-Syn: 
    /note=* likely a gene
    /note=* agreeance in the start sites (no change in start choice), 53 MAs, gap/overlap data does not provide additional support
    /note=* nrdh-like glutaredoxin - support from BLASTp sharing a 100% match with 6 other phages that have NrdH-like glutaredoxin and has this function called in Dashyla and Armawen (two most similar genomes) on Phamerator
    /note=*0 TMRs

CDS complement (6409 - 8628)
  /gene="10"
  /product="gp10"
  /function="DNA polymerase I"
  /locus tag="SwissCheezer_10"
    /note=Original Glimmer call @bp 8652 has strength 15.76; Genemark calls start at 8628
    /note=SSC: 8628-6409 CP: no SCS: both-gm ST: NI BLAST-Start: [DNA polymerase I [Microbacterium phage Phogo]],,NCBI, q1:s1 100.0% 0.0 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.791, -4.9912573797770525, no F: DNA polymerase I SIF-BLAST: ,,[DNA polymerase I [Microbacterium phage Phogo]],,QJD52808,99.8647,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=This is a large gene with very high coding potential. 
    /note=Start site was determined to be 8628 instead of 8652. There is more evidence that supports 8628, such as multiple manual annotations (20 MAs) and gap/overlap (1) 
    /note=There was a lot of information that supported the protein associated with this gene as DNA Polymerase I. Multiple sources such as Phamerator (similarity between Dashyla and Armawen), BlastP, and HHPred all point to the function call of DNA Polymerase I.
    /note=0 TMRs

CDS complement (8630 - 8842)
  /gene="11"
  /product="gp11"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_11"
    /note=Original Glimmer call @bp 8842 has strength 14.54; Genemark calls start at 8842
    /note=SSC: 8842-8630 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_LILYLOU_12 [Microbacterium phage LilyLou] ],,NCBI, q1:s1 100.0% 7.75795E-42 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.842, -2.827683592113848, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_LILYLOU_12 [Microbacterium phage LilyLou] ],,QDF16040,100.0,7.75795E-42 SIF-HHPRED:  SIF-Syn: 
    /note=this is likely a gene that is consistent with given the consistent coding potential. 
    /note=Glimmer, GeneMark, and Starterator all agree with a start at 8842. 
    /note=It doesn`t have -1 or -4 gap but the next best gap would be -8 with a start of 8842. 
    /note=Start auto annotated is a 5 with the start at 8842 with 10 possible MA`s. 
    /note=No function was called for this gene based on no evidence from blast p and Phamerator. 
    /note=There are no Transmembrane Regions

CDS complement (8835 - 9962)
  /gene="12"
  /product="gp12"
  /function="Cas4 exonuclease"
  /locus tag="SwissCheezer_12"
    /note=Original Glimmer call @bp 9962 has strength 15.19; Genemark calls start at 9962
    /note=SSC: 9962-8835 CP: no SCS: both ST: NI BLAST-Start: [Cas4 family exonuclease [Microbacterium phage DumpQuist]],,NCBI, q1:s1 100.0% 0.0 GAP: -20 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.904, -4.752447703791792, no F: Cas4 exonuclease SIF-BLAST: ,,[Cas4 family exonuclease [Microbacterium phage DumpQuist]],,WNM73223,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Start site 9962 has the most manual annotations (17), Glimmer & GeneMark agree
    /note=
    /note=Final function call of cas4-exonuclease is supported by phamerator (function called in Dashyla and Armawen), hhpred (There are 29 hits above 90 probability and 44 hits above 70% query coverage. There are function matches for DNA binding proteins.) and ncbi (There are many hits for cas4family exonuclease).
    /note=0 TMRs

CDS complement (9943 - 10074)
  /gene="13"
  /product="gp13"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_13"
    /note=Original Glimmer call @bp 10074 has strength 13.39; Genemark calls start at 10074
    /note=SSC: 10074-9943 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein HWC34_gp14 [Microbacterium phage Alex44] ],,NCBI, q1:s1 100.0% 9.15621E-24 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.994, -2.442961286954254, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein HWC34_gp14 [Microbacterium phage Alex44] ],,YP_009847695,100.0,9.15621E-24 SIF-HHPRED:  SIF-Syn: 
    /note=This gene candidate has high coding potential in GeneMark - likely a gene. Start site 10074 is supported by the -4 overlap, Glimmer & GeneMark agree, there are 17 MAs in starterator for start 10074. 
    /note=
    /note=The function call of hypothetical protein is supported by lack of evidence in BLASTp, phamerator ( no function called for Dashyla or Armawen), and HHPred.  There are no Trasmembrane Regions

CDS complement (10071 - 10202)
  /gene="14"
  /product="gp14"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_14"
    /note=Original Glimmer call @bp 10202 has strength 11.28; Genemark calls start at 10202
    /note=SSC: 10202-10071 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ARMAWEN_14 [Microbacterium phage ArMaWen] ],,NCBI, q1:s1 100.0% 5.22653E-22 GAP: 55 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.236, -2.45827804503836, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ARMAWEN_14 [Microbacterium phage ArMaWen] ],,AZV01777,100.0,5.22653E-22 SIF-HHPRED:  SIF-Syn: 
    /note=Likely a gene 
    /note=Start choice 10202 is supported by agreement between Glimmer & GeneMark.  Has 34 MAs in Starterator and a gap of 8 bp.
    /note=Hypothetical Function is supported because of lack of evidence in Phamerator (no fnc called in Armawen or Dashyla), BLASTp, and low probability and % coverage in HHPred. No Transmembrane Regions.

