CDS 10 - 807
  /gene="1"
  /product="gp1"
  /function="ParB-like nuclease domain"
  /locus tag="LittleMunchkin_1"
    /note=Original Glimmer call @bp 10 has strength 21.44; Genemark calls start at 1
    /note=SSC: 10-807 CP: yes SCS: both-gl ST: SS BLAST-Start: [ParB-like nuclease domain protein [Mycobacterium phage KayaCho] ],,NCBI, q1:s1 98.4906% 6.47418E-68 GAP: 0 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.877, -5.016377765385121, no F: ParB-like nuclease domain SIF-BLAST: ,,[ParB-like nuclease domain protein [Mycobacterium phage KayaCho] ],,YP_008409638,60.7407,6.47418E-68 SIF-HHPRED: Stage 0 sporulation protein J; ParB, Chromosome segregation, Chromosome organization, DNA BINDING PROTEIN; HET: CDP, MSE; 1.81A {Bacillus subtilis (strain 168)} SCOP: a.4.14.0, d.268.1.0,,,6SDK_A,52.0755,99.5 SIF-Syn: 
    /note=Start site is close enough to start of genome for coding potential to be obscured. All coding potential likely captured, but can`t be certain based on output.

CDS 804 - 1652
  /gene="2"
  /product="gp2"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_2"
    /note=Original Glimmer call @bp 804 has strength 15.63; Genemark calls start at 804
    /note=SSC: 804-1652 CP: yes SCS: both ST: NA BLAST-Start: [oxidoreductase [Gordonia phage CloverMinnie] ],,NCBI, q1:s1 99.6454% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.95, -2.9063687850157054, yes F: hypothetical protein SIF-BLAST: ,,[oxidoreductase [Gordonia phage CloverMinnie] ],,QFG11149,91.958,0.0 SIF-HHPRED: JBP-like; oxygenase domain of uncharacterized bacterial and phage proteins similar to kinetoplastid J-binding protein (JBP) 1 and JBP2.,,,cd20331,88.2979,100.0 SIF-Syn: 
    /note=Not the longest ORF. No 1:1 ratios are found.

CDS 1649 - 2506
  /gene="3"
  /product="gp3"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_3"
    /note=Original Glimmer call @bp 1649 has strength 8.35; Genemark calls start at 1649
    /note=SSC: 1649-2506 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_ANARQUE_3 [Gordonia phage AnarQue]],,NCBI, q1:s1 100.0% 7.45838E-164 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.234, -6.345829651909036, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ANARQUE_3 [Gordonia phage AnarQue]],,UBF41606,87.7193,7.45838E-164 SIF-HHPRED:  SIF-Syn: 
    /note=There were some indications on HHPRED that pyrophosphorylase was the correct choice for function. However, this was not an option available in the function.

CDS 2503 - 3048
  /gene="4"
  /product="gp4"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_4"
    /note=Original Glimmer call @bp 2503 has strength 15.85; Genemark calls start at 2503
    /note=SSC: 2503-3048 CP: yes SCS: both ST: NA BLAST-Start: [adenylate kinase [Gordonia phage AnarQue]],,NCBI, q2:s3 98.3425% 1.86987E-78 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.8, -3.4224590770118644, no F: hypothetical protein SIF-BLAST: ,,[adenylate kinase [Gordonia phage AnarQue]],,UBF41607,77.9006,1.86987E-78 SIF-HHPRED:  SIF-Syn: 
    /note=No 1:1 ratios

CDS 3045 - 3926
  /gene="5"
  /product="gp5"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_5"
    /note=Original Glimmer call @bp 3045 has strength 6.77; Genemark calls start at 3045
    /note=SSC: 3045-3926 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_ANARQUE_5 [Gordonia phage AnarQue]],,NCBI, q4:s3 98.6348% 1.11841E-168 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.97, -4.843798539558957, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ANARQUE_5 [Gordonia phage AnarQue]],,UBF41608,86.8966,1.11841E-168 SIF-HHPRED:  SIF-Syn: 
    /note=The best result in NCBI match did not have a one to one match. The Glimmer and GeneMark start site did not have the longest ORF and it didn`t have the best SD score. HHPred could not find a decent match and all the matches in PhagesDB were drafts, which was why NFK was chosen as the function.

CDS 3931 - 5658
  /gene="6"
  /product="gp6"
  /function="terminase"
  /locus tag="LittleMunchkin_6"
    /note=Original Glimmer call @bp 3931 has strength 13.53; Genemark calls start at 3931
    /note=SSC: 3931-5658 CP: yes SCS: both ST: NI BLAST-Start: [terminase [Gordonia phage CloverMinnie]],,NCBI, q1:s1 99.8261% 0.0 GAP: 4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.904, -2.9215542714922735, yes F: terminase SIF-BLAST: ,,[terminase [Gordonia phage CloverMinnie]],,QFG11153,83.9442,0.0 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,84.0,100.0 SIF-Syn: 

CDS complement (5655 - 6182)
  /gene="7"
  /product="gp7"
  /function="RuvC-like resolvase"
  /locus tag="LittleMunchkin_7"
    /note=Original Glimmer call @bp 6197 has strength 16.6; Genemark calls start at 6182
    /note=SSC: 6182-5655 CP: yes SCS: both-gm ST: SS BLAST-Start: [RuvC-like resolvase [Gordonia phage AnClar]],,NCBI, q1:s1 99.4286% 7.16031E-71 GAP: 54 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.18, -5.4374836651438505, no F: RuvC-like resolvase SIF-BLAST: ,,[RuvC-like resolvase [Gordonia phage AnClar]],,QIG58932,78.2857,7.16031E-71 SIF-HHPRED: RuvC endonuclease; endonuclease, DNA junctions, replication, recombination, phage packaging, Holliday junction, RNase-H fold, DNA junction endonuclease, Holliday junctions; 1.68A {Lactococcus phage bIL67},,,4KTW_A,86.2857,99.9 SIF-Syn: 
    /note=GeneMark and Glimmer scores do not match, GeneMark start site selected based on Starterator report.

CDS 6237 - 6560
  /gene="8"
  /product="gp8"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_8"
    /note=Original Glimmer call @bp 6237 has strength 18.92; Genemark calls start at 6237
    /note=SSC: 6237-6560 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_ANCLAR_6 [Gordonia phage AnClar]],,NCBI, q1:s1 100.0% 1.58107E-60 GAP: 54 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.857, -5.056409918993686, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ANCLAR_6 [Gordonia phage AnClar]],,QIG58933,95.3271,1.58107E-60 SIF-HHPRED:  SIF-Syn: 
    /note=Doesn`t have the most annotated start site. There was a hit in the TmHmm with 3 helices however in order to stay in agreement there we stayed also called no known function.

CDS 6586 - 8433
  /gene="9"
  /product="gp9"
  /function="portal protein"
  /locus tag="LittleMunchkin_9"
    /note=Original Glimmer call @bp 6586 has strength 12.83; Genemark calls start at 6586
    /note=SSC: 6586-8433 CP: yes SCS: both ST: SS BLAST-Start: [portal protein [Gordonia phage Sour] ],,NCBI, q1:s1 99.5122% 0.0 GAP: 25 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.554, -6.264935315460357, no F: portal protein SIF-BLAST: ,,[portal protein [Gordonia phage Sour] ],,YP_009625582,88.7789,0.0 SIF-HHPRED: Phage portal protein, HK97 family; "neck", "portal", "capsid", "tail tube", VIRUS; 3.58A {Rhodobacter capsulatus},,,6TE9_A,63.7398,100.0 SIF-Syn: 
    /note=Not the best SD score, but none are particularly good.

