Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007614.1 Corchorus capsularis cultivar CVL-1 contig07635, 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: 4272
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Found at i:3751 original size:438 final size:433
Alignment explanation
Indices: 2911--3892 Score: 1441
Period size: 438 Copynumber: 2.2 Consensus size: 433
2901 TATAATTAAC
* * * * * * *
2911 AAAATGTTTGTTGATAGAGA-TGAAACATAAAAATTATCTCTTGAACCCTTCATGAAACTCATGA
1 AAAATATTTGTTTATGGAGACT-AAACATAAAAATTCTCTCTCGAA-CCTTCACGAAACTCATTA
* * *** * *
2975 ATCAAATTCAACATTCAAACCCTTAGTGAAAGTCGTATATTACACAATAACATTTTAACCGCACT
64 ATCAAATTCAACTTTCAAGCCCTTAACAAAAGTCGTA-A-TATACAATAACATTGTAACCGCACT
* * *
3040 TGAACAACTTCAATCGGACAAGTTGAGCAAAAATTATACAATATTAAATAAACCGGCAATCAAAA
127 TGAACAACCTCAATCGGACAAGTGGACCAAAAATTATACAATATTAAATAAACCGGCAATCAAAA
** *
3105 CCACGAAATTTAAAAATCATTTTTTAGAATTGAAACATTATTTGGCTTCTGAGTCCTTCATGAAA
192 CCACGAAATTTAAAAATCATTTTTTAGAATCAAAACATTAATTGGCTTCTGAGTCCTTCATGAAA
*
3170 GTTCTAAATCATGAAATTACCTCATAATATACACTTGAATCACTTTGATCGAACAAATAGAACAG
257 GTTCTAAATCATGAAATTACCTCATAATATACACTTGAATCACCTTGATCGAACAAATAGAACAG
* *
3235 AAAATACAAAAATAAAAGTTCAAGCGTTAAATTGTCCAACCTATAATCTTAAAGGATTAAATAGC
322 AAAATACAAAAATAAAAGTTAAAGCGTTAAATCGTCCAACCTATAATCTTAAAGGATTAAATAGC
*
3300 GTAAAACATAAAAGTATGAGGATCATTTGATAGATAATCCAAC-AAA
387 ATAAAACATAAAAGTATGAGGATCATTTGATAGATAATCCAACAAAA
3346 AAAATATTTGTTTATGGAGACTAAACATAAAAATTCTCTCTCGAACCTTCCACGAAACTCATTAA
1 AAAATATTTGTTTATGGAGACTAAACATAAAAATTCTCTCTCGAACCTT-CACGAAACTCATTAA
* *
3411 TCAAATTCAACTTTCAAGCCCTTAACAAAAGTCGTAGATCATACAATAACCTTGTAATCGACACT
65 TCAAATTCAACTTTCAAGCCCTTAACAAAAGTCGTA-AT-ATACAATAACATTGTAACCG-CACT
* * *
3476 TGAACAACCTCAATCGGACAAGTGGACCGAAAATTATACAATATTAAATAGACTGGCAATCAAAA
127 TGAACAACCTCAATCGGACAAGTGGACCAAAAATTATACAATATTAAATAAACCGGCAATCAAAA
* *
3541 CCACGAAATTTAAAAATCATTTTTTAGAATCAAAACATTAAAATTGGCTTTTG-GCTCCTTTATG
192 CCACGAAATTTAAAAATCATTTTTTAGAATCAAAACATT--AATTGGCTTCTGAG-TCCTTCATG
* * *
3605 AAAGTTGTAGATCATTAAATTACCTCATAATATACACTTGAATCACCTTGATCGAACAAATAGAA
254 AAAGTTCTAAATCATGAAATTACCTCATAATATACACTTGAATCACCTTGATCGAACAAATAGAA
* *
3670 CAGAAAATACAAAAATAAAATTTAAAGCGTTAAATCGTCCAACCTATAATTTTAAAGGATTAAAT
319 CAGAAAATACAAAAATAAAAGTTAAAGCGTTAAATCGTCCAACCTATAATCTTAAAGGATTAAAT
* *
3735 AGCATAAAATATAAAAGTATGAGGATCATTTGATAGATAATCCAGCAAAA
384 AGCATAAAACATAAAAGTATGAGGATCATTTGATAGATAATCCAACAAAA
* *
3785 AAAATATTTGTTTATGGAGACCAAACAT-AAAATTACTCTCTCAAACCTTTCACGAAACTCATTA
1 AAAATATTTGTTTATGGAGACTAAACATAAAAATT-CTCTCTCGAACC-TTCACGAAACTCATTA
* *
3849 ATCAAATTCAGCTTTCAAGCGCTTAACAAAAGTCGTAATATACA
64 ATCAAATTCAACTTTCAAGCCCTTAACAAAAGTCGTAATATACA
3893 CTTGAAATTA
Statistics
Matches: 494, Mismatches: 43, Indels: 18
0.89 0.08 0.03
Matches are distributed among these distances:
434 5 0.01
435 99 0.20
436 101 0.20
437 6 0.01
438 191 0.39
439 90 0.18
440 2 0.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (433 bp):
AAAATATTTGTTTATGGAGACTAAACATAAAAATTCTCTCTCGAACCTTCACGAAACTCATTAAT
CAAATTCAACTTTCAAGCCCTTAACAAAAGTCGTAATATACAATAACATTGTAACCGCACTTGAA
CAACCTCAATCGGACAAGTGGACCAAAAATTATACAATATTAAATAAACCGGCAATCAAAACCAC
GAAATTTAAAAATCATTTTTTAGAATCAAAACATTAATTGGCTTCTGAGTCCTTCATGAAAGTTC
TAAATCATGAAATTACCTCATAATATACACTTGAATCACCTTGATCGAACAAATAGAACAGAAAA
TACAAAAATAAAAGTTAAAGCGTTAAATCGTCCAACCTATAATCTTAAAGGATTAAATAGCATAA
AACATAAAAGTATGAGGATCATTTGATAGATAATCCAACAAAA
Done.