CDS complement (10258 - 11025)
  /gene="15"
  /product="gp15"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_15"
    /note=Original Glimmer call @bp 11025 has strength 15.54; Genemark calls start at 11025
    /note=SSC: 11025-10258 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUMPQUIST_15 [Microbacterium phage DumpQuist]],,NCBI, q1:s1 100.0% 0.0 GAP: 40 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.0, -4.900166819979879, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_DUMPQUIST_15 [Microbacterium phage DumpQuist]],,WNM73226,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=High coding potential - Likely a gene 
    /note=Glimmer, GeneMark, and Starterator  (43 MAs) agree with start 11025 
    /note=Smallest gap of 40 basepairs
    /note=There are no functions called in Phamerator
    /note=no TMR predicted 
    /note=no hits that support a function with a probability greater than 90 or coverage greater than 70% for HHpred

CDS complement (11066 - 11242)
  /gene="16"
  /product="gp16"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_16"
    /note=Original Glimmer call @bp 11254 has strength 16.06; Genemark calls start at 11254
    /note=SSC: 11242-11066 CP: no SCS: both-cs ST: NI BLAST-Start: [hypothetical protein SEA_ARMAWEN_16 [Microbacterium phage ArMaWen] ],,NCBI, q1:s1 100.0% 2.60065E-34 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.253, -4.364952153961186, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ARMAWEN_16 [Microbacterium phage ArMaWen] ],,AZV01779,100.0,2.60065E-34 SIF-HHPRED:  SIF-Syn: 
    /note=High coding potential - likely a gene 
    /note=Glimmer and Genemark agree with 11254, however starterator has 13 MAs at start 11242 which also has an overlap of -1. Start choice is changed to 11242. 
    /note=There is similarity between the two closest relatives, and neither call a function. Other sources (HHpred and BLASTp) also lead to hypothetical protein.

CDS complement (11242 - 11853)
  /gene="17"
  /product="gp17"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_17"
    /note=Original Glimmer call @bp 11853 has strength 16.3; Genemark calls start at 11853
    /note=SSC: 11853-11242 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein HWC34_gp18 [Microbacterium phage Alex44] ],,NCBI, q1:s1 100.0% 2.12484E-149 GAP: 236 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.994, -2.442961286954254, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein HWC34_gp18 [Microbacterium phage Alex44] ],,YP_009847699,100.0,2.12484E-149 SIF-HHPRED:  SIF-Syn: 
    /note=- Likely a gene due to coding potential 
    /note=- glimmer and gene mark agree start choice is 11853, supported by starterator 
    /note=- the start site cannot be extended further because of stop codons in the same reading frame.
    /note=- function was called hypothetical protein because no functions assigned in phamerator, BLASTp, or HHpred
    /note=- No TMR

CDS complement (12090 - 12362)
  /gene="18"
  /product="gp18"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_18"
    /note=Original Glimmer call @bp 12362 has strength 13.51; Genemark calls start at 12362
    /note=SSC: 12362-12090 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein HWC34_gp19 [Microbacterium phage Alex44] ],,NCBI, q1:s1 100.0% 2.79321E-57 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.491, -3.5707972674952195, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein HWC34_gp19 [Microbacterium phage Alex44] ],,YP_009847700,100.0,2.79321E-57 SIF-HHPRED:  SIF-Syn: 
    /note=- Likely a gene due to coding potential
    /note=- Start choice supported by small gap, glimmer and GeneMark agree, and Starterator has 17 MAs at this location
    /note=- Phamerator does not show an annotated function in closest relatives therefore, we are unable to call a specific function  
    /note=- Nothing from HHPred or BlastP
    /note=- No TMR

CDS complement (12364 - 12732)
  /gene="19"
  /product="gp19"
  /function="membrane protein"
  /locus tag="SwissCheezer_19"
    /note=Original Glimmer call @bp 12732 has strength 12.27; Genemark calls start at 12732
    /note=SSC: 12732-12364 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein HWC34_gp20 [Microbacterium phage Alex44] ],,NCBI, q1:s1 100.0% 9.26918E-83 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.994, -2.583959800616441, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein HWC34_gp20 [Microbacterium phage Alex44] ],,YP_009847701,100.0,9.26918E-83 SIF-HHPRED:  SIF-Syn: 
    /note=Determined to be a gene due to high and consistent coding potential throughout the ORF
    /note=Final start call determined to be 12732, all sources support this start call  (overlap of -4, starterator supports, and Glimmer and GeneMark agree)
    /note=Function called is membrane protein,1 predicted unnamed transmembrane protein from DeepTMHMM, no evidence for any other function among any of the other sources

CDS complement (12729 - 13082)
  /gene="20"
  /product="gp20"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_20"
    /note=Original Glimmer call @bp 13070 has strength 13.02; Genemark calls start at 13070
    /note=SSC: 13082-12729 CP: no SCS: both-cs ST: NI BLAST-Start: [hypothetical protein SEA_PHOGO_21 [Microbacterium phage Phogo]],,NCBI, q1:s1 100.0% 1.67662E-79 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.57, -4.170102567841746, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_PHOGO_21 [Microbacterium phage Phogo]],,QJD52819,100.0,1.67662E-79 SIF-HHPRED:  SIF-Syn: 
    /note=Likely a gene, there is coding potential
    /note=Glimmer and GeneMark agree on Start choice 13070, however Starterator (8MAs) and Gap data (-4 overlap) support start choice of 13082 - start choice is changed to 13082 
    /note=There is no functions called in pahmerators closest relatives, No evidence for a function call in BLASTp or HHpred
    /note=No TMR