CDS 8441 - 10822
  /gene="10"
  /product="gp10"
  /function="capsid maturation protease"
  /locus tag="LittleMunchkin_10"
    /note=Original Glimmer call @bp 8441 has strength 13.81; Genemark calls start at 8441
    /note=SSC: 8441-10822 CP: yes SCS: both ST: NA BLAST-Start: [capsid maturation protease [Gordonia phage Ligma]],,NCBI, q1:s1 99.7478% 0.0 GAP: 7 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.193, -6.3486537515621615, no F: capsid maturation protease SIF-BLAST: ,,[capsid maturation protease [Gordonia phage Ligma]],,UJE15664,88.4131,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Does not have the best shine dalgarno sequence (-6.349).

CDS 10824 - 11030
  /gene="11"
  /product="gp11"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_11"
    /note=Original Glimmer call @bp 10824 has strength 12.94; Genemark calls start at 10824
    /note=SSC: 10824-11030 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_LIGMA_10 [Gordonia phage Ligma]],,NCBI, q1:s1 100.0% 3.2243E-37 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.665, -4.000400284422595, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LIGMA_10 [Gordonia phage Ligma]],,UJE15665,95.5882,3.2243E-37 SIF-HHPRED:  SIF-Syn: 
    /note=There was no known function to this because on HHPRED there was very little coverage % and with a lower probability along with this on phagesdb there was no function.

CDS 11125 - 12825
  /gene="12"
  /product="gp12"
  /function="major capsid protein"
  /locus tag="LittleMunchkin_12"
    /note=Original Glimmer call @bp 11125 has strength 17.5; Genemark calls start at 11125
    /note=SSC: 11125-12825 CP: yes SCS: both ST: NI BLAST-Start: [major capsid hexamer protein [Gordonia phage Yago84] ],,NCBI, q1:s1 100.0% 0.0 GAP: 94 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.696, -3.6360588251033645, no F: major capsid protein SIF-BLAST: ,,[major capsid hexamer protein [Gordonia phage Yago84] ],,QDF17543,94.5133,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Multiple 1:1 ratios. No results were produced from HHPRED, no probabilities of 100%. Most were below 35%. There is a huge gap of more than 100 with this gene and the next one. Though HHPRED didn`t give any results, PhagesDB and NCBI Blast was pretty confident with the function. Major capsid hexamer protein.

CDS 12925 - 13710
  /gene="13"
  /product="gp13"
  /function="major capsid protein"
  /locus tag="LittleMunchkin_13"
    /note=Original Glimmer call @bp 12925 has strength 11.6; Genemark calls start at 12925
    /note=SSC: 12925-13710 CP: yes SCS: both ST: SS BLAST-Start: [major capsid pentamer protein [Gordonia phage AnClar]],,NCBI, q1:s1 100.0% 5.60748E-144 GAP: 99 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.201, -2.394485424036831, yes F: major capsid protein SIF-BLAST: ,,[major capsid pentamer protein [Gordonia phage AnClar]],,QIG58939,89.2308,5.60748E-144 SIF-HHPRED:  SIF-Syn: Major capsid protein
    /note=There is a larger than normal gap in between this gene and the previous (99 base pairs). HHPred did not produce any results for this function but NCBI Blast and PhagesDB blast both were pretty confident in its function.

CDS 13719 - 14384
  /gene="14"
  /product="gp14"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_14"
    /note=Original Glimmer call @bp 13719 has strength 14.05; Genemark calls start at 13719
    /note=SSC: 13719-14384 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDJ57_gp16 [Gordonia phage Sour] ],,NCBI, q1:s1 88.6878% 4.73729E-70 GAP: 8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.185, -4.4057176022952405, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDJ57_gp16 [Gordonia phage Sour] ],,YP_009625587,69.7561,4.73729E-70 SIF-HHPRED:  SIF-Syn: 
    /note=There was no known function to this because on HHPRED there was little coverage % and the high probabilities were that of humans or yeast. Phagesdb also indicated there was no known function also proving that this was the case.

CDS 14381 - 14770
  /gene="15"
  /product="gp15"
  /function="membrane protein"
  /locus tag="LittleMunchkin_15"
    /note=Original Glimmer call @bp 14423 has strength 9.24; Genemark calls start at 14423
    /note=SSC: 14381-14770 CP: yes SCS: both-cs ST: NI BLAST-Start: [hypothetical protein SEA_YAGO84_14 [Gordonia phage Yago84] ],,NCBI, q1:s1 97.6744% 7.24875E-76 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.031, -3.5088110057482766, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein SEA_YAGO84_14 [Gordonia phage Yago84] ],,QDF17546,93.1298,7.24875E-76 SIF-HHPRED:  SIF-Syn: 
    /note=genemark and glimmer call a different start site, but that site is not the most called

CDS 14770 - 15246
  /gene="16"
  /product="gp16"
  /function="membrane protein"
  /locus tag="LittleMunchkin_16"
    /note=Original Glimmer call @bp 14770 has strength 15.49; Genemark calls start at 14770
    /note=SSC: 14770-15246 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_YAGO84_15 [Gordonia phage Yago84] ],,NCBI, q6:s5 96.8354% 1.6903E-78 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.097, -5.032276239276967, no F: membrane protein SIF-BLAST: ,,[hypothetical protein SEA_YAGO84_15 [Gordonia phage Yago84] ],,QDF17547,83.4395,1.6903E-78 SIF-HHPRED:  SIF-Syn: 
    /note=This gene does not have the longest ORF and it doesn`t have the best SD score out of the options. But it does capture all the coding potential. Tmhmm predicted 4 TMHs for this gene.

CDS 15243 - 15710
  /gene="17"
  /product="gp17"
  /function="membrane protein"
  /locus tag="LittleMunchkin_17"
    /note=Original Glimmer call @bp 15243 has strength 11.46; Genemark calls start at 15243
    /note=SSC: 15243-15710 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_YAGO84_16 [Gordonia phage Yago84] ],,NCBI, q1:s1 100.0% 7.7505E-76 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.539, -3.603870559007238, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein SEA_YAGO84_16 [Gordonia phage Yago84] ],,QDF17548,84.6154,7.7505E-76 SIF-HHPRED:  SIF-Syn: 
    /note=Do not have most annotated start site, Starterator was not applicable.

CDS 15707 - 16021
  /gene="18"
  /product="gp18"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_18"
    /note=Original Glimmer call @bp 15707 has strength 12.03; Genemark calls start at 15707
    /note=SSC: 15707-16021 CP: yes SCS: both ST: NA BLAST-Start: [membrane protein [Gordonia phage CloverMinnie]],,NCBI, q4:s3 97.1154% 6.89212E-49 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.679, -3.6701184301625793, yes F: hypothetical protein SIF-BLAST: ,,[membrane protein [Gordonia phage CloverMinnie]],,QFG11166,83.4951,6.89212E-49 SIF-HHPRED:  SIF-Syn: 
    /note=the phage does not have the most annotated start site, so starterator is not applicable. One TMH predicted, but lack of other evidence led to NKF

CDS 16116 - 16928
  /gene="19"
  /product="gp19"
  /function="major tail protein"
  /locus tag="LittleMunchkin_19"
    /note=Original Glimmer call @bp 16116 has strength 17.87; Genemark calls start at 16116
    /note=SSC: 16116-16928 CP: yes SCS: both ST: NA BLAST-Start: [major tail protein [Gordonia phage Ligma]],,NCBI, q1:s1 99.6296% 0.0 GAP: 94 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.696, -3.6360588251033645, yes F: major tail protein SIF-BLAST: ,,[major tail protein [Gordonia phage Ligma]],,UJE15673,97.4074,0.0 SIF-HHPRED: L_lac_phage_MSP ; Phage tail tube protein,,,PF06488.14,67.037,91.2 SIF-Syn: 
    /note=Does not have the most annotated start site, Starterator was non-informative.

