Phage AY216660.2

Gene Starts

Genes missing RBS 0 / 79

The following genes have issues with their RBS.

Since you have not annotated any possible RBSs, this does not count off from your overall score.

Feature Type ID Location Error Upstream (-15 .. -5)
gene CPT-T1_001.gene 40..576 [1] No RBS annotated, None found taaatgttaa
gene CPT-T1_002.gene 589..2184 [1] Unannotated but valid RBS taacttt AGG
gene CPT-T1_003.gene 2230..3522 [1] No RBS annotated, None found acggcccttt
gene CPT-T1_004.gene 3496..4273 [1] Unannotated but valid RBS cc GGAG ccgg
gene CPT-T1_005.gene 4264..5388 [1] No RBS annotated, None found tccagacttt
gene CPT-T1_006.gene 5389..5876 [1] No RBS annotated, None found agcaaagtaa
gene CPT-T1_007.gene 5926..6705 [1] No RBS annotated, None found tagtcctttt
gene CPT-T1_008.gene 6784..7755 [1] No RBS annotated, None found ttttttatta
gene CPT-T1_009.gene 7794..8093 [1] No RBS annotated, None found gtcccttttt
gene CPT-T1_010.gene 8127..8548 [1] No RBS annotated, None found agcgcctttt
gene CPT-T1_011.gene 8534..8919 [1] Unannotated but valid RBS atgac AGGA c
gene CPT-T1_012.gene 8897..9355 [1] No RBS annotated, None found atcgtccagt
gene CPT-T1_013.gene 9332..9743 [1] No RBS annotated, None found gcaatcaagc
gene CPT-T1_014.gene 9733..10414 [1] Unannotated but valid RBS tac GAG taga
gene CPT-T1_015.gene 10516..10845 [1] No RBS annotated, None found tgctatcaac
gene CPT-T1_016.gene 10516..11162 [1] No RBS annotated, None found tgctatcaac
gene CPT-T1_017.gene 11192..14076 [1] No RBS annotated, None found gttttttcgt
gene CPT-T1_018.gene 14067..14432 [1] Unannotated but valid RBS cattc AGGA a
gene CPT-T1_019.gene 14500..15294 [1] Unannotated but valid RBS gttgc AGGT a
gene CPT-T1_020.gene 15279..16025 [1] No RBS annotated, None found tgtcgcttca
gene CPT-T1_021.gene 16009..16621 [1] No RBS annotated, None found taatcgttcg
gene CPT-T1_022.gene 16688..20217 [1] No RBS annotated, None found ataaatagca
gene CPT-T1_023.gene 20251..20568 [1] No RBS annotated, None found atgccctttt
gene CPT-T1_024.gene 20556..21257 [1] No RBS annotated, None found cttaatagca
gene CPT-T1_025.gene 21279..21518 [-1] No RBS annotated, None found aatcacacta
gene CPT-T1_026.gene 21755..21906 [1] No RBS annotated, None found tgtatatcgt
gene CPT-T1_027.gene 22020..23098 [1] No RBS annotated, None found attcatcgta
gene CPT-T1_028.gene 23129..23820 [1] No RBS annotated, None found aaacaaataa
gene CPT-T1_029.gene 23854..24289 [1] No RBS annotated, None found tcgcccataa
gene CPT-T1_030.gene 24351..26550 [-1] No RBS annotated, None found cgtgctattt
gene CPT-T1_031.gene 26447..26600 [-1] No RBS annotated, None found tgcccattgc
gene CPT-T1_032.gene 26638..27585 [-1] No RBS annotated, None found cgcgtttttt
gene CPT-T1_033.gene 27635..28098 [-1] No RBS annotated, None found gcaaaaagtg
gene CPT-T1_034.gene 28168..30199 [1] No RBS annotated, None found gttacaacga
gene CPT-T1_035.gene 30181..30612 [1] No RBS annotated, None found caaagacttc
gene CPT-T1_036.gene 30669..31393 [1] No RBS annotated, None found atctcaccaa
gene CPT-T1_037.gene 31377..31641 [1] No RBS annotated, None found aaaacaaacg
gene CPT-T1_038.gene 31695..31917 [1] No RBS annotated, None found tcatagaaac
gene CPT-T1_039.gene 31881..32167 [1] No RBS annotated, None found cttcatctct
gene CPT-T1_040.gene 32099..32399 [1] Unannotated but valid RBS GAG ttttacc
gene CPT-T1_041.gene 32467..33611 [1] No RBS annotated, None found tttcattatc
gene CPT-T1_042.gene 33673..34166 [1] No RBS annotated, None found ttttatagaa
gene CPT-T1_043.gene 34226..34415 [1] No RBS annotated, None found accacatcga
gene CPT-T1_044.gene 34525..34749 [1] No RBS annotated, None found gttcaaaaaa
gene CPT-T1_045.gene 34739..35237 [1] Unannotated but valid RBS AGG cgcttaa
gene CPT-T1_046.gene 35227..35638 [1] No RBS annotated, None found acgcatattg
gene CPT-T1_047.gene 35761..36179 [-1] No RBS annotated, None found caatcctcga
gene CPT-T1_048.gene 36173..37755 [-1] No RBS annotated, None found tcacgccgtc
gene CPT-T1_049.gene 37741..38294 [-1] No RBS annotated, None found gacggcacaa
gene CPT-T1_050.gene 38277..38706 [-1] No RBS annotated, None found tcaagataac
gene CPT-T1_051.gene 38774..38994 [-1] No RBS annotated, None found tttacattaa
gene CPT-T1_052.gene 38987..39222 [-1] No RBS annotated, None found taccaaacaa
gene CPT-T1_053.gene 39289..39444 [-1] No RBS annotated, None found ggcatatcaa
gene CPT-T1_054.gene 39429..39758 [-1] No RBS annotated, None found tatcctgact
gene CPT-T1_055.gene 39766..39978 [-1] Unannotated but valid RBS tagc GGA tcg
gene CPT-T1_056.gene 39959..40342 [-1] No RBS annotated, None found acatcaacag
gene CPT-T1_057.gene 41020..41606 [1] No RBS annotated, None found tgtatattga
gene CPT-T1_058.gene 41606..41945 [1] Unannotated but valid RBS aaaatgt GGA
gene CPT-T1_059.gene 42013..42254 [1] Unannotated but valid RBS ac GAG atacc
gene CPT-T1_060.gene 42247..42487 [1] No RBS annotated, None found tcagcacttt
gene CPT-T1_061.gene 42473..42594 [1] No RBS annotated, None found ggcgacaaca
gene CPT-T1_062.gene 42580..42764 [1] No RBS annotated, None found ttgctactgt
gene CPT-T1_063.gene 42824..43324 [1] No RBS annotated, None found ccatcgacaa
gene CPT-T1_064.gene 43385..43881 [1] No RBS annotated, None found acatcaacca
gene CPT-T1_065.gene 43870..44030 [1] No RBS annotated, None found actcttgtcc
gene CPT-T1_066.gene 44098..44485 [1] No RBS annotated, None found gcacgacaac
gene CPT-T1_067.gene 44527..44649 [1] No RBS annotated, None found gttccccttt
gene CPT-T1_068.gene 44625..44852 [1] No RBS annotated, None found gacattatct
gene CPT-T1_069.gene 44898..45356 [1] No RBS annotated, None found cctacaccaa
gene CPT-T1_070.gene 45428..45970 [1] No RBS annotated, None found ttaagcaacc
gene CPT-T1_071.gene 45941..46451 [1] No RBS annotated, None found gcctgtgata
gene CPT-T1_072.gene 46444..47026 [1] No RBS annotated, None found tcacaaaaag
gene CPT-T1_073.gene 47085..47308 [1] No RBS annotated, None found ctcatcgaca
gene CPT-T1_074.gene 47293..47649 [1] No RBS annotated, None found cccgatcgaa
gene CPT-T1_075.gene 47637..47879 [1] No RBS annotated, None found aagtttttca
gene CPT-T1_076.gene 47864..48082 [1] Unannotated but valid RBS cgt AGGT aac
gene CPT-T1_077.gene 48235..48408 [1] No RBS annotated, None found gcggcaacaa
gene CPT-T1_078.gene 48377..48574 [1] No RBS annotated, None found ctggcgttat
gene CPT-T1_079.gene 48564..48803 [1] No RBS annotated, None found atattgaatt