CDS complement (13079 - 13282)
  /gene="21"
  /product="gp21"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_21"
    /note=Original Glimmer call @bp 13282 has strength 10.08; Genemark calls start at 13282
    /note=SSC: 13282-13079 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ARMAWEN_21 [Microbacterium phage ArMaWen] ],,NCBI, q1:s1 100.0% 1.03713E-42 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.597, -3.364992052816827, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ARMAWEN_21 [Microbacterium phage ArMaWen] ],,AZV01784,100.0,1.03713E-42 SIF-HHPRED:  SIF-Syn: 
    /note=Likely a gene due to having high coding potential in the ORF.
    /note=Starterator, Glimmer, and Genemark agree that the starting position is 13282.
    /note=Due to no reliable evidence signifying a specific function from multiple sources (Phamerator, BLASTp, or HHpred), it is considered a hypothetical protein. 
    /note=No TMR

CDS complement (13282 - 13569)
  /gene="22"
  /product="gp22"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_22"
    /note=Original Glimmer call @bp 13569 has strength 13.44; Genemark calls start at 13569
    /note=SSC: 13569-13282 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DASHYLA_22 [Microbacterium phage Dashyla]],,NCBI, q1:s1 100.0% 1.25637E-63 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.055, -4.431815568174083, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_DASHYLA_22 [Microbacterium phage Dashyla]],,XEN14144,100.0,1.25637E-63 SIF-HHPRED:  SIF-Syn: 
    /note=* Likely a gene has coding potential but not consistent 
    /note=* Glimmer, GeneMark and Starterator (23 MAs) all agree with a start 13569 and is the final start call
    /note=* The function is a Hypothetical Protein 
    /note=*Phamerator phages have nucleotide similarity and no function called, BLAST hits also hypothetical, HHpred hits do not give additional data, 0 TMRs

CDS complement (13566 - 13853)
  /gene="23"
  /product="gp23"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_23"
    /note=Original Glimmer call @bp 13853 has strength 13.69; Genemark calls start at 13853
    /note=SSC: 13853-13566 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein HWC34_gp24 [Microbacterium phage Alex44] ],,NCBI, q1:s1 100.0% 8.09116E-61 GAP: -17 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.865, -6.141009609660544, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein HWC34_gp24 [Microbacterium phage Alex44] ],,YP_009847705,100.0,8.09116E-61 SIF-HHPRED:  SIF-Syn: 
    /note=*Likely a gene
    /note=*Glimmer, GeneMark, Starterator agree on the start site ( No change needed)
    /note=*Phamerator phages have nucleotide similarity and no function called
    /note=BLAST hits also hypothetical
    /note=HHpred hits do not give additional data
    /note=0 TMRs

CDS complement (13837 - 14091)
  /gene="24"
  /product="gp24"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_24"
    /note=Original Glimmer call @bp 14091 has strength 13.12; Genemark calls start at 14091
    /note=SSC: 14091-13837 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein HWC34_gp25 [Microbacterium phage Alex44] ],,NCBI, q1:s1 100.0% 6.86141E-53 GAP: 76 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.105, -4.387988835334809, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein HWC34_gp25 [Microbacterium phage Alex44] ],,YP_009847706,100.0,6.86141E-53 SIF-HHPRED:  SIF-Syn: 
    /note=This gene has consistently high coding potential. 
    /note=Start Site 14091 was agreed upon by Glimmer and GeneMark, and this was also supported through Starterator with multiple manual annotators. 
    /note=No function was able to be called for the protein that this gene codes for. 
    /note=There were no clear matches or answers from Phamerator, BlastP, or HHPred. 
    /note=The function will continued to be labeled as a Hypothetical Protein.

CDS complement (14168 - 14644)
  /gene="25"
  /product="gp25"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_25"
    /note=Original Glimmer call @bp 14644 has strength 16.42; Genemark calls start at 14644
    /note=SSC: 14644-14168 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ARMAWEN_25 [Microbacterium phage ArMaWen] ],,NCBI, q1:s1 100.0% 1.2341E-107 GAP: 129 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.899, -2.6453814847322845, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ARMAWEN_25 [Microbacterium phage ArMaWen] ],,AZV01788,100.0,1.2341E-107 SIF-HHPRED:  SIF-Syn: 
    /note=This is likely a gene located at 13282 that is consistent with coding potential. 
    /note=Glimmer, GeneMark, Starterator, all agree and support this start site. 
    /note=There are also no -4 or -1 overlaps to this gene.
    /note= For the function no call was made making it a hypothetical protein. No evidence from phamerator or any blast gave support to a function.