CDS 17045 - 18409
  /gene="20"
  /product="gp20"
  /function="glucosaminyl deacetylase"
  /locus tag="LittleMunchkin_20"
    /note=Original Glimmer call @bp 17045 has strength 8.74; Genemark calls start at 17045
    /note=SSC: 17045-18409 CP: yes SCS: both ST: NA BLAST-Start: [glucosaminyl deacetylase [Gordonia phage Sanjuju]],,NCBI, q1:s1 99.7797% 0.0 GAP: 116 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.201, -2.3335289980954053, yes F: glucosaminyl deacetylase SIF-BLAST: ,,[glucosaminyl deacetylase [Gordonia phage Sanjuju]],,QUE25899,94.4812,0.0 SIF-HHPRED: Peptidoglycan N-acetylglucosamine deacetylase; tim barrel, hydrolase, polysaccharide deacetylase; HET: ACT, PXU, SO4; 2.336A {Bacillus cereus},,,4L1G_C,61.8943,99.9 SIF-Syn: 
    /note=Doesn`t have the most annotated start and does not call it.

CDS 18456 - 19184
  /gene="21"
  /product="gp21"
  /function="head-to-tail adaptor"
  /locus tag="LittleMunchkin_21"
    /note=Original Glimmer call @bp 18456 has strength 9.51; Genemark calls start at 18456
    /note=SSC: 18456-19184 CP: yes SCS: both ST: NI BLAST-Start: [head-to-tail adaptor [Gordonia phage Yago84]],,NCBI, q1:s1 100.0% 1.64684E-165 GAP: 46 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.584, -6.203622861102651, no F: head-to-tail adaptor SIF-BLAST: ,,[head-to-tail adaptor [Gordonia phage Yago84]],,QDF17551,96.6942,1.64684E-165 SIF-HHPRED: Adaptor protein Rcc01688; "neck", "portal", "capsid", "tail tube", VIRUS; 3.58A {Rhodobacter capsulatus},,,6TE9_D,87.6033,99.6 SIF-Syn: 
    /note=We have the most annotated start but do not call it, Starterator was not informative.

CDS 19184 - 19726
  /gene="22"
  /product="gp22"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_22"
    /note=Original Glimmer call @bp 19184 has strength 11.68; Genemark calls start at 19217
    /note=SSC: 19184-19726 CP: yes SCS: both-gl ST: NA BLAST-Start: [hypothetical protein SEA_ANCLAR_21 [Gordonia phage AnClar]],,NCBI, q1:s1 100.0% 1.31688E-108 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.272, -4.290417282676006, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ANCLAR_21 [Gordonia phage AnClar]],,QIG58948,92.3077,1.31688E-108 SIF-HHPRED: c.116.1.5 (A:67-228) Hypothetical protein TTHA0657 (TT1575) {Thermus thermophilus [TaxId: 274]},,,d1v6za2,3.33333,16.1 SIF-Syn: 
    /note=longest ORF has much larger overlap than chosen start site. the phage does not have the most annotated start site, so starterator is not applicable

CDS 19735 - 20055
  /gene="23"
  /product="gp23"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_23"
    /note=Original Glimmer call @bp 19735 has strength 18.7; Genemark calls start at 19735
    /note=SSC: 19735-20055 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_YAGO84_21 [Gordonia phage Yago84]],,NCBI, q1:s1 100.0% 3.06777E-51 GAP: 8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.201, -2.7806870294376242, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_YAGO84_21 [Gordonia phage Yago84]],,QDF17553,85.3211,3.06777E-51 SIF-HHPRED:  SIF-Syn: 
    /note=Has and calls the most annotated start site.

CDS 20052 - 20465
  /gene="24"
  /product="gp24"
  /function="tail assembly chaperone"
  /locus tag="LittleMunchkin_24"
    /note=Original Glimmer call @bp 20052 has strength 10.19; Genemark calls start at 20052
    /note=SSC: 20052-20465 CP: yes SCS: both ST: NA BLAST-Start: [tail assembly chaperone [Gordonia phage Mariokart]],,NCBI, q1:s1 100.0% 1.7932E-73 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.857, -6.044175462576674, no F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Gordonia phage Mariokart]],,QNL30149,89.0511,1.7932E-73 SIF-HHPRED: HK97-gp10_like ; Bacteriophage HK97-gp10, putative tail-component,,,PF04883.15,51.8248,99.2 SIF-Syn: 
    /note=Starteraror didn`t call as most annotated start site.

CDS 20512 - 21039
  /gene="25"
  /product="gp25"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_25"
    /note=Original Glimmer call @bp 20512 has strength 18.72; Genemark calls start at 20512
    /note=SSC: 20512-21039 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_ANCLAR_24 [Gordonia phage AnClar]],,NCBI, q5:s4 89.7143% 1.10143E-67 GAP: 46 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.191, -4.394706008439538, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ANCLAR_24 [Gordonia phage AnClar]],,QIG58951,70.0535,1.10143E-67 SIF-HHPRED:  SIF-Syn: 
    /note=Do not have most annotated start, Starterator not applicable.

CDS 21076 - 26559
  /gene="26"
  /product="gp26"
  /function="tape measure protein"
  /locus tag="LittleMunchkin_26"
    /note=Original Glimmer call @bp 21076 has strength 13.47; Genemark calls start at 21076
    /note=SSC: 21076-26559 CP: yes SCS: both ST: SS BLAST-Start: [tape measure protein [Gordonia phage AnClar]],,NCBI, q1:s1 100.0% 0.0 GAP: 36 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.663, -5.740791561519216, no F: tape measure protein SIF-BLAST: ,,[tape measure protein [Gordonia phage AnClar]],,QIG58952,90.0438,0.0 SIF-HHPRED: Tape Measure Protein, gp57; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alpha},,,6V8I_AF,3.0104,99.8 SIF-Syn: 

CDS 26568 - 28097
  /gene="27"
  /product="gp27"
  /function="minor tail protein"
  /locus tag="LittleMunchkin_27"
    /note=Original Glimmer call @bp 26568 has strength 15.48; Genemark calls start at 26568
    /note=SSC: 26568-28097 CP: yes SCS: both ST: NA BLAST-Start: [minor tail protein [Gordonia phage AnClar]],,NCBI, q1:s1 100.0% 0.0 GAP: 8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.185, -4.4057176022952405, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Gordonia phage AnClar]],,QIG58953,94.8919,0.0 SIF-HHPRED: HYPOTHETICAL PROTEIN 19.1; VIRAL PROTEIN, DISTAL TAIL PROTEIN; 2.95A {BACILLUS PHAGE SPP1},,,2X8K_C,65.2259,94.2 SIF-Syn: 
    /note=Do not have most annotated start, Starterator is not applicable.

CDS 28100 - 29137
  /gene="28"
  /product="gp28"
  /function="minor tail protein"
  /locus tag="LittleMunchkin_28"
    /note=Original Glimmer call @bp 28100 has strength 12.0; Genemark calls start at 28100
    /note=SSC: 28100-29137 CP: yes SCS: both ST: NA BLAST-Start: [minor tail protein [Gordonia phage Mariokart]],,NCBI, q1:s1 100.0% 0.0 GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.151, -4.4747668481608205, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Gordonia phage Mariokart]],,QNL30153,88.7283,0.0 SIF-HHPRED: Prophage MuSo2, 43 kDa tail protein; MuSo2, Shewanella oneidensis MR-1, Structural Genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG; HET: MSE; 2.1A {Shewanella oneidensis} SCOP: b.106.1.1,,,3CDD_D,94.7826,99.6 SIF-Syn: 
    /note=Do not have most annotated start, Starterator is not applicable.

CDS 29134 - 30714
  /gene="29"
  /product="gp29"
  /function="minor tail protein"
  /locus tag="LittleMunchkin_29"
    /note=Original Glimmer call @bp 29134 has strength 14.53; Genemark calls start at 29134
    /note=SSC: 29134-30714 CP: yes SCS: both ST: NA BLAST-Start: [minor tail protein [Gordonia phage Yago84]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.603, -5.574447489270071, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Gordonia phage Yago84]],,QDF17559,93.1818,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Do not have most annotated start, Starterator not applicable.

