CDS 53 - 535
    /note=Best Z and Final scores. Strong evidence for the function. Glimmer and GeneMark suggest same start.

CDS 1111 - 2790
    /note=The suggested start has the best Z and final score. Also has the maximum coding capacity.

CDS 2787 - 4241
    /note=The Glimmer start maximizes coding potential.

CDS 4216 - 4839
    /note=Both Glimmer and Gene Mark suggested the same start.
    /note=Some phages are calling the function of this gene as MuF-like minor capsid protein.

CDS 4889 - 5350
    /note=Both Glimmer and GeneMark have the same suggested start. Best Z and final score.

CDS 5370 - 6326
    /note=HHPRED also blast it for Major head protein; capsid, phage.

CDS 6393 - 6905
    /note=Both glimmer and GeneMark suggest the same start. Best final and Z score.

CDS 6902 - 7243
    /note=Suggested start has best Z and final score. Glimmer and GeneMark suggest same start.

CDS 7492 - 7902
    /note=Both Glimmer and GeneMark suggest same start. Best Z and final score. Evidence for tail terminator on HHPRED

CDS 7911 - 8756
    /note=Glimmer and gene mark start are same. The start avoids a 49bp overlap. Best Z and final score.

CDS 8858 - 9151
    /note=Glimmer and GeneMark suggest same start location. HHPRED signal this gene function as tail assembly protein.

CDS join(8858..9127,9127..9612)
    /note=This is a frameshift. The slippery nucleotide is 9127.

CDS 9629 - 14398
    /note=Glimmer and GeneMark suggest the same start. However, when we changed the start to expand coding potential and have better Z and Final scores, there is an increase in alignment, identity, and coverage when compared to other phages.

CDS 14395 - 15366
    /note=Glimmer suggests start and maximum coding capacity. Best Z and final score.

CDS 15360 - 17060
    /note=We picked GM suggested start to maximize coding capacity. There is evidence to transmembrane protein.

CDS 17071 - 17469
    /note=Glimmer suggested start have the best Z and final scores.

CDS 17466 - 18056
    /note=Glimmer and GeneMark suggest same start. Best Z and final score.

CDS 18060 - 19022
    /note=Same start with glimmer and GeneMark. Good Z and final score.

CDS 19019 - 19300
    /note=Glimmer and GeneMark suggest same start.

CDS 19350 - 19838
    /note=Glimmer and GeneMark suggest same start.

CDS 19945 - 20151
    /note=Glimmer suggest start location. Maximum coding capacity.

CDS 20151 - 21248
    /note=Glimmer and GeneMark suggest same start. Best Z and final score.

CDS 21259 - 21600
    /note=The glimmer and GeneMark have the same start. Best Z and final score.

CDS 21603 - 22553
    /note=Glimmer and GeneMark start in same location. Best Z and final score.

CDS 22557 - 23063
    /note=The Gene Mark starting point and glimmer starting point are the same.

CDS complement (23144 - 23653)
    /note=The glimmer and gene mark starting points are in the same spot. Best Z and final score.

CDS complement (23718 - 24002)
    /note=Glimmer and GeneMark suggest same start. Selected gene has best Z- and final score.

CDS complement (24123 - 24716)
    /note=Glimmer and GeneMark suggest best start. Best final and Z score.

CDS 24834 - 25118
    /note=GeneMark suggests a start site with maximum coding capacity, despite the lower Z and final scores.

CDS complement (25241 - 25597)
    /note=Glimmer and Gene Mark suggest same start. Best Z and final score.

CDS 25796 - 26188
    /note=Glimmer and GeneMark suggest same start. Best Z and final score.

CDS 26185 - 26280
    /note=Yummy and Horseradish (on the same cluster) have "membrane protein" for this gene function on NCBI, and that`s why we picked membrane protein as function assuming the genomes were QCed and corrections were made.

CDS 26335 - 26550
    /note=Glimmer and Genemark started in the same start.

CDS complement (26598 - 26885)
    /note=Glimmer and GeneMark suggest same start. HHPRED shows 99.5 and 95.7% of probability and coverage, respectively, for Nuclease, hydrolase.

