Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012286.1 Corchorus olitorius cultivar O-4 contig12319, 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: 2021
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1579 original size:322 final size:321
Alignment explanation
Indices: 53--2019 Score: 2852
Period size: 325 Copynumber: 6.1 Consensus size: 321
43 ATCCTTTACC
** *
53 TGACGGGATTTTCACGAATCTAAATATCGTTTTCGCATTTTTTTCCGAATTAAGTTCTAATTAAA
1 TGACGGGATTTTCACGCTTCTAAATATCGTTTTCGCA-TTTTTTCCGAATTAATTTCTAATTAAA
* *
118 TTGAAACAAGCTTCAGATACTCGTATAA-ACAAATCCTTATATCGAATGTAGCTGAGATTTGGTT
65 TTGAAACAAGATTCAGATACTCGTA-AAGACAAATCCTTATATCGAATGTGGCTGAGATTTGGTT
* *
182 AGATTATATATAAAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATTGAGCCGGACTCC
129 AGATTATATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATTGAGCCGGGCTCC
* *
247 GGAACGCG-TTTTATCCAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAAACTGACCCGAA
194 GGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAA
* * *
311 AATTTTTTTTACTTCAATTTTTTGCAACAATACTTACAAAAGATATATTATTCAACGCCAAAAAG
259 AA-TTTTTTT-C-TCAATTTTTTGCAACAATACTCAGAAAA-ATATATAATTCAACGCCAAAAAG
376 AT
320 AT
* *
378 TGACGGCATTTTCACGCTTCTAAATATCGTTTTCGCATTTTTTTCCGAATTAATTTTTAATTAAA
1 TGACGGGATTTTCACGCTTCTAAATATCGTTTTCGCA-TTTTTTCCGAATTAATTTCTAATTAAA
* *
443 TTG-AACTAA-ATTTTAGATACTCGTAGAA-ACAAATCCATATATCGAATGTGGCTGAGATTTGG
65 TTGAAAC-AAGA-TTCAGATACTCGTA-AAGACAAATCCTTATATCGAATGTGGCTGAGATTTGG
*
505 TTAGATTATATATAGAAACTTTTA-GACTCTTTGCGCCCAAAATCATGCAAAATTGAGCCGGGCT
127 TTAGATTATATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATTGAGCCGGGCT
* * * * * * * *
569 TCGGAACGCGTTTTTAGTCAAAAACAGTGATAGTTAATACACAATTTTGACTAAAAACTGACCCG
192 CCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCG
* *
634 AAAATTTTTTTTCTCAATTTTTTGCAACATTACTCGGAAAAATATATAATTCAACGCCAAAAAGA
257 AAAA-TTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAATATATAATTCAACGCCAAAAAGA
699 T
321 T
* * * ** * *
700 TGACGGGATTTTTATGTTTCTAAATATTATTTTTGCA-TTTTTCCGATTTAATTTCTAATTAAAT
1 TGACGGGATTTTCACGCTTCTAAATATCGTTTTCGCATTTTTTCCGAATTAATTTCTAATTAAAT
*
764 TGAAACAAGATTTAGATACTCGTAAAGACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTAG
66 TGAAACAAGATTCAGATACTCGTAAAGACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTAG
* * *
829 A-TAAATATAGAAACTTTTAGGAGTCTTTGTGCCCAAAATCATGCAAAATTGGGCCGGGCTCCGG
131 ATTATATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATTGAGCCGGGCTCCGG
* * * * * *
893 AACGCATTTTTAACCAAAAAAC----T-G-TCGTACACGGTTTAGGCTAAAAACTGACCCGAAAA
196 AACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAA
* * * * *
952 ATTTCTTCTCAGTTTTTTGCAACAACACTCAGAAATGATATATAATTCAACGCCAAAAAGAT
261 TTTTTTTCTCAATTTTTTGCAACAATACTCAGAAA-AATATATAATTCAACGCCAAAAAGAT
** *
1014 TGACGGGATTTTCACAATTCTAAATATCGTTTTCGCATTTTTTTTCCGAATTAATTTCTAATCAA
1 TGACGGGATTTTCACGCTTCTAAATATCGTTTTCGCA--TTTTTTCCGAATTAATTTCTAATTAA
* *
1079 ATTGAAAAAAGATTCAGATACTCGTAAAGAAAAATCCTTATATCGAATGTGGCTGAGATTTGGTT
64 ATTGAAACAAGATTCAGATACTCGTAAAGACAAATCCTTATATCGAATGTGGCTGAGATTTGGTT
* * *