CDS 30714 - 30905
  /gene="30"
  /product="gp30"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_30"
    /note=Original Glimmer call @bp 30714 has strength 15.67; Genemark calls start at 30714
    /note=SSC: 30714-30905 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_YAGO84_28 [Gordonia phage Yago84] ],,NCBI, q1:s1 100.0% 3.81113E-36 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.916, -2.916420155493201, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_YAGO84_28 [Gordonia phage Yago84] ],,QDF17560,100.0,3.81113E-36 SIF-HHPRED:  SIF-Syn: 
    /note=Do not have most annotated start, Starterator is not applicable.

CDS 30916 - 31530
  /gene="31"
  /product="gp31"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_31"
    /note=Original Glimmer call @bp 30916 has strength 14.86; Genemark calls start at 30916
    /note=SSC: 30916-31530 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_YAGO84_29 [Gordonia phage Yago84] ],,NCBI, q1:s1 100.0% 2.02278E-134 GAP: 10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.459, -6.635031505882524, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_YAGO84_29 [Gordonia phage Yago84] ],,QDF17561,95.5882,2.02278E-134 SIF-HHPRED:  SIF-Syn: 

CDS 31527 - 32156
  /gene="32"
  /product="gp32"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_32"
    /note=Original Glimmer call @bp 31527 has strength 13.76; Genemark calls start at 31527
    /note=SSC: 31527-32156 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Gordonia phage AnClar]],,NCBI, q1:s1 100.0% 9.91044E-132 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.404, -3.959465094810568, yes F: hypothetical protein SIF-BLAST: ,,[minor tail protein [Gordonia phage AnClar]],,QIG58958,96.1722,9.91044E-132 SIF-HHPRED:  SIF-Syn: 
    /note=The HHPRED had a very low coverage along with a very low probability, the hits that were found were from fungi. Along with that, there was very little evidence that was found within Phagesdb which was another indication of no known function.

CDS 32153 - 32749
  /gene="33"
  /product="gp33"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_33"
    /note=Original Glimmer call @bp 32153 has strength 16.37; Genemark calls start at 32153
    /note=SSC: 32153-32749 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_YAGO84_31 [Gordonia phage Yago84] ],,NCBI, q1:s1 100.0% 1.86707E-117 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.185, -4.85287563363746, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_YAGO84_31 [Gordonia phage Yago84] ],,QDF17563,89.3939,1.86707E-117 SIF-HHPRED:  SIF-Syn: 
    /note=Does not have the best SD score but everything else points to 32153 being the start site. HHPred results were horrible

CDS 32782 - 33129
  /gene="34"
  /product="gp34"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_34"
    /note=Original Glimmer call @bp 32782 has strength 12.56; Genemark calls start at 32782
    /note=SSC: 32782-33129 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_YAGO84_32 [Gordonia phage Yago84] ],,NCBI, q1:s1 100.0% 2.39054E-53 GAP: 32 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.232, -4.309437458116814, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_YAGO84_32 [Gordonia phage Yago84] ],,QDF17564,83.4783,2.39054E-53 SIF-HHPRED:  SIF-Syn: 
    /note=The HHPRED had very little coverage on most of theirs however with the little coverage there was a high probability. This however was still not enough information for it to have a function. Another thing that led us to believe that this had no function was that there were no functions that were listed in PhagesDB.

CDS 33126 - 33437
  /gene="35"
  /product="gp35"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_35"
    /note=Original Glimmer call @bp 33126 has strength 12.72; Genemark calls start at 33126
    /note=SSC: 33126-33437 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_LIGMA_33 [Gordonia phage Ligma]],,NCBI, q1:s1 100.0% 3.6061E-57 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.179, -7.682130123425133, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LIGMA_33 [Gordonia phage Ligma]],,UJE15688,94.1748,3.6061E-57 SIF-HHPRED:  SIF-Syn: 
    /note=Not the best SD score out of all the options but all other evidence points to 33126 being the start site. HHPred does not produce any relevant results for this protein`s function.

CDS 33451 - 33867
  /gene="36"
  /product="gp36"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_36"
    /note=Original Glimmer call @bp 33451 has strength 17.61; Genemark calls start at 33451
    /note=SSC: 33451-33867 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_YAGO84_34 [Gordonia phage Yago84]],,NCBI, q1:s1 100.0% 1.85862E-78 GAP: 13 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.787, -4.403467825203357, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_YAGO84_34 [Gordonia phage Yago84]],,QDF17566,92.029,1.85862E-78 SIF-HHPRED:  SIF-Syn: 
    /note=There was no coverage or function that was found on HHPRED. To confirm that this was the case we looked into the PHagesDB and this also agreed that there was no known function.

CDS 33864 - 34556
  /gene="37"
  /product="gp37"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_37"
    /note=Original Glimmer call @bp 33864 has strength 18.75; Genemark calls start at 33864
    /note=SSC: 33864-34556 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_LIGMA_35 [Gordonia phage Ligma]],,NCBI, q1:s1 100.0% 2.6144E-124 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.586, -6.375966011762079, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LIGMA_35 [Gordonia phage Ligma]],,UJE15690,87.8261,2.6144E-124 SIF-HHPRED:  SIF-Syn: 
    /note=Doesn`t have the best SD score but all the other evidence points to the suggested start site. HHPred suggests the levanase enzyme but the other evidence points to NKF.

CDS 34566 - 35381
  /gene="38"
  /product="gp38"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_38"
    /note=Original Glimmer call @bp 34566 has strength 20.19; Genemark calls start at 34566
    /note=SSC: 34566-35381 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Gordonia phage Sour] ],,NCBI, q1:s1 100.0% 5.37509E-138 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.185, -4.325675514574479, no F: hypothetical protein SIF-BLAST: ,,[minor tail protein [Gordonia phage Sour] ],,YP_009625612,81.0345,5.37509E-138 SIF-HHPRED:  SIF-Syn: 
    /note=There was little coverage with little probability on HHPRED and on however there was little evidence on PhagesDB that this could be a minor tail protein that was suggested. We do not feel comfortable calling a function with such little evidence to back this up.

CDS 35385 - 35948
  /gene="39"
  /product="gp39"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_39"
    /note=Original Glimmer call @bp 35385 has strength 13.17; Genemark calls start at 35385
    /note=SSC: 35385-35948 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_YAGO84_37 [Gordonia phage Yago84]],,NCBI, q1:s1 99.4652% 2.65682E-118 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.073, -4.9063858544558085, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_YAGO84_37 [Gordonia phage Yago84]],,QDF17569,94.1176,2.65682E-118 SIF-HHPRED:  SIF-Syn: 
    /note=Does not have the best SD score but all other evidence points to the suggested start site. Function is debated between minor tail protein and NKF. HHPred pointed to mice genes.

CDS complement (35945 - 36172)
  /gene="40"
  /product="gp40"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="LittleMunchkin_40"
    /note=Original Glimmer call @bp 36172 has strength 12.04; Genemark calls start at 36172
    /note=SSC: 36172-35945 CP: yes SCS: both ST: NA BLAST-Start: [LamD-like [Gordonia phage AnClar]],,NCBI, q1:s1 100.0% 3.23903E-42 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.201, -2.3335289980954053, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[LamD-like [Gordonia phage AnClar]],,QIG58966,93.3333,3.23903E-42 SIF-HHPRED: Putative DNA-binding protein; BldC, S. coelicolor, developmental switch, MerR-like, DNA BINDING PROTEIN-DNA complex; 3.09A {Streptomyces venezuelae},,,6AMA_A,85.3333,99.1 SIF-Syn: 
    /note=Starterator was inconclusive, did not call as the most annotated start. 
    /note=Not all of the coding potential was captured, but since it was the longest ORF it was the best option.

