Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014493.1 Corchorus capsularis cultivar CVL-1 contig14514, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 28644
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:6631 original size:113 final size:114
Alignment explanation
Indices: 6433--6667 Score: 454
Period size: 113 Copynumber: 2.1 Consensus size: 114
6423 TCCGAATTCA
*
6433 AAATAAATATTAAATATATAAAAGTGAGCTCTAAAATGCCATATTCAAAATGTCATAATCCAACT
1 AAATAAATATTAAATATATAAAAGTAAGCTCTAAAATGCCATATTCAAAATGTCATAATCCAACT
6498 AATTTAAGCACATAATGAA-TTTTTTTTTCTTCGAAAATTACAAAATGC
66 AATTTAAGCACATAATGAATTTTTTTTTTCTTCGAAAATTACAAAATGC
6546 AAATAAATATTAAATATATAAAAGTAAGCTCTAAAATGCCATATTCAAAATGTCATAATCCAACT
1 AAATAAATATTAAATATATAAAAGTAAGCTCTAAAATGCCATATTCAAAATGTCATAATCCAACT
6611 AATTTAAGCACATAATGAATTTTTTTTTTCTTCGAAAATTACAAAATGC
66 AATTTAAGCACATAATGAATTTTTTTTTTCTTCGAAAATTACAAAATGC
6660 AAATAAAT
1 AAATAAAT
6668 TCATTCAAAT
Statistics
Matches: 120, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
113 83 0.69
114 37 0.31
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.34
Consensus pattern (114 bp):
AAATAAATATTAAATATATAAAAGTAAGCTCTAAAATGCCATATTCAAAATGTCATAATCCAACT
AATTTAAGCACATAATGAATTTTTTTTTTCTTCGAAAATTACAAAATGC
Found at i:7859 original size:13 final size:13
Alignment explanation
Indices: 7841--7865 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7831 TGGCTGAGAA
7841 TATATATATATAG
1 TATATATATATAG
7854 TATATATATATA
1 TATATATATATA
7866 TATTAAGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
TATATATATATAG
Found at i:9571 original size:45 final size:46
Alignment explanation
Indices: 9493--9586 Score: 147
Period size: 45 Copynumber: 2.1 Consensus size: 46
9483 TAACTCATGT
9493 TTCTTTACTTTTACACATTTTGACAGAAATAATAGAAGGAAGGAAA
1 TTCTTTACTTTTACACATTTTGACAGAAATAATAGAAGGAAGGAAA
* *
9539 TTCTTTAC-TTTACCACATTTTGAC-GGAATAATAGATGGAAGGAAA
1 TTCTTTACTTTTA-CACATTTTGACAGAAATAATAGAAGGAAGGAAA
9584 TTC
1 TTC
9587 AAAAGACTGT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
45 26 0.58
46 19 0.42
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (46 bp):
TTCTTTACTTTTACACATTTTGACAGAAATAATAGAAGGAAGGAAA
Found at i:25160 original size:51 final size:52
Alignment explanation
Indices: 25056--25179 Score: 232
Period size: 51 Copynumber: 2.4 Consensus size: 52
25046 ATTTAAAAAG
25056 TTTAAAAGACTTAGTAATTAGGGAGACGGATGAGGGCTGTCCCTCCAAACAT
1 TTTAAAAGACTTAGTAATTAGGGAGACGGATGAGGGCTGTCCCTCCAAACAT
25108 TTTAAAAGACTTAGTAATTAGGGAGAC-GATGAGGGCTGTCCCTCCAAACAT
1 TTTAAAAGACTTAGTAATTAGGGAGACGGATGAGGGCTGTCCCTCCAAACAT
*
25159 TTTAAAAGATTTAGTAATTAG
1 TTTAAAAGACTTAGTAATTAG
25180 CATAGTGTGA
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
51 44 0.62
52 27 0.38
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.28
Consensus pattern (52 bp):
TTTAAAAGACTTAGTAATTAGGGAGACGGATGAGGGCTGTCCCTCCAAACAT
Found at i:25392 original size:5 final size:5
Alignment explanation
Indices: 25382--25422 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
25372 GCTGATAAAA
*
25382 TCTTT TCTTT TCTTT TCTTT TCTTT TTTCTT TC-TT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCT-TT TCTTT TCTTT T
25423 TTTCCCCTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 4 0.12
5 25 0.78
6 3 0.09
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TCTTT
Found at i:25423 original size:15 final size:15
Alignment explanation
Indices: 25382--25425 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
25372 GCTGATAAAA
*
25382 TCTTTTCTTTTCTTT
1 TCTTTTCTTTTTTTT
25397 TCTTTTCTTTTTTCTT
1 TCTTTTCTTTTTT-TT