1144 AGA-TAAATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCGAAATTGAGCTGGGCTCC
129 AGATTATATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATTGAGCCGGGCTCC
* *
1208 GGAACGCGATTTTAGCCAAAAACCGTGATGGTTAGTACACTATTTCGGCTAAAAACTGACCCGAA
194 GGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAA
*
1273 AATTTTTTTCTCAAATTTTTGCAACAATACTCAGAATAAATATATAATTCAACGCCAAAAAGAT
259 AATTTTTTTCTCAATTTTTTGCAACAATACTCAGAA-AAATATATAATTCAACGCCAAAAAGAT
* *
1337 TGACGGGATTTTCACGCTTCTAAATATCATTTTCGCA-TTTTTCCTGAATTAATTTATAATTAAA
1 TGACGGGATTTTCACGCTTCTAAATATCGTTTTCGCATTTTTTCC-GAATTAATTTCTAATTAAA
**
1401 TTGAAACAAGATTCAGATACAAGTAAAGACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTA
65 TTGAAACAAGATTCAGATACTCGTAAAGACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTA
*
1466 GATTATATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAACCATGCAAAATTGAGCCGGGCTCCG
130 GATTATATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATTGAGCCGGGCTCCG
1531 GAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAA
195 GAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAA
*
1596 ATTTTTTTCTCAATTTTTTGCAACAATACTCATAAAAAATATATAATTCAACGCCAAAAAGAT
260 ATTTTTTTCTCAATTTTTTGCAACAATACTCA-GAAAAATATATAATTCAACGCCAAAAAGAT
*
1659 TGACGGGATTTTCACGCTTCTAAATATCGTTTTCGCATTTTTTTCCCTAATTAATTTCTAATTAA
1 TGACGGGATTTTCACGCTTCTAAATATCGTTTTCGCA-TTTTTT-CCGAATTAATTTCTAATTAA
*
1724 ATTGAAACAAGATTCAAATACTCGTAAAGACAAATCCTTATATCGAATGTGGCTGAGATTTGGTT
64 ATTGAAACAAGATTCAGATACTCGTAAAGACAAATCCTTATATCGAATGTGGCTGAGATTTGGTT
*
1789 AGATTATATATAGAAACTTTTAGGAGTTCTTTGCGCCCAAAACCATGCAAAATTGAGCCGGGCTC
129 AGATTATATATAGAAACTTTTAGGAG-TCTTTGCGCCCAAAATCATGCAAAATTGAGCCGGGCTC
*
1854 CGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGAATTCGGCTAAAAACTTGCAAAA
193 CGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAA----C----
* * *
1919 TTGACCCGAAAAAGTTTTTTCTCAATTTTTTCGCAACAATACTCATAAAAAACTGTATAATTCAA
250 -TGACCCG-AAAATTTTTTTCTCAATTTTTT-GCAACAATACTCA-GAAAAA-TATATAATTCAA
1984 CG-CAAAAACGAT
310 CGCCAAAAA-GAT
1996 TGACGGGATTTTCACGCTTCTAAA
1 TGACGGGATTTTCACGCTTCTAAA
2020 AA
Statistics
Matches: 1487, Mismatches: 117, Indels: 64
0.89 0.07 0.04
Matches are distributed among these distances:
313 29 0.02
314 84 0.06
315 1 0.00
316 1 0.00
317 165 0.11
319 19 0.01
320 145 0.10
321 85 0.06
322 270 0.18
323 145 0.10
324 161 0.11
325 287 0.19
329 1 0.00
334 7 0.00
335 21 0.01
336 26 0.02
337 40 0.03
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Consensus pattern (321 bp):
TGACGGGATTTTCACGCTTCTAAATATCGTTTTCGCATTTTTTCCGAATTAATTTCTAATTAAAT
TGAAACAAGATTCAGATACTCGTAAAGACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTAG
ATTATATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATTGAGCCGGGCTCCGG
AACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAA
TTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAATATATAATTCAACGCCAAAAAGAT
Found at i:1771 original size:645 final size:643
Alignment explanation
Indices: 53--2019 Score: 2913
Period size: 645 Copynumber: 3.0 Consensus size: 643
43 ATCCTTTACC