CDS complement (36182 - 36568)
  /gene="41"
  /product="gp41"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="LittleMunchkin_41"
    /note=Original Glimmer call @bp 36568 has strength 12.97; Genemark calls start at 36568
    /note=SSC: 36568-36182 CP: yes SCS: both ST: NA BLAST-Start: [helix-turn-helix DNA binding protein [Gordonia phage Sour] ],,NCBI, q12:s4 91.4062% 1.97693E-48 GAP: 65 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.031, -2.66371296573402, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding protein [Gordonia phage Sour] ],,YP_009625615,74.1936,1.97693E-48 SIF-HHPRED: Endothelial differentiation-related factor 1; EDF1, HMBF1alpha, helix-turn-helix, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural; NMR {Homo sapiens} SCOP: l.1.1.1, a.35.1.12,,,1X57_A,57.0312,98.5 SIF-Syn: 
    /note=GeneMark makes it look as though chosen site doesn`t capture all coding potential, but the start site captures the maximum potential and there aren`t other viable options.

CDS complement (36634 - 37302)
  /gene="42"
  /product="gp42"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_42"
    /note=Original Glimmer call @bp 37302 has strength 14.85; Genemark calls start at 37302
    /note=SSC: 37302-36634 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_YAGO84_40 [Gordonia phage Yago84]],,NCBI, q1:s1 100.0% 1.22863E-98 GAP: 104 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.696, -4.113180079823027, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_YAGO84_40 [Gordonia phage Yago84]],,QDF17572,75.8475,1.22863E-98 SIF-HHPRED: DUF6011 ; Family of unknown function (DUF6011),,,PF19474.2,15.3153,99.1 SIF-Syn: 
    /note=Did not have the most annotated start.

CDS 37407 - 38561
  /gene="43"
  /product="gp43"
  /function="lysin A"
  /locus tag="LittleMunchkin_43"
    /note=Original Glimmer call @bp 37407 has strength 12.73; Genemark calls start at 37407
    /note=SSC: 37407-38561 CP: yes SCS: both ST: SS BLAST-Start: [lysin A [Gordonia phage Yago84]],,NCBI, q1:s1 100.0% 0.0 GAP: 104 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.174, -5.177338803001188, no F: lysin A SIF-BLAST: ,,[lysin A [Gordonia phage Yago84]],,QDF17573,96.875,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Has and calls the most annotated start site.

CDS 38558 - 39280
  /gene="44"
  /product="gp44"
  /function="lysin B"
  /locus tag="LittleMunchkin_44"
    /note=Original Glimmer call @bp 38558 has strength 9.64; Genemark calls start at 38558
    /note=SSC: 38558-39280 CP: yes SCS: both ST: NA BLAST-Start: [lysin B [Gordonia phage AnClar]],,NCBI, q1:s1 100.0% 3.02159E-148 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.153, -4.4713484557894425, no F: lysin B SIF-BLAST: ,,[lysin B [Gordonia phage AnClar]],,QIG58970,92.5311,3.02159E-148 SIF-HHPRED:  SIF-Syn: 
    /note=Does not have the most annotated start.

CDS complement (39398 - 39895)
  /gene="45"
  /product="gp45"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_45"
    /note=Original Glimmer call @bp 39895 has strength 15.9; Genemark calls start at 39895
    /note=SSC: 39895-39398 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_YAGO84_43 [Gordonia phage Yago84] ],,NCBI, q1:s1 100.0% 7.87511E-93 GAP: 72 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.652, -5.4121604219751855, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_YAGO84_43 [Gordonia phage Yago84] ],,QDF17575,92.7273,7.87511E-93 SIF-HHPRED: DUF3094 ; Protein of unknown function (DUF3094),,,PF11293.11,9.69697,35.5 SIF-Syn: 

tRNA 39949 - 40044
  /gene="46"
  /product="tRNA-Gln(ctg)"
  /locus tag="LITTLEMUNCHKIN_46"
    /note=tRNA-Gln(ctg)

CDS complement (39968 - 41233)
  /gene="47"
  /product="gp47"
  /function="exonuclease"
  /locus tag="LittleMunchkin_47"
    /note=Original Glimmer call @bp 41233 has strength 15.33; Genemark calls start at 41233
    /note=SSC: 41233-39968 CP: yes SCS: both ST: NA BLAST-Start: [exonuclease [Gordonia phage Yago84] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.102, -4.635604911695725, no F: exonuclease SIF-BLAST: ,,[exonuclease [Gordonia phage Yago84] ],,QDF17576,96.6746,0.0 SIF-HHPRED: Mitochondrial genome maintenance exonuclease 1; human MGME1, DNA complex, DNA exonuclease, DNA BINDING PROTEIN; 2.702A {Homo sapiens},,,5ZYT_C,66.0333,99.8 SIF-Syn: 
    /note=Does not have the most annotated start.

CDS complement (41230 - 42897)
  /gene="48"
  /product="gp48"
  /function="DNA helicase"
  /locus tag="LittleMunchkin_48"
    /note=Original Glimmer call @bp 42864 has strength 16.14; Genemark calls start at 42864
    /note=SSC: 42897-41230 CP: yes SCS: both-cs ST: NA BLAST-Start: [DNA helicase [Gordonia phage Ligma]],,NCBI, q1:s1 100.0% 0.0 GAP: 141 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.171, -2.3771126854926803, yes F: DNA helicase SIF-BLAST: ,,[DNA helicase [Gordonia phage Ligma]],,UJE15701,93.1408,0.0 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,62.8829,100.0 SIF-Syn: 
    /note=Glimmer and genemark both chose 42864 as start. 42897 has a better SD and is longest ORF, as well as undoubtedly capturing all coding potential.

CDS complement (43039 - 43521)
  /gene="49"
  /product="gp49"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_49"
    /note=Original Glimmer call @bp 43521 has strength 17.78; Genemark calls start at 43521
    /note=SSC: 43521-43039 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_ANARQUE_49 [Gordonia phage AnarQue]],,NCBI, q3:s2 93.75% 4.13451E-16 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.597, -4.3934175870462076, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ANARQUE_49 [Gordonia phage AnarQue]],,UBF41652,58.7097,4.13451E-16 SIF-HHPRED:  SIF-Syn: 
    /note=Does not have the most annotated start site.

CDS complement (43521 - 43895)
  /gene="50"
  /product="gp50"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_50"
    /note=Original Glimmer call @bp 43895 has strength 14.06; Genemark calls start at 43895
    /note=SSC: 43895-43521 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein [Mycolicibacterium conceptionense] ],,NCBI, q3:s1108 21.7742% 8.89001E-7 GAP: 28 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.091, -2.4787699911121788, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein [Mycolicibacterium conceptionense] ],,WP_048895554,1.72911,8.89001E-7 SIF-HHPRED:  SIF-Syn: 
    /note=This currently seems to be an orpham without close phage matches, the closest blast matches are from bacteria.

CDS complement (43924 - 44298)
  /gene="51"
  /product="gp51"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="LittleMunchkin_51"
    /note=Original Glimmer call @bp 44298 has strength 10.09; Genemark calls start at 44298
    /note=SSC: 44298-43924 CP: yes SCS: both ST: NA BLAST-Start: [helix-turn-helix DNA binding domain protein [Gordonia phage Ligma]],,NCBI, q1:s1 97.5806% 1.51346E-27 GAP: -14 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.911, -6.189096607906054, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding domain protein [Gordonia phage Ligma]],,UJE15703,68.9655,1.51346E-27 SIF-HHPRED: Putative uncharacterized protein; DNA BINDING PROTEIN; NMR {Hyperthermus butylicus},,,2LVS_A,73.3871,99.1 SIF-Syn: 
    /note=Starterator was inconclusive, did not call as the most annotated start.