Start Codon Usage

This section covers genes with unusual start codons

Start Codon Count
ATG74
GTG3
TTG2
Feature Type ID Location Error

Intergenic Gaps

Phage genomes are under pressure to maintain high coding density. Large intergenic gaps may be a sign of incorrect gene starts or missing genes.

Region Size Bounding Gene Transcription Direction Message
2184 .. 2238 54 → →
5876 .. 5937 61 → →
6705 .. 6795 90 → →
10414 .. 10527 113 → →
14432 .. 14511 79 → → 2 ORFs found in this region
16621 .. 16698 77 → →
21506 .. 21765 259 → →
21906 .. 22033 127 → →
24289 .. 24350 61 → → 1 ORFs found in this region
27573 .. 27634 61 → →
28087 .. 28180 93 → →
30612 .. 30679 67 → → 1 ORFs found in this region
31641 .. 31707 66 → →
32399 .. 32477 78 → → 1 ORFs found in this region
33611 .. 33683 72 → →
34166 .. 34238 72 → →
34415 .. 34533 118 → →
35638 .. 35760 122 → → 2 ORFs found in this region
38693 .. 38773 80 → → 2 ORFs found in this region
39211 .. 39288 77 → →
40330 .. 41030 700 → → 7 ORFs found in this region
41945 .. 42023 78 → →
42764 .. 42835 71 → →
43324 .. 43395 71 → →
44030 .. 44110 80 → →
44485 .. 44538 53 → →
44852 .. 44909 57 → →
45356 .. 45439 83 → → 6 ORFs found in this region
47026 .. 47098 72 → →
48082 .. 48246 164 → → 2 ORFs found in this region

Overlapping Genes

Large gene overlaps may indicate an incorrect gene start or miscalled gene.

Feature A Feature B Shared Region Overlap Length
CPT-T1_015.gene ([10516:10845](+)) CPT-T1_016.gene ([10516:11162](+)) 10527..10844 317 bp
CPT-T1_030.gene ([24351:26550](-)) CPT-T1_031.gene ([26447:26600](-)) 26446..26536 90 bp
CPT-T1_039.gene ([31881:32167](+)) CPT-T1_040.gene ([32099:32399](+)) 32111..32166 55 bp

Antisense Genes

Possible Morons 78 / 79 (Doesn't count towards score)

Feature RBS Surrounding Features
CPT-T1_025.gene No RBS Available → → → →

Annotation Issues

Missing Product Tags 79 / 79

Feature Qualifiers