** * *
53 TGACGGGATTTTCACGAATCTAAATATCGTTTTCGCATTTTTTTCCGAATTAAGTTCTAATTAAA
1 TGACGGGATTTTCACGCTTCTAAATATCATTTTCGCA--TTTTTCCGAATTAATTTCTAATTAAA
* *
118 TTGAAACAAGCTTCAGATACTCGTATAA-ACAAATCCTTATATCGAATGTAGCTGAGATTTGGTT
64 TTGAAACAAGATTCAGATACTCGTA-AAGACAAATCCTTATATCGAATGTGGCTGAGATTTGGTT
* *
182 AGATTATATATAAAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATTGAGCCGGACTCC
128 AGATTATATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATTGAGCCGGGCTCC
* *
247 GGAACGCG-TTTTATCCAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAAACTGACCCGAA
193 GGAACGCGTTTTTAACCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAA
* *
311 AATTTTTTTTACTTCAATTTTTTGCAACAATACTTACAAAAGATATATTATTCAACGCCAAAAAG
258 AA-TTTTTTT-C-TCAATTTTTTGCAACAATACTCACAAAAGATATATAATTCAACGCCAAAAAG
* *
376 ATTGACGGCATTTTCACGCTTCTAAATATCGTTTTCGCATTTTTTTCCGAATTAATTTTTAATTA
320 ATTGACGGGATTTTCACGCTTCTAAATATCGTTTTCGCATTTTTTTCCGAATTAATTTCTAATTA
* *
441 AATTG-AACTAA-ATTTTAGATACTCGTAGAA-ACAAATCCATATATCGAATGTGGCTGAGATTT
385 AATTGAAAC-AAGA-TTCAGATACTCGTA-AAGACAAATCCTTATATCGAATGTGGCTGAGATTT
*
503 GGTTAGATTATATATAGAAACTTTTA-GACTCTTTGCGCCCAAAATCATGCAAAATTGAGCCGGG
447 GGTTAGATTATATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATTGAGCCGGG
* * * * * * *
567 CTTCGGAACGCGTTTTTAGTCAAAAACAGTGATAGTTAATACACAATTTTGACTAAAAACTGACC
512 CTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGGCTAAAAACTGACC
* *
632 CGAAAATTTTTTTTCTCAATTTTTTGCAACATTACTCGGAAAAATATATAATTCAACGCCAAAAA
577 CGAAAA-TTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAATATATAATTCAACGCCAAAAA
697 GAT
641 GAT
* * * * * *
700 TGACGGGATTTTTATGTTTCTAAATATTATTTTTGCATTTTTCCGATTTAATTTCTAATTAAATT
1 TGACGGGATTTTCACGCTTCTAAATATCATTTTCGCATTTTTCCGAATTAATTTCTAATTAAATT
*
765 GAAACAAGATTTAGATACTCGTAAAGACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTAGA
66 GAAACAAGATTCAGATACTCGTAAAGACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTAGA
* * *
830 -TAAATATAGAAACTTTTAGGAGTCTTTGTGCCCAAAATCATGCAAAATTGGGCCGGGCTCCGGA
131 TTATATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATTGAGCCGGGCTCCGGA
* * * * * *
894 ACGCATTTTTAACCAAAAAAC----T-G-TCGTACACGGTTTAGGCTAAAAACTGACCCGAAAAA
196 ACGCGTTTTTAACCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAT
* * * * *
953 TTTCTTCTCAGTTTTTTGCAACAACACTCAGAAATGATATATAATTCAACGCCAAAAAGATTGAC
261 TTTTTTCTCAATTTTTTGCAACAATACTCACAAAAGATATATAATTCAACGCCAAAAAGATTGAC
** *
1018 GGGATTTTCACAATTCTAAATATCGTTTTCGCATTTTTTTTCCGAATTAATTTCTAATCAAATTG
326 GGGATTTTCACGCTTCTAAATATCGTTTTCGCA-TTTTTTTCCGAATTAATTTCTAATTAAATTG
* *
1083 AAAAAAGATTCAGATACTCGTAAAGAAAAATCCTTATATCGAATGTGGCTGAGATTTGGTTAGA-
390 AAACAAGATTCAGATACTCGTAAAGACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTAGAT
* * *
1147 TAAATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCGAAATTGAGCTGGGCTCCGGAA
455 TATATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATTGAGCCGGGCTCCGGAA
* *
1212 CGCGATTTTAGCCAAAAACCGTGATGGTTAGTACACTATTTCGGCTAAAAACTGACCCGAAAATT
520 CGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGGCTAAAAACTGACCCGAAAATT
*
1277 TTTTTCTCAAATTTTTGCAACAATACTCAGAATAAATATATAATTCAACGCCAAAAAGAT
585 TTTTTCTCAATTTTTTGCAACAATACTCAGAA-AAATATATAATTCAACGCCAAAAAGAT
*
1337 TGACGGGATTTTCACGCTTCTAAATATCATTTTCGCATTTTTCCTGAATTAATTTATAATTAAAT
1 TGACGGGATTTTCACGCTTCTAAATATCATTTTCGCATTTTTCC-GAATTAATTTCTAATTAAAT
**
1402 TGAAACAAGATTCAGATACAAGTAAAGACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTAG
65 TGAAACAAGATTCAGATACTCGTAAAGACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTAG
*
1467 ATTATATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAACCATGCAAAATTGAGCCGGGCTCCGG
130 ATTATATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATTGAGCCGGGCTCCGG
*
1532 AACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAA
195 AACGCGTTTTTAACCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAA
* *
1597 TTTTTTTCTCAATTTTTTGCAACAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGA
260 TTTTTTTCTCAATTTTTTGCAACAATACTCACAAAAGATATATAATTCAACGCCAAAAAGATTGA
*
1662 CGGGATTTTCACGCTTCTAAATATCGTTTTCGCATTTTTTTCCCTAATTAATTTCTAATTAAATT
325 CGGGATTTTCACGCTTCTAAATATCGTTTTCGCATTTTTTT-CCGAATTAATTTCTAATTAAATT
*
1727 GAAACAAGATTCAAATACTCGTAAAGACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTAGA
389 GAAACAAGATTCAGATACTCGTAAAGACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTAGA
*
1792 TTATATATAGAAACTTTTAGGAGTTCTTTGCGCCCAAAACCATGCAAAATTGAGCCGGGCTCCGG
454 TTATATATAGAAACTTTTAGGAG-TCTTTGCGCCCAAAATCATGCAAAATTGAGCCGGGCTCCGG
1857 AACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGAA-TTCGGCTAAAAACTTGCAAAATT
518 AACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACAC-AATTTCGGCTAAAAA----C-----T
* * *
1921 GACCCGAAAAAGTTTTTTCTCAATTTTTTCGCAACAATACTCATAAAAAACTGTATAATTCAACG
573 GACCCG-AAAATTTTTTTCTCAATTTTTT-GCAACAATACTCA-GAAAAA-TATATAATTCAACG
1986 -CAAAAACGAT
634 CCAAAAA-GAT
1996 TGACGGGATTTTCACGCTTCTAAA
1 TGACGGGATTTTCACGCTTCTAAA
2020 AA
Statistics
Matches: 1185, Mismatches: 101, Indels: 56
0.88 0.08 0.04
Matches are distributed among these distances:
636 132 0.11
637 245 0.21
638 89 0.08
639 109 0.09
640 1 0.00
641 1 0.00
643 1 0.00
644 73 0.06
645 303 0.26
646 21 0.02
647 117 0.10
648 1 0.00
651 1 0.00
656 7 0.01
657 20 0.02
658 22 0.02
659 42 0.04
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Consensus pattern (643 bp):
TGACGGGATTTTCACGCTTCTAAATATCATTTTCGCATTTTTCCGAATTAATTTCTAATTAAATT
GAAACAAGATTCAGATACTCGTAAAGACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTAGA
TTATATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATTGAGCCGGGCTCCGGA
ACGCGTTTTTAACCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAT
TTTTTTCTCAATTTTTTGCAACAATACTCACAAAAGATATATAATTCAACGCCAAAAAGATTGAC
GGGATTTTCACGCTTCTAAATATCGTTTTCGCATTTTTTTCCGAATTAATTTCTAATTAAATTGA
AACAAGATTCAGATACTCGTAAAGACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTAGATT
ATATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATTGAGCCGGGCTCCGGAAC
GCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGGCTAAAAACTGACCCGAAAATTT
TTTTCTCAATTTTTTGCAACAATACTCAGAAAAATATATAATTCAACGCCAAAAAGAT
Done.