CDS complement (26882 - 27277)
    /note=Glimmer and GeneMark suggest same start. We were conservative here, but NCBI suggests 93.12% and 96.18% for identity and alignment, respectively, for a peptidase function for the pham 72290.

CDS complement (27274 - 27432)
    /note=Glimmer and GeneMark suggest same start. Best Z and final score.

CDS complement (27436 - 27663)
    /note=We decided to call this gene function a "membrane protein" based on the results of the DeepTMHMM. The guide suggests that without evidence for a specific function, this protein could be annotated as a membrane protein.

CDS complement (27706 - 28251)
    /note=Best Z and final score.

CDS complement (28251 - 29087)
    /note=We picked the start suggested by GM because it maximizes coding capacity.

CDS complement (29112 - 30140)
    /note=Glimmer and GeneMark suggest same start. Best Z and final score.

CDS complement (30137 - 30445)
    /note=Best Z and final score. Glimmer and GeneMark suggest same start. Orphan pham.

CDS complement (30442 - 32832)
    /note=Glimmer Score and GeneMark suggest the same start.

CDS complement (32829 - 33296)
    /note=Glimmer and GeneMark suggest same start. Best Z and final score.

CDS complement (33293 - 33541)
    /note=Glimmer and GeneMark suggest same start.

CDS complement (33538 - 34386)
    /note=Glimmer and GeneMark suggest same start. Best Z and final score.

CDS complement (34383 - 34529)
    /note=Gimmer and GeneMark suggest same start. Best Z and final score.

CDS complement (34529 - 35377)
    /note=Glimmer and GeneMark suggest same start. Nor the best Z or Final scores, but maximizes coding potential.

CDS complement (36288 - 36524)
    /note=Glimmer and GeneMark suggest same start. Best Z and final score.

CDS complement (36526 - 36981)
    /note=The suggest start maximizes coding capacity. This function is not on the Function Assignments list provided by SEA.

CDS complement (36978 - 37490)
    /note=Glimmer and GeneMark suggest same start. In several phages, the fuction of this gene is "thymidylate kinase". However, the fucntion assignment list has two kinases: "polynucleotide kinase" or "serine/threonine kinase".

CDS complement (37487 - 38965)
    /note=Glimmer and GeneMark starting points are in the same position. Pham #212243 is associated with DNA helicase in several clusters.

CDS complement (38962 - 39234)
    /note=Glimmer and GeneMark suggest same start. Best Z and final score.

CDS complement (39234 - 39407)
    /note=Glimmer and GeneMark sugested start avoids major overlaps .

CDS complement (39400 - 39606)
    /note=Glimmer and GeneMark suggest same start.

CDS complement (39603 - 40046)
    /note=Glimmer Start and Gene Mark suggested start avoid major overlaps.

CDS 40074 - 42071
    /note=Glimmer and GeneMark suggest same start. Best final score and full coding capacity.

CDS 42399 - 42542
    /note=This is an orphan pham. However, when the start is changed to the largest possible ORF, we get a BLAST with PHAGESDB. No NCBI BLASTs.

CDS 42576 - 42899
    /note=We favored GM start.

CDS 42896 - 43027
    /note=Glimmer suggests the selected start. Best Z and final score. Orphan pham.

CDS 43345 - 43440
    /note=Orphan pham. Very low identity and alignment (40%) on NCBI.

CDS 43437 - 43544
    /note=Orphan pham. BLAST results are very poor and do not coincide with the pham number.

CDS 43928 - 44308
    /note=Glimmer start was selected because it has best Z- and Final score.

CDS 44746 - 45087
    /note=Selected gene start suggested by Glimmer. It has best Z- and final scores.

CDS complement (45698 - 46114)
    /note=GeneMark does not suggest a start fir this gene, and the start suggested by Glimmer have low Z and Final scores. NCBI Blast did not run in PECAAN, but when the gene sequence was copied and pasted on the NCBI website, it revealed high similarity with a gene on SweatNTears. We wonder if this gene should be deleted.