CDS complement (14774 - 14917)
  /gene="26"
  /product="gp26"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_26"
    /note=Original Glimmer call @bp 14902 has strength 7.36; Genemark calls start at 14917
    /note=SSC: 14917-14774 CP: no SCS: both-gm ST: NI BLAST-Start: [hypothetical protein SEA_ARMAWEN_26 [Microbacterium phage ArMaWen] ],,NCBI, q1:s1 100.0% 1.59918E-24 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.138, -7.203650105041291, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ARMAWEN_26 [Microbacterium phage ArMaWen] ],,AZV01817,100.0,1.59918E-24 SIF-HHPRED:  SIF-Syn: 
    /note=Start choices from glimmer (14902) and genemark (14917) disagree on start
    /note=14917 has 14 MAs and a -4 overlap
    /note=Phamerator phages have nucleotide similarity and no function called
    /note=BLAST hits also hypothetical
    /note=HHpred hits do not give additional data
    /note=0 TMRs

CDS complement (14914 - 15195)
  /gene="27"
  /product="gp27"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_27"
    /note=Original Glimmer call @bp 15195 has strength 16.78; Genemark calls start at 15195
    /note=SSC: 15195-14914 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ARMAWEN_27 [Microbacterium phage ArMaWen] ],,NCBI, q1:s1 100.0% 5.19966E-61 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.518, -3.5316035464369326, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ARMAWEN_27 [Microbacterium phage ArMaWen] ],,AZV01789,100.0,5.19966E-61 SIF-HHPRED:  SIF-Syn: 
    /note=High coding potential in the ORF and likely a gene
    /note=Start choice agreed upon by GeneMark and Glimmer as 15195, 12 MA`s, -1 overlap gives additional data to support start call
    /note=Phamerator phages have nucleotide similarity and no function called
    /note=BLAST hits also hypothetical
    /note=HHpred hits do not give additional data
    /note=0 TMRs

CDS complement (15195 - 15593)
  /gene="28"
  /product="gp28"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_28"
    /note=Original Glimmer call @bp 15593 has strength 12.9; Genemark calls start at 15599
    /note=SSC: 15593-15195 CP: no SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_DUMPQUIST_28 [Microbacterium phage DumpQuist]],,NCBI, q1:s1 100.0% 3.19324E-92 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.92, -3.9067510144203146, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_DUMPQUIST_28 [Microbacterium phage DumpQuist]],,WNM73239,100.0,3.19324E-92 SIF-HHPRED:  SIF-Syn: 
    /note=High coding potential in the ORF and likely a gene
    /note=Start choice not agreed upon- Glimmer calls 15593 and GeneMark calls 15559, 9 MA`s over 6 MA`s for start 15593, 15593 has -8 gap/overlap
    /note=Phamerator phages have nucleotide similarity and no function called
    /note=BLAST hits also hypothetical
    /note=HHpred hits do not give additional data
    /note=0 TMRs

CDS complement (15586 - 15834)
  /gene="29"
  /product="gp29"
  /function="membrane protein"
  /locus tag="SwissCheezer_29"
    /note=Original Glimmer call @bp 15795 has strength 14.53; Genemark calls start at 15813
    /note=SSC: 15834-15586 CP: no SCS: both-cs ST: NI BLAST-Start: [hypothetical protein SEA_ARMAWEN_29 [Microbacterium phage ArMaWen] ],,NCBI, q1:s1 100.0% 9.36283E-51 GAP: 691 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.702, -3.1417032362307356, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein SEA_ARMAWEN_29 [Microbacterium phage ArMaWen] ],,AZV01791,98.7805,9.36283E-51 SIF-HHPRED:  SIF-Syn: 
    /note=Changed start site to 15834 because had the most manual annotations with 11
    /note=GeneMark calls the start at 15813, Glimmer calls the start at 15795
    /note=Could extend the start site to make the gap smaller; however, it will not close the gap.  We went with the start site with the most MAs.  There is no coding potential between this gene and the next in sequence. 
    /note=
    /note=Phamerator phages have nucleotide similarity and no function called
    /note=BLAST hits also hypothetical
    /note=HHpred hits do not give additional data
    /note=
    /note=membrane protein- 1 TMR- DeepTMHMM

CDS 16526 - 16618
  /gene="30"
  /product="gp30"
  /locus tag="SwissCheezer_30"
    /note=Genemark calls start at 16526
    /note=SSC: 16526-16618 CP: no SCS: genemark ST: NI BLAST-Start: [hypothetical protein SEA_LILYLOU_31 [Microbacterium phage LilyLou]],,NCBI, q1:s1 100.0% 3.64207E-10 GAP: 691 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.865, -5.186767100221219, no F:  SIF-BLAST: ,,[hypothetical protein SEA_LILYLOU_31 [Microbacterium phage LilyLou]],,QDF16059,100.0,3.64207E-10 SIF-HHPRED:  SIF-Syn: 
    /note=GeneMark shows low and lack of coding potential in the ORF.
    /note=GeneMark calls a start for 16,526 and Glimmer does not
    /note=Start 16,526 has 2 MAs
    /note=Gap/Overlap is more than 400 bp
    /note=In Phamerator, ArMaWen and Dashyla do have nucleotide similarity to this "gene" but no gene called in either genome
    /note=It is a forward gene in a row of reverse genes
    /note=Not likely a gene

CDS complement (16742 - 17152)
  /gene="31"
  /product="gp31"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_31"
    /note=Original Glimmer call @bp 17152 has strength 13.41; Genemark calls start at 17152
    /note=SSC: 17152-16742 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_PHOGO_31 [Microbacterium phage Phogo] ],,NCBI, q1:s1 100.0% 1.96785E-94 GAP: 452 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.128, -6.537112064475647, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_PHOGO_31 [Microbacterium phage Phogo] ],,QJD52852,100.0,1.96785E-94 SIF-HHPRED:  SIF-Syn: 
    /note=-likely a gene 
    /note=-GeneMark and Glimmer have 17152 start called, 3 MA`s for this start
    /note=-no gaps and overlaps within consideration 
    /note=-We cannot close the gap by extending start site because there are stop codons in the same reading frame. -There is no coding potential in other reading frames.
    /note=-Phamerator phages have nucleotide similarity and no function called
    /note=-BLAST hits also hypothetical
    /note=-HHpred hits do not give additional data
    /note=-0 TMRs

