Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014157.1 Corchorus capsularis cultivar CVL-1 contig14178, 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: 35626
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:27978 original size:14 final size:14
Alignment explanation
Indices: 27959--28071 Score: 77
Period size: 14 Copynumber: 8.1 Consensus size: 14
27949 TTTATTTTAT
27959 AAATTCATTTAAGA
1 AAATTCATTTAAGA
*
27973 AAATTCAGTTAAGA
1 AAATTCATTTAAGA
* * * *
27987 AATTTTATTTTA-T
1 AAATTCATTTAAGA
*
28000 AAATTCTTTTAAGA
1 AAATTCATTTAAGA
*
28014 AAATTCAGTTAAGA
1 AAATTCATTTAAGA
* * ***
28028 AATTTTATTT-TTT
1 AAATTCATTTAAGA
*
28041 AAATTCTTTTAAGAA
1 AAATTCATTTAAG-A
*
28056 AAATTCAGTTAAGA
1 AAATTCATTTAAGA
28070 AA
1 AA
28072 TGAAATTTTG
Statistics
Matches: 69, Mismatches: 27, Indels: 6
0.68 0.26 0.06
Matches are distributed among these distances:
13 15 0.22
14 43 0.62
15 11 0.16
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.42
Consensus pattern (14 bp):
AAATTCATTTAAGA
Found at i:28005 original size:41 final size:41
Alignment explanation
Indices: 27948--28072 Score: 223
Period size: 41 Copynumber: 3.0 Consensus size: 41
27938 CGTGCGGCTG
*
27948 TTTTATTTTATAAATTCATTTAAGAAAATTCAGTTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
27989 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
*
28030 TTTTATTTTTTAAATTCTTTTAAGAAAAATTCAGTTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAG-AAAATTCAGTTAAGAAA
28072 T
1 T
28073 GAAATTTTGT
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
41 63 0.78
42 18 0.22
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (41 bp):
TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
Found at i:28030 original size:27 final size:27
Alignment explanation
Indices: 27959--28031 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 27
27949 TTTATTTTAT
27959 AAATTCATTTAAGAAAATTCAGTTAAGA
1 AAATTCATTTAAG-AAATTCAGTTAAGA
* * * * **
27987 AATTTTATTTTATAAATTCTTTTAAGA
1 AAATTCATTTAAGAAATTCAGTTAAGA
*
28014 AAATTCAGTTAAGAAATT
1 AAATTCATTTAAGAAATT
28032 TTATTTTTTA
Statistics
Matches: 34, Mismatches: 11, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
27 25 0.74
28 9 0.26
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.41
Consensus pattern (27 bp):
AAATTCATTTAAGAAATTCAGTTAAGA
Found at i:33011 original size:324 final size:322
Alignment explanation
Indices: 32206--33690 Score: 2207
Period size: 324 Copynumber: 4.6 Consensus size: 322
32196 ATATAAATCA
* *
32206 AATATCGTTTTTTCCATTTTTTTCCCGAATTTATTTCTAATTAAATCGAAAAAAAATTCAGATGC
1 AATATCG-TTTTTCCATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGC
* * *
32271 TCGTAAAAAGAAATACTTAAATCCATTGTCGCTGAAATTTGGTTAGATGAATATAGATATTTCAA
65 TCGTAAAAAGAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAA
* * * * * * *
32336 GTAGTCTTTCGGTAAAAAATCATGCAAAATTGAGTCGGGTCTCCAGAACGTG-TTTTAGTCAAAA
130 GGAGTCTTTCTGCAAAAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCAAAA
* * *
32400 ACCGAGATGGTTAGTAAATGATTTCGGCTAAAAATTGA-CACGAAAAAGTTTTTCCTCAATTTTT
195 ACCGTGATGGTTAGTACACGATTTCGGCTAAAAATTGACCA-G-AAAAGTTTTTCCTCAA-TTTT
32464 TTGCCACAATACTCAGAAAAAATATATAAATCAACGCCAAAAAAA-GATGGGTTTTTCACGCTTC
257 TTGCCACAATACTCAGAAAAAATATATAAATCAACGCCAAAAAAATGATGGGTTTTTCACGCTTC
32528 T
322 T
* *
32529 AATATCGTTTTTCCATTTTTTTT-CGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCT
1 AATATCGTTTTTCCATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCT
* * * * *
32593 C--AAAAAAAAATCCTTAAATCCATCGTAGCTGAGATTTGATTAGATGAATATAAATATTTCAAG
66 CGTAAAAAGAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAG
* * * *
32656 GAGTTTTTCTGCAAAAAATCATGCAAAATTGAGCCGGGTCTGCGGAACGCGTCTTTAGCAAAAAA
131 GAGTCTTTCTGCAAAAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCAAAAA
*
32721 CCGTGATTGTTAGTACACGATTTCGGCTAAAAATTGACCAGAAAAGTTTTTCCTCAATTTTTTTG
196 CCGTGATGGTTAGTACACGATTTCGGCTAAAAATTGACCAGAAAAGTTTTTCCTCAA-TTTTTTG
* * *
32786 CGACAATACTCATG-AAAAATATATAATTCAACGCCCAAAAAATGATGGGTTTTTCACGCTTCT
260 CCACAATACTCA-GAAAAAATATATAAATCAACGCCAAAAAAATGATGGGTTTTTCACGCTTCT
*
32849 AATATCGTTTTTCCATTCTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCCGATGC
1 AATATCGTTTTTCCATT-TTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGC
*
32914 TCGTAGAAAGAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAA
65 TCGTAAAAAGAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAA
* * *
32979 GGAGCCTTTCTGCAAAAAATCATGCAAAATTGAGCAGAGTCTCCGGAACGCGTTTTTAGCCAAAA
130 GGAGTCTTTCTGCAAAAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCAAAA
* * * * *
33044 ACCGTGATGGTTAGTACACGATTTCAGCTAAAAGTTGACCCGAAAACTTTTTCCTCAATTTATTG
195 ACCGTGATGGTTAGTACACGATTTCGGCTAAAAATTGACCAGAAAAGTTTTTCCTCAATTTTTTG
* * *
33109 CCACAATACTCAGAAAAAATATATAAATGAACGCCAAAAAAATGAAGGGGTTTTCACGCTTCT
260 CCACAATACTCAGAAAAAATATATAAATCAACGCCAAAAAAATGATGGGTTTTTCACGCTTCT
*
33172 AATATCGTTTTTCCATTTTTTTTTTCAGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATG
1 AATATCGTTTTTCCA--TTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATG
* *
33237 CTCGTAAAAAGGAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGATTATAGATATTTCA
64 CTCGTAAAAAGAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCA
* * * * *
33302 AGGAGTCTTTCTGCAAAAAAATCATGCATAATTAAGCCGGGTCTCCCGTACGCGTTTTTAGCCTA
129 AGGAGTCTTTCTGC-AAAAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCAA
* * *
33367 AAACGGTGATGATTAGTACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCCTCAATTTTT
193 AAACCGTGATGGTTAGTACACGATTTCGGCTAAAAATTGACCAGAAAAGTTTTTCCTCAATTTTT
*
33432 TGCCACAATACTCAGAAAAAATATATAAATCAACGCAAAAAAAATGATGGGTTTTTTCACGCTTC
258 TGCCACAATACTCAGAAAAAATATATAAATCAACGCCAAAAAAATGATGGG-TTTTTCACGCTTC
33497 T
322 T
* *
33498 AATATCGTTTTCCCA-TTTTTTT-CGAATTTATTT-TAAATTAAATCGAAACAAGATTCAGATGC
1 AATATCGTTTTTCCATTTTTTTTCCGAATTTATTTCT-AATTAAATCGAAACAAAATTCAGATGC
