Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012409.1 Corchorus capsularis cultivar CVL-1 contig12430, 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: 12893
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Found at i:895 original size:21 final size:22
Alignment explanation
Indices: 869--914 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
859 ATACAAAAGG
*
869 AAATT-AA-AAGAAAATATAAAA
1 AAATTAAATAAGAAAA-AGAAAA
890 AAATTAAATAAGAAAAAGAAAA
1 AAATTAAATAAGAAAAAGAAAA
912 AAA
1 AAA
915 AAATCAGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 10 0.45
23 7 0.32
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (22 bp):
AAATTAAATAAGAAAAAGAAAA
Found at i:2484 original size:13 final size:13
Alignment explanation
Indices: 2463--2504 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
2453 GATGTTGGCC
* *
2463 ATAATAAATATAA
1 ATAAAAAATAAAA
2476 ATAAAAAATAAAAA
1 ATAAAAAAT-AAAA
2490 ATAAAAAATAAAA
1 ATAAAAAATAAAA
2503 AT
1 AT
2505 GGTTTTGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
ATAAAAAATAAAA
Found at i:2504 original size:6 final size:7
Alignment explanation
Indices: 2474--2503 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
2464 TAATAAATAT
2474 AAATAAA
1 AAATAAA
2481 AAATAAA
1 AAATAAA
2488 AAATAAA
1 AAATAAA
2495 AAATAAA
1 AAATAAA
2502 AA
1 AA
2504 TGGTTTTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAATAAA
Found at i:4853 original size:4 final size:4
Alignment explanation
Indices: 4846--4872 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
4836 TATATATATA
4846 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
4873 CTGACGGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:12438 original size:334 final size:332
Alignment explanation
Indices: 11387--12892 Score: 2439
Period size: 334 Copynumber: 4.5 Consensus size: 332
11377 GCGACCCGCA
* *
11387 CCGAGACCTCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAATACACAATTTCGACTAAAAT
1 CCGAGACCTCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGACTAAAAT
*
11452 TTCGCAAAAAGTTACCCCAAAAGATTTTTCCTCAATATTTGGCCAAAATACTCATAATAAAT-CA
66 TTCGCAAAAAGTTACCCCAAAAGATTTTTCCTCAATATTTGGCCAAAATACTCATAATAAATATA
* * *
11516 TTATTAAAGGCCAAAAATACTGGAGGGATTTTCACGGTTTTAATGTAATTTTTACTATTTTTTTT
131 TTATTAAAGGCCAAAAATATTGGAGGGATTTTCACGGTTTTAATGTCATTTTTACTATTTTTTCT
*
11581 GAATTAATTTCTATTTAATTCGAAAAAGATTCAGATACTCAG-AAAAACAAATCCTTAAATCCAT
196 GAATTAATTTCTATTTAATTCGAAAAAGATTCAGATGCTC-GTAAAAACAAATCCTTAAATCCAT
*
11645 AGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCA
260 AGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTGGCGCCAAAAATCATGCA
*
11710 CAACTGAG
325 AAACTGAG
* * * *
11718 CTGAGACCTCGGAACGCATTTTTAGCCAAAAACTGTGATGGTTAGTACATGATTTCGACTACAAT
