Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012410.1 Corchorus capsularis cultivar CVL-1 contig12431, 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: 2795
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Found at i:1703 original size:333 final size:332
Alignment explanation
Indices: 1--2096 Score: 3549
Period size: 332 Copynumber: 6.3 Consensus size: 332
1 ACTGTGATGGTTAGTACACGATTTCGACTAAAATTTCGCAAAAATTGACCCCAAAAGATTTTTCC
1 ACTGTGATGGTTAGTACACGATTTCGACTAAAATTTCGCAAAAATTGACCCCAAAAGATTTTTCC
*
66 TCAATATTTGGCCAAAATACTAATAAAAAATATATTATTAAAGGCCAAAAATATTGGAGGGATTT
66 TCAATATTTGGCCAAAATACTCATAAAAAATATATTATTAAAGGCCAAAAATATTGGAGGGATTT
*
131 TCACGGTTTTAATGTCATTTTTACTATTTTTTCTGAATTACTTTCTATTTAATTCGAAAAAGATT
131 TCACGGTTTTAATGTCATTTTTACTATTTTTTCTGAATTAATTTCTATTTAATTCGAAAAAGATT
196 CAGATGCTCGTAAAAACAAATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATAGAT
196 CAGATGCTCGTAAAAACAAATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATAGAT
*
261 ATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAATACTGAGCCGAGACCTCGGAACGCGTTTTTA
261 ATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGAGACCTCGGAACGCGTTTTTA
326 GCCAAAA
326 GCCAAAA
*
333 ACTGTGATCGGTTAGTACACGATTTCGACTAAAATTTCGCAAAAGTTGACCCCAAAAGATTTTTC
1 ACTGTGAT-GGTTAGTACACGATTTCGACTAAAATTTCGCAAAAATTGACCCCAAAAGATTTTTC
* *
398 CAT-AATATTTGGCCAAAATACTCATAATAAATATATTATTAAAGGCC-AAAATACTGGAGGGAT
65 C-TCAATATTTGGCCAAAATACTCATAAAAAATATATTATTAAAGGCCAAAAATATTGGAGGGAT
* * *
461 TTTCACGGTTTTAATGTCATTTTGACTATTTTTTCTGAATTAATTTCTATTTAGTTGGAAAAAGA
129 TTTCACGGTTTTAATGTCATTTTTACTATTTTTTCTGAATTAATTTCTATTTAATTCGAAAAAGA
*
526 TTCAGATGCTCGTAAAACCAAATTCC-TAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATA
194 TTCAGATGCTCGTAAAAACAAA-TCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATA
* * *
590 GATATTTGAAGGAGTCTTGGCGCCAAAAATCATGCAATACTGAGCCGAGACCTCGGAACGCGCTT
258 GATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGAGACCTCGGAACGCGTTT
655 TTAGCCAAAA
323 TTAGCCAAAA
*
665 ACTGTGATGGTTAGTACAAGATTTCGACTAAAATTTCGCAAAAATTGACCCCAAAAGATTTTTCC
1 ACTGTGATGGTTAGTACACGATTTCGACTAAAATTTCGCAAAAATTGACCCCAAAAGATTTTTCC
* *
730 TCAATATTTGGCCAAAATACTAATAAAAAATATATTATTAAAGGCCAAAAATATTGAAGGGATTT
66 TCAATATTTGGCCAAAATACTCATAAAAAATATATTATTAAAGGCCAAAAATATTGGAGGGATTT
795 TCACGGTTTTAATGTCATTTTTACTATTTTTTCTGAATTAATTTC-ATTTTAATTCGAAAAAGAT
131 TCACGGTTTTAATGTCATTTTTACTATTTTTTCTGAATTAATTTCTA-TTTAATTCGAAAAAGAT
*
859 TCAGATGCTCGTAAAAACAAATCCTTAAATCTATAGTGGCTGAGATTTGGTTAGATGAATATAGA
195 TCAGATGCTCGTAAAAACAAATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATAGA
924 TATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGAGACCTCGGAACGCGTTTTT
260 TATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGAGACCTCGGAACGCGTTTTT
*
989 AGCCCAAA
325 AGCCAAAA
*
997 ACTGTGATCGGTTAGTACACGATTTTGGACTAAAATTTCGCAAAAAGTT-ACCCCAAAAGATTTT
1 ACTGTGAT-GGTTAGTACACGA-TTTCGACTAAAATTTCGCAAAAA-TTGACCCCAAAAGATTTT
*
1061 TCCTCAATATTTGGCCAAAATACTCATAATAAATATATTATTAAAGGCCAAAAATATTGGAGGGA
63 TCCTCAATATTTGGCCAAAATACTCATAAAAAATATATTATTAAAGGCCAAAAATATTGGAGGGA
