Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009642.1 Corchorus capsularis cultivar CVL-1 contig09663, 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: 7737
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Found at i:653 original size:332 final size:332
Alignment explanation
Indices: 6--1290 Score: 1515
Period size: 333 Copynumber: 3.9 Consensus size: 332
1 AGTCT
* * * **
6 TGTTTCGATTTAATTAGAAAATAATTCAGAATAAAAT-GGAAAAGCGATATTATATAATTGAAAA
1 TGTTTCGATTTAATCAGAAATTAATTCAGAA-AAAATAGGAAAAGCGATATTAGATGCTTGAAAA
* * * *
70 GCTCTTCAATATTTTTGGCGTTGAATTATATATCTTTTTTTGA-TAATTGTGGTC-AAAATTGAT
65 GCCCTTCAATCTTTTTGGCGTTGAATTATATAT-TTTTTCTGAGT-ATTGTGGTCAAAAATTGAG
* * *
133 GCAAACATTTTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTCTACGTAACCATCACAG-T
128 GAAAAC-TTTTCGGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTACGTAACCATCACAGAT
* * * *
197 TTTTGGCTAAAAACGCGTTCCGGAGCCCCGACTCGGTTTTGCTTGATTTTTGGC-CCCTAGAGTC
192 TTTTGGCTAAAAACGCGTTCCGGGGCCCCAACTCAGTTTTGCTTGATTTTTGGCGCCC-AGACTC
***
261 CTTGAAATATCTATATTCATCTAACCAAATCTCGGTCACATTGGATTTAAGGATTTGTTTTTACG
256 CTTGAAATATCTATATTCATCTAACCAAATCTCAACCACATT-GATTTAAGGATTTGTTTTTACG
326 ATCATCTGAATAA
320 ATCATCTGAATAA
339 TGTTTCGATTTAATCAGAAATTAATTCTA-AAAAAATAGGAAAAGCGATATTAGATGCTTGAAAA
1 TGTTTCGATTTAATCAGAAATTAATTC-AGAAAAAATAGGAAAAGCGATATTAGATGCTTGAAAA
** * * * * * * *
403 GCAATTCTATCTTTTTGACATTGAATTATTTATTTTTTCTGAGTATTGTGGCCAAAAATTAAAGA
65 GCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGTCAAAAATTGAGGA
* *
468 ATAACTTTTCGGATCATTTTTTGCAAAA-TTTATGCCGAAATCGTGTAC-TAACCATCACAG-TT
130 A-AACTTTTCGGGTCATTTTTTGCAAAATTTTA-GCCAAAATCGTGTACGTAACCATCACAGATT
* * * * * * *
530 TTCGGCTAAAAACGTGTTCCGGGGCCCCAGCTCAATTTTGTTTGATTTTGGGCGCCCAGACTCAT
193 TTTGGCTAAAAACGCGTTCCGGGGCCCCAACTCAGTTTTGCTTGATTTTTGGCGCCCAGACTCCT
* * * *
595 TGAAACATAC-ATATGCATCTAATCAAATCTTAACCACATTGCATTTAAGG-TCTTGTTTTTACG
258 TGAAATAT-CTATATTCATCTAACCAAATCTCAACCACATTG-ATTTAAGGAT-TTGTTTTTACG
* *
658 AGT-ATCTAAATAT
320 A-TCATCTGAATAA
* * * * *
671 TGTTTCTATTTAATTAGAAATTAATTC-GTAGAGAAATAGGAAAAGCAATATTAGATGCTTGTAA
1 TGTTTCGATTTAATCAGAAATTAATTCAG-A-AAAAATAGGAAAAGCGATATTAGATGCTTGAAA
* *
735 AGCCCTTCAATCTTCTTGGCGTTGAATTATATATTTTTTCTGAGTGTTGTGGTCAAAAATTGAGG
64 AGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGTCAAAAATTGAGG
* * * * *
800 TAAAACTATTCAGGTTATTTTTTGCAAAAATTTAGCCAAAATCGTGTAC-TAACCATCA-TGATT
129 -AAAACTTTTCGGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTACGTAACCATCACAGATT
* *** * *
863 TTTGGCTAAAAACACGTTATAGGGCCCCAACTCAGTTTTGCTTGATTTTTAGCGTCCAGACTCCT
193 TTTGGCTAAAAACGCGTTCCGGGGCCCCAACTCAGTTTTGCTTGATTTTTGGCGCCCAGACTCCT
* * * *
928 TGAAATATCTATTTTCATCTAACCAAATCTCAACCATATTAGATTTAAGGATTTGTTTTTATGAG
258 TGAAATATCTATATTCATCTAACCAAATCTCAACCACATT-GATTTAAGGATTTGTTTTTACGAT