CDS 17605 - 31056
  /gene="32"
  /product="gp32"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_32"
    /note=Original Glimmer call @bp 17605 has strength 12.08; Genemark calls start at 17605
    /note=SSC: 17605-31056 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DASHYLA_31 [Microbacterium phage Dashyla]],,NCBI, q1:s1 100.0% 0.0 GAP: 452 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.994, -2.970161406017234, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_DASHYLA_31 [Microbacterium phage Dashyla]],,XEN14153,99.8662,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Very large gene with high coding potential in the ORF and likely a gene
    /note=Start choice agreed upon by GeneMark and Glimmer as 17,605, 23 MA`s, overlap doesn`t give additional data to support start call
    /note=Phamerator phages have nucleotide similarity and no function called
    /note=BLAST hits also hypothetical
    /note=HHpred hits do not give additional data
    /note=0 TMRs

CDS 31053 - 33128
  /gene="33"
  /product="gp33"
  /function="portal protein"
  /locus tag="SwissCheezer_33"
    /note=Original Glimmer call @bp 31053 has strength 12.98; Genemark calls start at 31053
    /note=SSC: 31053-33128 CP: no SCS: both ST: NI BLAST-Start: [portal protein [Microbacterium phage Alex44] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.697, -6.2909565709011765, no F: portal protein SIF-BLAST: ,,[portal protein [Microbacterium phage Alex44] ],,YP_009847714,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=High coding potential in the ORF and likely a gene
    /note=Start choice agreed upon by GeneMark and Glimmer as 31,053, 47 MA`s, -4 overlap supports start call
    /note=Phamerator phages have nucleotide similarity and function called as portal protein
    /note=BLAST hits also point to portal protein
    /note=HHpred hits for portal protein
    /note=0 TMRs

CDS 33178 - 34848
  /gene="34"
  /product="gp34"
  /function="major capsid protein"
  /locus tag="SwissCheezer_34"
    /note=Original Glimmer call @bp 33178 has strength 13.99; Genemark calls start at 33178
    /note=SSC: 33178-34848 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein HWC34_gp34 [Microbacterium phage Alex44] ],,NCBI, q1:s1 100.0% 0.0 GAP: 49 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.13, -2.2364030944336752, yes F: major capsid protein SIF-BLAST: ,,[hypothetical protein HWC34_gp34 [Microbacterium phage Alex44] ],,YP_009847715,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Definitely a gene.  
    /note=Start sites are good- Glimmer and GeneMark call the same starts. 51 MA`s is great evidence for the start site chosen at 33178. 
    /note=No functions called on Phamerator for its closest related ones. BLAST hits also no function but some hits for major capsid protein (forums suggest wet bench evidence for major capsid protein directly following portal protein), HHpred no function, and 0 TMRs.

CDS 34916 - 35074
  /gene="35"
  /product="gp35"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_35"
    /note=Original Glimmer call @bp 34916 has strength 14.65; Genemark calls start at 34916
    /note=SSC: 34916-35074 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein HWC34_gp35 [Microbacterium phage Alex44] ],,NCBI, q1:s1 100.0% 1.0771E-23 GAP: 67 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.13, -2.2364030944336752, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein HWC34_gp35 [Microbacterium phage Alex44] ],,YP_009847716,100.0,1.0771E-23 SIF-HHPRED:  SIF-Syn: 
    /note=-coding Potential demonstrated on GeneMark - Likely a gene
    /note=-Glimmer and GeneMark agree on start site, Starterator data is confirmed with 42 MAs
    /note=-Phamerator phages have nucleotide similarity but no function called, BLAST hits also no function, HHpred no function, and 0 TMRs

CDS 35150 - 36004
  /gene="36"
  /product="gp36"
  /function="minor tail protein"
  /locus tag="SwissCheezer_36"
    /note=Original Glimmer call @bp 35150 has strength 12.25; Genemark calls start at 35150
    /note=SSC: 35150-36004 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein HWC34_gp36 [Microbacterium phage Alex44] ],,NCBI, q1:s1 100.0% 0.0 GAP: 75 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.225, -2.0162541296952132, yes F: minor tail protein SIF-BLAST: ,,[hypothetical protein HWC34_gp36 [Microbacterium phage Alex44] ],,YP_009847717,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=High consistent coding potential 
    /note=Likely a gene 
    /note=Has 47 MA`s 
    /note=Glimmer, GeneMark and Starterator have the same start choice as 35150
    /note=Function: minior tail protein
    /note=No membrane bound regions

CDS 36013 - 37788
  /gene="37"
  /product="gp37"
  /function="minor tail protein"
  /locus tag="SwissCheezer_37"
    /note=Original Glimmer call @bp 36013 has strength 5.84; Genemark calls start at 36013
    /note=SSC: 36013-37788 CP: no SCS: both ST: NI BLAST-Start: [minor tail protein [Microbacterium phage ArMaWen] ],,NCBI, q1:s1 100.0% 0.0 GAP: 8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.105, -4.4057176022952405, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage ArMaWen] ],,AZV01798,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Glimmer, GeneMark, and Starterator agree on the same start making it likely a gene. Though there is no gap and overlap that directly supports it, there is a gap close to -4 that does. Start 2 at 36013 is auto-annoted, along with the fact that it was MA. There are 26 possible start sites for this gene. The most considerable gap was 8 for start 36013.
    /note=
    /note=NCBI BLAST results with high percent identity and high alignment to minor tail protein function
    /note=HHPred hits have high coverage for interleukin receptor type tyrosine phosphatase but in a eukaryote
    /note=0 TMRs

