Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007714.1 Corchorus capsularis cultivar CVL-1 contig07735, 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: 2062
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:1610 original size:333 final size:333
Alignment explanation
Indices: 1--2062 Score: 3160
Period size: 334 Copynumber: 6.2 Consensus size: 333
* *
1 TTTTGCGATAATTGACCCGAACAATTTTCCTCAGATTTTTTGCCACAATACTCATAAGAATTATA
1 TTTTGCGAAAATTGACCCGAACGATTTTCCTCA-ATTTTTTGCCACAATACTCATAAGAATTATA
*
66 TAATTCATTGCCAAAAGTATTGAAGGGCTTTTCATTCATCCAATATCATATATCCTATTTTTTTT
65 TAATTCATTGCCAAAAGTATTGAAGGGCTTTTCATTCTTCCAATATCATATATCCTA-TTTTTTT
131 TCCGAATTAATTTCCATCTAAATCGAAACAAGATTCTGATCCTAG-AGAAAACAAATCCTCAAAT
129 TCCGAATTAATTTCCATCTAAATCGAAACAAGATTCTGATCCTAGTA-AAAACAAATCCTCAAAT
* *
195 CCAACATGGCTGAGATTTGGTTAGATGAATACAGATATTTTAATGAGTCTTGGCGCCAAAATTCA
193 CCAACATGGCTGAGATTTGGTTAGATGAATACAGATATTTTAATGAGCCTTGGCGCCAAAAATCA
* * *
260 TGCAAAACCGAGTCGGGACCCCGGAATGCATTTTTACCCCAAAACTGTGATGGTTAGTACACGTT
258 TGCAAAACCGAGTCGGGACCCCGGAATGCGTTTTTAGCACAAAACTGTGATGGTTAGTACACGTT
325 TTCGGCTAAAA
323 TTCGGCTAAAA
* *
336 TTTTGCGAAAATTGACCCGAACAATTTTCCTAAATTTTTTTGCCACAATACTCATAAGAATTATA
1 TTTTGCGAAAATTGACCCGAACGATTTTCCTCAA-TTTTTTGCCACAATACTCATAAGAATTATA
*
401 TAATTCATTGCCAAAAGTATTGAAGGGCTTTTCATTCATCCAATATCATATATCCTATTTTTTTT
65 TAATTCATTGCCAAAAGTATTGAAGGGCTTTTCATTCTTCCAATATCATATATCCTATTTTTTTT
*
466 CCGAATTAATTTCCATCTAAATCGAAACAAGATTCTGATCCTAGTGAAAACAAATCCTCAAATCC
130 CCGAATTAATTTCCATCTAAATCGAAACAAGATTCTGATCCTAGTAAAAACAAATCCTCAAATCC
* * * *
531 AACATGGCTGAGATTTGGTTAGATGAATATAGATATTTTAATGAGCCTTGGCGCCAAAATTCGTA
195 AACATGGCTGAGATTTGGTTAGATGAATACAGATATTTTAATGAGCCTTGGCGCCAAAAATCATG
* * * * * * *
596 CATAACTGCGTCGGGATCCCGAAACGCGTTTTTAGCCCAAAACTGTGATGGTTAGTACACGTTTT
260 CAAAACCGAGTCGGGACCCCGGAATGCGTTTTTAGCACAAAACTGTGATGGTTAGTACACGTTTT
661 CGGCTAAAA
325 CGGCTAAAA
670 TTTTGCGAAAATTGACCCGAACGATTTTCCTCAATTTTTTTGCCACAATACTCATAAGAATTATA
1 TTTTGCGAAAATTGACCCGAACGATTTTCCTCAA-TTTTTTGCCACAATACTCATAAGAATTATA
*
735 TAATTCATTGCCAAAAGTATTGAAGGGCTTTTCATTCTTCCAATATCATATATCATATTTTTTTT
65 TAATTCATTGCCAAAAGTATTGAAGGGCTTTTCATTCTTCCAATATCATATATCCTATTTTTTTT
* *
800 CTGAATTAATTTCCATTTAAATCGAAACAAGATTCTGATCCTAGTAAAAACAAATCCTCAAATCC
130 CCGAATTAATTTCCATCTAAATCGAAACAAGATTCTGATCCTAGTAAAAACAAATCCTCAAATCC
*
865 AACATGGCTGAGATTTGGTTAGATGAATACAGATATTTTAATGAGTCTTGGCGCCAAAAATCATG
195 AACATGGCTGAGATTTGGTTAGATGAATACAGATATTTTAATGAGCCTTGGCGCCAAAAATCATG
*
930 CAAAACCGAGTCGGGACCCCGGAATGCGTTTTTAGCCCAAAACTGTGATGGTTAGTACACGTTTT
260 CAAAACCGAGTCGGGACCCCGGAATGCGTTTTTAGCACAAAACTGTGATGGTTAGTACACGTTTT
995 CGGCTAAAA
325 CGGCTAAAA
** * * * * * * *
1004 TTTTGCGAAAAAAGACCCGAAAGATTTTTCCTCAATTTTTGGCAAGAATACTCACAAAAAATATA
1 TTTTGCGAAAATTGACCCGAACGA-TTTTCCTCAATTTTTTGCCACAATACTCATAAGAATTATA
* * * * * * * * *
1069 TAATTCATCGCCAAAAAG-GTTGAAGGGTTTTTTTATGCTTCTATTATCGTTTATCCTA-TTTTT
