Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010688.1 Corchorus capsularis cultivar CVL-1 contig10709, 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: 78097
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:5424 original size:2 final size:2
Alignment explanation
Indices: 5417--5443 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5407 TCATGGATTC
5417 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
5444 TCTTAAGCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:12490 original size:3 final size:3
Alignment explanation
Indices: 12470--12504 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
12460 TTGCTGTTAG
* *
12470 TGA TGA AGA TGG TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
12505 CAGAGTCATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.31, C:0.00, G:0.37, T:0.31
Consensus pattern (3 bp):
TGA
Found at i:14861 original size:6 final size:6
Alignment explanation
Indices: 14850--14875 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
14840 CTCAACTCCG
14850 TCTTCA TCTTCA TCTTCA TCTTCA TC
1 TCTTCA TCTTCA TCTTCA TCTTCA TC
14876 CCCGCTATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.35, G:0.00, T:0.50
Consensus pattern (6 bp):
TCTTCA
Found at i:34646 original size:1 final size:1
Alignment explanation
Indices: 34635--34680 Score: 65
Period size: 1 Copynumber: 46.0 Consensus size: 1
34625 CTTCTTCTTC
* **
34635 TTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAATTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
34681 AATACACTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.04, C:0.02, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:38949 original size:14 final size:14
Alignment explanation
Indices: 38930--38958 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
38920 TGAAGGAAAA
38930 TTACATATTGATAT
1 TTACATATTGATAT
38944 TTACATATTGATAT
1 TTACATATTGATAT
38958 T
1 T
38959 GCTTGTTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (14 bp):
TTACATATTGATAT
Found at i:42688 original size:26 final size:26
Alignment explanation
Indices: 42652--42702 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
42642 TTCGATCCCC
*
42652 TGCATCTCCAATATTTGTTTTCTTTT
1 TGCATCTCCAATATTTGTTATCTTTT
42678 TGCATCTCCAATATTTGTTATCTTT
1 TGCATCTCCAATATTTGTTATCTTT
42703 ATTTATTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.18, C:0.20, G:0.08, T:0.55
Consensus pattern (26 bp):
TGCATCTCCAATATTTGTTATCTTTT
Found at i:52507 original size:41 final size:41
Alignment explanation
Indices: 52462--52571 Score: 211
Period size: 41 Copynumber: 2.7 Consensus size: 41
52452 AGTGATTCTA
*
52462 GAAACTCTTCTTAATGTTTATCCCATAAGGGCTTCATATAT
1 GAAACTATTCTTAATGTTTATCCCATAAGGGCTTCATATAT
52503 GAAACTATTCTTAATGTTTATCCCATAAGGGCTTCATATAT
1 GAAACTATTCTTAATGTTTATCCCATAAGGGCTTCATATAT
52544 GAAACTATTCTTAATGTTTATCCCATAA
1 GAAACTATTCTTAATGTTTATCCCATAA
52572 TTAGATTGAG
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 68 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (41 bp):
GAAACTATTCTTAATGTTTATCCCATAAGGGCTTCATATAT
Found at i:55869 original size:31 final size:31
Alignment explanation
Indices: 55834--55940 Score: 133
Period size: 31 Copynumber: 3.5 Consensus size: 31
55824 CATGTGGCAT
* * *
55834 GTGGCATGCCATGTGTCACTTTTTGGTACAT
1 GTGGCATGACACGTGTCACTTTTTGGTACAC
