CDS 1 - 792
  /gene="1"
  /product="gp1"
  /function="ParB-like nuclease domain"
  /locus tag="Phantasmagoria_1"
    /note=Original Glimmer call @bp 37 has strength 15.05; Genemark calls start at 76
    /note=SSC: 1-792 CP: yes SCS: both-cs ST: SS BLAST-Start: [DNA binding protein [Mycobacterium phage Tres] ],,NCBI, q1:s1 100.0% 0.0 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.688, -5.711596282398514, no F: ParB-like nuclease domain SIF-BLAST: ,,[DNA binding protein [Mycobacterium phage Tres] ],,ALF01286,100.0,0.0 SIF-HHPRED: Chromosome-partitioning protein ParB; chromosome segregation, CTP, molecular gates, protein-DNA recognition, DNA BINDING PROTEIN; HET: CTP; 2.73A {Caulobacter vibrioides (strain NA1000 / CB15N)} SCOP: a.4.14.0, d.268.1.0,,,7BM8_A,57.7947,99.7 SIF-Syn: ⅘ using blast were parb-like nuclease domain protein 
12% frequency for parb-like nuclease domain protein 15% frequency for helix-turn-helix dna binding protein for B2 Cluster

CDS 789 - 1829
  /gene="2"
  /product="gp2"
  /function="dpdA-like tRNA-guanine transglycosylase"
  /locus tag="Phantasmagoria_2"
    /note=Original Glimmer call @bp 789 has strength 13.88; Genemark calls start at 789
    /note=SSC: 789-1829 CP: yes SCS: both ST: SS BLAST-Start: [queuine tRNA-ribosyltransferase [Mycobacterium phage Opia] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.003, -5.246974731142583, no F: dpdA-like tRNA-guanine transglycosylase SIF-BLAST: ,,[queuine tRNA-ribosyltransferase [Mycobacterium phage Opia] ],,AVE00290,100.0,0.0 SIF-HHPRED: Queuine tRNA-ribosyltransferase; tm1561, Queuine tRNA-ribosyltransferase, tRNA-guanine, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI; HET: EDO; 1.9A {Thermotoga maritima} SCOP: c.1.20.1,,,2ASH_B,71.6763,99.9 SIF-Syn: Faze9, Coffee, Lephleur, Sabella, Eaglehorse all have Queuine tRNA-ribosyltransferase as their function
    /note=Queuine tRNA-ribosyltransferase

CDS 1826 - 2533
  /gene="3"
  /product="gp3"
  /function="Pre Qo pathway, queC-like"
  /locus tag="Phantasmagoria_3"
    /note=Original Glimmer call @bp 1826 has strength 14.79; Genemark calls start at 1826
    /note=SSC: 1826-2533 CP: yes SCS: both ST: SS BLAST-Start: [Pre Qo pathway QueC-like protein [Mycobacterium phage Allegro]],,NCBI, q1:s1 100.0% 3.33011E-171 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.12, -3.095100142625534, yes F: Pre Qo pathway, queC-like SIF-BLAST: ,,[Pre Qo pathway QueC-like protein [Mycobacterium phage Allegro]],,QYC54247,100.0,3.33011E-171 SIF-HHPRED: c.26.2.1 (A:1-230) Queuosine biosynthesis protein QueC {Erwinia carotovora [TaxId: 554]},,,d2pg3a1,94.8936,100.0 SIF-Syn: Faze9: Pre qo pathway queC-like protein 
Coffee: Pre qo pathway queC-like protein 
Lephleur: Pre qo pathway queC-like protein

CDS 2530 - 2961
  /gene="4"
  /product="gp4"
  /function="Pre Qo pathway, queD-like"
  /locus tag="Phantasmagoria_4"
    /note=Original Glimmer call @bp 2530 has strength 16.73; Genemark calls start at 2530
    /note=SSC: 2530-2961 CP: yes SCS: both ST: SS BLAST-Start: [QueD-like queosine biosynthesis protein [Mycobacterium phage ItsyBitsy1]],,NCBI, q1:s1 100.0% 1.89141E-99 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.951, -4.966271270034708, no F: Pre Qo pathway, queD-like SIF-BLAST: ,,[QueD-like queosine biosynthesis protein [Mycobacterium phage ItsyBitsy1]],,AUX82214,99.3007,1.89141E-99 SIF-HHPRED: d.96.1.0 (A:) automated matches {Escherichia coli [TaxId: 469008]},,,d4ntka_,97.2028,100.0 SIF-Syn: Faze 9: queD-like queosine biosynthesis protein
Coffee:queD-like queosine biosynthesis protein
Lephleur: queD-like queosine biosynthesis protein

CDS 2958 - 3671
  /gene="5"
  /product="gp5"
  /function="Pre Qo pathway, queE-like"
  /locus tag="Phantasmagoria_5"
    /note=Original Glimmer call @bp 2958 has strength 11.34; Genemark calls start at 2958
    /note=SSC: 2958-3671 CP: yes SCS: both ST: SS BLAST-Start: [QueE-like queosine biosynthesis protein [Mycobacterium phage Glass] ],,NCBI, q1:s1 100.0% 6.87706E-171 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.083, -4.696275508110696, no F: Pre Qo pathway, queE-like SIF-BLAST: ,,[QueE-like queosine biosynthesis protein [Mycobacterium phage Glass] ],,AMB17319,99.5781,6.87706E-171 SIF-HHPRED: 7-carboxy-7-deazaguanine synthase; S-Adenosylmethionine radical enzyme, 7-Carboxy-7-deazaguanine synthase, LYASE; HET: SF4, 7C5, MET; 2.407A {Bacillus subtilis},,,5TH5_A,98.7342,99.9 SIF-Syn: Faze9: QueE-like queosine biosynthesis protein 
Coffee:QueE-like queosine biosynthesis protein
Lephleur: QueE-like queosine biosynthesis protein
Sabella: QueE-like queosine biosynthesis protein

CDS 3671 - 4246
  /gene="6"
  /product="gp6"
  /function="folE-like GTP cyclohydrolase I"
  /locus tag="Phantasmagoria_6"
    /note=Original Glimmer call @bp 3671 has strength 12.36; Genemark calls start at 3671
    /note=SSC: 3671-4246 CP: yes SCS: both ST: SS BLAST-Start: [gp6 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 2.05584E-135 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.837, -3.5466635877785, yes F: folE-like GTP cyclohydrolase I SIF-BLAST: ,,[gp6 [Mycobacterium phage Rosebush] ],,NP_817767,100.0,2.05584E-135 SIF-HHPRED: d.96.1.1 (A:) GTP cyclohydrolase I {Norway rat (Rattus norvegicus) [TaxId: 10116]},,,d1is8a_,95.8115,100.0 SIF-Syn: Faze9: GTP cyclohydrochlorase I
Coffee: GTP cyclohydrochlorase I
Lephleur: GTP cyclohydrochlorase I
    /note=called 3671 as the start site for Phantasmagoria_6 due to strong evidence from the Starterator report with this start being highly conserved in the pham, this particular start having a good gap value, and a notably good z-score. I also called the function of Phantasmagoria_6 to be a GTP cyclohydrochlorase I because this was the function in the same gene in the five closest related phages. The SIF-BLAST and SIF-HHPred were also very supportive of this function because very low e-values and high alignment and coverage percentages, as well as probability scores of 100.

CDS 4230 - 5924
  /gene="7"
  /product="gp7"
  /function="terminase"
  /locus tag="Phantasmagoria_7"
    /note=Original Glimmer call @bp 4230 has strength 14.51; Genemark calls start at 4230
    /note=SSC: 4230-5924 CP: yes SCS: both ST: NI BLAST-Start: [gp7 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 0.0 GAP: -17 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.848, -3.077027835973012, no F: terminase SIF-BLAST: ,,[gp7 [Mycobacterium phage Rosebush] ],,NP_817768,100.0,0.0 SIF-HHPRED: DNA packaging protein Gp17; large terminase, Alternative initiation, ATP-binding, DNA-binding, Hydrolase, Nuclease, Nucleotide-binding; HET: PO4; 2.8A {Bacteriophage T4},,,3CPE_A,86.3475,100.0 SIF-Syn: Faze9: terminase
Coffee: terminase
Lephleur: terminase
    /note=Called 4230 as the start site for Phantasmagoria_7 because is was the start site suggested by both Glimmer and Genemark and it had a strong z-score. I also chose the function of Phantasmagoria_7 to be a terminase because it is the function in the same gene in its closest related phages.

CDS complement (5921 - 6391)
  /gene="8"
  /product="gp8"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_8"
    /note=Original Glimmer call @bp 6391 has strength 21.97; Genemark calls start at 6391
    /note=SSC: 6391-5921 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDI79_gp08 [Mycobacterium phage Godines] ],,NCBI, q1:s1 100.0% 1.93606E-107 GAP: 82 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.12, -2.442961286954254, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI79_gp08 [Mycobacterium phage Godines] ],,YP_009616342,99.359,1.93606E-107 SIF-HHPRED: UPF0246 protein YaaA; UNKNOWN FUNCTION; HET: MSE; 1.65A {Escherichia coli},,,5CAJ_B,58.3333,99.5 SIF-Syn: 
    /note=I called 6391 as the start site for Phantasamagoria_8 because it is the suggested start by both Glimmer and Genemark and it has a very high z-score compared to the other candidates. I found that Phantasmagoria_8 has no known function since the same gene in its closest related phages also have no known function for this gene

CDS 6474 - 7049
  /gene="9"
  /product="gp9"
  /function="RuvC-like resolvase"
  /locus tag="Phantasmagoria_9"
    /note=Original Glimmer call @bp 6474 has strength 14.97; Genemark calls start at 6561
    /note=SSC: 6474-7049 CP: yes SCS: both-gl ST: SS BLAST-Start: [RuvC-like resolvase [Mycobacterium virus TA17a] ],,NCBI, q1:s40 100.0% 5.51208E-138 GAP: 82 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.851, -5.935104314925138, no F: RuvC-like resolvase SIF-BLAST: ,,[RuvC-like resolvase [Mycobacterium virus TA17a] ],,YP_009667163,83.0435,5.51208E-138 SIF-HHPRED: c.55.3.6 (A:) RuvC resolvase {Thermus thermophilus [TaxId: 300852]},,,d4ep4a_,90.0524,99.9 SIF-Syn: Faze9: RuvC-like resolvase
Coffee: RuvC-like resolvase
Lephleur: RuvC-like resolvase
    /note=I called 6474 as the start site for Phantasamagoria_9 because is was the start that was relatively highly conserved in the pham, and it has a more negative final score than the suggested Genemark start (6561). I chose the function of Phantasmagoria_9 to be a RuvC-like resolvase because it is the function in the same gene in Phantasmagoria’s closest related phages.

CDS 7046 - 7366
  /gene="10"
  /product="gp10"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_10"
    /note=Original Glimmer call @bp 7046 has strength 11.18; Genemark calls start at 7046
    /note=SSC: 7046-7366 CP: yes SCS: both ST: SS BLAST-Start: [gp10 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 1.81918E-72 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.676, -3.4892599424135016, yes F: hypothetical protein SIF-BLAST: ,,[gp10 [Mycobacterium phage Rosebush] ],,NP_817771,100.0,1.81918E-72 SIF-HHPRED: DUF5810 ; Family of unknown function (DUF5810),,,PF19126.3,44.3396,58.5 SIF-Syn: 
    /note=I called 7046 as the start site for Phantasamagoria_10 because it is the start suggested by both Glimmer and Genemark, it is a very highly conserved start in the pham, it makes for a -4 gap, and it has the highest z-score of all the top candidates. I found that Phantasmagoria_10 does not have a known function because its closest phage relative also have no function for the same gene.

