Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006229.1 Corchorus capsularis cultivar CVL-1 contig06248, 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: 2396
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:671 original size:334 final size:332
Alignment explanation
Indices: 62--1621 Score: 2256
Period size: 333 Copynumber: 4.7 Consensus size: 332
52 TCGTGTGCTA
*
62 ACCCACATTAGATTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTCGATATAATTAAAAA
1 ACCCACATTAGATTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTCGATTTAATT-AAAA
* *
127 TTAATTCGGGAAAAAAAGAAAAATAATATTAGAAGCATGAGAAACCCGTCAATATTTTTGGCGTT
65 TTAATTCGGGAAAAAAAGAAAAATGATATTAGAAGCATGAGAAACCCGTCAATTTTTTTGGCGTT
* *
192 GACTTGTATATATATTTTTAGGAGTATTATGGCCAAAAATTGAGGAGAAATGTTTCAGATCAATT
130 GAGTTATATATAT-TTTTTAGGAGTATTATGGCCAAAAATTGAGGAGAAATGTTTCAGATCAATT
*
257 TTGGCGAAATTTTACCCGAAATCGTGTGCTAACCATCACAGTTTTGGACCAAAAATGCGTTCCGG
194 TTGGCAAAATTTTACCCGAAATCGTGTGCTAACCATCACAGTTTTGGACCAAAAATGCGTTCCGG
322 AGCCCCGGCTCTGTTTTGCATGATTTTTGGCGCCAAGTCTCTTTGAAATATCTATATCCATCTGA
259 AGCCCCGGCTCTGTTTTGCATGATTTTTGGCGCCAAGTCTCTTTGAAATATCTATATCCATCTGA
387 CAAAATCTT
324 CAAAATCTT
396 ACCCACATTAGATTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTCGATTTAATTAAAAT
1 ACCCACATTAGATTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTCGATTTAATTAAAAT
*
461 TAATTCGGGAAAAAAAGAAAAATGATATTAGAAGCATGAGAAACCCGTCAATTTTTTTGACGTTG
66 TAATTCGGGAAAAAAAGAAAAATGATATTAGAAGCATGAGAAACCCGTCAATTTTTTTGGCGTTG
526 AGTTATATATATGTTTTTAGGA-TAATTATGGCCAAAAATTGAGGAGAAATGTTTCAGATCAATT
131 AGTTATATATAT-TTTTTAGGAGT-ATTATGGCCAAAAATTGAGGAGAAATGTTTCAGATCAATT
*
590 TTGGAAACAATTTTACCCGAAATCGTGTGCTAACCATCACAGTTTTGGACCAAAAATGCGTTCCG
194 TTGGCAA-AATTTTACCCGAAATCGTGTGCTAACCATCACAGTTTTGGACCAAAAATGCGTTCCG
* ** *
655 GAGCCCCGGCTCTGTTTTGCATGATTTTTTGCTTCAAGTCTCTTTGAAATATCTATATTCATCTG
258 GAGCCCCGGCTCTGTTTTGCATGATTTTTGGCGCCAAGTCTCTTTGAAATATCTATATCCATCTG
720 ACAAAATCTT
323 ACAAAATCTT
* * * * *
730 ACGCACATTAGATTTAAAGCTTTGTACTTACGACTATGTCAATCCAGTTTCGATTTAATTAAAAT
1 ACCCACATTAGATTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTCGATTTAATTAAAAT
* *
795 TAATTCGGGAAAAAAAGAAAAATGATATTAGAAGCATGAGAAAACCGTAAATTTTTTTGGCGTTG
66 TAATTCGGGAAAAAAAGAAAAATGATATTAGAAGCATGAGAAACCCGTCAATTTTTTTGGCGTTG
860 AGTTATATATATATTTTTAGGA-TAATTATGGCCAAAAATTGAGGAGAAATGTTTCAGATCAATT
131 AGTTATATATAT-TTTTTAGGAGT-ATTATGGCCAAAAATTGAGGAGAAATGTTTCAGATCAATT
* * * * *