* *
55865 GTGGCTTGACACGTGTCACTTTTGGGTACAC
1 GTGGCATGACACGTGTCACTTTTTGGTACAC
* *
55896 GTGGCGTGACACGTGTCACTTTTTGATACAC
1 GTGGCATGACACGTGTCACTTTTTGGTACAC
* *
55927 ATGGCATGCCACGT
1 GTGGCATGACACGT
55941 CGGGCACTGT
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 65 1.00
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (31 bp):
GTGGCATGACACGTGTCACTTTTTGGTACAC
Found at i:62392 original size:17 final size:17
Alignment explanation
Indices: 62370--62405 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
62360 GATTATGTGA
62370 TTAACTACTTTTTTTTT
1 TTAACTACTTTTTTTTT
62387 TTAACTACTTTTTTTTT
1 TTAACTACTTTTTTTTT
62404 TT
1 TT
62406 CCTGCAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (17 bp):
TTAACTACTTTTTTTTT
Found at i:71460 original size:31 final size:31
Alignment explanation
Indices: 71424--71510 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 31
71414 TTTTGTGCAC
* *
71424 GTGGCATATCACGTGCCATTTTTTGAAACAT
1 GTGGCATACCACGTGCCACTTTTTGAAACAT
* * **
71455 GTGGCATGCCACGTGTCACTTTTTGGTACAT
1 GTGGCATACCACGTGCCACTTTTTGAAACAT
* * * *
71486 GTGGCGTGCCACATGTCACTTTTTG
1 GTGGCATACCACGTGCCACTTTTTG
71511 GTACACGTGG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (31 bp):
GTGGCATACCACGTGCCACTTTTTGAAACAT
Found at i:71511 original size:31 final size:31
Alignment explanation
Indices: 71451--71528 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
71441 ATTTTTTGAA
* *
71451 ACATGTGGCATGCCACGTGTCACTTTTTGGT
1 ACATGTGGCGTGCCACATGTCACTTTTTGGT
71482 ACATGTGGCGTGCCACATGTCACTTTTTGGT
1 ACATGTGGCGTGCCACATGTCACTTTTTGGT
*
71513 ACACGTGGCGTGCCAC
1 ACATGTGGCGTGCCAC
71529 GTCGGACACC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.17, C:0.26, G:0.27, T:0.31
Consensus pattern (31 bp):
ACATGTGGCGTGCCACATGTCACTTTTTGGT
Found at i:75042 original size:14 final size:15
Alignment explanation
Indices: 75006--75042 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
74996 TGATTTAAAA
75006 AAACAGAAAAAATAG
1 AAACAGAAAAAATAG
75021 AAACAGAAAAAATAG
1 AAACAGAAAAAATAG
75036 AAA-AGAA
1 AAACAGAA
75043 GAGAAATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.76, C:0.05, G:0.14, T:0.05
Consensus pattern (15 bp):
AAACAGAAAAAATAG
Found at i:75224 original size:18 final size:21
Alignment explanation
Indices: 75190--75235 Score: 71
Period size: 19 Copynumber: 2.3 Consensus size: 21
75180 TTTTTTTTAA
75190 AAAAAATTATATATATT-ATC
1 AAAAAATTATATATATTAATC
75210 AAAAAATTAT-T-TATTAATC
1 AAAAAATTATATATATTAATC
75229 AAAAAAT
1 AAAAAAT
75236 ATGACGTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.16
19 11 0.44
20 10 0.40
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAAAATTATATATATTAATC
Found at i:76472 original size:323 final size:323
Alignment explanation
Indices: 75432--78095 Score: 3790
Period size: 324 Copynumber: 8.3 Consensus size: 323
75422 CTTTTACCTC
* * *
75432 ATAAAAACAAATCCATAAAATCGAATGTGGCTGGGATTTGCTTCGATAAATATAGATATTTCGAA
1 ATAAAAACAAATCCAT-AAATCGAATGTGGCTGAGATTTGCTTCGATGAATATAGATATTTCAAA
* *
75497 GAGTCTTTCTGCCAAAAATCATACAAAACTGATTCAGGACCCCGAAACGCGTTTTTAGCCCATAA
65 GAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAA
*
75562 ACTGTGATGGTTAGTACATGA-TTTCGGCTAAAAACTGACCCGGAAATTATTTTCCTAAATTTTT
130 ACTGTGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGGAAATT-TTTTCCTAAATTTTT