CDS 7363 - 7701
  /gene="11"
  /product="gp11"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_11"
    /note=Original Glimmer call @bp 7363 has strength 14.52; Genemark calls start at 7363
    /note=SSC: 7363-7701 CP: yes SCS: both ST: SS BLAST-Start: [gp11 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 8.86629E-71 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.608, -3.627004739933808, yes F: hypothetical protein SIF-BLAST: ,,[gp11 [Mycobacterium phage Rosebush] ],,NP_817772,100.0,8.86629E-71 SIF-HHPRED: DUF1360 ; Protein of unknown function (DUF1360),,,PF07098.14,75.8929,99.9 SIF-Syn: 
    /note=I called 7363 as the start site for Phantasamagoria_11 because it is the start suggested by both Glimmer and Genemark, it makes for a gap of -4, and it has the highest z-score of the top candidates. I found that Phantasmagoria_11 does not have a known function because its closest phage relative also have no function for the same gene.

CDS 7728 - 9617
  /gene="12"
  /product="gp12"
  /function="portal protein"
  /locus tag="Phantasmagoria_12"
    /note=Original Glimmer call @bp 7728 has strength 18.32; Genemark calls start at 7800
    /note=SSC: 7728-9617 CP: yes SCS: both-gl ST: SS BLAST-Start: [portal protein [Mycobacterium phage Allegro]],,NCBI, q1:s1 100.0% 0.0 GAP: 26 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 0.997, -6.8474408907317805, no F: portal protein SIF-BLAST: ,,[portal protein [Mycobacterium phage Allegro]],,QYC54256,100.0,0.0 SIF-HHPRED: Phage portal protein, HK97 family; "neck", "portal", "capsid", "tail tube", VIRUS; 3.58A {Rhodobacter capsulatus},,,6TE9_A,63.434,100.0 SIF-Syn: I called 7728 as the start site for Phantasamagoria_12 because it is the start the includes the most coding potential, it is the start that was pretty highly conserved in the pham, and the final score is among the more negative among the other top candidates. I chose Phantasmagoria_12 to be a portal protein because the same gene in the closest related phages is also a portal protein.
    /note=I called 7728 as the start site for Phantasamagoria_12 because it is the start the includes the most coding potential, it is the start that was pretty highly conserved in the pham, and the final score is among the more negative among the other top candidates. I chose Phantasmagoria_12 to be a portal protein because the same gene in the closest related phages is also a portal protein.

CDS 9617 - 12064
  /gene="13"
  /product="gp13"
  /function="minor capsid protein"
  /locus tag="Phantasmagoria_13"
    /note=Original Glimmer call @bp 9617 has strength 17.41; Genemark calls start at 9617
    /note=SSC: 9617-12064 CP: yes SCS: both ST: SS BLAST-Start: [gp13 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.517, -3.75071250087134, no F: minor capsid protein SIF-BLAST: ,,[gp13 [Mycobacterium phage Rosebush] ],,NP_817774,100.0,0.0 SIF-HHPRED: Phage_Mu_F ; Phage Mu protein F like protein,,,PF04233.17,15.8282,99.3 SIF-Syn: Faze9: MuF-like minor capsid protein
Coffee: MuF-like minor capsid protein
Lephleur: MuF-like minor capsid protein
    /note=I called 9617 as the start site for Phantasamagoria_13 because that start was very highly conserved in the pham and the spacer and z-scores for this start were particularly strong. I found the function of Phantasmagoria_13 to be a MuF-like minor capsid protein because it was the function in the same gene in Phantasmagoria’s closest related phages.

CDS 12064 - 12237
  /gene="14"
  /product="gp14"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_14"
    /note=Original Glimmer call @bp 12064 has strength 7.88; Genemark calls start at 12064
    /note=SSC: 12064-12237 CP: yes SCS: both ST: SS BLAST-Start: [gp14 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 1.09299E-32 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.625, -3.513874779476501, yes F: hypothetical protein SIF-BLAST: ,,[gp14 [Mycobacterium phage Rosebush] ],,NP_817775,100.0,1.09299E-32 SIF-HHPRED: DUF6316 ; Domain of unknown function (DUF6316),,,PF19837.2,45.614,89.9 SIF-Syn: 
    /note=I called 12064 as the start site for Phantasamagoria_14 because of the notably good z-score that was the only start candidate to have a z-score greater than 2, the good gap value of -1 which was only found for this start candidate. I found Phantasmagoria_14 to have no known function because the closest related phages also had no known function for the same gene.

CDS 12411 - 14438
  /gene="15"
  /product="gp15"
  /function="major capsid hexamer protein"
  /locus tag="Phantasmagoria_15"
    /note=Original Glimmer call @bp 12411 has strength 17.75; Genemark calls start at 12411
    /note=SSC: 12411-14438 CP: yes SCS: both ST: SS BLAST-Start: [gp15 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 0.0 GAP: 173 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.282, -2.17469248771465, yes F: major capsid hexamer protein SIF-BLAST: ,,[gp15 [Mycobacterium phage Rosebush] ],,NP_817776,100.0,0.0 SIF-HHPRED: Med21 ; Subunit 21 of Mediator complex,,,PF11221.11,10.963,43.8 SIF-Syn: Faze9: major capsid hexamer protein
Coffee: major capsid hexamer protein
Lephleur: major capsid hexamer protein
    /note=I chose 12411 as the start site for Phantasmagoria_15 because it is the start suggested by both Glimmer and Genemark, there`s a high coding capacity for the entire gene region, it makes for the longest oen reading frame, and it has the highest z-score of all top gene candidates. I found the function of Phantasmagoria_15 to be a major capsid hexamer protein because the closest related phages have this as the function for the same gene.

CDS 14532 - 15350
  /gene="16"
  /product="gp16"
  /function="major capsid pentamer protein"
  /locus tag="Phantasmagoria_16"
    /note=Original Glimmer call @bp 14532 has strength 12.25; Genemark calls start at 14532
    /note=SSC: 14532-15350 CP: yes SCS: both ST: SS BLAST-Start: [major capsid pentamer protein [Mycobacterium phage LizLemon] ],,NCBI, q1:s1 100.0% 0.0 GAP: 93 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.202, -2.9284886490054283, yes F: major capsid pentamer protein SIF-BLAST: ,,[major capsid pentamer protein [Mycobacterium phage LizLemon] ],,AIK68790,100.0,0.0 SIF-HHPRED: PhiRv1 phage protein; bacterial toxin, TOXIN; 1.90057258182A {Mycobacterium tuberculosis},,,6LG3_A,19.1176,24.2 SIF-Syn: Faze9: major capsid pentamer protein
Coffee: major capsid pentamer protein
Lephleur: major capsid pentamer protein
    /note=I chose 14532 as the start site for Phantasmagoria_16 because it contains all of the coding potential, it is the start suggested by both Glimmer and Genemark, it makes for the longest open reading frame, and the z-score at this start is the highest of all other top gene candidates. I found the function of Phantasmagoria_16 to be a major capsid pentamer protein because that function was in the same gene in the closest related phages.

CDS 15350 - 16099
  /gene="17"
  /product="gp17"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_17"
    /note=Original Glimmer call @bp 15350 has strength 15.2; Genemark calls start at 15350
    /note=SSC: 15350-16099 CP: yes SCS: both ST: SS BLAST-Start: [gp17 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 8.65755E-175 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.213, -2.3335289980954053, yes F: hypothetical protein SIF-BLAST: ,,[gp17 [Mycobacterium phage Rosebush] ],,NP_817778,99.5984,8.65755E-175 SIF-HHPRED: a.140.2.1 (A:71-114) Rififylin (FYVE-RING finger protein Sakura) {Human (Homo sapiens) [TaxId: 9606]},,,d1y02a1,13.253,93.8 SIF-Syn: 
    /note=I chose 15350 as the start site for Phantasmagoria_17 because it contains all of the coding potential, it is the suggest start by both Glimmer and Genemark, it was the start that was highly conserved in the pham, it has a very good gap value, it makes for the longest open reading frame, it has the highest z-score of all the other top gene candidates. I found that Phantasmagoria_17 has no known function because the same gene in the closest related phages also had no known function.

CDS 16136 - 16678
  /gene="18"
  /product="gp18"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_18"
    /note=Original Glimmer call @bp 16136 has strength 12.0; Genemark calls start at 16232
    /note=SSC: 16136-16678 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein J3996_gp18 [Mycobacterium phage Laurie] ],,NCBI, q1:s1 100.0% 4.09302E-127 GAP: 36 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.213, -2.3335289980954053, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J3996_gp18 [Mycobacterium phage Laurie] ],,YP_010012386,100.0,4.09302E-127 SIF-HHPRED: p53-inducible11 ; Tumour protein p53-inducible protein 11,,,PF14936.9,68.8889,95.8 SIF-Syn: 
    /note=I chose 16136 as the start site for Phantasmagoria_18 because it contains the entire coding potential, makes for the longest open reading frame, and has the highest z-score of all the other top gene candidates. I found that Phantasmagoria_18 has no known function because the same gene in its closest related phages also had no known function.

CDS 16675 - 17157
  /gene="19"
  /product="gp19"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_19"
    /note=Original Glimmer call @bp 16912 has strength 6.58; Genemark calls start at 16675
    /note=SSC: 16675-17157 CP: no SCS: both-gm ST: SS BLAST-Start: [gp19 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 8.07292E-112 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.509, -4.03953528405695, no F: hypothetical protein SIF-BLAST: ,,[gp19 [Mycobacterium phage Rosebush] ],,NP_817780,100.0,8.07292E-112 SIF-HHPRED: YrhC ; YrhC-like protein,,,PF14143.9,36.875,80.4 SIF-Syn: 
    /note=I chose 16675 as the start site for Phantasmagoria_19 because it contains all of the detected coding potential, eventhough that potenial is very weak, it is the only start to have a very good gap value, it makes for the longest open reading frame, and it has a z-score greater than 2. I also found the Phantasmagoria_19 has no known function becuase the same gene in Phantasmagoria’s closest related phages is also listed as no known function.

CDS 17154 - 17486
  /gene="20"
  /product="gp20"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_20"
    /note=Original Glimmer call @bp 17154 has strength 11.29; Genemark calls start at 17154
    /note=SSC: 17154-17486 CP: yes SCS: both ST: SS BLAST-Start: [gp20 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 6.41851E-71 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.598, -3.6476983004329377, yes F: hypothetical protein SIF-BLAST: ,,[gp20 [Mycobacterium phage Rosebush] ],,NP_817781,100.0,6.41851E-71 SIF-HHPRED: BLOC1_2 ; Biogenesis of lysosome-related organelles complex-1 subunit 2,,,PF10046.12,61.8182,92.4 SIF-Syn: 
    /note=I chose 17154 as the start site for Phantasmagoria_20 because it contains all of the predicted coding potential, it is the start suggested by both Glimmer and Genemark, is was a pretty highly conserved start in the pham, it was the only start to have a very good gap value, and it was the start with the highest z-score greater than 2. I found Phantasmagoria_20 to have no known function because the same gene in the closest related phages also had no known function for this same gene.

CDS 17576 - 18652
  /gene="21"
  /product="gp21"
  /function="major tail protein"
  /locus tag="Phantasmagoria_21"
    /note=Original Glimmer call @bp 17576 has strength 20.37; Genemark calls start at 17576
    /note=SSC: 17576-18652 CP: yes SCS: both ST: SS BLAST-Start: [gp20 [Mycobacterium phage Qyrzula] ],,NCBI, q1:s1 100.0% 0.0 GAP: 89 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.042, -3.2535385006449706, no F: major tail protein SIF-BLAST: ,,[gp20 [Mycobacterium phage Qyrzula] ],,YP_655700,100.0,0.0 SIF-HHPRED: L_lac_phage_MSP ; Phage tail tube protein,,,PF06488.14,51.1173,88.7 SIF-Syn: Faze9: major tail protein
Coffee: major tail protein
Sabella: major tail protein
    /note=I chose 17576 as the start site for Phantasmagoria_21 becuase it contains all of the predicted coding potential, it is the start predicted by both Glimmer and Genemark, it makes for the longest open reading frame, and it has the highest z-score. I also found Phantasmagoria_21 to be a major tail protein becuase most of the closest related phages also had the function for the same gene called as a major tail protein.