924 TTGGGAAAATTTTACCCAAAACCGTGTGCTAACAATCACAGTTTTGGACCAAAAATGAGTTCCGG
194 TTGGCAAAATTTTACCCGAAATCGTGTGCTAACCATCACAGTTTTGGACCAAAAATGCGTTCCGG
* * *
989 AGCCCCGGCTATGTTTTG-ATTGATTTTTGGCGCCAAGTCACTTTGAAATATCTATATCCATTTG
259 AGCCCCGGCTCTGTTTTGCA-TGATTTTTGGCGCCAAGTCTCTTTGAAATATCTATATCCATCTG
1053 ACAAAATCTT
323 ACAAAATCTT
** * *
1063 ACCCACATTA-ATTTTAAAGATTTGTATTTACGACCATCTCAATTAAGTTTTGATTTATTTAGAA
1 ACCCACATTAGA-TTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTCGATTTAATTA-AA
** * * * * ** *
1127 ATTAATTC-GGAAAAATATCAAAAACGATATTAGAAACGTGATAAGTCCTTCAATTTTTTTGGCG
64 ATTAATTCGGGAAAAA-AAGAAAAATGATATTAGAAGCATGAGAAACCCGTCAATTTTTTTGGCG
* * * *
1191 TTGAGTTATATATATTATTTATGAGTATTGTGAG-CAAAAATTGAGGAGAAATGTTTCGGATCAA
128 TTGAGTTATATATATTTTTTAGGAGTATTATG-GCCAAAAATTGAGGAGAAATGTTTCAGATCAA
*
1255 TTTTGGCAAAATTTTACCCGAAATCATGTGCTAACCATCACAGTTTTGGACCAAAAATGCGTTCC
192 TTTTGGCAAAATTTTACCCGAAATCGTGTGCTAACCATCACAGTTTTGGACCAAAAATGCGTTCC
* * * **
1320 GGAACCCCGACTCTGTTTTGCATGATTTTTGACGCCAAGTCTCTTTGAAATATCTATATTAATCT
257 GGAGCCCCGGCTCTGTTTTGCATGATTTTTGGCGCCAAGTCTCTTTGAAATATCTATATCCATCT
*
1385 GACAAAATATT
322 GACAAAATCTT
* * * *
1396 ACCCACATTAAATTTTAAGATTTGTATTTACGACCATCTCAATCCAGTTTTGATTTATTTAGAAA
1 ACCCACATTAGATTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTCGATTTAATTA-AAA
** * * * * ** * *
1461 TTAATTC-GGAAAAATCTGAAAAACGATATTAGAAACGTGATAAGTCCTTCAATATTTTTGGCGT
65 TTAATTCGGGAAAAA-AAGAAAAATGATATTAGAAGCATGAGAAACCCGTCAATTTTTTTGGCGT
* * * * * * *
1525 TTA--CATGTATATTTTTTATGAGTATTGTGGCCAAAAATTGAAGAGAAATGTTTCGGATCAATT
129 TGAGTTATATATATTTTTTAGGAGTATTATGGCCAAAAATTGAGGAGAAATGTTTCAGATCAATT
* **
1588 TTAGTTAAATTTTACCCGAAATCGTGTGCTAACC
194 TTGGCAAAATTTTACCCGAAATCGTGTGCTAACC
1622 CACATTAGAT
Statistics
Matches: 1128, Mismatches: 87, Indels: 25
0.91 0.07 0.02
Matches are distributed among these distances:
330 1 0.00
331 84 0.07
332 3 0.00
333 595 0.53
334 445 0.39
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (332 bp):
ACCCACATTAGATTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTCGATTTAATTAAAAT
TAATTCGGGAAAAAAAGAAAAATGATATTAGAAGCATGAGAAACCCGTCAATTTTTTTGGCGTTG
AGTTATATATATTTTTTAGGAGTATTATGGCCAAAAATTGAGGAGAAATGTTTCAGATCAATTTT
GGCAAAATTTTACCCGAAATCGTGTGCTAACCATCACAGTTTTGGACCAAAAATGCGTTCCGGAG
CCCCGGCTCTGTTTTGCATGATTTTTGGCGCCAAGTCTCTTTGAAATATCTATATCCATCTGACA
AAATCTT
Found at i:1464 original size:667 final size:665
Alignment explanation
Indices: 62--1620 Score: 2296