* * * *
75626 TGGCACAATACTCAGAATGAATAAATAATTCAACGTCAAATAGATTGACAGGCTTTTCACGCAAC
194 TGGCACAATACTCAGAATGAATAAATAATTCAACGCCAAAAAGATTGACAGACTTTTCACGCATC
* *
75691 TAATATCGTTTTT-TATTTTTTTCTGATTAATTTCTAA-TAAATCGAAACAAGATTCAGATGC-A
259 TAATATCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTA
* * ** *
75753 TATAAAAACAAATCCATAAATCAAATTTGAATGGGATTTGCTTCGATGAATATAGATATTTCAAA
1 -ATAAAAACAAATCCATAAATCGAATGTGGCTGAGATTTGCTTCGATGAATATAGATATTTCAAA
* * ** *
75818 GAGTCTTTATGCCAAAAATCATGCAAAATTGAGTCAGGACCTTGAAACGCGTTTTTAGCCTATAA
65 GAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAA
* * * *
75883 ACTATGATGGTTAGTACACGATTCTCGGCTAAAAACTGAACCGGAAATTTTTTCCTCAATTTTTT
130 ACTGTGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGGAAATTTTTTCCTAAATTTTTT
75948 GGCACAATACTCAGAATGAATAAATAATTCAACGCCAAAAAGATTGACAGACTTTTCACGCATCT
195 GGCACAATACTCAGAATGAATAAATAATTCAACGCCAAAAAGATTGACAGACTTTTCACGCATCT
* * *
76013 AATAT--TGTTT-T-TTTTTTCCCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTC
260 AATATCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTA
*
76073 ATAAAAACAAATCCATAAATCGACTGTGGCTGAGATTTGCTTCGATGAATATAGATATTTCAAAG
1 ATAAAAACAAATCCATAAATCGAATGTGGCTGAGATTTGCTTCGATGAATATAGATATTTCAAAG
* * *
76138 AGTCTTTCTGCCAAAAATCATGCAAAACTGTGTCAGGACCCCGAAACGCGTTTTTAGCTCTTAAA
66 AGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAA
* * *
76203 CTATGATGGTAAGTACACAATTTTCAGG-TAAAAACTGACCCGGAAATTTATTTCCTAAATTTTT
131 CTGTGATGGTTAGTACACGATTTTC-GGCTAAAAACTGACCCGGAAATTT-TTTCCTAAATTTTT
*
76267 TGGTACAATACTCAGAATGAATAAATAATTCAACGCCAAAAAGATTGACAGACTTTTCACGCATC
194 TGGCACAATACTCAGAATGAATAAATAATTCAACGCCAAAAAGATTGACAGACTTTTCACGCATC
* *
76332 TAATATTGTTTTTCTA-TTTTTTCCGATTAACTTCTAATTAAATCGAAACATGATTCAGATGCTA
259 TAATATCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTA
* * * * * *
76396 ATAAATACAAATCTATTATTCTAATGTGGCTGAGATTTGCTTCGATGAATATAGATATTTCAAGG
1 ATAAAAACAAATCCATAAATCGAATGTGGCTGAGATTTGCTTCGATGAATATAGATATTTCAAAG
* * * * *
76461 AGTCATTCTGCCAAAAATCTTGCAAAACTAAGTCAGGACCCCGAAACGCATTTTTAGCCCACAAA
66 AGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAA
* * * *
76526 CTGTGATGGTTAGTACACGATTTTCGGCTAAAAACTTAACTGGAAAATATTTTTCCTAATTTTTT
131 CTGTGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGG-AAAT-TTTTTCCTAAATTTTT
* * *
76591 TGGCACAATACTCAGAATAAATAAATAATTCAATGTCAAAAAGATTGACAGACTTTTCACGCATC
194 TGGCACAATACTCAGAATGAATAAATAATTCAACGCCAAAAAGATTGACAGACTTTTCACGCATC
* *
76656 TAATATCGTTTTTCTA-TTTTTTCCGATTAATTTCTAATTAAATCGAAACATGATTCATATGCTC
259 TAATATCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTA
* * *
76720 CTAAAAACAAATCCATAAATCGAATGTGGCTGTGATTTGGTTCGATGAATATAGATATTTCAAAG
1 ATAAAAACAAATCCATAAATCGAATGTGGCTGAGATTTGCTTCGATGAATATAGATATTTCAAAG
* * * * * *
76785 AGTCTTTTTGCCCAAAATCATGCAAAATTGGGTCAGGACCCCGAAACGCGTTTTTAACTCATAAA
66 AGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAA
* * * * *
76850 CTGTGACGGTTAGTACACGATTTTCGGCTAAAAACTGACCCAGAAATTTTTTTCTTAATTTTTTC
131 CTGTGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGGAAATTTTTTCCTAAATTTTTTG
* * *
76915 GCACAATACTCAGAATGAATAAATAATTCCACGCCCAAAAGATTGACAGACTTTTCAAGCATCTA
196 GCACAATACTCAGAATGAATAAATAATTCAACGCCAAAAAGATTGACAGACTTTTCACGCATCTA
* * * *
76980 ATATCCTTTTCCTATTTTTTTTTCCGATTAATTTCTAA-TAAATCGAAAAATGATTCATATGCTA