CDS complement (18711 - 18824)
  /gene="22"
  /product="gp22"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_22"
    /note=Original Glimmer call @bp 18824 has strength 8.79; Genemark calls start at 18824
    /note=SSC: 18824-18711 CP: yes SCS: both ST: SS BLAST-Start: [gp22 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 1.73316E-17 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.201, -4.455662434380964, no F: hypothetical protein SIF-BLAST: ,,[gp22 [Mycobacterium phage Rosebush] ],,NP_817783,100.0,1.73316E-17 SIF-HHPRED: g.41.3.1 (I:1-49) RBP9 subunit of RNA polymerase II {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]},,,d1twfi1,35.1351,94.9 SIF-Syn: 
    /note=I chose 18824 as the start site for Phantasmagoria_22 because it contains all of the predicted coding capacity, it is the start suggested by both Glimmer and Genemark, it was a very highly conserved start in the pham, it has a very good gap value, and it has a z-score greater than 2. I found Phantasmagoria_22 to have no known function because the closest related phages have the same gene called as having no known function.

CDS complement (18824 - 19015)
  /gene="23"
  /product="gp23"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_23"
    /note=Original Glimmer call @bp 19015 has strength 19.12; Genemark calls start at 19015
    /note=SSC: 19015-18824 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein J3996_gp23 [Mycobacterium phage Laurie] ],,NCBI, q1:s1 100.0% 4.87121E-38 GAP: 110 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.865, -3.0425830684175623, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein J3996_gp23 [Mycobacterium phage Laurie] ],,YP_010012391,100.0,4.87121E-38 SIF-HHPRED: Rv1761c; PROTEIN, integral membrane protein, MEMBRANE PROTEIN; HET: MTN; NMR {Mycobacterium tuberculosis},,,2K3M_A,28.5714,58.0 SIF-Syn: 
    /note=I chose 19015 as the start site for Phantasmagoria_23 because it contains the entire predicted coding potential, it is the start suggested by both Glimmer and Genemark, it is the start that`s highly conserved in the pham, and it`s the only start to have a z-score greater than 2. I found Phantasmagoria_23 to have no known function because the closest related phages also called this same gene as having no known function.

CDS 19126 - 19911
  /gene="24"
  /product="gp24"
  /function="head-to-tail adaptor"
  /locus tag="Phantasmagoria_24"
    /note=Original Glimmer call @bp 19126 has strength 10.36; Genemark calls start at 19126
    /note=SSC: 19126-19911 CP: yes SCS: both ST: SS BLAST-Start: [head-to-tail adaptor [Mycobacterium phage Hedgerow] ],,NCBI, q1:s1 100.0% 0.0 GAP: 110 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.301, -6.976929056182261, no F: head-to-tail adaptor SIF-BLAST: ,,[head-to-tail adaptor [Mycobacterium phage Hedgerow] ],,AER47256,100.0,0.0 SIF-HHPRED: Adaptor protein Rcc01688; "neck", "portal", "capsid", "tail tube", VIRUS; 3.58A {Rhodobacter capsulatus},,,6TE9_D,81.2261,99.5 SIF-Syn: Faze9: head-to-tail adaptor
Coffee: head-to-tail adaptor
Lephleur: head-to-tail adaptor
    /note=I chose 19126 as the start site for Phantasmagoria_24 because it contains all of the predicted coding potential, it is the start suggested by both Glimmer and Genemark, and it makes for the longest open reading frame. I found Phantasmagoria_24 to be a head-to-tail adaptor because the closest related phages called this same gene as being that function.

CDS 19908 - 20468
  /gene="25"
  /product="gp25"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_25"
    /note=Original Glimmer call @bp 19908 has strength 15.06; Genemark calls start at 19908
    /note=SSC: 19908-20468 CP: yes SCS: both ST: SS BLAST-Start: [gp25 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 2.23579E-132 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.271, -4.252323739694084, no F: hypothetical protein SIF-BLAST: ,,[gp25 [Mycobacterium phage Rosebush] ],,NP_817786,100.0,2.23579E-132 SIF-HHPRED: KBTB_W-LIR ; KBTB, W-type LIR motif,,,PF20165.1,2.68817,15.8 SIF-Syn: 
    /note=I chose 19908 as the start site for Phantasmagoria_25 because is includes all of the proposed coding potential for the area and the coding potential is high, it is the start suggested by both Glimmer and Genemark, it has a very good gap value (-4), the spacer is within the accepted range, and the z-score is greater than 2. I found Phantasmagoria_25 to have no known function because the closest related phages called the same gene as having no known function.

CDS 20477 - 20830
  /gene="26"
  /product="gp26"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_26"
    /note=Original Glimmer call @bp 20477 has strength 17.03; Genemark calls start at 20477
    /note=SSC: 20477-20830 CP: yes SCS: both ST: SS BLAST-Start: [gp26 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 2.7679E-78 GAP: 8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.436, -3.9166971242758706, no F: hypothetical protein SIF-BLAST: ,,[gp26 [Mycobacterium phage Rosebush] ],,NP_817787,100.0,2.7679E-78 SIF-HHPRED: Mu-like prophage FluMu protein gp35, Protein HI1507 in Mu-like prophage FluMu region; structural genomics, Haemophilus influenzae, hypothetical protein, Structure 2 Function Project, S2F, UNKNOWN FUNCTION; NMR {Haemophilus influenzae} SCOP: a.140.3.2, d.344.1.1, l.1.1.1,,,2OUT_A,98.2906,94.7 SIF-Syn: 
    /note=I chose 20477 as the start site for Phantasmagoria_26 because it includes all of the predicted coding potential for the area and the potential is high, it is the start suggested by both Glimmer and Genemark, it is a highly conserved start in the pham, it has a spacer value within the acceptable range, and a z-score greater than 2. I found Phantasmagoria_26 to have no known function because the closest related phages also called this same gene as having no known function.

CDS 20830 - 21258
  /gene="27"
  /product="gp27"
  /function="tail assembly chaperone"
  /locus tag="Phantasmagoria_27"
    /note=Original Glimmer call @bp 20830 has strength 8.66; Genemark calls start at 20830
    /note=SSC: 20830-21258 CP: yes SCS: both ST: SS BLAST-Start: [gp27 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 2.27414E-96 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.608, -3.627004739933808, yes F: tail assembly chaperone SIF-BLAST: ,,[gp27 [Mycobacterium phage Rosebush] ],,NP_817788,100.0,2.27414E-96 SIF-HHPRED: Minor_capsid_2 ; Minor capsid protein,,,PF11114.11,88.7324,99.5 SIF-Syn: Allergro, arbiter, ares
    /note=We called 20,830 (start site) - 21,258  because it does have coding potential although this start site is not conserved and it is not in the LORF. We call a function of tail assembly chaperone function because it is the overall SYN function and most of the Blast and HHPRED data also indicates this function.

CDS 21313 - 21798
  /gene="28"
  /product="gp28"
  /function="tail assembly chaperone"
  /locus tag="Phantasmagoria_28"
    /note=Original Glimmer call @bp 21340 has strength 16.57; Genemark calls start at 21313
    /note=SSC: 21313-21798 CP: yes SCS: both-gm ST: SS BLAST-Start: [tail assembly chaperone [Mycobacterium phage Opia] ],,NCBI, q1:s1 100.0% 2.32846E-113 GAP: 54 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.836, -5.585253183906189, no F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Mycobacterium phage Opia] ],,AVE00316,100.0,2.32846E-113 SIF-HHPRED: Phage_TAC_10 ; Phage tail assembly chaperone,,,PF10963.11,48.4472,94.2 SIF-Syn: Opia, allegro, ares
    /note=Start: 21313 (less gap, better cluster in starterator, better spacer, better final score, LORF). Improves over autoannotation call. tail assembly chaperone based on pham calls,

CDS 21824 - 27478
  /gene="29"
  /product="gp29"
  /function="tape measure protein"
  /locus tag="Phantasmagoria_29"
    /note=Original Glimmer call @bp 21824 has strength 15.6; Genemark calls start at 21824
    /note=SSC: 21824-27478 CP: yes SCS: both ST: NI BLAST-Start: [tape measure protein [Mycobacterium phage Faze9]],,NCBI, q1:s1 100.0% 0.0 GAP: 25 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 0.928, -7.560645402102623, no F: tape measure protein SIF-BLAST: ,,[tape measure protein [Mycobacterium phage Faze9]],,AZF93671,99.947,0.0 SIF-HHPRED: Tape Measure Protein, gp57; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alpha},,,6V8I_AF,13.9597,99.7 SIF-Syn: Faze9, Calamitous, rosebush
    /note=We called 21,842 the start site because it had coding potential and was in the LORF.
    /note=We call tape measure protein function because the Blast, HHPRED and SYN all listed that as the function and overall SYN function tape measure protein also

CDS 27487 - 28923
  /gene="30"
  /product="gp30"
  /function="minor tail protein"
  /locus tag="Phantasmagoria_30"
    /note=Original Glimmer call @bp 27487 has strength 12.8; Genemark calls start at 27487
    /note=SSC: 27487-28923 CP: yes SCS: both ST: NI BLAST-Start: [gp30 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 0.0 GAP: 8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.196, -4.4057176022952405, no F: minor tail protein SIF-BLAST: ,,[gp30 [Mycobacterium phage Rosebush] ],,NP_817791,100.0,0.0 SIF-HHPRED: ORF46; Distal tail protein, Receptor-binding protein, Phage baseplate, host adsorption apparatus, genome injection device, VIRAL PROTEIN; 3.8A {Lactococcus phage TP901-1},,,4V96_AX,30.7531,93.7 SIF-Syn: allegro, arbiter
    /note=I called 27,487 the start site because it is in the LORF and had coding potential. 
    /note=I call protein function because overall functions says minor tail but the probabilities from HHPRED for a vial protein were high as well.

CDS 28926 - 29975
  /gene="31"
  /product="gp31"
  /function="minor tail protein"
  /locus tag="Phantasmagoria_31"
    /note=Original Glimmer call @bp 28926 has strength 14.73; Genemark calls start at 28926
    /note=SSC: 28926-29975 CP: yes SCS: both ST: NI BLAST-Start: [minor tail protein [Mycobacterium phage Arbiter] ],,NCBI, q1:s1 100.0% 0.0 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.193, -4.6836130299641985, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Mycobacterium phage Arbiter] ],,AEN79532,100.0,0.0 SIF-HHPRED: Sipho_Gp37 ; Siphovirus ReqiPepy6 Gp37-like protein,,,PF14594.9,89.1117,99.9 SIF-Syn: Allegro, arbiter, bananafish
    /note=We called this start site because it does have coding potential although this start site is not conserved and it is not in the LORF. We call minor tail protein due to NCBI and phagesDB results.

CDS 29972 - 32692
  /gene="32"
  /product="gp32"
  /function="minor tail protein"
  /locus tag="Phantasmagoria_32"
    /note=Original Glimmer call @bp 29972 has strength 16.56; Genemark calls start at 29972
    /note=SSC: 29972-32692 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Mycobacterium phage Arbiter]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.292, -4.271082485841055, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Mycobacterium phage Arbiter]],,AEN79533,100.0,0.0 SIF-HHPRED: b.18.1.7 (A:) Xylan-binding domain {Clostridium thermocellum [TaxId: 1515]},,,d1h6ya_,17.66,97.8 SIF-Syn: Lephleur, arbiter
    /note=I called 29,972 the start site because it is in the LORF and conserved in Pfam. I call this function a minor tail protein due to the evidence from all SIF sources except HHPRED.