25413 TC-TTTCTTTTTTT
1 TCTTTTCTTTTTTT
25426 CCCCTAAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 1 0.04
15 22 0.81
16 4 0.15
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TCTTTTCTTTTTTTT
Found at i:28190 original size:315 final size:318
Alignment explanation
Indices: 27630--28597 Score: 1039
Period size: 315 Copynumber: 3.0 Consensus size: 318
27620 AAATTTTTTA
* * * * * * *
27630 CCACGATACTCATAAAAAATATATAATTCAACGCCAGAAAGATTGAAAAGTTTTTCACACTTCTA
1 CCACCATACTCATAAAAAATATATAATTCAAAGCCAAAAAGATTGAAAGGCTTCTCACGCTTCTA
* * * * *
27695 ATATTGGTTTTCATATTTTT-CCGAATTAATTTCTGATAAAATCGAAACATGATTCAGATGGTCG
66 ATATTGG-TTTCATATTTTTCCCGAATTAATTTCTAATTAAATCGAAACAGGATTCAGATGCTCA
*
27759 TAAAAAAAAACCTTAAATCCAATGT-AGTTGATATTTGGTTAGATGGATATAGATATTTCAATGA
130 TAAAAACAAA---TAAATCCAATGTGA-TTGATATTTGGTTAGATGGATATAGATATTTCAATGA
* *
27823 GACTTGGTGACAAAAATCATGCAAAACAGAGCTGGGACCTCGAAACGCGTTTTTAGTCAAAAACT
191 GACTTGGTGCCAAAAATCATGCAAAATAGAGC-GGGACC-CGAAACGCGTTTTTAGTCAAAAACT
27888 GTAATGGTTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACACGAAACATTTT-TCAA-G
254 GTAATGGTTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACACGAAACATTTTCTCAATG
* * *
27951 CCACCATAGTCA-AAAAAATATATAACTT-AACGCCAAAAAGATTGAAGGGCTTCTCACGCTT-T
1 CCACCATACTCATAAAAAATATATAA-TTCAAAGCCAAAAAGATTGAAAGGCTTCTCACGCTTCT
* * ** * *
28013 AAATATT-TTTTTATATTATTT-TTGAATTAATTTCTAATTAAATCGAAACCGGATTGAGATGCT
65 -AATATTGGTTTCATATT-TTTCCCGAATTAATTTCTAATTAAATCGAAACAGGATTCAGATGCT
* * * * * ** * *
28076 TATAAAACCAAA-AAATCCAATGTGACTGAGATTTCGTTAGATAAATATAGATAATTCAATGAGT
128 CATAAAAACAAATAAATCCAATGTGATTGATATTTGGTTAGATGGATATAGATATTTCAATGAGA
* * * * *
28140 CTTGGCGCCAAAAATCATGCAAAATTGAGACGGAGTCCC-AGAATGCGTTTTTAGCCAAAAAC--
193 CTTGGTGCCAAAAATCATGCAAAATAGAG-CGG-GACCCGA-AACGCGTTTTTAGTCAAAAACTG
* * * * *
28202 CAGAT-ATTAGTACACGATTTCGGCTAAAA-TTTATAAAAATTGACCCGAAAGAATTTTCCTCAA
255 TA-ATGGTTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACACGAAA-CATTTT-CTCAA
28265 TTTTTGG
317 ----T-G
* * *
28272 CCACGATACTCATAAAAAATATATAATTCAAAGCCAAAAATATTGAAAGGCTTTTCACGCTTCTA
1 CCACCATACTCATAAAAAATATATAATTCAAAGCCAAAAAGATTGAAAGGCTTCTCACGCTTCTA
* * *
28337 ATATTGGTTTCCTATTTTTCCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGT
66 ATATTGGTTTCATATTTTTCCCGAATTAATTTCTAATTAAATCGAAACAGGATTCAGATGCTCAT
* *
28402 AAAAATAAATCCTTAAATCCAATGTGGTTGATATTTGGTTAGATGGATATAGATATTTCAATGAG
131 AAAAACAAA----TAAATCCAATGTGATTGATATTTGGTTAGATGGATATAGATATTTCAATGAG
* * * * *
28467 AGTTGGTGCCAAAAATCATGCAAAATAGAGTTGGGACCCCGAAACACGATTTTAGTAAAAAAACT
192 ACTTGGTGCCAAAAATCATGCAAAATAGAG-CGGGA-CCCGAAACGCGTTTTTAGT-CAAAAACT
* *
28532 GTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACACGAAACATTTCTCCTCAA
254 GTAATGGTTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACACGAAACATTT-T-CTCAA
28597 T
317 T
28598 TACCGGCCAC
Statistics
Matches: 527, Mismatches: 85, Indels: 63
0.78 0.13 0.09
Matches are distributed among these distances:
312 19 0.04
313 29 0.06
314 3 0.01
315 94 0.18
316 5 0.01
318 8 0.02
319 46 0.09
320 46 0.09
321 25 0.05
322 51 0.10
323 53 0.10
327 1 0.00
328 86 0.16
329 7 0.01
330 2 0.00
331 27 0.05
332 25 0.05
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (318 bp):
CCACCATACTCATAAAAAATATATAATTCAAAGCCAAAAAGATTGAAAGGCTTCTCACGCTTCTA
ATATTGGTTTCATATTTTTCCCGAATTAATTTCTAATTAAATCGAAACAGGATTCAGATGCTCAT
AAAAACAAATAAATCCAATGTGATTGATATTTGGTTAGATGGATATAGATATTTCAATGAGACTT
GGTGCCAAAAATCATGCAAAATAGAGCGGGACCCGAAACGCGTTTTTAGTCAAAAACTGTAATGG
TTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACACGAAACATTTTCTCAATG
Done.