CDS 37813 - 38778
  /gene="38"
  /product="gp38"
  /function="lysin A"
  /locus tag="SwissCheezer_38"
    /note=Original Glimmer call @bp 37813 has strength 10.17; Genemark calls start at 37813
    /note=SSC: 37813-38778 CP: no SCS: both ST: NI BLAST-Start: [lysin A [Microbacterium phage Phogo]],,NCBI, q1:s1 100.0% 0.0 GAP: 24 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.899, -2.7254235724530456, yes F: lysin A SIF-BLAST: ,,[lysin A [Microbacterium phage Phogo]],,QJD52835,99.0654,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=There is high coding for the gene according to GeneMark. Start site was agreed upon by multiple databases, such as Glimmer, GeneMark, and Starterator. 
    /note=
    /note=There was some discrepancy between whether or not the function of the protein is Lysin A or Endolysin.
    /note=
    /note=After further look at the official function list, calling the function lysinA because Swisscheezer is a mycobacteriophage.

CDS 38780 - 39274
  /gene="39"
  /product="gp39"
  /function="membrane protein"
  /locus tag="SwissCheezer_39"
    /note=Original Glimmer call @bp 38780 has strength 4.97; Genemark calls start at 38780
    /note=SSC: 38780-39274 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ARMAWEN_38 [Microbacterium phage ArMaWen] ],,NCBI, q1:s1 100.0% 6.28374E-113 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.576, -6.0980816910293765, no F: membrane protein SIF-BLAST: ,,[hypothetical protein SEA_ARMAWEN_38 [Microbacterium phage ArMaWen] ],,AZV01800,100.0,6.28374E-113 SIF-HHPRED:  SIF-Syn: 
    /note=Start choice agreed upon by GeneMark and Glimmer as 38,780, 13 MA`s
    /note=Gap/overlap of 1
    /note=
    /note=Phamerator phages have nucleotide similarity but no function called, BLAST hits are membrane protein, HHpred hits to membrane protein, and 4 TMRs.
    /note=Membrane protein function call.

CDS 39267 - 39665
  /gene="40"
  /product="gp40"
  /function="membrane protein"
  /locus tag="SwissCheezer_40"
    /note=Original Glimmer call @bp 39267 has strength 7.62; Genemark calls start at 39267
    /note=SSC: 39267-39665 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein HWC34_gp40 [Microbacterium phage Alex44] ],,NCBI, q1:s1 100.0% 2.57738E-90 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.236, -1.993391246735709, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein HWC34_gp40 [Microbacterium phage Alex44] ],,YP_009847721,100.0,2.57738E-90 SIF-HHPRED:  SIF-Syn: 
    /note=It is likely a gene due to the consistent and high coding potential found throughout the ORF.
    /note=Both Glimmer and Genemark agree that the starting position is at 39267.
    /note=Starterator has 11 MAs for that start
    /note=Gap/overlap of -8
    /note=Blastp, HHPred, and DeepTMHMM agree that it is a membrane protein.

CDS 39658 - 39909
  /gene="41"
  /product="gp41"
  /function="membrane protein"
  /locus tag="SwissCheezer_41"
    /note=Original Glimmer call @bp 39658 has strength 13.43; Genemark calls start at 39658
    /note=SSC: 39658-39909 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_LILYLOU_42 [Microbacterium phage LilyLou] ],,NCBI, q1:s1 100.0% 2.36707E-48 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.899, -2.707694805492614, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein SEA_LILYLOU_42 [Microbacterium phage LilyLou] ],,QDF16070,100.0,2.36707E-48 SIF-HHPRED:  SIF-Syn: 
    /note=High coding potential in the ORF and likely a gene
    /note=Start choice agreed upon by GeneMark and Glimmer as 39,658, 13 MA`s
    /note=Gap/overlap of -8
    /note=Phamerator phages have nucleotide similarity and no function called
    /note=BLAST hits also hypothetical
    /note=HHpred hits do not give additional data
    /note=0 TMRs
    /note=
    /note=There are two hits on Deep TMHMM showing two transmembrane regions. NCBI Blast on PECAAN also shows membrane protein.

CDS 39946 - 41211
  /gene="42"
  /product="gp42"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_42"
    /note=Original Glimmer call @bp 39946 has strength 10.02; Genemark calls start at 39946
    /note=SSC: 39946-41211 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ARMAWEN_41 [Microbacterium phage ArMaWen] ],,NCBI, q1:s1 100.0% 0.0 GAP: 36 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.225, -1.953940808934884, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ARMAWEN_41 [Microbacterium phage ArMaWen] ],,AZV01803,99.7625,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=-likely a gene 
    /note=-start site called the same for both GeneMark and Glimmer 39,946, Supported by Starterator (11 MAs)
    /note=-Gap/overlap of 36
    /note=-Phamerator phages have nucleotide similarity but no function called, BLAST hits also no function, HHpred no function, and 0 TMRs 
    /note=-hypothetical protein

CDS 41222 - 42307
  /gene="43"
  /product="gp43"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_43"
    /note=Original Glimmer call @bp 41222 has strength 10.87; Genemark calls start at 41234
    /note=SSC: 41222-42307 CP: no SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_UNPHAZED_43 [Microbacterium phage Unphazed]],,NCBI, q1:s1 100.0% 0.0 GAP: 10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.13, -2.6835611257758942, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_UNPHAZED_43 [Microbacterium phage Unphazed]],,QJD52787,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Starterator (50 MAs) and Glimmer support 41222 as the start, GeneMark does not agree.
    /note=Gap/overlap of 10
    /note=Phamerator phages have nucleotide similarity and no function called
    /note=BLAST hits also hypothetical
    /note=HHpred hits do not give additional data
    /note=0 TMRs