CDS complement (44285 - 46795)
  /gene="52"
  /product="gp52"
  /function="DNA primase/helicase"
  /locus tag="LittleMunchkin_52"
    /note=Original Glimmer call @bp 46795 has strength 14.82; Genemark calls start at 46795
    /note=SSC: 46795-44285 CP: yes SCS: both ST: SS BLAST-Start: [DNA primase/helicase [Gordonia phage Yago84]],,NCBI, q1:s1 99.7608% 0.0 GAP: 49 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.696, -4.113180079823027, yes F: DNA primase/helicase SIF-BLAST: ,,[DNA primase/helicase [Gordonia phage Yago84]],,QDF17580,85.6341,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Does not the the best SD score but all other evidence points to this being the suggested start site

CDS complement (46845 - 48656)
  /gene="53"
  /product="gp53"
  /function="DNA polymerase I"
  /locus tag="LittleMunchkin_53"
    /note=Original Glimmer call @bp 48656 has strength 19.87; Genemark calls start at 48656
    /note=SSC: 48656-46845 CP: yes SCS: both ST: NI BLAST-Start: [DNA polymerase I [Gordonia phage AnClar]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.517, -3.7300189403722097, no F: DNA polymerase I SIF-BLAST: ,,[DNA polymerase I [Gordonia phage AnClar]],,QIG58977,85.0993,0.0 SIF-HHPRED: Prex DNA polymerase; DNA polymerase, TRANSFERASE; HET: SO4; 2.9A {Plasmodium falciparum},,,5DKT_A,98.1758,100.0 SIF-Syn: 
    /note=This is believed to be a DNA polymerase. There was great coverage and a high probability on HHPRED. Another form of evidence would be that the PhagesDB also showed that DNA polymerase 1 is the correct function.

CDS complement (48653 - 48964)
  /gene="54"
  /product="gp54"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_54"
    /note=Original Glimmer call @bp 48964 has strength 14.62; Genemark calls start at 48964
    /note=SSC: 48964-48653 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_YAGO84_50 [Gordonia phage Yago84] ],,NCBI, q1:s1 100.0% 1.16042E-34 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.032, -4.717114992838803, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_YAGO84_50 [Gordonia phage Yago84] ],,QDF17582,74.5098,1.16042E-34 SIF-HHPRED:  SIF-Syn: 
    /note=This start site does not have the longest ORF and it also does not have the best SD score but all other evidence points to this being the correct start site.

CDS complement (48961 - 49386)
  /gene="55"
  /product="gp55"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_55"
    /note=Original Glimmer call @bp 49386 has strength 16.53; Genemark calls start at 49386
    /note=SSC: 49386-48961 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_MARIOKART_52 [Gordonia phage Mariokart]],,NCBI, q3:s1 97.8723% 4.5671E-46 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.827, -3.1586778224135674, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_MARIOKART_52 [Gordonia phage Mariokart]],,QNL30179,68.0,4.5671E-46 SIF-HHPRED:  SIF-Syn: 
    /note=There was very little coverage and a very little percentage that was on HHPRED which was an indication that there was no function. Along with that, there was a great amount of unknown function on the PhagesDB which again was an indication that there was no function.

CDS complement (49383 - 49817)
  /gene="56"
  /product="gp56"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_56"
    /note=Original Glimmer call @bp 49817 has strength 16.14; Genemark calls start at 49817
    /note=SSC: 49817-49383 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_MARIOKART_53 [Gordonia phage Mariokart]],,NCBI, q1:s1 95.1389% 4.30098E-14 GAP: 113 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.201, -2.253486910374644, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_MARIOKART_53 [Gordonia phage Mariokart]],,QNL30180,48.6486,4.30098E-14 SIF-HHPRED:  SIF-Syn: 
    /note=Not the longest ORF but all other evidence points to this being the correct start site.

CDS complement (49931 - 50239)
  /gene="57"
  /product="gp57"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_57"
    /note=Original Glimmer call @bp 50239 has strength 14.87; Genemark calls start at 50239
    /note=SSC: 50239-49931 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_YAGO84_53 [Gordonia phage Yago84]],,NCBI, q1:s1 97.0588% 3.72414E-31 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.95, -2.9063687850157054, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_YAGO84_53 [Gordonia phage Yago84]],,QDF17585,71.0,3.72414E-31 SIF-HHPRED:  SIF-Syn: 
    /note=There was very little coverage and very little percentage that there was a function on HHPRED which indicated no function. Along with that, there was no function that was listed on any of the PhagesDB blast which confirmed no known function.

CDS complement (50236 - 50529)
  /gene="58"
  /product="gp58"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_58"
    /note=Original Glimmer call @bp 50529 has strength 12.69; Genemark calls start at 50529
    /note=SSC: 50529-50236 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein FDJ57_gp57 [Gordonia phage Sour] ],,NCBI, q1:s1 89.6907% 1.4479E-8 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.597, -3.627004739933808, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDJ57_gp57 [Gordonia phage Sour] ],,YP_009625628,59.1398,1.4479E-8 SIF-HHPRED:  SIF-Syn: 
    /note=Not the longest ORF or best SD score but all other evidence points to this being the correct start site.

CDS complement (50529 - 51077)
  /gene="59"
  /product="gp59"
  /function="phosphatase"
  /locus tag="LittleMunchkin_59"
    /note=Original Glimmer call @bp 51077 has strength 13.69; Genemark calls start at 51077
    /note=SSC: 51077-50529 CP: yes SCS: both ST: NA BLAST-Start: [phosphatase [Gordonia phage Yago84]],,NCBI, q1:s1 100.0% 5.31555E-120 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.95, -2.9063687850157054, yes F: phosphatase SIF-BLAST: ,,[phosphatase [Gordonia phage Yago84]],,QDF17587,94.5055,5.31555E-120 SIF-HHPRED: HAD_PNKP-C; C-terminal phosphatase domain of T4 polynucleotide kinase/phosphatase (PNKP) and related phosphatases.,,,cd07502,76.9231,99.8 SIF-Syn: 
    /note=There was good coverage and a solid percentage on HHPRED that indicated this was a phosphatase. Along with that, on PhagesDB there were good matches that showed that this also agrees with phosphatase.

CDS complement (51074 - 51484)
  /gene="60"
  /product="gp60"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_60"
    /note=Original Glimmer call @bp 51481 has strength 16.06; Genemark calls start at 51481
    /note=SSC: 51484-51074 CP: no SCS: both-cs ST: SS BLAST-Start:  GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.291, -6.289697455117486, no F: hypothetical protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Does not have the longest ORF or the best SD score but all other evidence points to this being the correct start site.

CDS complement (51481 - 51846)
  /gene="61"
  /product="gp61"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_61"
    /note=Original Glimmer call @bp 51846 has strength 14.15; Genemark calls start at 51846
    /note=SSC: 51846-51481 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_MARIOKART_56 [Gordonia phage Mariokart]],,NCBI, q1:s1 93.3884% 2.19184E-42 GAP: 54 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.723, -3.2921018957843318, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_MARIOKART_56 [Gordonia phage Mariokart]],,QNL30183,77.0642,2.19184E-42 SIF-HHPRED:  SIF-Syn: 
    /note=There was very little coverage and the percentage that was on HHPRED was not the greatest, this was an indication that there wasn`t a function. Along with that, there was little evidence that this could have a function on PhagesDB.

CDS complement (51901 - 52110)
  /gene="62"
  /product="gp62"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_62"
    /note=Original Glimmer call @bp 52110 has strength 8.64; Genemark calls start at 52110
    /note=SSC: 52110-51901 CP: yes SCS: both ST: SS BLAST-Start:  GAP: 370 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.348, -2.033982896655645, yes F: hypothetical protein SIF-BLAST:  SIF-HHPRED: DUF2710 ; Protein of unknown function (DUF2710),,,PF10921.11,63.7681,62.3 SIF-Syn: 
    /note=No data was available in NCBI BLAST.

