CDS 1 - 525 /note=no functional matches in databases CDS 522 - 1922 /note=clear function and synteny CDS 1953 - 3350 /note=clear function and synteny CDS 3356 - 4024 /note=clear function and synteny CDS 4108 - 4668 /note=clear function and synteny CDS 4708 - 5634 /note=clear function and synteny CDS 5631 - 5879 /note=no functional matches in databases CDS 5951 - 6085 /note=This start site is the least negatvie final score and highest Z-score. Neither start sites had all GM coding capacity. Other similar phages like BigRedClifford and BonesMcCoy also called this start site. CDS 6114 - 6527 /note=no functional matches in database CDS 6493 - 6906 /note=Glimmer and Starterator both call this start site, and it is the most annotated start in this pham. CDS 6903 - 7244 /note=Called the function minor capsid protein but some phages called minor tail protein, and both of these functions are coming up in HHPred. Also this gene is upstream from the tapemeasure protein, so it is unlikely that it is a minor tail protein. CDS 7247 - 7606 /note=clear function and synteny CDS 7603 - 7839 /note=no functional matches in databases CDS 7854 - 8351 /note=clear function and synteny CDS 8382 - 8951 /note=clear function and synteny CDS 8966 - 9337 /note=Chose this start site becasue this covers the maxium amount of coding potential without overlap of the nex gene. Other annotations hafve also extended the length beyond what starterator is calling. CDS 9362 - 11632 /note=clear function and synteny CDS 11629 - 12402 /note=clear function and synteny CDS 12402 - 14828 /note=clear function and synteny CDS 14828 - 15013 /note=no functional matches in databases CDS 15010 - 15606 /note=no functional matches in databases CDS 15606 - 16094 /note=no functional matches in database CDS 16091 - 18229 /note=This start site has the ideal gap of -4 and it is the LORF. In addition of members of this pham also call this start site. CDS 18259 - 19065 /note=Calling the protein function endolysin because it is not a mycobacterium and there is no lysin b, so it does not qualify to be a lysin a. CDS 19100 - 19489 /note=Cannot be membrane protein because not enough TMHs were predicted. CDS 19494 - 19835 /note=clear function and synteny CDS 19895 - 20305 /note=no functional matches in databases CDS complement (20373 - 20561) /note=no functional matches in databases CDS complement (20632 - 20784) /note=no functional matches in databases CDS complement (20799 - 20957) /note=no functional matches in databases CDS complement (20954 - 21796) /note=no functional matches in databases CDS complement (21840 - 22178) /note=Called the function membrane protein because of NCBI blast and the similarity to membrane protein in Alyxandracam, Strathdee, and WildNOut. CDS complement (22188 - 22430) /note=clear function and synteny CDS complement (22427 - 24028) /note=There is too much overlap with the start site predicted by genemark. CDS complement (24073 - 24366) /note=clear function and synteny CDS complement (24370 - 25212) /note=no functional matches in databases CDS complement (25245 - 25913) /note=clear function and synteny CDS complement (25910 - 27085) /note=Although Genemark predicted the start site of 27094, both Starterator and Glimmer predicted the start site 27085. In addition, the start site 27085 has the least negative final score and the highest Z-score. It also has a smaller gap than 27094. Chose this function due to similarity to BigRedClifford, WildNOut, and Klimt. CDS complement (27072 - 28937) /note=Start site 28937 is the most annotated start, least negative final score, and highest z-score. It also maximizes potential coding capacity. For these reasons I chose this even though genemark and starterator did not. CDS complement (29137 - 29562) /note=No functional matches in databases; there is no open reading frame between gene 40 ad 41. CDS complement (29733 - 31121) /note=clear function and synteny CDS complement (31121 - 31714) /note=clear function and synteny CDS complement (31711 - 32007) /note=no functional matches in databases CDS complement (32007 - 32285) /note=no functional matches in databases CDS complement (32285 - 33091) /note=clear function and synteny CDS complement (33088 - 33813) /note=Genemark, Glimmer, and Starterator all called this start site, and phages in this pham have this large of overlap too. CDS complement (33791 - 34372) /note=clear function and synteny CDS complement (34385 - 35317) /note=clear function and synteny CDS complement (35310 - 35543) /note=no functional matches in databases CDS complement (35606 - 35902) /note=no functional matches in databases CDS complement (35899 - 36666) /note=clear function and synteny CDS complement (36786 - 36998) /note=no functional matches in databases CDS complement (37077 - 37301) /note=Although Genemark called the start site 3782, Starterator and glimmer both called the start 37301. Start 37382 is the LORF, but start site 37301 is the least negative final score and highest Z score. Both of them have all GM coding capacity. CDS complement (37366 - 37632) /note=no functional matches in databases CDS complement (37704 - 38000) /note=no functional matches in databases CDS complement (38092 - 38286) /note=No functional matches in databases CDS complement (38325 - 38630) /note=No functional matches in databases CDS complement (38627 - 38812) /note=No functional matches in databases CDS complement (38814 - 39545) /note=No functional matches in databases CDS complement (39639 - 40025) /note=Both Glimmer and Starterator called the start site 39977, but GeneMark called the start site of 40025. I chose the start site 40025 because it is the LORF, and it has the ideal gap of -4. CDS complement (40022 - 40381) /note=Both Glimmer and Starterator called the start site 40351, but GeneMark called the start site of 40381. I chose the start site 40381 because it is the LORF, and it has the ideal gap of -4. CDS complement (40378 - 40611) /note=This start site does not agree with starterator, but it maximizes coding capacity coverage, and it is the msot called start. /note=There are no hits on BLASTx in NCBI for this gap. CDS 40975 - 41616 /note=Although genemark and starterator did not predict this start site, this start site is the LORF and the most called start.