CDS 42307 - 43095
  /gene="44"
  /product="gp44"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_44"
    /note=Original Glimmer call @bp 42307 has strength 9.98; Genemark calls start at 42307
    /note=SSC: 42307-43095 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein HWC34_gp44 [Microbacterium phage Alex44] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.938, -4.741583905672826, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein HWC34_gp44 [Microbacterium phage Alex44] ],,YP_009847725,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=High and consistent coding potential - likely a gene
    /note=Gene Mark and Glimmer agree on start at 42307, 13 MA`s, -1gap
    /note=Hypothetical protein - 0 hits on DeepTMHMM, no significant hits on HHPred, no function called for BLASTp, nucleotide similarity in Pharmerator but no function called

CDS 43095 - 45770
  /gene="45"
  /product="gp45"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_45"
    /note=Original Glimmer call @bp 43095 has strength 10.16; Genemark calls start at 43095
    /note=SSC: 43095-45770 CP: no SCS: both ST: NI BLAST-Start: [minor tail protein [Microbacterium phage Dashyla]],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.545, -3.9209593204668103, no F: Hypothetical Protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage Dashyla]],,XEN14166,99.8878,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=High coding potential in the ORF and likely a gene
    /note=Start choice agreed upon by GeneMark and Glimmer as 43,095, 42 MA`s, gap/overlap of -1
    /note=
    /note=There is only one hit that shows minor tail protein from a pham member, the rest of the hits lean towards hypothetical protein. There is not enough information to say minor tail protein.

CDS 45779 - 46006
  /gene="46"
  /product="gp46"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_46"
    /note=Original Glimmer call @bp 45779 has strength 10.38; Genemark calls start at 45779
    /note=SSC: 45779-46006 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein HWC34_gp46 [Microbacterium phage Alex44] ],,NCBI, q1:s1 100.0% 2.35335E-44 GAP: 8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.105, -4.4057176022952405, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein HWC34_gp46 [Microbacterium phage Alex44] ],,YP_009847727,100.0,2.35335E-44 SIF-HHPRED:  SIF-Syn: 
    /note=-small coding potential 
    /note=-same start call 45779 called Glimmer and GeneMark
    /note=-Starterator has 14 MAs
    /note=-Gap/overlap of 8
    /note=-Phamerator phages have nucleotide similarity but no function called, BLAST hits also no function, HHpred no function, and 0 TMRs
    /note=-no function called so hypothetical protein

CDS 46010 - 48019
  /gene="47"
  /product="gp47"
  /function="purple acid phosphatase"
  /locus tag="SwissCheezer_47"
    /note=Original Glimmer call @bp 46010 has strength 12.38; Genemark calls start at 46010
    /note=SSC: 46010-48019 CP: no SCS: both ST: NI BLAST-Start: [purple acid phosphatase [Microbacterium phage Dashyla]],,NCBI, q1:s1 100.0% 0.0 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.518, -3.4515614587161716, no F: purple acid phosphatase SIF-BLAST: ,,[purple acid phosphatase [Microbacterium phage Dashyla]],,XEN14168,99.2526,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Start site of 46010 is supported by Glimmer and GeneMark, Starterator has 17 MAs
    /note=Gap/overlap of 3
    /note=Phamerator phages have nucleotide similarity and purple acid phosphatase function called, BLAST hits also this function, HHpred no additional information, and 0 TMRs
    /note=Purple acid phosphatase is the function with lots of support.

CDS 48102 - 49040
  /gene="48"
  /product="gp48"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_48"
    /note=Original Glimmer call @bp 48102 has strength 12.73; Genemark calls start at 48102
    /note=SSC: 48102-49040 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ARMAWEN_47 [Microbacterium phage ArMaWen] ],,NCBI, q1:s1 100.0% 0.0 GAP: 82 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.92, -2.66371296573402, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ARMAWEN_47 [Microbacterium phage ArMaWen] ],,AZV01809,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Genemark concludes that it is likely a gene due to having high coding potential within the reading frame.
    /note=Both Glimmer and Starterator (39 MAs) agree that the starting position is 48102.
    /note=Gap/overlap of 82
    /note=Phamerator phages have nucleotide similarity but no function called, BLAST hits also no function, HHpred no function, and 0 TMRs
    /note=No reliable evidence regarding function from any source.

CDS 49040 - 49750
  /gene="49"
  /product="gp49"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_49"
    /note=Original Glimmer call @bp 49040 has strength 18.52; Genemark calls start at 49040
    /note=SSC: 49040-49750 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ARMAWEN_48 [Microbacterium phage ArMaWen]],,NCBI, q1:s1 100.0% 4.99422E-175 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.899, -2.996490344739583, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ARMAWEN_48 [Microbacterium phage ArMaWen]],,AZV01810,100.0,4.99422E-175 SIF-HHPRED:  SIF-Syn: 
    /note=High coding potential in the ORF and likely a gene
    /note=Start choice agreed upon by GeneMark and Glimmer as 49,040, 23 MA`s, gap/overlap of -1
    /note=
    /note=There are hits on NCBI Blast with high E-values and probability for hypothetical protein. Phamerator also has similarity, but no function called. HHpred called functions but the coverage was not high enough. There are zero transmembrane regions called.