65 TAATTCATTGCC-AAAAGTATTGAAGGG-CTTTTCATTCTTCCAATATCATATATCCTATTTTTT
* * * *
1132 TTCGGAATTAATTTCTAAT-TAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAATCCTCAAA
128 TTCCGAATTAATTTC-CATCTAAATCGAAACAAGATTCTGATCCTAGTAAAAACAAATCCTCAAA
** * *
1196 TCCAATGTGGCGGAGATTTGGTTAGATGAATACAGATATTTTAATGAGCCTTGGCGTCAAAAATC
192 TCCAACATGGCTGAGATTTGGTTAGATGAATACAGATATTTTAATGAGCCTTGGCGCCAAAAATC
* * * * * *
1261 GTACAAAACAGAGTCGGGACCCCGGAACGCGTTTTTAGCATAAAACTGTAATGGTTAGTACACGT
257 ATGCAAAACCGAGTCGGGACCCCGGAATGCGTTTTTAGCACAAAACTGTGATGGTTAGTACACGT
1326 TTTCGGCTAAAA
322 TTTCGGCTAAAA
*
1338 TTTTGCGAAAATTGACCCGAACGATTTTCCTCAATTTTTTTGCCAAAATACTCATAAGAATTATA
1 TTTTGCGAAAATTGACCCGAACGATTTTCCTCAA-TTTTTTGCCACAATACTCATAAGAATTATA
*
1403 TAATTCATTGCCAAAAGTATTGAAGGGCTTTTCATTCTTCCAATATCATATATCCTA-ATTTTTT
65 TAATTCATTGCCAAAAGTATTGAAGGGCTTTTCATTCTTCCAATATCATATATCCTATTTTTTTT
* * * *
1467 CAGAATTAATTACTATTTAAATCGAAACAAGATTCTGATCCTAGTAAAAACAAATCCTCAAATCC
130 CCGAATTAATTTCCATCTAAATCGAAACAAGATTCTGATCCTAGTAAAAACAAATCCTCAAATCC
* * *
1532 AACATGGCTGAAATTTGATTAGATGAATACAGATATTATAATGAGCCTTGGCGCCAAAAATCATG
195 AACATGGCTGAGATTTGGTTAGATGAATACAGATATTTTAATGAGCCTTGGCGCCAAAAATCATG
1597 CAAAACCGAGTCGGGACCCCGGAATGCGTTTTTAGCACAAAACTGTGATGGTTAGTACACGTTTT
260 CAAAACCGAGTCGGGACCCCGGAATGCGTTTTTAGCACAAAACTGTGATGGTTAGTACACGTTTT
1662 CGGCTAAAA
325 CGGCTAAAA
* *
1671 TTTTGCGAAAATTGACCCGAACGATTTTCTTCAATTTTTTGTCACAATACTCAT--GAATTATAT
1 TTTTGCGAAAATTGACCCGAACGATTTTCCTCAATTTTTTGCCACAATACTCATAAGAATTATAT
* *
1734 AATTCATTGCCAAAAGTATTGAAGGGCTTTCCATTCTTCCAATATCATATAT-C-ATATTTTTTC
66 AATTCATTGCCAAAAGTATTGAAGGGCTTTTCATTCTTCCAATATCATATATCCTATTTTTTTTC
*
1797 TGAATTAATTTCCATCTAAATCGAAACAAGATTCTGATCCTAGTAAAAACAAATCCTCAAATCCA
131 CGAATTAATTTCCATCTAAATCGAAACAAGATTCTGATCCTAGTAAAAACAAATCCTCAAATCCA
* * *
1862 ACATGGCTGAGATTTGGTTAGATGAATACAGATATTTTAACGAGTCATGGCGCCAAAAATCATGC
196 ACATGGCTGAGATTTGGTTAGATGAATACAGATATTTTAATGAGCCTTGGCGCCAAAAATCATGC
1927 AAAACCGAGTCGGGACCCCGGAATGCGTTTTTAGC-CAGAAACTGTGATGG-T--TACACGTTTT
261 AAAACCGAGTCGGGACCCCGGAATGCGTTTTTAGCACA-AAACTGTGATGGTTAGTACACGTTTT
1988 CGGCTAAAA
325 CGGCTAAAA
** * * * * * *
1997 TTTTGCGAAAAAAGACCCGAAAGATTTTTCCTCAATTTTTGGCTAGAATACTCACAAAAATTATA
1 TTTTGCGAAAATTGACCCGAACGA-TTTTCCTCAATTTTTTGCCACAATACTCATAAGAATTATA
2062 T
65 T
Statistics
Matches: 1584, Mismatches: 129, Indels: 34
0.91 0.07 0.02
Matches are distributed among these distances:
326 40 0.03
327 24 0.02
328 4 0.00
329 184 0.12
330 60 0.04
332 20 0.01
333 260 0.16
334 835 0.53
335 157 0.10
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (333 bp):
TTTTGCGAAAATTGACCCGAACGATTTTCCTCAATTTTTTGCCACAATACTCATAAGAATTATAT
AATTCATTGCCAAAAGTATTGAAGGGCTTTTCATTCTTCCAATATCATATATCCTATTTTTTTTC
CGAATTAATTTCCATCTAAATCGAAACAAGATTCTGATCCTAGTAAAAACAAATCCTCAAATCCA
ACATGGCTGAGATTTGGTTAGATGAATACAGATATTTTAATGAGCCTTGGCGCCAAAAATCATGC
AAAACCGAGTCGGGACCCCGGAATGCGTTTTTAGCACAAAACTGTGATGGTTAGTACACGTTTTC
GGCTAAAA
Done.