Period size: 667 Copynumber: 2.3 Consensus size: 665
52 TCGTGTGCTA
*
62 ACCCACATTAGATTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTCGATATAATTAAAAA
1 ACCCACATTAGATTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTCGATTTAATT-AAAA
* *
127 TTAATTCGGGAAAAAAAGAAAAATAATATTAGAAGCATGAGAAACCCGTCAATATTTTTGGCGTT
65 TTAATTCGGGAAAAAAAGAAAAATGATATTAGAAGCATGAGAAAACCGTCAATATTTTTGGCGTT
*
192 GACTTGTATATATATTTTTAGGAGTATTATGGCCAAAAATTGAGGAGAAATGTTTCAGATCAATT
130 GA-TTATATATATATTTTTAGGAGTATTATGGCCAAAAATTGAGGAGAAATGTTTCAGATCAATT
* *
257 TTGGCGAAATTTTACCCGAAATCGTGTGCTAACCATCACAGTTTTGGACCAAAAATGCGTTCCGG
194 TTGG-GAAATTTTACCCGAAATCGTGTGCTAACAATCACAGTTTTGGACCAAAAATGAGTTCCGG
* *
322 AGCCCCGGCTCTGTTTTGCATGATTTTTGGCGCCAAGTCTCTTTGAAATATCTATATCCATCTGA
258 AGCCCCGGCTATGTTTTGCATGATTTTTGGCGCCAAGTCACTTTGAAATATCTATATCCATCTGA
*
387 CAAAATCTTACCCACATTAGATTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTCGATTT
323 CAAAATCTTACCCACATTAGATTTAAAGATTTGTATTTACGACCATCTCAATCAAGTTTCGATTT
* * *
452 AATTAAAATTAATTCGGGAAAAAAAGAAAAATGATATTAGAAGCATGAGAAACCCGTCAATTTTT
388 AATTAAAATTAATTCGGGAAAAAAACAAAAACGATATTAGAAACATGAGAAACCCGTCAATTTTT
*
517 TTGACGTTGAGTTATATATATGTTTTTAGGATAATTATGGCCAAAAATTGAGGAGAAATGTTTCA
453 TTGACGTTGAGTTATATATATGTATTTAGGATAATTATGGCCAAAAATTGAGGAGAAATGTTTCA
*
582 GATCAATTTTGGAAACAATTTTACCCGAAATCGTGTGCTAACCATCACAGTTTTGGACCAAAAAT
518 GATCAATTTTGGAAACAATTTTACCCGAAATCATGTGCTAACCATCACAGTTTTGGACCAAAAAT
* * **
647 GCGTTCCGGAGCCCCGGCTCTGTTTTGCATGATTTTTTGCTTCAAGTCTCTTTGAAATATCTATA
583 GCGTTCCGGAACCCCGACTCTGTTTTGCATGATTTTTTGCGCCAAGTCTCTTTGAAATATCTATA
* *
712 TTCATCTGACAAAATCTT
648 TTAATCTGACAAAATATT
* * * * *
730 ACGCACATTAGATTTAAAGCTTTGTACTTACGACTATGTCAATCCAGTTTCGATTTAATTAAAAT
1 ACCCACATTAGATTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTCGATTTAATTAAAAT
* *
795 TAATTCGGGAAAAAAAGAAAAATGATATTAGAAGCATGAGAAAACCGTAAATTTTTTTGGCGTTG
66 TAATTCGGGAAAAAAAGAAAAATGATATTAGAAGCATGAGAAAACCGTCAATATTTTTGGCGTTG
860 AGTTATATATATATTTTTAGGA-TAATTATGGCCAAAAATTGAGGAGAAATGTTTCAGATCAATT
131 A-TTATATATATATTTTTAGGAGT-ATTATGGCCAAAAATTGAGGAGAAATGTTTCAGATCAATT
* *
924 TTGGGAAAATTTTACCCAAAACCGTGTGCTAACAATCACAGTTTTGGACCAAAAATGAGTTCCGG
194 TTGGG-AAATTTTACCCGAAATCGTGTGCTAACAATCACAGTTTTGGACCAAAAATGAGTTCCGG
*
989 AGCCCCGGCTATGTTTTG-ATTGATTTTTGGCGCCAAGTCACTTTGAAATATCTATATCCATTTG
258 AGCCCCGGCTATGTTTTGCA-TGATTTTTGGCGCCAAGTCACTTTGAAATATCTATATCCATCTG
* *
1053 ACAAAATCTTACCCACATTA-ATTTTAAAGATTTGTATTTACGACCATCTCAATTAAGTTTTGAT
322 ACAAAATCTTACCCACATTAGA-TTTAAAGATTTGTATTTACGACCATCTCAATCAAGTTTCGAT
* * * * ** *
1117 TTATTTAGAAATTAATTC-GGAAAAATATCAAAAACGATATTAGAAACGTGATAAGTCCTTCAAT
386 TTAATTA-AAATTAATTCGGGAAAAA-AACAAAAACGATATTAGAAACATGAGAAACCCGTCAAT
* * *
1181 TTTTTTGGCGTTGAGTTATATATAT-TATTTATGAGT-ATTGTGAG-CAAAAATTGAGGAGAAAT
449 TTTTTTGACGTTGAGTTATATATATGTATTTAGGA-TAATTATG-GCCAAAAATTGAGGAGAAAT
* *
1243 GTTTCGGATCAATTTTGGCAA-AATTTTACCCGAAATCATGTGCTAACCATCACAGTTTTGGACC
512 GTTTCAGATCAATTTTGGAAACAATTTTACCCGAAATCATGTGCTAACCATCACAGTTTTGGACC
1307 AAAAATGCGTTCCGGAACCCCGACTCTGTTTTGCATGA-TTTTTGACGCCAAGTCTCTTTGAAAT
577 AAAAATGCGTTCCGGAACCCCGACTCTGTTTTGCATGATTTTTTG-CGCCAAGTCTCTTTGAAAT
1371 ATCTATATTAATCTGACAAAATATT
641 ATCTATATTAATCTGACAAAATATT
* * * *
1396 ACCCACATTAAATTTTAAGATTTGTATTTACGACCATCTCAATCCAGTTTTGATTTATTTAGAAA
1 ACCCACATTAGATTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTCGATTTAATTA-AAA
** * * * * ** *
1461 TTAATTC-GGAAAAATCTGAAAAACGATATTAGAAACGTGATAAGTCCTTCAATATTTTTGGCGT
65 TTAATTCGGGAAAAA-AAGAAAAATGATATTAGAAGCATGAGAAAACCGTCAATATTTTTGGCGT
* * * * * * *
1525 TTA-CATGTATAT-TTTTTATGAGTATTGTGGCCAAAAATTGAAGAGAAATGTTTCGGATCAATT
129 TGATTATATATATATTTTTAGGAGTATTATGGCCAAAAATTGAGGAGAAATGTTTCAGATCAATT
**
1588 TTAGTTAAATTTTACCCGAAATCGTGTGCTAAC
194 TT-GGGAAATTTTACCCGAAATCGTGTGCTAAC
1621 CCACATTAGA
Statistics
Matches: 802, Mismatches: 76, Indels: 30
0.88 0.08 0.03
Matches are distributed among these distances:
664 72 0.09
665 15 0.02
666 181 0.23
667 415 0.52
668 119 0.15
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (665 bp):
ACCCACATTAGATTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTCGATTTAATTAAAAT
TAATTCGGGAAAAAAAGAAAAATGATATTAGAAGCATGAGAAAACCGTCAATATTTTTGGCGTTG
ATTATATATATATTTTTAGGAGTATTATGGCCAAAAATTGAGGAGAAATGTTTCAGATCAATTTT
GGGAAATTTTACCCGAAATCGTGTGCTAACAATCACAGTTTTGGACCAAAAATGAGTTCCGGAGC
CCCGGCTATGTTTTGCATGATTTTTGGCGCCAAGTCACTTTGAAATATCTATATCCATCTGACAA
AATCTTACCCACATTAGATTTAAAGATTTGTATTTACGACCATCTCAATCAAGTTTCGATTTAAT
TAAAATTAATTCGGGAAAAAAACAAAAACGATATTAGAAACATGAGAAACCCGTCAATTTTTTTG
ACGTTGAGTTATATATATGTATTTAGGATAATTATGGCCAAAAATTGAGGAGAAATGTTTCAGAT
CAATTTTGGAAACAATTTTACCCGAAATCATGTGCTAACCATCACAGTTTTGGACCAAAAATGCG
TTCCGGAACCCCGACTCTGTTTTGCATGATTTTTTGCGCCAAGTCTCTTTGAAATATCTATATTA
ATCTGACAAAATATT
Found at i:2383 original size:332 final size:334
Alignment explanation
Indices: 1619--2396 Score: 1224
Period size: 333 Copynumber: 2.3 Consensus size: 334
1609 TCGTGTGCTA
* * * * *
1619 ACCCACATTAGATTTAAAGATTTGTATTTACGACCATCTCAAACCAGTTTCGATTTAATTAAAAA
1 ACCCACATTAAATTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTTGATTTATTTAGAAA
* ** * * * **
1684 TTAATTCGGGAAAAA-AAGAAAAATTATATTAGAAGCATGAGAAACCCGTCAATTTTTTTGGCGT
66 TTAATTC-GGAAAAATATGAAAAACGATATTAGAAACGTGATAAGTCCGTCAATTTTTTTGGCGT
* **
1748 TGAGTTATATATATATTTTTAGGATAATTGTGGCCAAAAATTGAGGAGAAATGTTTCAGATCAAT
130 TGAGTTATATATATATATTTAGGATAATTGTGGAAAAAAATTGAGGAGAAATGTTTCAGATCAAT
*
1813 TTTGGCAAAATTTTACACGAAATCGTATGCTAACCATCACAGTTTTGGACCAAAAATGAGTTCCG
195 TTTGGCAAAATTTTACACGAAATCATATGCTAACCATCACAGTTTTGGACCAAAAATGAGTTCCG
1878 GAGCCCCGGCTATGTTTTGATTGATTTTTGGCGCCAAGTCTCTTTGAAATATCTATATCCATCTG
260 GAGCCCCGGCTATGTTTTGATTGATTTTTGGCGCCAAGTCTCTTTGAAATATCTATATCCATCTG
1943 ACAAAATCTT
325 ACAAAATCTT
** * *
1953 ACCCACATTATGTTTAAAGATTTGTATTTACGACCATCTCAATCAAATTTTGATTTATTTAGAAA
1 ACCCACATTAAATTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTTGATTTATTTAGAAA
* *
2018 TTAATTCCGAAAAATATGAAAAACGATATTAGAAACGTGATAAGTCCTTCAATTTTTTTGGCGTT
66 TTAATTCGGAAAAATATGAAAAACGATATTAGAAACGTGATAAGTCCGTCAATTTTTTTGGCGTT
*
2083 GAGTTATATATAT-TATTTATGAGT-ATTGTGGAAAAAAATTGAGGAGAAATGTTTCAGATCAAT
131 GAGTTATATATATATATTTAGGA-TAATTGTGGAAAAAAATTGAGGAGAAATGTTTCAGATCAAT
* * *
2146 TTTGGCAAAATTTTACCCGAAATCATGTGCTAACCATCACAGTTTTGGACCAAAAATGCGTTCCG
195 TTTGGCAAAATTTTACACGAAATCATATGCTAACCATCACAGTTTTGGACCAAAAATGAGTTCCG
*
2211 GAGCCCCGGCTCTGTTTTGCA-TGATTTTTGGCGCCAAGTCTCTTTGAAATATCTATATCCATCT
260 GAGCCCCGGCTATGTTTTG-ATTGATTTTTGGCGCCAAGTCTCTTTGAAATATCTATATCCATCT
2275 GA-AAAATCTT
324 GACAAAATCTT
* *
2285 ACCCACATTAAATTTAAAGATTTGTATTTACGACAATCTCAATCCAGTTTTGATTTATTTAGAGA
1 ACCCACATTAAATTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTTGATTTATTTAGAAA
2350 TTAATTCGGAAAAATATGAAAAACGATATTAGAAACGTGATAAGTCC
66 TTAATTCGGAAAAATATGAAAAACGATATTAGAAACGTGATAAGTCC
Statistics
Matches: 407, Mismatches: 34, Indels: 8
0.91 0.08 0.02
Matches are distributed among these distances:
332 113 0.28
333 174 0.43
334 120 0.29
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (334 bp):
ACCCACATTAAATTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTTGATTTATTTAGAAA
TTAATTCGGAAAAATATGAAAAACGATATTAGAAACGTGATAAGTCCGTCAATTTTTTTGGCGTT
GAGTTATATATATATATTTAGGATAATTGTGGAAAAAAATTGAGGAGAAATGTTTCAGATCAATT
TTGGCAAAATTTTACACGAAATCATATGCTAACCATCACAGTTTTGGACCAAAAATGAGTTCCGG
AGCCCCGGCTATGTTTTGATTGATTTTTGGCGCCAAGTCTCTTTGAAATATCTATATCCATCTGA
CAAAATCTT
Done.