CDS 32695 - 33858
  /gene="33"
  /product="gp33"
  /function="minor tail protein"
  /locus tag="Phantasmagoria_33"
    /note=Original Glimmer call @bp 32695 has strength 12.93; Genemark calls start at 32695
    /note=SSC: 32695-33858 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Mycobacterium phage LizLemon]],,NCBI, q1:s1 100.0% 0.0 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.415, -4.020421520751994, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Mycobacterium phage LizLemon]],,AIK68807,100.0,0.0 SIF-HHPRED:  SIF-Syn: LizLemmon, Eaglehorse
    /note=I called 32,695 the start site because it is conserved in the Pfam, although not in LORF 
    /note=I call minor tail protein function because every SYN function is a minor tail but at the very least its a protein.

CDS 33889 - 34278
  /gene="34"
  /product="gp34"
  /function="NFK"
  /locus tag="Phantasmagoria_34"
    /note=Original Glimmer call @bp 33889 has strength 8.69; Genemark calls start at 33889
    /note=SSC: 33889-34278 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_LIZLEMON_34 [Mycobacterium phage LizLemon] ],,NCBI, q1:s1 100.0% 1.54228E-85 GAP: 30 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.128, -4.52735728736575, yes F: NFK SIF-BLAST: ,,[hypothetical protein PBI_LIZLEMON_34 [Mycobacterium phage LizLemon] ],,AIK68808,100.0,1.54228E-85 SIF-HHPRED: Uncharacterized protein; Protein NMR, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), Target TR5, PSI-2, Protein Structure Initiative, Methanothermobacter thermautotrophicus, O26567_METTH; NMR {Methanothermobacter thermautotrophicus str. Delta H},,,2KKE_B,10.0775,32.6 SIF-Syn: 
    /note=We called 33,889 the start site because it is conserved in the Pfam and in LORF.
    /note=We call this function a hypothetical protein because most of the blast indicates that and the probability of the functions in HHPRED are somewhat low.

CDS 34287 - 34676
  /gene="35"
  /product="gp35"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_35"
    /note=Original Glimmer call @bp 34287 has strength 8.1; Genemark calls start at 34287
    /note=SSC: 34287-34676 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FPF50_gp36 [Mycobacterium virus TA17a] ],,NCBI, q1:s1 100.0% 7.76959E-88 GAP: 8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.848, -3.523800704818996, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FPF50_gp36 [Mycobacterium virus TA17a] ],,YP_009667190,100.0,7.76959E-88 SIF-HHPRED: pGolemi; protein design, miniature protein, aPP, beta-hairpin, ActA homolog, DE NOVO PROTEIN; NMR {N/A},,,2K76_A,24.8062,87.1 SIF-Syn: 
    /note=I called 34,287 start site because it is themost annotated start site and conserved in Pfam but not in LORF .I call this function unknown because most of the sources are unsure of it being a protein in general and high probability of de novo/ hormone as well.

CDS 34688 - 35332
  /gene="36"
  /product="gp36"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_36"
    /note=Original Glimmer call @bp 34688 has strength 17.81; Genemark calls start at 34697
    /note=SSC: 34688-35332 CP: yes SCS: both-gl ST: SS BLAST-Start: [gp36 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 6.12821E-156 GAP: 11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.321, -4.133270333136946, no F: hypothetical protein SIF-BLAST: ,,[gp36 [Mycobacterium phage Rosebush] ],,NP_817797,100.0,6.12821E-156 SIF-HHPRED: DUF6807 ; Family of unknown function (DUF6807),,,PF14100.9,7.47664,38.3 SIF-Syn: 
    /note=We called 34,688 the start site because it had coding potential even though it is not in the LORF. I call this function a protein  because BLAST talks about proteins and the enzymes HHPRED denotes are also proteins.

CDS 35329 - 35481
  /gene="37"
  /product="gp37"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_37"
    /note=Original Glimmer call @bp 35356 has strength 3.46
    /note=SSC: 35329-35481 CP: yes SCS: glimmer-cs ST: SS BLAST-Start: [hypothetical protein FDI79_gp37 [Mycobacterium phage Godines] ],,NCBI, q1:s1 100.0% 6.48973E-27 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.164, -4.4713484557894425, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI79_gp37 [Mycobacterium phage Godines] ],,YP_009616371,100.0,6.48973E-27 SIF-HHPRED: NinF ; NinF protein,,,PF05810.15,54.0,98.4 SIF-Syn: 
    /note=Moved start to 35329 (better gap, longer, fits size of genes in pham better, better spacer). Improvement over autoannoation.

CDS 35478 - 36077
  /gene="38"
  /product="gp38"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_38"
    /note=Original Glimmer call @bp 35478 has strength 12.29; Genemark calls start at 35478
    /note=SSC: 35478-36077 CP: yes SCS: both ST: SS BLAST-Start: [gp37 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 8.39327E-145 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.962, -2.8454123590742793, yes F: hypothetical protein SIF-BLAST: ,,[gp37 [Mycobacterium phage Rosebush] ],,NP_817798,100.0,8.39327E-145 SIF-HHPRED: ChiC ; Chitinase C,,,PF06483.14,43.2161,47.1 SIF-Syn: 
    /note=I called 35,478 the  start site because its in the LORF and SS ( meaning the start site is conserved in the Pfam.
    /note=I call this gene as NKF because it seems to be the overall consensus even if the sources say different types of proteins

CDS 36074 - 37387
  /gene="39"
  /product="gp39"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_39"
    /note=Original Glimmer call @bp 36074 has strength 17.17; Genemark calls start at 36131
    /note=SSC: 36074-37387 CP: yes SCS: both-gl ST: SS BLAST-Start: [gp38 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.355, -4.081238041395941, no F: hypothetical protein SIF-BLAST: ,,[gp38 [Mycobacterium phage Rosebush] ],,NP_817799,100.0,0.0 SIF-HHPRED: AvrPib protein; Magnaporthe oryzae, MAX effector, protein crystal structure, UNKNOWN FUNCTION; HET: MSE; 1.661A {Magnaporthe oryzae},,,5Z1V_D,10.2975,37.5 SIF-Syn: 
    /note=I called 36,074 the start site because even though it is not in the LORF it does have coding potential. I call this function unknown because the probabilities given in HHPRED are relatively low.

CDS 37418 - 37774
  /gene="40"
  /product="gp40"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_40"
    /note=Original Glimmer call @bp 37418 has strength 11.15; Genemark calls start at 37418
    /note=SSC: 37418-37774 CP: yes SCS: both ST: SS BLAST-Start: [gp39 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 2.0923E-79 GAP: 30 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.436, -3.9166971242758706, no F: hypothetical protein SIF-BLAST: ,,[gp39 [Mycobacterium phage Rosebush] ],,NP_817800,100.0,2.0923E-79 SIF-HHPRED: Phage_TAC_10 ; Phage tail assembly chaperone,,,PF10963.11,64.4068,94.6 SIF-Syn: 
    /note=37,418-37,774 are called as the start and stop sites because it is called by both the Glimmer and Genemark starts. This start was also favored in both the Starterator report and phamerator report (the top three closest phage have the same start and stop sites). It has a z-score over 2, a spacer between 9-13, and the smallest negative value. It also has the longest open reading frame. This start and stop site also has the longest open reading frame Function is a hypothetical protein due to Blast evidence and Phamerator evidence.

CDS 37780 - 38100
  /gene="41"
  /product="gp41"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_41"
    /note=Original Glimmer call @bp 37735 has strength 16.81; Genemark calls start at 37735
    /note=SSC: 37780-38100 CP: yes SCS: both-cs ST: NI BLAST-Start: [gp40 [Mycobacterium phage Rosebush] ],,NCBI, q1:s16 100.0% 5.44444E-72 GAP: 5 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.221, -6.8398696868981075, no F: hypothetical protein SIF-BLAST: ,,[gp40 [Mycobacterium phage Rosebush] ],,NP_817801,87.6033,5.44444E-72 SIF-HHPRED: AvrE_T3Es ; AvrE-family Type-III effector proteins (T3Es),,,PF11725.11,90.566,74.7 SIF-Syn: 
    /note=Move start to 37780 (better spacer, better gap, still called a lot in starterator).

CDS 38126 - 38542
  /gene="42"
  /product="gp42"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_42"
    /note=Original Glimmer call @bp 38126 has strength 16.67; Genemark calls start at 38126
    /note=SSC: 38126-38542 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HEDGEROW_42 [Mycobacterium phage Hedgerow] ],,NCBI, q1:s1 100.0% 8.62602E-92 GAP: 25 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.787, -6.463418594059808, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HEDGEROW_42 [Mycobacterium phage Hedgerow] ],,AER47273,100.0,8.62602E-92 SIF-HHPRED: DUF1816 ; Domain of unknown function (DUF1816),,,PF08846.13,7.97101,8.6 SIF-Syn: 
    /note=I called the gene at 38,126 - 38,524 because it is conserved in Glimmer, Genemark, starterator, and phamerator. It also has a very negative final score and is very highly conserved in its pham.
    /note=I called an unknown function for this gene because the five most similar phages all report the same function. THE SIF-BLAST and SIF-HHPRED also reported high alignment and probability for a gene of unknown function.

CDS 38543 - 39238
  /gene="43"
  /product="gp43"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_43"
    /note=Original Glimmer call @bp 38543 has strength 14.31; Genemark calls start at 38543
    /note=SSC: 38543-39238 CP: yes SCS: both ST: SS BLAST-Start: [gp42 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 8.47178E-162 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.221, -5.103811796665142, no F: hypothetical protein SIF-BLAST: ,,[gp42 [Mycobacterium phage Rosebush] ],,NP_817803,100.0,8.47178E-162 SIF-HHPRED: LEVANASE; HYDROLASE, LEVAN; HET: FRU; 1.65A {BACILLUS SUBTILIS},,,4B1L_A,75.3247,97.6 SIF-Syn: 
    /note=I called the gene at 38,543-39,238 because it is conserved in Glimmer, Genemark, starterator, and phamerator. It has a very negative final score, a z-score over 2, and is the LORF. It is also a start that is highly conserved throughout the pham.
    /note=I called an unknown function for this gene because the five most similar phages all report an unknown function.

CDS complement (39235 - 39441)
  /gene="44"
  /product="gp44"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Phantasmagoria_44"
    /note=Original Glimmer call @bp 39441 has strength 8.31; Genemark calls start at 39441
    /note=SSC: 39441-39235 CP: yes SCS: both ST: SS BLAST-Start: [helix-turn-helix DNA binding domain protein [Mycobacterium phage Godines] ],,NCBI, q1:s1 100.0% 3.93318E-41 GAP: 30 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.851, -5.935104314925138, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding domain protein [Mycobacterium phage Godines] ],,YP_009616378,100.0,3.93318E-41 SIF-HHPRED: Putative DNA-binding protein; BldC, S. coelicolor, developmental switch, MerR-like, DNA BINDING PROTEIN-DNA complex; 3.09A {Streptomyces venezuelae},,,6AMA_A,86.7647,99.3 SIF-Syn: Faze9: helix-turn-helix DNA-binding protein 
Coffee: helix-turn-helix DNA-binding protein
Lephleur: helix-turn-helix DNA-binding protein
    /note=I called the gene at 39,441-39,235 because it is conserved in Glimmer, Genemark, starterator, and phamerator. It also has a very negative final score and is the LORF.
    /note=I called the function as helix-turn-helix DNA-binding protein because the five most similar phages all report the same function and it has very high frequency within the pham. THE SIF-BLAST and SIF-HHPRED also reported high alignment and probability with a helix-turn-helix DNA-binding protein.