261 ATATCGTTTTTCTA--TTTTTTTCCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTA
* * * * * *
77044 ATGAAAAGAAATCTATAAATCGAATGTGGTTAAGATTTGCTTCGATGAATATAGATATTTGAAAG
1 ATAAAAACAAATCCATAAATCGAATGTGGCTGAGATTTGCTTCGATGAATATAGATATTTCAAAG
* * *
77109 AGTCTTTCTTCCAAAAATCATACAAAACTGAGAT-AGGACCCCGAAACGCGTTTTTAGCCTATAA
66 AGTCTTTCTGCCAAAAATCATGCAAAACTGAG-TCAGGACCCCGAAACGCGTTTTTAGCCCATAA
* * * *
77173 ATTGTGATTGTTAGTACATGATTTTCGGCTAAAAACTTACCCGGAAATTTTTTTCCTAAATTTTT
130 ACTGTGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGGAAA-TTTTTTCCTAAA-TTTT
* * * * * * * *
77238 TTGACACAATACTAAGAATGAATAAATAATTCAATGCCGAAAAGATTAAAATACTTTTCATGCAT
193 TTGGCACAATACTCAGAATGAATAAATAATTCAACGCCAAAAAGATTGACAGACTTTTCACGCAT
* *
77303 CTAATATCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAGTCGAAACATGATTTAGATGCT
258 CTAATATCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCT
77368 CA
323 -A
* * * * * *
77370 A-AAAAATAAATTCATAAATAGAATGTGGCTGGGATTTGCTTCGATGAATATAAATATTTAAAAG
1 ATAAAAACAAATCCATAAATCGAATGTGGCTGAGATTTGCTTCGATGAATATAGATATTTCAAAG
* * *
77434 AGTCTTTCTACCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAACGCGGTTTTAGCTCATAAA
66 AGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAA
* * * * *
77499 CTGTGATTGTTAGTACACGATTTTCGGGTAAAAACTGACCCAGAAATTGTTTTTCTTAATTTTTT
131 CTGTGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGGAAATT-TTTTCCTAAATTTTTT
* *
77564 GGCACAATACTCAGAATGAATAAATAATTCAACG-CAGAAAAAATTGATAGACTTTTCACGCATC
195 GGCACAATACTCAGAATGAATAAATAATTCAACGCCA-AAAAGATTGACAGACTTTTCACGCATC
77628 TAATATCGTTTTTCTATTTTTTTCCGATTAATTTCTAA-TAAATCGAAACATGATTCAGATGCTA
259 TAATATCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTA
*
77692 ATAAAAACAAATCCATAAATCGAATGTGGCTGAGATTTGCTTCGATAAATATAGATATTTCAAAG
1 ATAAAAACAAATCCATAAATCGAATGTGGCTGAGATTTGCTTCGATGAATATAGATATTTCAAAG
* * *
77757 AGTCTTTCTGCCAAAAATCATGCAAAATTGGGTCAGGACCCCGAAACGCGTTTTTAACCCATAAA
66 AGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAA
* *
77822 C-G-G-T-G--ACGTACACGATTCTCGGCTAAAAACTGACCTGGAAATTTTTTTCCTAAATTTTT
131 CTGTGATGGTTA-GTACACGATTTTCGGCTAAAAACTGACCCGGAAA-TTTTTTCCTAAA-TTTT
*
77881 TTGGTACAATACTCAGAATGAATAAATAATTCAACGCCAAAAAGATTGACAGACTTTTCACGCAT
193 TTGGCACAATACTCAGAATGAATAAATAATTCAACGCCAAAAAGATTGACAGACTTTTCACGCAT
*
77946 CTAATATTGTTTTTCTA-TTTTTTCCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCT
258 CTAATATCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCT
78010 A
323 A
* * * * * *
78011 ATAAATACAAATCTATTATTCTAATGTGGTTGAGATTTGCTTCGATGAATATAGATATTTCAAAG
1 ATAAAAACAAATCCATAAATCGAATGTGGCTGAGATTTGCTTCGATGAATATAGATATTTCAAAG
*
78076 TAGACTTTCTGCCAAAAATC
66 -AGTCTTTCTGCCAAAAATC
78096 TT
Statistics
Matches: 2086, Mismatches: 226, Indels: 62
0.88 0.10 0.03
Matches are distributed among these distances:
317 1 0.00
318 79 0.04
319 352 0.17
320 106 0.05
321 201 0.10
322 135 0.06
323 339 0.16
324 582 0.28
325 215 0.10
326 76 0.04
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (323 bp):
ATAAAAACAAATCCATAAATCGAATGTGGCTGAGATTTGCTTCGATGAATATAGATATTTCAAAG
AGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAA
CTGTGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGGAAATTTTTTCCTAAATTTTTTG
GCACAATACTCAGAATGAATAAATAATTCAACGCCAAAAAGATTGACAGACTTTTCACGCATCTA
ATATCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTA
Done.