* * * *
1126 CTTTCACGGTTTTAATTTCATTTTTACTATATTTTTCTGAATTTATTTCTAATTAATTTTCGAAA
128 TTTTCACGGTTTTAATGTCATTTTTACTAT-TTTTTCTGAATTAATTTCTATTTAA--TTCG-AA
* *
1191 AAAGATTCAGATGCTCGTAAAACCAAATCTTTAAATCCATAGTGGCTGAGATTTGGTTAGATCG-
189 AAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGAT-GA
* *
1255 ATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGACATCGGAACG
253 ATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGAGACCTCGGAACG
*
1320 CGTTTTTAGCAAAAA
318 CGTTTTTAGCCAAAA
1335 ACTGTGATGGTTAGTACACGATTTCGACTAAAATTTCGCAAAAATTGACCCCAAAAGATTTTTCC
1 ACTGTGATGGTTAGTACACGATTTCGACTAAAATTTCGCAAAAATTGACCCCAAAAGATTTTTCC
*
1400 TCAATATTTGGCCAAAATACTAATAAAAAATATATTATTAAAGGCCAAAAATAATTGGAGGGATT
66 TCAATATTTGGCCAAAATACTCATAAAAAATATATTATTAAAGGCCAAAAAT-ATTGGAGGGATT
*
1465 TTCACGGTTTTAATTTCATTTTTACTATTTTTTTCTGAATTAATTTCTATTTAATTCGAAAAAGA
130 TTCACGGTTTTAATGTCATTTTTACTA-TTTTTTCTGAATTAATTTCTATTTAATTCGAAAAAGA
* *
1530 TTCAGATGCTCGTAAAAACAAATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATAAAA
194 TTCAGATGCTCGTAAAAACAAATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATAG
** * * *
1595 ATATTTCAA-TTGTCTTGACGCTAAAAATCATGCAAAACTGAGCCGAGACCTTGGAACGCGTTTT
259 ATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGAGACCTCGGAACGCGTTTT
1659 TAGCCAAAA
324 TAGCCAAAA
* *
1668 ACTGTGATGGTTATTACACGATTTCGAGTAAAATTTCGCAAAAATTGACCCCAAAAGATTTTTCC
1 ACTGTGATGGTTAGTACACGATTTCGACTAAAATTTCGCAAAAATTGACCCCAAAAGATTTTTCC
* *
1733 TCAATATTTGGCCAAAATACTCATAAAAAATATACTATTAAACGCCAAAAATATTGGAGGGATTT
66 TCAATATTTGGCCAAAATACTCATAAAAAATATATTATTAAAGGCCAAAAATATTGGAGGGATTT
1798 TCACGGTTTTAATGTCATTTTTACTATTTTTTTCTGAATTAATTTCTATTTAATTCGAAAAAGAT
131 TCACGGTTTTAATGTCATTTTTACTA-TTTTTTCTGAATTAATTTCTATTTAATTCGAAAAAGAT
* *
1863 TCAGATGCTCGTAAAAACAAATCCTTAAATCCATAGCGGTTGAGATTTGGTTAGATGAATATAGA
195 TCAGATGCTCGTAAAAACAAATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATAGA
* * *
1928 TATTTCAAAGAGTCTTGGTGCCAAAAATCATGCAAAACTGAGACGAGACCTCGGAACGCGTTTTT
260 TATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGAGACCTCGGAACGCGTTTTT
*
1993 AGACAAAA
325 AGCCAAAA
*
2001 ACTGTGATTGTTAGTACACGATTTCGACTAAAATTTCGCAAAAATTGACCCCAAAAGATTTTTCC
1 ACTGTGATGGTTAGTACACGATTTCGACTAAAATTTCGCAAAAATTGACCCCAAAAGATTTTTCC
* *
2066 TCTATATTTGGCCAAAATACTCATAATAAAT
66 TCAATATTTGGCCAAAATACTCATAAAAAAT
2097 GATACGAATC
Statistics
Matches: 1660, Mismatches: 83, Indels: 41
0.93 0.05 0.02
Matches are distributed among these distances:
330 1 0.00
331 101 0.06
332 581 0.35
333 429 0.26
334 203 0.12
335 29 0.02
336 91 0.05
337 78 0.05
338 146 0.09
339 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (332 bp):
ACTGTGATGGTTAGTACACGATTTCGACTAAAATTTCGCAAAAATTGACCCCAAAAGATTTTTCC
TCAATATTTGGCCAAAATACTCATAAAAAATATATTATTAAAGGCCAAAAATATTGGAGGGATTT
TCACGGTTTTAATGTCATTTTTACTATTTTTTCTGAATTAATTTCTATTTAATTCGAAAAAGATT
CAGATGCTCGTAAAAACAAATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATAGAT
ATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGAGACCTCGGAACGCGTTTTTA
GCCAAAA
Done.