CDS complement (39472 - 39861)
  /gene="45"
  /product="gp45"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Phantasmagoria_45"
    /note=Original Glimmer call @bp 39861 has strength 16.11; Genemark calls start at 39861
    /note=SSC: 39861-39472 CP: yes SCS: both ST: SS BLAST-Start: [gp44 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 1.01962E-88 GAP: 74 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.282, -2.1123791669543204, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[gp44 [Mycobacterium phage Rosebush] ],,NP_817805,100.0,1.01962E-88 SIF-HHPRED: a.35.1.6 (A:5-166) Hypothetical protein SO3848 {Shewanella oneidensis [TaxId: 70863]},,,d2ox6a1,86.0465,98.6 SIF-Syn: Coffee: helix-turn-helix DNA-binding protein
Lephleur: helix-turn-helix DNA-binding protein
Sabella: helix-turn-helix DNA-binding protein
    /note=39861-39472 are called as the start and stop sites because it is called by both the Glimmer and Genemark starts. This start was also favored in both the Starterator report and phamerator report (the top five closest phage have the same start and stop sites). It has a z-score over 2, a spacer between 9-13, and the smallest negative value. It also has the longest open reading frame. Function is helix-turn-helix DNA-binding protein due to Blast, HHPRED, and Phamerator evidence.

CDS complement (39936 - 40700)
  /gene="46"
  /product="gp46"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_46"
    /note=Original Glimmer call @bp 40700 has strength 16.35; Genemark calls start at 40700
    /note=SSC: 40700-39936 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_FAZE9_45 [Mycobacterium phage Faze9]],,NCBI, q1:s1 100.0% 0.0 GAP: 107 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.865, -3.0248543014571307, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_FAZE9_45 [Mycobacterium phage Faze9]],,AZF93687,100.0,0.0 SIF-HHPRED: DUF6011 ; Family of unknown function (DUF6011),,,PF19474.2,13.7795,99.0 SIF-Syn: 
    /note=40700-39936 are called as the start and stop sites because it is called by both the Glimmer and Genemark starts. This start was also favored in both the Starterator report and phamerator report (the top five closest phage have the same start and stop sites). It has a z-score over 2, a spacer between 9-13, and the smallest negative value. It also has the longest open reading frame. Function is a hypothetical protein due to HHPRED evidence, Blast evidence and Phamerator evidence.

CDS 40808 - 42307
  /gene="47"
  /product="gp47"
  /function="lysin A"
  /locus tag="Phantasmagoria_47"
    /note=Original Glimmer call @bp 40808 has strength 17.03; Genemark calls start at 40808
    /note=SSC: 40808-42307 CP: yes SCS: both ST: SS BLAST-Start: [lysin A [Mycobacterium phage Hedgerow] ],,NCBI, q1:s1 100.0% 0.0 GAP: 107 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.488, -5.768351819757361, no F: lysin A SIF-BLAST: ,,[lysin A [Mycobacterium phage Hedgerow] ],,AER47278,100.0,0.0 SIF-HHPRED: Peptidase_M15_4 ; D-alanyl-D-alanine carboxypeptidase,,,PF13539.9,15.2305,99.3 SIF-Syn: Faze9: lysin A
Coffee: lysin A
Lephleur: lysin A
    /note=40808-42307 are called as the start and stop sites because it is called by both the Glimmer and Genemark starts. This start was also favored in both the Starterator report and phamerator report (the top five closest phage have the same start and stop sites). Function is lysin A due to Blast evidence and Phamerator evidence.

CDS 42307 - 42840
  /gene="48"
  /product="gp48"
  /function="holin"
  /locus tag="Phantasmagoria_48"
    /note=Original Glimmer call @bp 42307 has strength 14.11; Genemark calls start at 42307
    /note=SSC: 42307-42840 CP: yes SCS: both ST: SS BLAST-Start: [holin [Mycobacterium phage Faze9]],,NCBI, q1:s1 100.0% 1.13129E-117 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.221, -4.337049294579155, no F: holin SIF-BLAST: ,,[holin [Mycobacterium phage Faze9]],,AZF93689,99.435,1.13129E-117 SIF-HHPRED: Phage_holin_7_1 ; Mycobacterial 2 TMS Phage Holin (M2 Hol) Family,,,PF16081.8,81.9209,100.0 SIF-Syn: Faze9: holin
Coffee: holin
Lephleur:holin
    /note=42,307-42840 are called as the start and stop sites because it is called by both the Glimmer and Genemark starts. This start was also favored in both the Starterator report and phamerator report (the top four closest phage have the same start and stop sites). It has a z-score over 2, a spacer between 9-13, and the smallest negative value. It also has a gap of -1. Function is holin due to HHPRED evidence, Blast evidence and Phamerator evidence.

CDS complement (42958 - 43482)
  /gene="49"
  /product="gp49"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_49"
    /note=Original Glimmer call @bp 43482 has strength 15.58; Genemark calls start at 43482
    /note=SSC: 43482-42958 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FPF50_gp50 [Mycobacterium virus TA17a] ],,NCBI, q1:s1 100.0% 5.54859E-119 GAP: 14 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.371, -2.58321678164666, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FPF50_gp50 [Mycobacterium virus TA17a] ],,YP_009667204,100.0,5.54859E-119 SIF-HHPRED: Enterobactin biosynthesis protein YbdZ; NONRIBOSOMAL PEPTIDE SYNTHETASE, NRPS, CONDENSATION, ADENYLATION, PCP, THIOESTERASE, MBTH-LIKE PROTEIN, PHOSPHOPANTETHEINE, BIOSYNTHETIC PROTEIN, LIGASE; HET: 75C; 3.0A {Escherichia coli (strain K12)} SCOP: d.100.2.0,,,5JA1_B,4.02299,34.6 SIF-Syn: 
    /note=43,482-42,958 are called as the start and stop sites because it is called by both the Glimmer and Genemark starts. This start was also favored in both the Starterator report and phamerator report (the top five closest phage have the same start and stop sites).  There is also coding potential in this region. Function is a hypothetical protein due to Blast evidence and Phamerator evidence.

CDS complement (43497 - 44864)
  /gene="50"
  /product="gp50"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_50"
    /note=Original Glimmer call @bp 44864 has strength 16.56; Genemark calls start at 44864
    /note=SSC: 44864-43497 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_FAZE9_49 [Mycobacterium phage Faze9]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.635, -5.531579584701049, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_FAZE9_49 [Mycobacterium phage Faze9]],,AZF93691,100.0,0.0 SIF-HHPRED: Mitochondrial genome maintenance exonuclease 1; human MGME1, DNA complex, DNA exonuclease, DNA BINDING PROTEIN; 2.702A {Homo sapiens},,,5ZYT_C,55.3846,99.8 SIF-Syn: Faze9: function unknown
Coffee: function unknown
Lephleur: function unknown
    /note=I called the gene at 44,864 - 43,497 because it is conserved in Glimmer and Genemark as well as starterator and phamerator(it is highly conserved in its pham). It also has high coding potential, a final score below -2, and the longest open reading frame.
    /note=NKF since this corresponds to most SIF data.

CDS complement (44861 - 46576)
  /gene="51"
  /product="gp51"
  /function="DNA helicase"
  /locus tag="Phantasmagoria_51"
    /note=Original Glimmer call @bp 46576 has strength 20.72; Genemark calls start at 46564
    /note=SSC: 46576-44861 CP: yes SCS: both-gl ST: SS BLAST-Start: [gp48 [Mycobacterium phage Qyrzula] ],,NCBI, q1:s1 100.0% 0.0 GAP: 70 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.282, -2.1924212546750814, yes F: DNA helicase SIF-BLAST: ,,[gp48 [Mycobacterium phage Qyrzula] ],,YP_655728,100.0,0.0 SIF-HHPRED: TFIIH basal transcription factor complex helicase XPB subunit,XPB,TFIIH basal transcription factor complex helicase XPB subunit; transcription initiation, DNA repair, multiprotein complex, kinase, helicase, TRANSCRIPTION; 4.4A {Homo sapiens},,,5OF4_A,60.9457,100.0 SIF-Syn: Faze9: DNA Helicase
Coffee: DNA Helicase
Lephleur: DNA Helicase
    /note=I called the gene at 46,576 - 44,861 because it is conserved in Glimmer as well as starterator; and four of the most similar phages have a gene of the same length which suggests they have the same start. It also has high coding potential, a z-score over 2 and final score below -2.
    /note=I called the function as DNA Helicase because it has a high probability and alignment through SIF-HHPRED and SIF-BLAST; and it is called in all five most similar phages.

CDS complement (46647 - 46808)
  /gene="52"
  /product="gp52"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_52"
    /note=Original Glimmer call @bp 46808 has strength 3.41
    /note=SSC: 46808-46647 CP: yes SCS: glimmer ST: SS BLAST-Start: [gp51 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 3.23212E-29 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.971, -5.884306463368766, no F: hypothetical protein SIF-BLAST: ,,[gp51 [Mycobacterium phage Rosebush] ],,NP_817812,100.0,3.23212E-29 SIF-HHPRED: DUF740 ; Protein of unknown function (DUF740),,,PF05340.15,50.9434,70.1 SIF-Syn: 
    /note=I called the gene at 46,808 - 46,647 because it is conserved in Glimmer, phamerator, and starterator; and all of the five most similar phages have a gene of the same length which suggests they have the same start. It also is very highly conserved in its pham, has high coding potential, a final score below -2, and is the LORF.
    /note=I called function unknown for this gene because the five most similar phages all reported no known function for this gene. SIF-HHPRED also reported the highest alignment and probability with a protein of unknown function.

CDS complement (46810 - 47145)
  /gene="53"
  /product="gp53"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_53"
    /note=Original Glimmer call @bp 47145 has strength 4.52; Genemark calls start at 47145
    /note=SSC: 47145-46810 CP: yes SCS: both ST: SS BLAST-Start: [gp52 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 3.67483E-73 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.951, -4.905314844093283, no F: hypothetical protein SIF-BLAST: ,,[gp52 [Mycobacterium phage Rosebush] ],,NP_817813,100.0,3.67483E-73 SIF-HHPRED: Tetronasin; Complex, cyclase, UNKNOWN FUNCTION; HET: KUJ; 1.7A {Streptomyces longisporoflavus},,,6NNW_B,42.3423,89.7 SIF-Syn: 
    /note=I called the gene at 47,145 - 46,810 because it is conserved in Glimmer, Genemark, phamerator, and starterator; and all of the five most similar phages have a gene of the same length which suggests they have the same start. It also is highly conserved in its pham, has a final score under -2, and has high coding potential.
    /note=I called function unknown for this gene because the five most similar phages all reported no known function for this gene. SIF-HHPRED also reported the highest alignment and probability with a protein of unknown function.

CDS complement (47145 - 47636)
  /gene="54"
  /product="gp54"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_54"
    /note=Original Glimmer call @bp 47636 has strength 15.36; Genemark calls start at 47636
    /note=SSC: 47636-47145 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_FAZE9_53 [Mycobacterium phage Faze9] ],,NCBI, q1:s1 100.0% 4.3744E-116 GAP: 64 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.36, -2.0162541296952132, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_FAZE9_53 [Mycobacterium phage Faze9] ],,AZF93695,100.0,4.3744E-116 SIF-HHPRED: Surface protein adhesin; Streptococcus mutans, AgI/II, spaP (variable domain), CELL ADHESION; HET: SO4; 1.6A {Streptococcus mutans},,,6TZL_C,24.5399,71.4 SIF-Syn: 
    /note=I called the gene at 47,636 - 47,145 because it is conserved in Glimmer, Genemark, phamerator, and starterator; and all of the five most similar phages have a gene of the same length which suggests they have the same start. It also has high coding potential, a z-score over 2, final score below -2, and is the LORF.
    /note=I called function unknown for this gene because the five most similar phages all reported no known function for this gene. SIF-BLAST also reported high alignment with hypothetical proteins(unknown function).