1 CCGAGACCTCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGACTAAAAT
*
11783 TTCGCAAAAA-TTGACCTCAAAAGATTTTTCCTCAATATTTGGCCAAAATACTCATAATAAATAT
66 TTCGCAAAAAGTT-ACCCCAAAAGATTTTTCCTCAATATTTGGCCAAAATACTCATAATAAATAT
** * *
11847 ATTATTAAACACCAAAAATATTGGAGGGACTTTCACGGTTTTAATTTCATTTTTACTATTTTTTC
130 ATTATTAAAGGCCAAAAATATTGGAGGGATTTTCACGGTTTTAATGTCATTTTTACTATTTTTTC
* * * *
11912 TGAATTTATTTCTAATTAATTTTCGAAAAAAGATTCAGATGCTCGTAAAACCAAATCTTTAAATC
195 TGAATTAATTTCTATTTAA--TTCG-AAAAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATC
* *
11977 CATAGTGGCTGAGATTTGGTTAGATGAATATATATATTTGAAGAAGTCTTGGCGCCAAAAATCAT
257 CATAGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTGGCGCCAAAAATCAT
*
12042 GCAATACTGAG
322 GCAAAACTGAG
12053 CCGAGACCTCGGAACGCGTTTTTAGCCAAAAACTGTGATCGGTTAGTACACGATTTCGACTAAAA
1 CCGAGACCTCGGAACGCGTTTTTAGCCAAAAACTGTGAT-GGTTAGTACACGATTTCGACTAAAA
12118 TTTCGCAAAAAGTTACCCCAAAAGATTTTTCCAT-AATATTTGGCCAAAATACTCATAATAAATA
65 TTTCGCAAAAAGTTACCCCAAAAGATTTTTCC-TCAATATTTGGCCAAAATACTCATAATAAATA
12182 TATTATTAAAGGCCAAAAATATTGGAGGGATTTTCACGGTTTTAATGTCATTTTTACTATTTTTT
129 TATTATTAAAGGCCAAAAATATTGGAGGGATTTTCACGGTTTTAATGTCATTTTTACTA-TTTTT
* *
12247 TCTGAATTACTTTTTATTTAATTCGAAAAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCC
193 TCTGAATTAATTTCTATTTAATTCGAAAAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCC
* * *
12312 ATAGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATG
258 ATAGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTGGCGCCAAAAATCATG
*
12377 CAAAACTGCG
323 CAAAACTGAG
* *
12387 CCGAGACCTCAGAACGCGTTTTTAGTCAAAAACTGTGATCGGTTAGTACACGATTTCGACTAAAA
1 CCGAGACCTCGGAACGCGTTTTTAGCCAAAAACTGTGAT-GGTTAGTACACGATTTCGACTAAAA
* *
12452 TTTCGCAAAAAGTTACCCCAAAATATTTTTCCTTAATATTTGGCCAAAATACTCATAATAAATAT
65 TTTCGCAAAAAGTTACCCCAAAAGATTTTTCCTCAATATTTGGCCAAAATACTCATAATAAATAT
* *
12517 ATTTTTAAAGGCCAAAAATACTGGAGGGATTTTCACGGTTTTAATGTCATTTTTACTATTTTTTC
130 ATTATTAAAGGCCAAAAATATTGGAGGGATTTTCACGGTTTTAATGTCATTTTTACTATTTTTTC
* *
12582 TGAATTAATTTCTATTTAATTCGAATAAGATTCATATGCTCGTAAAAACAAATCCTTAAATCCAT
195 TGAATTAATTTCTATTTAATTCGAAAAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAT
* *
12647 AGTGGCTGAGATTTGGTTAGATGAATATATATATTTGAAGAAGTCTTGGCGCCAAAAATCATGCA
260 AGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTGGCGCCAAAAATCATGCA
*
12712 ATACTGAG
325 AAACTGAG
* *
12720 CCGAGACCTCGGAACGCATTTTTAGCCAAAAACTGTGATGGTTAGTACATGATTTCGACTAAAAT
1 CCGAGACCTCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGACTAAAAT
* * *
12785 TTCGCAAAAA-TTGACCTCAAAAGATTTTTCCTCAATATTTGGCCAAAATATTTATAATAAATAT
66 TTCGCAAAAAGTT-ACCCCAAAAGATTTTTCCTCAATATTTGGCCAAAATACTCATAATAAATAT
* *
12849 ATTATTAAACGCC-AAAATATTGGAGGGACTTTCACGGTTTTAAT
130 ATTATTAAAGGCCAAAAATATTGGAGGGATTTTCACGGTTTTAAT
12893 T
Statistics
Matches: 1087, Mismatches: 76, Indels: 24
0.92 0.06 0.02
Matches are distributed among these distances:
330 2 0.00
331 148 0.14
332 167 0.15
333 171 0.16
334 292 0.27
335 146 0.13
336 136 0.13
337 25 0.02
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (332 bp):
CCGAGACCTCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGACTAAAAT
TTCGCAAAAAGTTACCCCAAAAGATTTTTCCTCAATATTTGGCCAAAATACTCATAATAAATATA
TTATTAAAGGCCAAAAATATTGGAGGGATTTTCACGGTTTTAATGTCATTTTTACTATTTTTTCT
GAATTAATTTCTATTTAATTCGAAAAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATA
GTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTGGCGCCAAAAATCATGCAA
AACTGAG
Found at i:12679 original size:667 final size:666
Alignment explanation
Indices: 11387--12892 Score: 2524
Period size: 667 Copynumber: 2.3 Consensus size: 666
11377 GCGACCCGCA
* *
11387 CCGAGACCTCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAATACACAATTTCGACTAAAAT
1 CCGAGACCTCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGACTAAAAT
*
11452 TTCGCAAAAAGTTACCCCAAAAGATTTTTCCTCAATATTTGGCCAAAATACTCATAATAAAT-CA
66 TTCGCAAAAAGTTACCCCAAAAGATTTTTCCTCAATATTTGGCCAAAATACTCATAATAAATATA
*
11516 TTATTAAAGGCCAAAAATACTGGAGGGATTTTCACGGTTTTAATGTAATTTTTACTATTTTTTTT
131 TTATTAAAGGCCAAAAATATTGGAGGGATTTTCACGGTTTTAATGTAATTTTTACTATTTTTTTT
11581 GAATTAATTTCTATTTAATTCGAAAAAGATTCAGATACTCAGAAAAACAAATCCTTAAATCCATA
196 GAATTAATTTCTATTTAATTCGAAAAAGATTCAGATACTCAGAAAAACAAATCCTTAAATCCATA
*
11646 GTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAC
261 GTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAA
* * *
11711 AACTGAGCTGAGACCTCGGAACGCATTTTTAGCCAAAAACTGTGATGGTTAGTACATGATTTCGA
326 AACTGAGCCGAGACCTCAGAACGCATTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGA
* *
11776 CTACAATTTCGCAAAAATTGACCTCAAAAGATTTTTCCTCAATATTTGGCCAAAATACTCATAAT
391 CTAAAATTTCGCAAAAATTGACCCCAAAAGATTTTTCCTCAATATTTGGCCAAAATACTCATAAT
* *
11841 AAATATATTATTAAACACCAAAAATATTGGAGGGACTTTCACGGTTTTAATTTCATTTTTACTAT
456 AAATATATTATTAAACACCAAAAATACTGGAGGGACTTTCACGGTTTTAATGTCATTTTTACTAT
* * *
11906 TTTTTCTGAATTTATTTCTAATTAATTTTCGAAAAAAGATTCAGATGCTCGTAAAACCAAATCTT
521 TTTTTCTGAATTAATTTCTAATTAA-TTTCGAAAAAAGATTCAGATGCTCGTAAAAACAAATCCT
11971 TAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATATATATTTGAAGAAGTCTTGGCGCCAAA
585 TAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATATATATTTGAAGAAGTCTTGGCGCCAAA
12036 AATCATGCAATACTGAG
650 AATCATGCAATACTGAG
12053 CCGAGACCTCGGAACGCGTTTTTAGCCAAAAACTGTGATCGGTTAGTACACGATTTCGACTAAAA
1 CCGAGACCTCGGAACGCGTTTTTAGCCAAAAACTGTGAT-GGTTAGTACACGATTTCGACTAAAA
12118 TTTCGCAAAAAGTTACCCCAAAAGATTTTTCCAT-AATATTTGGCCAAAATACTCATAATAAATA
65 TTTCGCAAAAAGTTACCCCAAAAGATTTTTCC-TCAATATTTGGCCAAAATACTCATAATAAATA
*
12182 TATTATTAAAGGCCAAAAATATTGGAGGGATTTTCACGGTTTTAATGTCATTTTTACTATTTTTT
129 TATTATTAAAGGCCAAAAATATTGGAGGGATTTTCACGGTTTTAATGTAATTTTTACTATTTTTT
* * *
12247 TCTGAATTACTTTTTATTTAATTCGAAAAAGATTCAGATGCTC-GTAAAAACAAATCCTTAAATC
194 T-TGAATTAATTTCTATTTAATTCGAAAAAGATTCAGATACTCAG-AAAAACAAATCCTTAAATC
* *
12311 CATAGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCAT
257 CATAGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCAT
* * *
12376 GCAAAACTGCGCCGAGACCTCAGAACGCGTTTTTAGTCAAAAACTGTGATCGGTTAGTACACGAT
322 GCAAAACTGAGCCGAGACCTCAGAACGCATTTTTAGCCAAAAACTGTGAT-GGTTAGTACACGAT
* *
12441 TTCGACTAAAATTTCGCAAAAAGTT-ACCCCAAAATATTTTTCCTTAATATTTGGCCAAAATACT
386 TTCGACTAAAATTTCGCAAAAA-TTGACCCCAAAAGATTTTTCCTCAATATTTGGCCAAAATACT
* ** *
12505 CATAATAAATATATTTTTAAAGGCCAAAAATACTGGAGGGATTTTCACGGTTTTAATGTCATTTT
450 CATAATAAATATATTATTAAACACCAAAAATACTGGAGGGACTTTCACGGTTTTAATGTCATTTT
* * *
12570 TACTATTTTTTCTGAATTAATTTCTATTTAA-TTCG-AATAAGATTCATATGCTCGTAAAAACAA
515 TACTATTTTTTCTGAATTAATTTCTAATTAATTTCGAAAAAAGATTCAGATGCTCGTAAAAACAA
12633 ATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATATATATTTGAAGAAGTCTTGGCG
580 ATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATATATATTTGAAGAAGTCTTGGCG
12698 CCAAAAATCATGCAATACTGAG
645 CCAAAAATCATGCAATACTGAG
* *
12720 CCGAGACCTCGGAACGCATTTTTAGCCAAAAACTGTGATGGTTAGTACATGATTTCGACTAAAAT
1 CCGAGACCTCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGACTAAAAT
* * *
12785 TTCGCAAAAA-TTGACCTCAAAAGATTTTTCCTCAATATTTGGCCAAAATATTTATAATAAATAT
66 TTCGCAAAAAGTT-ACCCCAAAAGATTTTTCCTCAATATTTGGCCAAAATACTCATAATAAATAT
* *
12849 ATTATTAAACGCC-AAAATATTGGAGGGACTTTCACGGTTTTAAT
130 ATTATTAAAGGCCAAAAATATTGGAGGGATTTTCACGGTTTTAAT
12893 T
Statistics
Matches: 791, Mismatches: 40, Indels: 19
0.93 0.05 0.02
Matches are distributed among these distances:
665 33 0.04
666 132 0.17
667 233 0.29
668 69 0.09
669 164 0.21
670 158 0.20
671 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (666 bp):
CCGAGACCTCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGACTAAAAT
TTCGCAAAAAGTTACCCCAAAAGATTTTTCCTCAATATTTGGCCAAAATACTCATAATAAATATA
TTATTAAAGGCCAAAAATATTGGAGGGATTTTCACGGTTTTAATGTAATTTTTACTATTTTTTTT
GAATTAATTTCTATTTAATTCGAAAAAGATTCAGATACTCAGAAAAACAAATCCTTAAATCCATA
GTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAA
AACTGAGCCGAGACCTCAGAACGCATTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGA
CTAAAATTTCGCAAAAATTGACCCCAAAAGATTTTTCCTCAATATTTGGCCAAAATACTCATAAT
AAATATATTATTAAACACCAAAAATACTGGAGGGACTTTCACGGTTTTAATGTCATTTTTACTAT
TTTTTCTGAATTAATTTCTAATTAATTTCGAAAAAAGATTCAGATGCTCGTAAAAACAAATCCTT
AAATCCATAGTGGCTGAGATTTGGTTAGATGAATATATATATTTGAAGAAGTCTTGGCGCCAAAA
ATCATGCAATACTGAG
Done.