Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005683.1 Corchorus capsularis cultivar CVL-1 contig05701, 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: 3753
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Found at i:656 original size:26 final size:26
Alignment explanation
Indices: 627--687 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
617 TAAATTCGGC
627 TATTAGATTTAG-GCATTTAGCTGTGT
1 TATT-GATTTAGAGCATTTAGCTGTGT
** *
653 TATTTTTTTTAGATCATTTAGCTGTGT
1 TA-TTGATTTAGAGCATTTAGCTGTGT
680 TATTGATT
1 TATTGATT
688 GGTCAAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
26 11 0.39
27 17 0.61
ACGTcount: A:0.21, C:0.07, G:0.18, T:0.54
Consensus pattern (26 bp):
TATTGATTTAGAGCATTTAGCTGTGT
Found at i:1728 original size:441 final size:436
Alignment explanation
Indices: 819--1932 Score: 1479
Period size: 441 Copynumber: 2.5 Consensus size: 436
809 TGAAGCATTT
* * * * * *
819 TCAAAACA-TCAAATTGGCTTTAGAGTTCTTCATGAAAGTTGTAAATCATTAAATTACCTCTCAA
1 TCAAAACATTAAAATTGGCTTTA-AGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTTTAAA
* * * *
883 TAGACACTTGAATCACCTTGATCCGACAAATAGAACAAAAAATACAAAAATAAAAGCCAACATGT
65 TAGAAACTTGAATCATCTTGATCGGACAAATAGAACAAAAAATACAAAAATAAAAGCCAACACGT
* *
948 TAAATCGTCCAACCTATAATTGTAAAGGATTAAATAGCATAAAACATAAAAGTATGATGG-TCAT
130 TAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAAGCATAAAAGTATGA-GGATCAT
* * *
1012 TTGATAAATAATCCAGGGAAAAAAATATTTGTTCATGAAGACCAAACATAAAAATTCCCTCTTGA
194 TTGATAAATAATCCA-GCAAAAAAATATTTGTTTATG-AGACCAAACATAAAAATTCCCTCTCGA
* *
1077 ACTCCCCACGAAACTCATTAATCAAATTCAGCTTTCAGGCCCCTGGCGAAAGTCGTAGCTAACAC
257 ACTCCCCACGAAACTCATTAATCAAATTCAGCTTTCAGGCCCCTGACGAAAGTCGTAGATAACAC
* * *
1142 AATAACCTTTCAACTGACACTTGAACAACCTCAATCGGACAAGTGGACCGAAAATTATACAATAT
322 AATAACCTTTCAACTGACACTTAAACAACCTCAATCGGACAAGTGAAACGAAAATTATACAATAT
* * *
1207 TAGATAGACCGACAATCGAGACCACAAAATTTTAGAAGCTTTTTTTAGAA
387 TAGAGAGACCGACAATCGAGACCACAAAATTTCAGAAGCATTTTTTAGAA
* * *
1257 TCAAAACATCAAAATTGGCTTTTGAGTCCTTCATGAAAGTTGTAGACCATGAAATTACCTTTAAA
1 TCAAAACATTAAAATTGGC-TTTAAGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTTTAAA
* *
1322 TAGAAACCTGAATCATCTTGATCGGACAAATAGAACAAAAAATACAAAAATAAAAGCCAACGCGT
65 TAGAAACTTGAATCATCTTGATCGGACAAATAGAACAAAAAATACAAAAATAAAAGCCAACACGT
* *
1387 TAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAAGCATAAAAAGTGTGAGAATCAT
130 TAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAAGCAT-AAAAGTATGAGGATCAT
*
1452 TTGATAAATAATCCAGCAAAAAAAATATTTGTTTATAGAGACCAAACATAAAAATTCTCTCTCGA
194 TTGATAAATAATCCAGC-AAAAAAATATTTGTTTAT-GAGACCAAACATAAAAATTCCCTCTCGA
*
1517 AC-CCTCCACGAAACTCATTTAATCAAATTCAGCTTTCAGG-CCCTCGACGAAAGTCGTAGATCA
257 ACTCC-CCACGAAACTCA-TTAATCAAATTCAGCTTTCAGGCCCCT-GACGAAAGTCGTAGATAA
* * * *
1580 CACGATAACCTTTTAA-TAGACACTTAAACAATCTCAATCGGACAAGTGAAACGAAAATTATACG
319 CACAATAACCTTTCAACT-GACACTTAAACAACCTCAATCGGACAAGTGAAACGAAAATTATACA
*
1644 ATATTAGAGAGACCGGCAATCGAGACCACAAAATTTCAGAAGCATTTTTTAGAA
383 ATATTAGAGAGACCGACAATCGAGACCACAAAATTTCAGAAGCATTTTTTAGAA
* ** *
1698 TCAAAACATTAAAATTGACTTCTAAGTCCTTCATGGGAGTTGTAGATCATGAAATTACCTTTTAA
1 TCAAAACATTAAAATTGGCTT-TAAGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTTTAAA
* ** * * * * *
1763 TAGATACTTGAATCATCTTGATCGGACAAGCAAAACAAAAAATATAAGAATTAAAGTCGAA-ACG
65 TAGAAACTTGAATCATCTTGATCGGACAAATAGAACAAAAAATACAAAAATAAAAG-CCAACACG
* *** * *
1827 TTCAAA-CGTCCAACCCAAAACTTGTGGGGGACTAAATAGCATAAAGCATAAAGGTAT-AGGGAT
129 TT-AAATCGTCCAACCCATAA-TTGTAAAGGATTAAATAGCATAAAGCATAAAAGTATGA-GGAT
* * * *
1890 CATTTCATAAATACTCCAACAAAAAAATGTTTGTTTATTGAGA
191 CATTTGATAAATAATCCAGCAAAAAAATATTTGTTTA-TGAGA
1933 ATGGGACCCA
Statistics
Matches: 594, Mismatches: 66, Indels: 30
0.86 0.10 0.04
Matches are distributed among these distances:
438 8 0.01
439 151 0.25
440 115 0.19
441 290 0.49
442 30 0.05
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (436 bp):
TCAAAACATTAAAATTGGCTTTAAGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTTTAAAT
AGAAACTTGAATCATCTTGATCGGACAAATAGAACAAAAAATACAAAAATAAAAGCCAACACGTT
AAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAAGCATAAAAGTATGAGGATCATTT
GATAAATAATCCAGCAAAAAAATATTTGTTTATGAGACCAAACATAAAAATTCCCTCTCGAACTC
CCCACGAAACTCATTAATCAAATTCAGCTTTCAGGCCCCTGACGAAAGTCGTAGATAACACAATA
ACCTTTCAACTGACACTTAAACAACCTCAATCGGACAAGTGAAACGAAAATTATACAATATTAGA
GAGACCGACAATCGAGACCACAAAATTTCAGAAGCATTTTTTAGAA
Done.