*
993 CATCTGAATCA
322 CATCTGAATAA
* * *
1004 TTTTTCGATTTAATCAGAAATTAATTCAGAAAAAATAGGAAAACCGATATTATATGCTTGAAAAG
1 TGTTTCGATTTAATCAGAAATTAATTCAGAAAAAATAGGAAAAGCGATATTAGATGCTTGAAAAG
* *
1069 CCCTTCAATCTTTTTGGCGTTGAATTATATAATTTTTTCCGAGTATTGTGGGCAAAAATTGAGGA
66 CCCTTCAATCTTTTTGGCGTTGAATTATAT-ATTTTTTCTGAGTATTGTGGTCAAAAATTGAGGA
* * * * *
1134 AAACTTTTTGGGTCATTATTTTGTAAAATTTTAGCTAAAATCGTGTACGTTA-CATCACGGA-TT
130 AAACTTTTCGGGTCATT-TTTTGCAAAATTTTAGCCAAAATCGTGTACGTAACCATCACAGATTT
* * * * * * *
1197 TTGGCTAAAAACGTGTTCCGAGACCCCAACTCAGTTTTGCTTGATTGTTGACACCGAGACTCCTT
194 TTGGCTAAAAACGCGTTCCGGGGCCCCAACTCAGTTTTGCTTGATTTTTGGCGCCCAGACTCCTT
* *
1262 GAAATATGTATATCCATCTAACCAAATCT
259 GAAATATCTATATTCATCTAACCAAATCT
1291 TGGTCACGTT
Statistics
Matches: 804, Mismatches: 122, Indels: 52
0.82 0.12 0.05
Matches are distributed among these distances:
331 2 0.00
332 249 0.31
333 536 0.67
334 17 0.02
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (332 bp):
TGTTTCGATTTAATCAGAAATTAATTCAGAAAAAATAGGAAAAGCGATATTAGATGCTTGAAAAG
CCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGTCAAAAATTGAGGAA
AACTTTTCGGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTACGTAACCATCACAGATTTTT
GGCTAAAAACGCGTTCCGGGGCCCCAACTCAGTTTTGCTTGATTTTTGGCGCCCAGACTCCTTGA
AATATCTATATTCATCTAACCAAATCTCAACCACATTGATTTAAGGATTTGTTTTTACGATCATC
TGAATAA
Found at i:3492 original size:40 final size:40
Alignment explanation
Indices: 3437--3515 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
3427 ATGCGGCACA
** *
3437 TTCACATTTAACTTTCCCAATTGACATTGAACTTGCCTTG
1 TTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTG
*
3477 TTCACATCCAACTTTCTCAAATGACATTGAACTTGCCTT
1 TTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTT
3516 AATTCACAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.38
Consensus pattern (40 bp):
TTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTG
Found at i:3621 original size:31 final size:32
Alignment explanation
Indices: 3494--3682 Score: 346
Period size: 32 Copynumber: 6.0 Consensus size: 32
3484 CCAACTTTCT
*
3494 CAAATGACATTGAACTTGCCTTAATTCACAAC
1 CAAATGACATTGAACTTGCCTTAATTCACATC
3526 CAAATGACATTGAACTTGCCTTAATTCACATC
1 CAAATGACATTGAACTTGCCTTAATTCACATC
3558 CAAATGACATTGAACTTGCCTTAATTCACATC
1 CAAATGACATTGAACTTGCCTTAATTCACATC
*
3590 CAAAAGACATTGAACTTGCCTTAA-TCACATC
1 CAAATGACATTGAACTTGCCTTAATTCACATC
3621 CAAATGACATTGAACTTGCCTTAA-TCACATC
1 CAAATGACATTGAACTTGCCTTAATTCACATC
3652 CAAATGACATTGAACTTGCCTTAATTCACAT
1 CAAATGACATTGAACTTGCCTTAATTCACAT
3683 TGGCCCTCAA
Statistics
Matches: 153, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
31 61 0.40
32 92 0.60
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.30
Consensus pattern (32 bp):
CAAATGACATTGAACTTGCCTTAATTCACATC
Done.