CDS 49747 - 50859
  /gene="50"
  /product="gp50"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_50"
    /note=Original Glimmer call @bp 49747 has strength 14.55; Genemark calls start at 49747
    /note=SSC: 49747-50859 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ARMAWEN_49 [Microbacterium phage ArMaWen]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.204, -4.197185411639505, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ARMAWEN_49 [Microbacterium phage ArMaWen]],,AZV01811,99.7297,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=- coding potential 
    /note=- start sites agree 49747 for Glimmer and GeneMark, Starterator agrees with 28 MAs for that start, gap/overlap of -4
    /note=-Phamerator phages have nucleotide similarity but no function called, BLAST hits also no function, HHpred no function, and 0 TMRs
    /note=-hypothetical protein

CDS 50936 - 51175
  /gene="51"
  /product="gp51"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_51"
    /note=Original Glimmer call @bp 50936 has strength 12.18; Genemark calls start at 50936
    /note=SSC: 50936-51175 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ARMAWEN_50 [Microbacterium phage ArMaWen]],,NCBI, q1:s1 100.0% 2.37411E-50 GAP: 76 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.225, -1.953940808934884, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_ARMAWEN_50 [Microbacterium phage ArMaWen]],,AZV01812,100.0,2.37411E-50 SIF-HHPRED:  SIF-Syn: 
    /note=-start sites agree with 6 MAs 50936 as the start site 
    /note=-viral protein called by HHPRED but not enough info to support as the final function
    /note=-Phamerator phages have nucleotide similarity but no function called, BLAST hits also no function, HHpred no function, and 0 TMRs
    /note=-no function called, so hypothetical protein

CDS 51206 - 51646
  /gene="52"
  /product="gp52"
  /function="minor tail protein"
  /locus tag="SwissCheezer_52"
    /note=Original Glimmer call @bp 51206 has strength 17.57; Genemark calls start at 51203
    /note=SSC: 51206-51646 CP: no SCS: both-gl ST: NI BLAST-Start: [minor tail protein [Microbacterium phage ArMaWen]],,NCBI, q1:s1 100.0% 3.37224E-96 GAP: 30 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.225, -2.033982896655645, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage ArMaWen]],,AZV01813,100.0,3.37224E-96 SIF-HHPRED:  SIF-Syn: 
    /note=Genemark agrees that this is a gene due to high coding potential within the reading frame.
    /note=Starterator agrees that the starting point is 51206 (17 MAs) with GeneMark and Glimmer
    /note=30 gap/overlap
    /note=Phamerator phages have nucleotide similarity and called minor tail protein
    /note=BLAST hits also minor tail protein
    /note=HHpred hits do not give additional data
    /note=0 TMRs

CDS 51649 - 53163
  /gene="53"
  /product="gp53"
  /function="terminase"
  /locus tag="SwissCheezer_53"
    /note=Original Glimmer call @bp 51649 has strength 10.0; Genemark calls start at 51649
    /note=SSC: 51649-53163 CP: no SCS: both ST: NI BLAST-Start: [terminase large subunit [Microbacterium phage Alex44] ],,NCBI, q1:s1 100.0% 0.0 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.694, -5.547625656018686, no F: terminase SIF-BLAST: ,,[terminase large subunit [Microbacterium phage Alex44] ],,YP_009847734,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=High coding potential and likely a gene
    /note=Glimmer and GeneMark agree on start choice 51,649, 41 MAs, gap/overlap of 2
    /note=Related nucleotides in Phamerator for terminase 
    /note=BLAST multiple 100% matches with genes for terminase 
    /note=HHPred multiple hits with probability greater than 90% and coverage greater than 70
    /note=0 TMRs

CDS 53153 - 53512
  /gene="54"
  /product="gp54"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_54"
    /note=Original Glimmer call @bp 53153 has strength 4.52; Genemark calls start at 53153
    /note=SSC: 53153-53512 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein HWC34_gp54 [Microbacterium phage Alex44] ],,NCBI, q1:s1 100.0% 4.36546E-80 GAP: -11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.842, -4.946058559219759, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein HWC34_gp54 [Microbacterium phage Alex44] ],,YP_009847735,100.0,4.36546E-80 SIF-HHPRED:  SIF-Syn: 
    /note=-coding potential 
    /note=-43 MAs agree with 53153 as the start site, Glimmer and GeneMark agree, gap/overlap of -11
    /note=-Phamerator phages have nucleotide similarity but no function called, BLAST hits also no function, HHpred no function, and 0 TMRs
    /note=-so hypothetical protein

CDS 53466 - 53792
  /gene="55"
  /product="gp55"
  /function="Hypothetical Protein"
  /locus tag="SwissCheezer_55"
    /note=Original Glimmer call @bp 53466 has strength 8.22; Genemark calls start at 53466
    /note=SSC: 53466-53792 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein HWC34_gp55 [Microbacterium phage Alex44] ],,NCBI, q1:s1 100.0% 3.98057E-73 GAP: -47 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.899, -2.6453814847322845, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein HWC34_gp55 [Microbacterium phage Alex44] ],,YP_009847736,100.0,3.98057E-73 SIF-HHPRED:  SIF-Syn: 
    /note=-high coding potential and likely a gene 
    /note=-start call 53466 called by both glimmer and gene mark, 22 MAs, -47 gap/overlap
    /note=-Phamerator phages have nucleotide similarity but no function called, BLAST hits also no function, HHpred no function, and 0 TMRs
    /note=-hypothetical protein