CDS 52481 - 53263
  /gene="63"
  /product="gp63"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_63"
    /note=Original Glimmer call @bp 52481 has strength 15.85; Genemark calls start at 52481
    /note=SSC: 52481-53263 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_ANCLAR_57 [Gordonia phage AnClar]],,NCBI, q1:s1 94.2308% 8.44867E-49 GAP: 370 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.201, -2.253486910374644, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ANCLAR_57 [Gordonia phage AnClar]],,QIG58984,56.5385,8.44867E-49 SIF-HHPRED: DUF6444 ; Family of unknown function (DUF6444),,,PF20042.2,20.0,29.1 SIF-Syn: 

CDS 53357 - 53581
  /gene="64"
  /product="gp64"
  /function="ribbon-helix-helix DNA binding domain"
  /locus tag="LittleMunchkin_64"
    /note=Original Glimmer call @bp 53357 has strength 9.18; Genemark calls start at 53357
    /note=SSC: 53357-53581 CP: yes SCS: both ST: NA BLAST-Start: [ribbon-helix-helix DNA binding domain protein [Gordonia phage AnClar]],,NCBI, q11:s4 85.1351% 2.48238E-12 GAP: 93 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.307, -7.1656611020127885, no F: ribbon-helix-helix DNA binding domain SIF-BLAST: ,,[ribbon-helix-helix DNA binding domain protein [Gordonia phage AnClar]],,QIG58985,61.5385,2.48238E-12 SIF-HHPRED:  SIF-Syn: 
    /note=Does not have most annotated start, Starterator is not applicable.

CDS 53578 - 54135
  /gene="65"
  /product="gp65"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_65"
    /note=Original Glimmer call @bp 53578 has strength 12.92; Genemark calls start at 53578
    /note=SSC: 53578-54135 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_YAGO84_60 [Gordonia phage Yago84]],,NCBI, q1:s1 95.6757% 1.2999E-16 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.191, -4.393431483114409, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_YAGO84_60 [Gordonia phage Yago84]],,QDF17591,49.1329,1.2999E-16 SIF-HHPRED: DUF983 ; Protein of unknown function (DUF983),,,PF06170.15,4.86486,28.1 SIF-Syn: 

CDS 54116 - 54709
  /gene="66"
  /product="gp66"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="LittleMunchkin_66"
    /note=Original Glimmer call @bp 54116 has strength 17.95; Genemark calls start at 54116
    /note=SSC: 54116-54709 CP: yes SCS: both ST: NI BLAST-Start: [helix-turn-helix DNA binding domain protein [Gordonia phage AnarQue]],,NCBI, q1:s1 100.0% 2.69437E-79 GAP: -20 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.685, -4.6114151184034835, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding domain protein [Gordonia phage AnarQue]],,UBF41670,81.383,2.69437E-79 SIF-HHPRED: HTH_58 ; Helix-turn-helix domain,,,PF19575.2,28.4264,97.2 SIF-Syn: 
    /note=Has the most annotated start, but does not call it.

CDS 54718 - 55008
  /gene="67"
  /product="gp67"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_67"
    /note=Original Glimmer call @bp 54718 has strength 7.74; Genemark calls start at 54718
    /note=SSC: 54718-55008 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_ANCLAR_61 [Gordonia phage AnClar]],,NCBI, q1:s1 100.0% 3.04358E-45 GAP: 8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.201, -2.7806870294376242, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ANCLAR_61 [Gordonia phage AnClar]],,QIG58988,89.4737,3.04358E-45 SIF-HHPRED: DUF6360 ; Family of unknown function (DUF6360),,,PF19887.2,35.4167,75.7 SIF-Syn: 

CDS 55005 - 55526
  /gene="68"
  /product="gp68"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_68"
    /note=Original Glimmer call @bp 55005 has strength 11.78; Genemark calls start at 55023
    /note=SSC: 55005-55526 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein SEA_ANCLAR_62 [Gordonia phage AnClar]],,NCBI, q4:s6 98.2659% 6.34858E-102 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.506, -3.8116689268127657, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ANCLAR_62 [Gordonia phage AnClar]],,QIG58989,88.5714,6.34858E-102 SIF-HHPRED: g.41.3.5 (A:3-40) Hypothetical protein PA0128, N-terminal domain {Pseudomonas aeruginosa [TaxId: 287]},,,d2akla2,5.78035,60.2 SIF-Syn: 

CDS 55523 - 56035
  /gene="69"
  /product="gp69"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_69"
    /note=Original Glimmer call @bp 55523 has strength 13.82; Genemark calls start at 55523
    /note=SSC: 55523-56035 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_ANCLAR_63 [Gordonia phage AnClar]],,NCBI, q3:s6 98.8235% 4.20442E-54 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.281, -4.192397292939198, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ANCLAR_63 [Gordonia phage AnClar]],,QIG58990,76.5363,4.20442E-54 SIF-HHPRED: DUF2197 ; Uncharacterized protein conserved in bacteria (DUF2197),,,PF09963.12,8.82353,63.2 SIF-Syn: 

CDS 56035 - 56247
  /gene="70"
  /product="gp70"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_70"
    /note=Original Glimmer call @bp 56035 has strength 15.76; Genemark calls start at 56035
    /note=SSC: 56035-56247 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_YAGO84_66 [Gordonia phage Yago84]],,NCBI, q1:s1 100.0% 1.0169E-43 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.961, -4.924073590240254, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_YAGO84_66 [Gordonia phage Yago84]],,QDF17597,100.0,1.0169E-43 SIF-HHPRED:  SIF-Syn: 
    /note=Do not have most annotated start, Starterator is not applicable.

CDS 56247 - 56384
  /gene="71"
  /product="gp71"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_71"
    /note=Original Glimmer call @bp 56247 has strength 12.2; Genemark calls start at 56247
    /note=SSC: 56247-56384 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_YAGO84_65 [Gordonia phage Yago84]],,NCBI, q1:s1 100.0% 7.40319E-21 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.175, -5.447869148985249, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_YAGO84_65 [Gordonia phage Yago84]],,QDF17596,97.7778,7.40319E-21 SIF-HHPRED:  SIF-Syn: 
    /note=One possible TMH, no sure function based on this.

CDS 56388 - 56942
  /gene="72"
  /product="gp72"
  /function="HNH endonuclease"
  /locus tag="LittleMunchkin_72"
    /note=Original Glimmer call @bp 56388 has strength 8.51; Genemark calls start at 56388
    /note=SSC: 56388-56942 CP: yes SCS: both ST: NA BLAST-Start: [HNH endonuclease [Gordonia phage Yago84]],,NCBI, q3:s13 98.913% 1.52641E-100 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.324, -4.105706954229964, yes F: HNH endonuclease SIF-BLAST: ,,[HNH endonuclease [Gordonia phage Yago84]],,QDF17602,77.6699,1.52641E-100 SIF-HHPRED:  SIF-Syn: 
    /note=Do not have most annotated start, Starterator not applicable.

CDS complement (56916 - 57116)
  /gene="73"
  /product="gp73"
  /function="toxin in toxin/antitoxin system, HicA-like"
  /locus tag="LittleMunchkin_73"
    /note=Original Glimmer call @bp 57116 has strength 13.67; Genemark calls start at 57116
    /note=SSC: 57116-56916 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_MARIOKART_70 [Gordonia phage Mariokart]],,NCBI, q1:s1 100.0% 1.49414E-28 GAP: 48 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.031, -3.2535385006449706, yes F: toxin in toxin/antitoxin system, HicA-like SIF-BLAST: ,,[hypothetical protein SEA_MARIOKART_70 [Gordonia phage Mariokart]],,QNL30197,86.3636,1.49414E-28 SIF-HHPRED:  SIF-Syn: 
    /note=Do not have most annotated start, Starterator is not applicable.