CDS complement (47701 - 50457)
  /gene="55"
  /product="gp55"
  /function="DNA primase/helicase"
  /locus tag="Phantasmagoria_55"
    /note=Original Glimmer call @bp 50409 has strength 19.15; Genemark calls start at 50409
    /note=SSC: 50457-47701 CP: yes SCS: both-cs ST: NI BLAST-Start: [DNA primase/helicase [Mycobacterium phage Ares] ],,NCBI, q1:s1 100.0% 0.0 GAP: 44 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.825, -5.432024807810012, no F: DNA primase/helicase SIF-BLAST: ,,[DNA primase/helicase [Mycobacterium phage Ares] ],,AER48677,99.7821,0.0 SIF-HHPRED: c.37.1.11 (A:) Hexameric replicative helicase repA {Escherichia coli [TaxId: 562]},,,d1nlfa_,25.1634,99.8 SIF-Syn: Ares, sabella
    /note=Moved start to 50457 (better fit with like-phages in starterator, better gap, better spacer, better  final score, LORF). SIF sources all suggest DNA primase/helicase.

CDS complement (50502 - 50666)
  /gene="56"
  /product="gp56"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_56"
    /note=Original Glimmer call @bp 50666 has strength 9.37; Genemark calls start at 50666
    /note=SSC: 50666-50502 CP: yes SCS: both ST: SS BLAST-Start: [gp55 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 6.61909E-31 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.676, -3.4283035164720754, yes F: hypothetical protein SIF-BLAST: ,,[gp55 [Mycobacterium phage Rosebush] ],,NP_817816,100.0,6.61909E-31 SIF-HHPRED: TREH_N ; Trehalase-like, N-terminal,,,PF19291.2,31.4815,90.4 SIF-Syn: 
    /note=I called the gene at 50,666 - 50,502 because it is conserved in Glimmer, Genemark, phamerator, and starterator. It also has high coding potential, is very highly conserved in its pham, and has a z-score over 2 and final score below -2
    /note=I called function unknown for this gene because the five most similar phages all reported function unknown for this gene.

CDS complement (50669 - 52498)
  /gene="57"
  /product="gp57"
  /function="DNA polymerase I"
  /locus tag="Phantasmagoria_57"
    /note=Original Glimmer call @bp 52498 has strength 18.95; Genemark calls start at 52498
    /note=SSC: 52498-50669 CP: yes SCS: both ST: SS BLAST-Start: [DNA polymerase I [Mycobacterium phage Faze9]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.922, -5.410945357522411, no F: DNA polymerase I SIF-BLAST: ,,[DNA polymerase I [Mycobacterium phage Faze9]],,AZF93698,100.0,0.0 SIF-HHPRED: Prex DNA polymerase; DNA polymerase, TRANSFERASE; HET: SO4; 2.9A {Plasmodium falciparum},,,5DKT_A,97.2085,100.0 SIF-Syn: Faze9 - DNA polymerase I
Coffee - DNA polymerase I
Lephleur - DNA polymerase I
    /note=52,498-50,669 because agreement between Starterator, Glimmer, and GeneMark; -4 gap suggesting transcriptional re-initiation, LORF, favorable final score, and relatively favorable Z-score and spacer.

CDS complement (52495 - 52884)
  /gene="58"
  /product="gp58"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_58"
    /note=Original Glimmer call @bp 52884 has strength 16.42; Genemark calls start at 52884
    /note=SSC: 52884-52495 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_FAZE9_57 [Mycobacterium phage Faze9]],,NCBI, q1:s1 100.0% 9.36358E-88 GAP: -13 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.12, -2.523003374675015, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_FAZE9_57 [Mycobacterium phage Faze9]],,AZF93699,100.0,9.36358E-88 SIF-HHPRED: zinc_ribbon_4 ; zinc-ribbon domain,,,PF13717.9,19.3798,85.7 SIF-Syn: 
    /note=52,884-52,495 because agreement between Starterator, Glimmer, and GeneMark; -4 gap suggesting transcriptional re-initiation, LORF, favorable Z-score and spacer, and relatively favorable final score. SIF data was inconsistent, so NKF.

CDS complement (52872 - 53363)
  /gene="59"
  /product="gp59"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_59"
    /note=Original Glimmer call @bp 53363 has strength 17.26; Genemark calls start at 53363
    /note=SSC: 53363-52872 CP: yes SCS: both ST: SS BLAST-Start: [gp54 [Mycobacterium phage Qyrzula] ],,NCBI, q1:s1 100.0% 1.36069E-113 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.467, -3.8540125308361968, no F: hypothetical protein SIF-BLAST: ,,[gp54 [Mycobacterium phage Qyrzula] ],,YP_655734,100.0,1.36069E-113 SIF-HHPRED: DUF2161 ; Putative PD-(D/E)XK phosphodiesterase (DUF2161),,,PF09929.12,19.0184,25.1 SIF-Syn: 
    /note=53,363-52,872 because agreement between Starterator, Glimmer, and GeneMark; -4 gap suggesting transcriptional re-initiation, and favorable Z-score and spacer.

CDS complement (53360 - 53830)
  /gene="60"
  /product="gp60"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_60"
    /note=Original Glimmer call @bp 53830 has strength 11.02; Genemark calls start at 53830
    /note=SSC: 53830-53360 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_FAZE9_59 [Mycobacterium phage Faze9]],,NCBI, q1:s1 100.0% 2.19613E-108 GAP: 267 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.221, -4.354778061539587, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_FAZE9_59 [Mycobacterium phage Faze9]],,AZF93701,100.0,2.19613E-108 SIF-HHPRED: ESPFU; WASP, EspFU, GBD, autoinhibition, Cytoplasm, Cytoskeleton, Disease mutation, Phosphoprotein, SIGNALING PROTEIN; NMR {Homo sapiens},,,2K42_B,10.8974,60.6 SIF-Syn: 
    /note=I called 53830 as the start site since it was suggested by both Glimmer and Genemark, had a decent z-score, and was conserved in the pham. I called the function as a hypothetical protein since all compared BLASTed genes were hypothetical proteins and all HHPRED compared genes were a type of protein.

CDS 54098 - 54274
  /gene="61"
  /product="gp61"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_61"
    /note=Genemark calls start at 54116
    /note=SSC: 54098-54274 CP: yes SCS: genemark-cs ST: NA BLAST-Start:  GAP: 267 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.108, -4.505076120213986, no F: hypothetical protein SIF-BLAST:  SIF-HHPRED: b.1.1.1 (C:) automated matches {Human herpesvirus 2 [TaxId: 10315]},,,d3w9ec_,56.8966,28.4 SIF-Syn: 
    /note=Move TSS to 54098 (better spacer, zscore, overall score, fills CP). NKF as SIF sources are inconsistent. Possibly DNA methylase

CDS 54761 - 55462
  /gene="62"
  /product="gp62"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_62"
    /note=Original Glimmer call @bp 54761 has strength 16.06; Genemark calls start at 54728
    /note=SSC: 54761-55462 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein FPF50_gp65 [Mycobacterium virus TA17a] ],,NCBI, q1:s12 100.0% 1.63291E-167 GAP: 486 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.042, -3.429629759700652, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FPF50_gp65 [Mycobacterium virus TA17a] ],,YP_009667219,95.4918,1.63291E-167 SIF-HHPRED: DUF2710 ; Protein of unknown function (DUF2710),,,PF10921.11,33.9056,64.3 SIF-Syn: 
    /note=54,761-55,462 because agreement with Glimmer and Starterator, most favorable Z-score, and most favorable final score.

CDS 55526 - 55732
  /gene="63"
  /product="gp63"
  /function="ribbon-helix-helix DNA binding domain"
  /locus tag="Phantasmagoria_63"
    /note=Original Glimmer call @bp 55526 has strength 1.25; Genemark calls start at 55553
    /note=SSC: 55526-55732 CP: yes SCS: both-gl ST: NI BLAST-Start: [ribbon-helix-helix DNA binding domain protein [Mycobacterium phage Faze9] ],,NCBI, q1:s1 100.0% 2.35705E-40 GAP: 63 bp gap LO: no RBS: Kibler 6, Karlin Medium, 0.776, -7.298011797352949, no F: ribbon-helix-helix DNA binding domain SIF-BLAST: ,,[ribbon-helix-helix DNA binding domain protein [Mycobacterium phage Faze9] ],,AZF93705,100.0,2.35705E-40 SIF-HHPRED: a.43.1.4 (A:) Omega transcriptional repressor {Streptococcus pyogenes [TaxId: 1314]},,,d1irqa_,61.7647,98.8 SIF-Syn: ribbon-helix-helix DNA binding domain protein, Faze9_63, 55651-55857
ribbon-helix-helix DNA binding domain protein, Coffee_64, 55626-55832
ribbon-helix-helix DNA binding domain protein, Lephleur_64, 55428-55688
    /note=I called 55526 as the start site since it was suggested by Glimmer, had a strong z-score, and was conserved in the pham. I called the function as a ribbon helix-helix DNA binding domain protein since all compared genes were ribbon helix-helix DNA binding domain proteins.

CDS 55764 - 56105
  /gene="64"
  /product="gp64"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_64"
    /note=Original Glimmer call @bp 55764 has strength 16.59; Genemark calls start at 55785
    /note=SSC: 55764-56105 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein SEA_GLASS_66 [Mycobacterium phage Glass] ],,NCBI, q1:s1 100.0% 2.68643E-73 GAP: 31 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.984, -4.7584729022291805, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_GLASS_66 [Mycobacterium phage Glass] ],,AMB17380,100.0,2.68643E-73 SIF-HHPRED: Bbox1_TRIM66; B-box-type 1 zinc finger found in tripartite motif-containing protein 66 (TRIM66) and similar proteins.,,,cd19811,14.1593,47.8 SIF-Syn: 
    /note=I called 55764 as the start site since it was suggested by Glimmer, had a strong z-score, and was conserved in the pham. I called the function as a hypothetical protein since all compared BLASTed genes were hypothetical proteins.

CDS 56102 - 56755
  /gene="65"
  /product="gp65"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Phantasmagoria_65"
    /note=Original Glimmer call @bp 56108 has strength 14.92; Genemark calls start at 56102
    /note=SSC: 56102-56755 CP: yes SCS: both-gm ST: SS BLAST-Start: [gp65 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 4.73218E-152 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.232, -5.159669614130143, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[gp65 [Mycobacterium phage Rosebush] ],,NP_817826,99.5392,4.73218E-152 SIF-HHPRED: Small Terminase subunit; viral genome packaging motor, small terminase, Pseudomonas phage PaP3, DNA BINDING PROTEIN, VIRAL PROTEIN; 3.95A {Pseudomonas phage NV1},,,7JOQ_i,49.7696,98.2 SIF-Syn: helix-turn-helix DNA binding domain protein, Faze9_65, 56233-56880
DNA binding protein, Coffee_66, 56202-56855
helix-turn-helix DNA-binding protein, Lephleur_66, 56058-56708
    /note=Move TSS to 56102 (-4 gap, better zscore, better final score, fits with cluster in starterator better, longer ORF). I called the function as a helix-turn-helix DNA-binding protein since all compared BLASTed genes were hypothetical proteins and all HHPRED compared genes support this conclusion.

CDS 56757 - 57290
  /gene="66"
  /product="gp66"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_66"
    /note=Original Glimmer call @bp 56766 has strength 11.17; Genemark calls start at 56757
    /note=SSC: 56757-57290 CP: yes SCS: both-gm ST: SS BLAST-Start: [hypothetical protein SEA_GLASS_68 [Mycobacterium phage Glass]],,NCBI, q1:s68 100.0% 4.47177E-121 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.669, -6.307317900605185, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_GLASS_68 [Mycobacterium phage Glass]],,AMB17382,72.1311,4.47177E-121 SIF-HHPRED: UPF0158 ; Uncharacterised protein family (UPF0158),,,PF03682.16,12.4294,31.0 SIF-Syn: 
    /note=Move TSS to 56757 (better gap, fills CP/length, fits cluster in starterator better). SIF sources inconsistent or indicate NKF.

CDS 57331 - 57714
  /gene="67"
  /product="gp67"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_67"
    /note=Original Glimmer call @bp 57409 has strength 12.09; Genemark calls start at 57409
    /note=SSC: 57331-57714 CP: yes SCS: both-cs ST: SS BLAST-Start: [hypothetical protein PBI_LIZLEMON_68 [Mycobacterium phage LizLemon] ],,NCBI, q1:s1 100.0% 1.83721E-86 GAP: 40 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.294, -4.2661880578013545, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_LIZLEMON_68 [Mycobacterium phage LizLemon] ],,AIK68842,100.0,1.83721E-86 SIF-HHPRED: fragment of Vesicle-associated membrane protein 2; Clostridium botulinum, BoNT F, VAMP, inhibitor, complex structure, Acetylation, Cell junction, HYDROLASE, TOXIN-PROTEIN TRANSPORT COMPLEX; HET: DCY; 2.1A {Clostridium botulinum},,,3FIE_D,20.4724,51.8 SIF-Syn: 
    /note=Moved start to 57331 (better starterator match, length, spacer, gap, zscore, final score, LORF) (already changed)

CDS 57711 - 58424
  /gene="68"
  /product="gp68"
  /function="DNA binding protein"
  /locus tag="Phantasmagoria_68"
    /note=Original Glimmer call @bp 57711 has strength 10.63; Genemark calls start at 57711
    /note=SSC: 57711-58424 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_FAZE9_68 [Mycobacterium phage Faze9]],,NCBI, q1:s1 100.0% 7.69767E-169 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.003, -5.627185972854188, no F: DNA binding protein SIF-BLAST: ,,[hypothetical protein SEA_FAZE9_68 [Mycobacterium phage Faze9]],,AZF93710,100.0,7.69767E-169 SIF-HHPRED: ECF RNA polymerase sigma factor SigL; Mycobacterium tuberculosis, RNA polymerase, ECF sigma factor, TRANSFERASE, TRANSFERASE-DNA-RNA complex; 3.3A {Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)},,,6DVC_F,28.27,98.4 SIF-Syn: DNA binding protein, Coffee_69, 57812-58525
DNA binding protein, Lephleur_69, 57664-58377
    /note=I called 57711 as the start site since it was suggested by both Glimmer and Genemark, has a decent z-score, and was conserved in the pham. I called the function as a DNA binding protein since the PhagesDB function call for this subcluster was a DNA binding protein and many of the compared BLASTed genes were helix-turn-helix DNA binding proteins.

CDS complement (58655 - 58957)
  /gene="69"
  /product="gp69"
  /function="HNH endonuclease"
  /locus tag="Phantasmagoria_69"
    /note=Original Glimmer call @bp 58957 has strength 7.61; Genemark calls start at 58957
    /note=SSC: 58957-58655 CP: yes SCS: both ST: SS BLAST-Start: [gp69 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 7.27568E-66 GAP: -14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.808, -5.767499571029442, no F: HNH endonuclease SIF-BLAST: ,,[gp69 [Mycobacterium phage Rosebush] ],,NP_817830,100.0,7.27568E-66 SIF-HHPRED: d.4.1.8 (A:513-673) CRISPR-associated endonuclease Cas9/Csn1, HNH domain {Actinomyces naeslundii [TaxId: 1115803]},,,d4ogca2,81.0,98.5 SIF-Syn: Lephleur - HNH endonuclease
Sabella - HNH endonuclease
Eaglehorse - HNH endonuclease
    /note=58,957-58,655 because agreement between Glimmer and GeneMark; and LORF.

CDS complement (58944 - 59048)
  /gene="70"
  /product="gp70"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_70"
    /note=Genemark calls start at 59048
    /note=SSC: 59048-58944 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein FDI79_gp72 [Mycobacterium phage Godines] ],,NCBI, q1:s1 100.0% 1.51568E-14 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.848, -3.077027835973012, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDI79_gp72 [Mycobacterium phage Godines] ],,YP_009616406,100.0,1.51568E-14 SIF-HHPRED: LapA_dom ; Lipopolysaccharide assembly protein A domain,,,PF06305.14,52.9412,92.8 SIF-Syn: 
    /note=59,048-58,944 because agreement between Starterator and GeneMark; -4 gap suggesting transcriptional re-initiation, most favorable final score, most favorable Z-score, and most favorable spacer.

CDS complement (59045 - 59269)
  /gene="71"
  /product="gp71"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_71"
    /note=Original Glimmer call @bp 59269 has strength 13.19; Genemark calls start at 59269
    /note=SSC: 59269-59045 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SABELLA_72 [Mycobacterium phage Sabella] ],,NCBI, q1:s1 100.0% 1.87626E-46 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.962, -2.8454123590742793, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SABELLA_72 [Mycobacterium phage Sabella] ],,AXH69077,100.0,1.87626E-46 SIF-HHPRED: d.50.3.2 (A:) Hypothetical protein TTHA1913 {Thermus thermophilus [TaxId: 274]},,,d1whza_,90.5405,99.6 SIF-Syn: 
    /note=59,269-59,045 because agreement between Starterator, Glimmer, and GeneMark; -4 gap suggesting transcriptional re-initiation, most favorable final score, most favorable Z-score, and most favorable spacer. SIF sources indicate NKF, potentially HicA toxin.

CDS complement (59266 - 59775)
  /gene="72"
  /product="gp72"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_72"
    /note=Original Glimmer call @bp 59775 has strength 9.11; Genemark calls start at 59775
    /note=SSC: 59775-59266 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_FAZE9_72 [Mycobacterium phage Faze9]],,NCBI, q1:s1 100.0% 4.63097E-118 GAP: -7 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.576, -5.650089995820535, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_FAZE9_72 [Mycobacterium phage Faze9]],,AZF93714,100.0,4.63097E-118 SIF-HHPRED: zinc_ribbon_4 ; zinc-ribbon domain,,,PF13717.9,17.1598,91.4 SIF-Syn: 
    /note=59,775-59,266 because agreement between Starterator, Glimmer, and GeneMark; -7 gap suggesting transcriptional re-initiation, relatively favorable final score, Z-score, and spacer. SIF sources indicate NKF

CDS complement (59769 - 60047)
  /gene="73"
  /product="gp73"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_73"
    /note=Original Glimmer call @bp 60047 has strength 8.71; Genemark calls start at 60047
    /note=SSC: 60047-59769 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_FAZE9_73 [Mycobacterium phage Faze9]],,NCBI, q1:s1 100.0% 1.18367E-60 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.511, -5.72088676244897, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_FAZE9_73 [Mycobacterium phage Faze9]],,AZF93715,98.913,1.18367E-60 SIF-HHPRED: Stomagen ; Stomagen,,,PF16851.8,18.4783,75.7 SIF-Syn: 
    /note=60,047-59,769 because agreement between Starterator, Glimmer, and GeneMark; -4 gap suggesting transcriptional re-initiation, and favorable spacer.

CDS complement (60044 - 60355)
  /gene="74"
  /product="gp74"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_74"
    /note=Original Glimmer call @bp 60355 has strength 14.51; Genemark calls start at 60355
    /note=SSC: 60355-60044 CP: yes SCS: both ST: SS BLAST-Start: [gp67 [Mycobacterium phage Qyrzula] ],,NCBI, q1:s1 100.0% 6.75086E-69 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.553, -4.249702485847477, no F: hypothetical protein SIF-BLAST: ,,[gp67 [Mycobacterium phage Qyrzula] ],,YP_655747,100.0,6.75086E-69 SIF-HHPRED: SIGNAL RECOGNITION PARTICLE PROTEIN; PROTEIN-RNA COMPLEX, DOUBLE HELIX, TETRALOOP, INTERNAL LOOP, SIGNAL RECOGNITION PARTICLE, SRP, RIBONUCLEOPROTEIN, SIGNALING PROTEIN-RNA COMPLEX; HET: CCC; 1.52A {Escherichia coli} SCOP: a.36.1.1,,,1HQ1_A,52.4272,46.7 SIF-Syn: 
    /note=60,355-60,044 because agreement between Starterator, Glimmer, and GeneMark; -4 gap suggesting transcriptional re-initiation, relatively favorable final score, and favorable Z-score.

CDS complement (60352 - 60663)
  /gene="75"
  /product="gp75"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_75"
    /note=Original Glimmer call @bp 60663 has strength 17.34; Genemark calls start at 60663
    /note=SSC: 60663-60352 CP: yes SCS: both ST: SS BLAST-Start: [gp74 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 1.45346E-65 GAP: 62 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.261, -2.5074698667202133, yes F: hypothetical protein SIF-BLAST: ,,[gp74 [Mycobacterium phage Rosebush] ],,NP_817835,100.0,1.45346E-65 SIF-HHPRED: Elongation factor P; aminoacyl-tRNA synthetase paralog, Translation, tRNA, Lysyl-tRNA synthetase, Elongation Factor, Structural Genomics, NPPSFA, National Project on Protein; HET: KAA; 2.5A {Escherichia coli},,,3A5Z_H,98.0583,97.1 SIF-Syn: 
    /note=60,663-60,352 because agreement between Starterator, Glimmer, and GeneMark; LORF, most favorable final score, most favorable Z-score, and favorable spacer.

CDS complement (60726 - 60971)
  /gene="76"
  /product="gp76"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_76"
    /note=Original Glimmer call @bp 60971 has strength 21.11; Genemark calls start at 60971
    /note=SSC: 60971-60726 CP: yes SCS: both ST: SS BLAST-Start: [gp75 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 2.67664E-49 GAP: 97 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.261, -2.6835611257758942, yes F: hypothetical protein SIF-BLAST: ,,[gp75 [Mycobacterium phage Rosebush] ],,NP_817836,100.0,2.67664E-49 SIF-HHPRED: lipocalin_NP2; nitrophorin 2. Nitrophorins (NPs) represent a group of nitric oxide (NO)-carrying heme proteins found in the saliva of Rhodnius prolixus.,,,cd19453,27.1605,71.5 SIF-Syn: 
    /note=60,971-60,726 because agreement between Starterator, Glimmer, and GeneMark; LORF, most favorable final score, and most favorable Z-score.

CDS complement (61069 - 61386)
  /gene="77"
  /product="gp77"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_77"
    /note=Original Glimmer call @bp 61335 has strength 20.13; Genemark calls start at 61377
    /note=SSC: 61386-61069 CP: yes SCS: both-cs ST: SS BLAST-Start: [gp76 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 9.4779E-70 GAP: 47 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.031, -4.723615450753023, no F: hypothetical protein SIF-BLAST: ,,[gp76 [Mycobacterium phage Rosebush] ],,NP_817837,99.0476,9.4779E-70 SIF-HHPRED: c.47.1.10 (A:1-170) automated matches {Ancylostoma ceylanicum [TaxId: 53326]},,,d4fh8a1,38.0952,90.5 SIF-Syn: 
    /note=Moved start to 61386 (more coverage, good spacer, less gap). SIF sources indicate NFK

CDS complement (61434 - 61859)
  /gene="78"
  /product="gp78"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_78"
    /note=Original Glimmer call @bp 61859 has strength 12.89; Genemark calls start at 61859
    /note=SSC: 61859-61434 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein ARBITER_76 [Mycobacterium phage Arbiter] ],,NCBI, q1:s1 100.0% 6.36058E-98 GAP: -11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.757, -3.243963255891538, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein ARBITER_76 [Mycobacterium phage Arbiter] ],,AEN79565,99.2908,6.36058E-98 SIF-HHPRED: CpG_bind_C ; CpG binding protein C-terminal domain,,,PF12269.11,73.7589,88.0 SIF-Syn: 
    /note=61,859-61,434 because agreement between Starterator, Glimmer, and GeneMark; LORF, most favorable final score, most favorable Z-score, and favorable spacer.

CDS complement (61849 - 62010)
  /gene="79"
  /product="gp79"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_79"
    /note=Original Glimmer call @bp 62010 has strength 0.59
    /note=SSC: 62010-61849 CP: yes SCS: glimmer ST: SS BLAST-Start: [gp78 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 3.68768E-29 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.951, -4.887586077132851, no F: hypothetical protein SIF-BLAST: ,,[gp78 [Mycobacterium phage Rosebush] ],,NP_817839,100.0,3.68768E-29 SIF-HHPRED: DUF6085 ; Family of unknown function (DUF6085),,,PF19563.2,83.0189,82.1 SIF-Syn: 
    /note=We called 62,010 the start site because it is conserved throughout the gene family.
    /note=We call it an  unknown function because no source can agree if this gene codes for a protein or if it does encode for a protein if there is no determinate function.

CDS complement (62012 - 62224)
  /gene="80"
  /product="gp80"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_80"
    /note=Original Glimmer call @bp 62224 has strength 18.26; Genemark calls start at 62224
    /note=SSC: 62224-62012 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_TRES_81 [Mycobacterium phage Tres] ],,NCBI, q1:s1 100.0% 1.06439E-43 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.585, -5.649978513542845, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_TRES_81 [Mycobacterium phage Tres] ],,ALF01366,100.0,1.06439E-43 SIF-HHPRED: Bot.2110.4; mini-protein binder, inhibitor, TOXIN; 1.95A {Clostridium botulinum},,,5VMR_D,28.5714,92.7 SIF-Syn: 
    /note=We called the start site 62,224 because it is conserved in the pfam and it is in the LORF. We called a hypothetical function because the HHPRED scores in similar phages are low and do not report similar functions if a function is listed.

CDS complement (62221 - 62715)
  /gene="81"
  /product="gp81"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_81"
    /note=Original Glimmer call @bp 62715 has strength 16.54; Genemark calls start at 62715
    /note=SSC: 62715-62221 CP: yes SCS: both ST: SS BLAST-Start: [gp80 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 3.89866E-113 GAP: 66 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.12, -2.5052746077145835, yes F: hypothetical protein SIF-BLAST: ,,[gp80 [Mycobacterium phage Rosebush] ],,NP_817841,100.0,3.89866E-113 SIF-HHPRED: Ish1 ; Putative nuclear envelope organisation protein,,,PF10281.12,21.3415,73.5 SIF-Syn: 
    /note=We called the start site 62,715 because it is conserved in the pfam and it is in the LORF. We called a hypothetical function and an unknown function  because the HHPRED scores in similar phages are low and do not report similar functions if a function is listed.

CDS complement (62782 - 63003)
  /gene="82"
  /product="gp82"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_82"
    /note=Original Glimmer call @bp 63003 has strength 15.61; Genemark calls start at 63003
    /note=SSC: 63003-62782 CP: yes SCS: both ST: SS BLAST-Start: [gp74 [Mycobacterium phage Qyrzula] ],,NCBI, q1:s1 100.0% 1.64488E-42 GAP: 109 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.407, -5.932167120701517, yes F: hypothetical protein SIF-BLAST: ,,[gp74 [Mycobacterium phage Qyrzula] ],,YP_655754,100.0,1.64488E-42 SIF-HHPRED: Serine/threonine-protein kinase B-raf; kinase, inhibitor, cancer, melanoma, TRANSFERASE-TRANSFERASE INHIBITOR complex, ONCOPROTEIN; HET: SO4, 0LI; 2.11A {Homo sapiens},,,6P3D_A,35.6164,21.3 SIF-Syn: 
    /note=We called the start site 63,003 because it is conserved in the pfam and it is in the LORF. We called a hypothetical function and unknown function  because the HHPRED scores in similar phages are low and do not report similar functions if a function is listed.

CDS complement (63113 - 63643)
  /gene="83"
  /product="gp83"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_83"
    /note=Original Glimmer call @bp 63643 has strength 14.09; Genemark calls start at 63643
    /note=SSC: 63643-63113 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_KHETH_84 [Mycobacterium phage Kheth]],,NCBI, q1:s27 100.0% 1.78504E-125 GAP: 76 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.282, -2.639579286017301, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_KHETH_84 [Mycobacterium phage Kheth]],,AVO21931,87.1287,1.78504E-125 SIF-HHPRED: DUF1192 ; Protein of unknown function (DUF1192),,,PF06698.14,19.8864,76.0 SIF-Syn: 
    /note=I called 63,643 the start site because it is in LORF. I call a hypothetical protein and unknown function because there`s no data available for the ultimate function.

CDS complement (63720 - 64790)
  /gene="84"
  /product="gp84"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_84"
    /note=Original Glimmer call @bp 64790 has strength 20.24; Genemark calls start at 64790
    /note=SSC: 64790-63720 CP: yes SCS: both ST: SS BLAST-Start: [gp83 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 0.0 GAP: 73 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.12, -2.442961286954254, yes F: hypothetical protein SIF-BLAST: ,,[gp83 [Mycobacterium phage Rosebush] ],,NP_817844,100.0,0.0 SIF-HHPRED: DUF932 ; Domain of unknown function (DUF932),,,PF06067.14,60.9551,99.9 SIF-Syn: 
    /note=I called 64,790 the start site because it is conserved in the Pfam genome.
    /note=I call an unknown function because HHPRED calls for a lot of that plus a hypothetical protein function in BLAST.

CDS complement (64864 - 65121)
  /gene="85"
  /product="gp85"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_85"
    /note=Original Glimmer call @bp 65121 has strength 18.68; Genemark calls start at 65121
    /note=SSC: 65121-64864 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BANANAFISH_87 [Mycobacterium phage Bananafish]],,NCBI, q1:s16 100.0% 5.19542E-50 GAP: 73 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.021, -2.7863799983944713, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_BANANAFISH_87 [Mycobacterium phage Bananafish]],,QCG77149,84.0,5.19542E-50 SIF-HHPRED: CELL DIVISION PROTEIN SEPF; CELL CYCLE; 2.0A {BACILLUS SUBTILIS},,,3ZIH_B,29.4118,34.5 SIF-Syn: 
    /note=I called this start site bc its in the longest reading frame but also coding is really teeny tiny.
    /note=I call hypothetical protein function as this is what SIF indicates.

CDS complement (65195 - 65341)
  /gene="86"
  /product="gp86"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_86"
    /note=Original Glimmer call @bp 65341 has strength 10.12; Genemark calls start at 65341
    /note=SSC: 65341-65195 CP: yes SCS: both ST: SS BLAST-Start: [gp85 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 7.4006E-21 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.971, -4.845388397338397, no F: hypothetical protein SIF-BLAST: ,,[gp85 [Mycobacterium phage Rosebush] ],,NP_817846,100.0,7.4006E-21 SIF-HHPRED: DUF6768 ; Family of unknown function (DUF6768),,,PF20556.1,89.5833,79.5 SIF-Syn: 
    /note=I called the start site 65,341  because it is conserved in the Pfam genome.
    /note=I call this genome to code for a hypothetical protein with an unknown function due to the low HHPRED scores and no similar proteins found in the similar phages.

CDS complement (65338 - 65475)
  /gene="87"
  /product="gp87"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_87"
    /note=Original Glimmer call @bp 65475 has strength 9.05; Genemark calls start at 65475
    /note=SSC: 65475-65338 CP: yes SCS: both ST: SS BLAST-Start: [gp86 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 9.92921E-24 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.042, -2.66371296573402, yes F: hypothetical protein SIF-BLAST: ,,[gp86 [Mycobacterium phage Rosebush] ],,NP_817847,100.0,9.92921E-24 SIF-HHPRED: DUF6776 ; Family of unknown function (DUF6776),,,PF20567.1,68.8889,54.2 SIF-Syn: 
    /note=I called the gene at 65,475 - 65,338 because it is conserved in Glimmer, Genemark, starterator, and phamerator.It is also a very highly conserved start in its pham. The five most similar phages all had genes of the same length which suggests the same start site. It also has a z-score over 2, final score below -2, and high coding potential.
    /note=I called function unknown for this gene because all five of the most similar phages reported function unknown, also the SIF-HHPRED reported the highest alignment and probability for Family of unknown function.

CDS complement (65472 - 65849)
  /gene="88"
  /product="gp88"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_88"
    /note=Original Glimmer call @bp 65849 has strength 13.13; Genemark calls start at 65849
    /note=SSC: 65849-65472 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein ARBITER_86 [Mycobacterium phage Arbiter]],,NCBI, q1:s1 100.0% 2.88438E-84 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.12, -2.583959800616441, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein ARBITER_86 [Mycobacterium phage Arbiter]],,AEN79555,99.2,2.88438E-84 SIF-HHPRED: DUF2497 ; Protein of unknown function (DUF2497),,,PF10691.12,20.0,77.5 SIF-Syn: 
    /note=Despite the few number of calls in the pham, the start and stop sites 65,849-65,472 are called for this gene. The most called start site (start 8) in the pham, does not exist for phantasmagoria, and thus start 7 must be called. This start site also has a z-score over two, a spacer between 9-13 and the smallest negative value. Function is a hypothetical protein due to BLAST, HHPRED, and Phamerator evidence.

CDS complement (65852 - 66043)
  /gene="89"
  /product="gp89"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_89"
    /note=Original Glimmer call @bp 66043 has strength 14.37; Genemark calls start at 66043
    /note=SSC: 66043-65852 CP: yes SCS: both ST: SS BLAST-Start: [gp89 [Mycobacterium phage Rosebush] ],,NCBI, q1:s1 100.0% 5.03443E-38 GAP: 95 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.962, -2.7653702713535186, yes F: hypothetical protein SIF-BLAST: ,,[gp89 [Mycobacterium phage Rosebush] ],,NP_817850,100.0,5.03443E-38 SIF-HHPRED: DUF4314 ; Domain of unknown function (DUF4314),,,PF14192.9,85.7143,95.9 SIF-Syn: 
    /note=66,043-65,852 are called as the start and stop sites because it is called by both the Glimmer and Genemark starts. This start was also favored in both the Starterator report and phamerator report (the top five closest phage have the same start and stop sites). It has a z-score over 2, a spacer between 9-13, and the smallest negative value. It also has the longest open reading frame. Function is a hypothetical protein due to BLAST, HHPRED, and Phamerator evidence.

CDS complement (66139 - 66882)
  /gene="90"
  /product="gp90"
  /function="hypothetical protein"
  /locus tag="Phantasmagoria_90"
    /note=Original Glimmer call @bp 66882 has strength 19.29; Genemark calls start at 66882
    /note=SSC: 66882-66139 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_LEPHLEUR_92 [Mycobacterium phage Lephleur]],,NCBI, q1:s1 100.0% 1.4565E-165 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.261, -2.2364030944336752, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LEPHLEUR_92 [Mycobacterium phage Lephleur]],,QHB36789,96.4286,1.4565E-165 SIF-HHPRED: Rhabdo_NV ; Rhabdovirus Non-virion protein,,,PF02484.18,4.45344,33.7 SIF-Syn: 
    /note=66,882-66,139 are called as the start and stop sites because it is called by both the Glimmer and Genemark starts. This start was also favored in the Starterator report in relation to other phages in this cluster. t has a z-score over 2, a spacer between 9-13, and the smallest negative value. It also has the longest open reading frame. Function is a hypothetical protein due to BLAST, and Phamerator evidence.