* *
33560 TCGTAGAAAGAAATCCTTAAATCCATTGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAA
65 TCGTAAAAAGAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAA
* * * * * *
33625 GGAGTCTTTCTGCAAAAAACCATGCAAAATTGTGCTGGGTCACCGGAATGCGTTTTTAACCAAAA
130 GGAGTCTTTCTGCAAAAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCAAAA
33690 A
195 A
33691 AAAAAAAACG
Statistics
Matches: 1050, Mismatches: 98, Indels: 30
0.89 0.08 0.03
Matches are distributed among these distances:
319 159 0.15
320 82 0.08
321 90 0.09
322 165 0.16
323 90 0.09
324 285 0.27
325 152 0.14
326 27 0.03
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (322 bp):
AATATCGTTTTTCCATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCT
CGTAAAAAGAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAG
GAGTCTTTCTGCAAAAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCAAAAA
CCGTGATGGTTAGTACACGATTTCGGCTAAAAATTGACCAGAAAAGTTTTTCCTCAATTTTTTGC
CACAATACTCAGAAAAAATATATAAATCAACGCCAAAAAAATGATGGGTTTTTCACGCTTCT
Found at i:33590 original size:646 final size:641
Alignment explanation
Indices: 32206--33690 Score: 2239
Period size: 643 Copynumber: 2.3 Consensus size: 641
32196 ATATAAATCA
*
32206 AATATCGTTTTTTCCATTTTTTTCCCGAATTTATTTCTAATTAAATCGAAAAAAAATTCAGATGC
1 AATATCG-TTTTTCCATTTTTTT-CCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGC
* * * *
32271 TCGTAAAAAGAAATACTTAAATCCATTGTCGCTGAAATTTGGTTAGATGAATATAGATATTTCAA
64 TCGTAGAAAGAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAA
* * * * * *
32336 GTAGTCTTTCGGTAAAAAATCATGCAAAATTGAGTCGGGTCTCCAGAACGTG-TTTTAGTCAAAA
129 GGAGTCTTTCTGCAAAAAATCATGCAAAATTGAG-CGGGTCTCCGGAACGCGTTTTTAGCCAAAA
* * * *
32400 ACCGAGATGGTTAGTAAATGATTTCGGCTAAAAATTGACACGAAAAAGTTTTTCCTCAATTTTTT
193 ACCGAGATGGTTAGTAAACGATTTCAGCTAAAAATTGACACGAAAAACTTTTTCCTCAATTTTAT
* *
32465 TGCCACAATACTCAGAAAAAATATATAAATCAACGCCAAAAAAAGATGGGTTTTTCACGCTTCTA
258 TGCCACAATACTCAGAAAAAATATATAAATCAACGCCAAAAAAAGAAGGGGTTTTCACGCTTCTA
*
32530 ATATCGTTTTTCCATTTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCA
323 ATATCGTTTTTCCATTTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAAATTCAGATGCTCA
32595 AAAAAAAATCCTTAAATCCATCGTAGCTGAGATTTGATTAGATGAATATAAATATTTCAAGGAGT
388 AAAAAAAATCCTTAAATCCATCGTAGCTGAGATTTGATTAGATGAATATAAATATTTCAAGGAGT
* * * *
32660 TTTTCTGCAAAAAATCATGCAAAATTGAGCCGGGTCTGCGGAACGCGTCTTTAGCAAAAAACCGT
453 CTTTCTGCAAAAAATCATGCAAAATTAAGCCGGGTCTCCCGAACGCGTCTTTAGCAAAAAACCGT
*
32725 GATTGTTAGTACACGATTTCGGCTAAAAATTGACCAGAAAAGTTTTTCCTCAATTTTTTTGCGAC
518 GATTGTTAGTACACGATTTCGGCTAAAAATTGACCAGAAAAGTTTTTCCTCAATTTTTTTGCCAC
* **
32790 AATACTCATGAAAAATATATAATTCAACGCCCAAAAAATGATGGGTTTTTCACGCTTCT
583 AATACTCATGAAAAATATATAAATCAACGCAAAAAAAATGATGGGTTTTTCACGCTTCT
*
32849 AATATCGTTTTTCCATTCTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCCGATGC
1 AATATCGTTTTTCCA-T-TTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGC
32914 TCGTAGAAAGAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAA
64 TCGTAGAAAGAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAA
* *
32979 GGAGCCTTTCTGCAAAAAATCATGCAAAATTGAGCAGAGTCTCCGGAACGCGTTTTTAGCCAAAA
129 GGAGTCTTTCTGCAAAAAATCATGCAAAATTGAGC-GGGTCTCCGGAACGCGTTTTTAGCCAAAA
* * * *
33044 ACCGTGATGGTTAGTACACGATTTCAGCTAAAAGTTGACCCG-AAAACTTTTTCCTCAA-TTTAT
193 ACCGAGATGGTTAGTAAACGATTTCAGCTAAAAATTGACACGAAAAACTTTTTCCTCAATTTTAT
*
33107 TGCCACAATACTCAGAAAAAATATATAAATGAACGCCAAAAAAATGAAGGGGTTTTCACGCTTCT
258 TGCCACAATACTCAGAAAAAATATATAAATCAACGCCAAAAAAA-GAAGGGGTTTTCACGCTTCT
*
33172 AATATCGTTTTTCCATTTTTTTTTTCAGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATG
322 AATATCGTTTTTCCA--TTTTTTTTC-GAATTTATTTCAAATTAAATCGAAACAAAATTCAGATG
** * * * * *
33237 CTCGTAAAAAGGAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGATTATAGATATTTCA
384 CTC--AAAAAAAAATCCTTAAATCCATCGTAGCTGAGATTTGATTAGATGAATATAAATATTTCA
* * * **
33302 AGGAGTCTTTCTGCAAAAAAATCATGCATAATTAAGCCGGGTCTCCCGTACGCGTTTTTAGCCTA
447 AGGAGTCTTTCTGC-AAAAAATCATGCAAAATTAAGCCGGGTCTCCCGAACGCGTCTTTAGCAAA
* *
33367 AAACGGTGA-TGATTAGTACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTCCTCAA-TTT
511 AAACCGTGATTG-TTAGTACACGATTTCGGCTAAAAATTGACCAGAAAAGTTTTTCCTCAATTTT
33430 TTTGCCACAATACTCA-GAAAAAATATATAAATCAACGCAAAAAAAATGATGGGTTTTTTCACGC
575 TTTGCCACAATACTCATG-AAAAATATATAAATCAACGCAAAAAAAATGATGGG-TTTTTCACGC
33494 TTCT
638 TTCT
* *
33498 AATATCGTTTTCCCATTTTTTT-CGAATTTATTT-TAAATTAAATCGAAACAAGATTCAGATGCT
1 AATATCGTTTTTCCATTTTTTTCCGAATTTATTTCT-AATTAAATCGAAACAAAATTCAGATGCT
*
33561 CGTAGAAAGAAATCCTTAAATCCATTGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAG
65 CGTAGAAAGAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAG
* * * * *
33626 GAGTCTTTCTGCAAAAAACCATGCAAAATTGTGCTGGGTCACCGGAATGCGTTTTTAACCAAAAA
130 GAGTCTTTCTGCAAAAAATCATGCAAAATTGAGC-GGGTCTCCGGAACGCGTTTTTAGCCAAAAA
33691 AAAAAAAACG
Statistics
Matches: 766, Mismatches: 61, Indels: 27
0.90 0.07 0.03
Matches are distributed among these distances:
642 56 0.07
643 199 0.26
644 53 0.07
645 10 0.01
646 197 0.26
647 7 0.01
648 119 0.16
649 125 0.16
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (641 bp):
AATATCGTTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTC
GTAGAAAGAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGG
AGTCTTTCTGCAAAAAATCATGCAAAATTGAGCGGGTCTCCGGAACGCGTTTTTAGCCAAAAACC
GAGATGGTTAGTAAACGATTTCAGCTAAAAATTGACACGAAAAACTTTTTCCTCAATTTTATTGC
CACAATACTCAGAAAAAATATATAAATCAACGCCAAAAAAAGAAGGGGTTTTCACGCTTCTAATA
TCGTTTTTCCATTTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAAATTCAGATGCTCAAAA
AAAAATCCTTAAATCCATCGTAGCTGAGATTTGATTAGATGAATATAAATATTTCAAGGAGTCTT
TCTGCAAAAAATCATGCAAAATTAAGCCGGGTCTCCCGAACGCGTCTTTAGCAAAAAACCGTGAT
TGTTAGTACACGATTTCGGCTAAAAATTGACCAGAAAAGTTTTTCCTCAATTTTTTTGCCACAAT
ACTCATGAAAAATATATAAATCAACGCAAAAAAAATGATGGGTTTTTCACGCTTCT
Done.