CDS complement (57165 - 57560)
  /gene="74"
  /product="gp74"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_74"
    /note=Original Glimmer call @bp 57560 has strength 15.88; Genemark calls start at 57560
    /note=SSC: 57560-57165 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_ANCLAR_72 [Gordonia phage AnClar]],,NCBI, q1:s1 100.0% 2.64058E-67 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.456, -3.8362837638757656, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ANCLAR_72 [Gordonia phage AnClar]],,QIG58999,84.7328,2.64058E-67 SIF-HHPRED:  SIF-Syn: 

CDS complement (57553 - 58287)
  /gene="75"
  /product="gp75"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_75"
    /note=Original Glimmer call @bp 58287 has strength 13.94; Genemark calls start at 58287
    /note=SSC: 58287-57553 CP: no SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_YAGO84_73 [Gordonia phage Yago84]],,NCBI, q13:s5 89.3443% 1.85713E-85 GAP: 40 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.201, -2.253486910374644, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_YAGO84_73 [Gordonia phage Yago84]],,QDF17604,63.0597,1.85713E-85 SIF-HHPRED:  SIF-Syn: 
    /note=Do not have most annotated start, Starterator is not applicable.

CDS complement (58328 - 58648)
  /gene="76"
  /product="gp76"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_76"
    /note=Original Glimmer call @bp 58648 has strength 19.35; Genemark calls start at 58648
    /note=SSC: 58648-58328 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_CLOVERMINNIE_74 [Gordonia phage CloverMinnie]],,NCBI, q1:s1 92.4528% 6.47683E-34 GAP: 114 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.696, -3.284949965096066, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_CLOVERMINNIE_74 [Gordonia phage CloverMinnie]],,QFG11221,72.449,6.47683E-34 SIF-HHPRED:  SIF-Syn: 
    /note=NCBI Blast gave a good ratio and % coverage is good. HHPRED is not helpful, the probability is not good. Starterator shows LittleMunchkin in Most annotated

CDS complement (58763 - 59392)
  /gene="77"
  /product="gp77"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_77"
    /note=Original Glimmer call @bp 59392 has strength 10.26; Genemark calls start at 59392
    /note=SSC: 59392-58763 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_YAGO84_75 [Gordonia phage Yago84]],,NCBI, q3:s5 87.5598% 5.00582E-61 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.417, -6.419545529284328, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_YAGO84_75 [Gordonia phage Yago84]],,QDF17606,55.2419,5.00582E-61 SIF-HHPRED:  SIF-Syn: 
    /note=NCBI Blast isn`t helpful in showing what the function is. The ratio was off and the percent coverage is not much. Phagesdb gave no known function. Probability from HHPRED isn`t helpful as well and coverage is not great. Not the longest ORF. Starterator is not informative.

CDS complement (59389 - 59781)
  /gene="78"
  /product="gp78"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_78"
    /note=Original Glimmer call @bp 59781 has strength 8.82; Genemark calls start at 59781
    /note=SSC: 59781-59389 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_YAGO84_76 [Gordonia phage Yago84]],,NCBI, q11:s49 92.3077% 7.1533E-40 GAP: 31 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.113, -5.3013323934651755, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_YAGO84_76 [Gordonia phage Yago84]],,QDF17607,52.2472,7.1533E-40 SIF-HHPRED:  SIF-Syn: 
    /note=Did not call most annotated start, Starterator not informative. Selected start site captures the most coding potential out of possible start sites. Both host-trained and self-trained GeneMarks were considered.

CDS complement (59813 - 59953)
  /gene="79"
  /product="gp79"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_79"
    /note=Original Glimmer call @bp 59953 has strength 3.95
    /note=SSC: 59953-59813 CP: yes SCS: glimmer ST: NA BLAST-Start: [HNH endonuclease [Gordonia phage Skog] ],,NCBI, q1:s1 78.2609% 5.35713E-12 GAP: 62 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.19, -2.338663114094478, yes F: hypothetical protein SIF-BLAST: ,,[HNH endonuclease [Gordonia phage Skog] ],,YP_010059282,19.2771,5.35713E-12 SIF-HHPRED:  SIF-Syn: 

CDS complement (60016 - 61029)
  /gene="80"
  /product="gp80"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_80"
    /note=Original Glimmer call @bp 61029 has strength 21.1; Genemark calls start at 61029
    /note=SSC: 61029-60016 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_YAGO84_77 [Gordonia phage Yago84]],,NCBI, q1:s1 99.7033% 0.0 GAP: 198 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.201, -2.604595770381943, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_YAGO84_77 [Gordonia phage Yago84]],,QDF17608,89.5833,0.0 SIF-HHPRED: DUF932 ; Domain of unknown function (DUF932),,,PF06067.14,71.2166,99.9 SIF-Syn: 
    /note=Glimmer and genemark agree on the start site. Starterator not informative. Not the longest ORF. No useful information from HHPRED and Phagesdb about function. The ratios and probability shown are very off so none are useful. NCBI blast shows okay coverage but the ratios are off.

CDS complement (61228 - 61488)
  /gene="81"
  /product="gp81"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_81"
    /note=Original Glimmer call @bp 61488 has strength 19.05; Genemark calls start at 61488
    /note=SSC: 61488-61228 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein FDJ57_gp75 [Gordonia phage Sour] ],,NCBI, q1:s1 100.0% 2.6213E-14 GAP: 155 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.614, -3.4515614587161716, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein FDJ57_gp75 [Gordonia phage Sour] ],,YP_009625646,63.0952,2.6213E-14 SIF-HHPRED:  SIF-Syn: 
    /note=Do not have most annotated start, Starterator is not informative.

CDS complement (61644 - 61979)
  /gene="82"
  /product="gp82"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_82"
    /note=Original Glimmer call @bp 61979 has strength 15.99; Genemark calls start at 61979
    /note=SSC: 61979-61644 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein KNU14_gp77 [Gordonia phage Buggaboo] ],,NCBI, q1:s1 100.0% 1.18314E-30 GAP: 441 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.201, -2.3335289980954053, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein KNU14_gp77 [Gordonia phage Buggaboo] ],,YP_010098871,75.4545,1.18314E-30 SIF-HHPRED:  SIF-Syn: 
    /note=Do not have most annotated start, Starterator is not informative., single transmembrane domain predicted by TmHmm

CDS complement (62421 - 62678)
  /gene="83"
  /product="gp83"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_83"
    /note=Original Glimmer call @bp 62678 has strength 17.84; Genemark calls start at 62678
    /note=SSC: 62678-62421 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_YAGO84_81 [Gordonia phage Yago84] ],,NCBI, q1:s1 100.0% 7.58983E-49 GAP: 11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.696, -3.364992052816827, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_YAGO84_81 [Gordonia phage Yago84] ],,QDF17612,94.1176,7.58983E-49 SIF-HHPRED:  SIF-Syn: 
    /note=Went with 62678 start site to agree with AnClar and Yago84 start sites and capture better Shine-Dalgarno score and agree with Glimmer and GeneMark, even though start site 62693 has 4 base pair overlap

CDS complement (62690 - 62848)
  /gene="84"
  /product="gp84"
  /function="membrane protein"
  /locus tag="LittleMunchkin_84"
    /note=Original Glimmer call @bp 62848 has strength 15.53; Genemark calls start at 62848
    /note=SSC: 62848-62690 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_UPYO_34 [Gordonia phage Upyo]],,NCBI, q4:s3 94.2308% 2.54789E-13 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.193, -6.347770337501965, no F: membrane protein SIF-BLAST: ,,[hypothetical protein SEA_UPYO_34 [Gordonia phage Upyo]],,QLF84013,78.8462,2.54789E-13 SIF-HHPRED:  SIF-Syn: 
    /note=Do not have most annotated start, Starterator is not informative.

CDS complement (62845 - 63081)
  /gene="85"
  /product="gp85"
  /function="hypothetical protein"
  /locus tag="LittleMunchkin_85"
    /note=Original Glimmer call @bp 63081 has strength 17.46; Genemark calls start at 63081
    /note=SSC: 63081-62845 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_YAGO84_83 [Gordonia phage Yago84] ],,NCBI, q1:s1 100.0% 1.29647E-41 GAP: 0 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.696, -3.4259484787582526, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_YAGO84_83 [Gordonia phage Yago84] ],,QDF17614,91.0256,1.29647E-41 SIF-HHPRED:  SIF-Syn: