Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014159.1 Corchorus capsularis cultivar CVL-1 contig14180, 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: 1805
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Found at i:1042 original size:322 final size:322
Alignment explanation
Indices: 4--1805 Score: 2473
Period size: 323 Copynumber: 5.6 Consensus size: 322
1 AAA
* *
4 TAAATCGAAA-AAACATTCAGATGCTCGTAAATAGAAATCCTTAAAT-CATTGTGGATGAGATTT
1 TAAATCGAAACAAA-ATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCATTGTGGCTGAGATTT
* * *
67 GATTAGATGAACATAAATATTTCAAGGAGTCTTTCTGC-GAAAAATCATGCAAAATTGAGCCAGG
65 GGTTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCAAAAAAATCATGCAAAATTGAGCCAGG
*
131 TCTCCGGAATACGTTTTTAGCCAAAAAACGTGATGGTTAGTACACGATTTCGGCTAAAAATTGAC
130 TCTCCGGAACACGTTTTTAGCCAAAAAACGTGATGGTTAGTACACGATTTCGGCTAAAAATTGAC
* * * * * *
196 CCGAAATGATTTTCCTCAATTTTTTGCCACAACAATCAGAGAAAATATAGAAATCAACGCCAAAA
195 CCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAATCAACGCCAAAA
* * * *
261 AAATTAAGGGTTCTTCACGCTTCTAATATCG-TTTTCCTATGTTTTCTCCCGAATTTATTTTTAA
260 AAATGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCC-AT-TTTT-TTCCGAATTTATTTCTAA
325 T
322 T
* * *
326 TAAATCGAAACAAAATTCAGAAGCTCGTAAAATGAAATCCTTAAAGCCATTGTGGCTGAGATTTG
1 TAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCATTGTGGCTGAGATTTG
* * * * * *
391 GTTGGATGACTATAAATATTTCAAGGGGTCTTTCTGCAAAAAGATCATCCAAAATTGAGCCGGGT
66 GTTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCAAAAAAATCATGCAAAATTGAGCCAGGT
* * * * * *
456 CTCCGGAACGC-ATTTTAGCC-AAAAACGGTGATTGTTAATACACAATTTCGGCTAAAAATGGAC
131 CTCCGGAACACGTTTTTAGCCAAAAAAC-GTGATGGTTAGTACACGATTTCGGCTAAAAATTGAC
* * *
519 CCGAAAAGTATTTCATCAATTTTTTGCCACAATACTAAGAAAAAATATATAAATCAACGCCAAAA
195 CCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAATCAACGCCAAAA
* *
584 AAATGATGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAACTTTTATTTCAAAT
260 AAATGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAA--TTTATTTCTAAT
*
649 TAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCATTGTGGCTGAGATTTG
1 TAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCATTGTGGCTGAGATTTG
* ** *
714 GTTAGATGAATATAGATATTTCAAGGACACTTTCTGCAAAAAAATCATGCAAAATTGAGCC-GGA
66 GTTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCAAAAAAATCATGCAAAATTGAGCCAGGT
** * * *
778 CTCCGGAACGTGTTTTTAGCCAAAAACCGCGATGGTTAGTACACGATTTCGGCTAAAAATTGAGC
131 CTCCGGAACACGTTTTTAGCCAAAAAACGTGATGGTTAGTACACGATTTCGGCTAAAAATTGACC
* * *
843 CGAAAAGTTTTTCCTCAATTTATTGCGACAATACTCAGAAAAAATATATAAATCAACACC-AAAA
196 CGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAATCAACGCCAAAAA
* * *
907 AATGAAGGGTTTTTCATGCTTCTTATATCGTTTTTCCAGTTTTTTTTTCGAATTTATTTCTAAT
261 AATGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCA--TTTTTTTCCGAATTTATTTCTAAT
* * * * *
971 TAAATCGAAACAAGATTCAGGTGCTCGTAAAAAGAAATCCTTAAATCGATGGTGGCTGAGATTTC
1 TAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCATTGTGGCTGAGATTTG
* * * * **
1036 GTTAGATGAATATAGATATTTCAAGGAGTCTTTCTTCCAAAAAATCATGAAAAATTGAGCTGGGT
66 GTTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCAAAAAAATCATGCAAAATTGAGCCAGGT
* *
1101 CTCCGGAACGCGTTTTTAGCC-AAAAACGGTGATGTTTAGTACACGATTTCGGCTAAAAATTGAC
131 CTCCGGAACACGTTTTTAGCCAAAAAAC-GTGATGGTTAGTACACGATTTCGGCTAAAAATTGAC
* * *
1165 CCGAAAA-TTTTTCCTCAATTTTTTGCCACAATACTAAGAAAAAATATATAAATCAATGCCCAAA
195 CCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAATCAACGCCAAAA
* * * * * * *
1229 AAATGATGGATTTTTCACGCTTCTAATATCGTTTTTTCTTTTTTTTCTGAACTTTTATTTCAAAA
260 AAATGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAA--TTTATTTCTAAT
* * *
1294 TAAATCGAAA-AAACATTCAGATGCTCGTAAATAGAAATCCTTAAATCCATTATGGATGAGATTT
1 TAAATCGAAACAAA-ATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCATTGTGGCTGAGATTT
* *
1358 GATTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCGAAAAAATCATGCAAAATTGAGCCAGG
65 GGTTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCAAAAAAATCATGCAAAATTGAGCCAGG
*
1423 TCTCCGGAATACGTTTTTAGCCAAAAAAACGTGATGGTTAGTACACGATTTCGGCTAAAAATTGA
130 TCTCCGGAACACGTTTTTAGCC-AAAAAACGTGATGGTTAGTACACGATTTCGGCTAAAAATTGA
* *
1488 CCCGAAATGATTTTCCTCAATTTTTTGCCACAACT-CTCAGAAAAAATATATAAATCAACGCCAA
194 CCCGAAAAGTTTTTCCTCAATTTTTTGCCACAA-TACTCAGAAAAAATATATAAATCAACGCCAA
* * * * *
1552 AAAAATTAAGGGTTCTTCACGCTTCTAATATCGTTTTTCCATATTTTCCCTAATTTATTTCTAAT
258 AAAAATGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTTATTTCTAAT
* * *
1617 TAAATCGAAACAAAATTAAGATGCTCGTAGAAAGAAATCCTTAAATCCATTGTGGCTAAGATTTG
1 TAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCATTGTGGCTGAGATTTG
* * * * * *
1682 GTGAGATTAATATAGATATTTCAAGGAGTCTTTC-GGAAAAAAATCATGCTAAATTGAGCCGGGT
66 GTTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCAAAAAAATCATGCAAAATTGAGCCAGGT
* *
1746 CTCCGGAATACGTTTTTAGCCAAAAAACGTGACGG--AGTACACGATTTCGGCTAAAAATTG
131 CTCCGGAACACGTTTTTAGCCAAAAAACGTGATGGTTAGTACACGATTTCGGCTAAAAATTG
Statistics
Matches: 1308, Mismatches: 150, Indels: 47
0.87 0.10 0.03
Matches are distributed among these distances:
319 25 0.02
321 29 0.02
322 328 0.25
323 729 0.56
324 98 0.07
325 98 0.07
326 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Consensus pattern (322 bp):
TAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCATTGTGGCTGAGATTTG
GTTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCAAAAAAATCATGCAAAATTGAGCCAGGT
CTCCGGAACACGTTTTTAGCCAAAAAACGTGATGGTTAGTACACGATTTCGGCTAAAAATTGACC
CGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAATCAACGCCAAAAA
AATGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTTATTTCTAAT
Found at i:1234 original size:645 final size:645
Alignment explanation
Indices: 1--1805 Score: 2725
Period size: 645 Copynumber: 2.8 Consensus size: 645
1 AAATAAATCGAAAAAACATTCAGATGCTCGTAAATAGAAATCCTTAAAT-CATTGTGGATGAGAT
1 AAATAAATCGAAAAAACATTCAGATGCTCGTAAATAGAAATCCTTAAATCCATTGTGGATGAGAT
* *
65 TTGATTAGATGAACATAAATATTTCAAGGAGTCTTTCTGCGAAAAATCATGCAAAATTGAGCCAG
66 TTGATTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCAAAAAATCATGCAAAATTGAGCCAG
130 GTCTCCGGAATACGTTTTTAGCCAAAAAACGTGATGGTTAGTACACGATTTCGGCTAAAAATTGA
131 GTCTCCGGAATACGTTTTTAGCCAAAAAACGTGATGGTTAGTACACGATTTCGGCTAAAAATTGA
* * * *
195 CCCGAAATGATTTTCCTCAATTTTTTGCCACAACAATCAGAGAAAATATAGAAATCAACGCCAAA
196 CCCGAAATGATTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAATCAACGCCAAA
* *
260 AAAATTAAGGGTTCTTCACGCTTCTAATATCG-TTTTCCTATGTTTTCTCCCGAATTTATTTTTA
261 AAAATTAAGGGTTCTTCACGCTTCTAATATCGTTTTTCC-AT-TTTTTTCCCGAATTTATTTCTA
* * *
324 ATTAAATCGAAACAAAATTCAGAAGCTCGTAAAATGAAATCCTTAAAGCCATTGTGGCTGAGATT
324 ATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCATTGTGGCTGAGATT
* * * * *
389 TGGTTGGATGACTATAAATATTTCAAGGGGTCTTTCTGCAAAAAGATCATCCAAAATTGAGCCGG
389 TGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCAAAAA-ATCATGCAAAATTGAGCCGG
* * * *
454 GTCTCCGGAACGC-ATTTTAGCCAAAAACGGTGAT-TGTTAATACACAATTTCGGCTAAAAATGG
453 GTCTCCGGAACGCGTTTTTAGCCAAAAACGGTGATGT-TTAGTACACGATTTCGGCTAAAAATTG
517 ACCCGAAAAGTATTTCATCAATTTTTTGCCACAATACTAAGAAAAAATATATAAATCAACGCCAA
517 ACCCGAAAAGTATTTCATCAATTTTTTGCCACAATACTAAGAAAAAATATATAAATCAACGCCAA
*
582 AAAAATGATGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAACTTTTATTTCA
582 AAAAATGATGGATTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAACTTTTATTTCA
* * * * *
646 AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCATTGTGGCTGAGAT
1 AAATAAATCGAAAAAACATTCAGATGCTCGTAAATAGAAATCCTTAAATCCATTGTGGATGAGAT
* * **
711 TTGGTTAGATGAATATAGATATTTCAAGGACACTTTCTGCAAAAAAATCATGCAAAATTGAGCC-
66 TTGATTAGATGAATATAAATATTTCAAGGAGTCTTTCTGC-AAAAAATCATGCAAAATTGAGCCA
* *** * *
775 GGACTCCGGAACGTGTTTTTAGCCAAAAACCGCGATGGTTAGTACACGATTTCGGCTAAAAATTG
130 GGTCTCCGGAATACGTTTTTAGCCAAAAAACGTGATGGTTAGTACACGATTTCGGCTAAAAATTG
* * * * * *
840 AGCCGAAAAGTTTTTCCTCAATTTATTGCGACAATACTCAGAAAAAATATATAAATCAACACC-A
195 ACCCGAAATGATTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAATCAACGCCAA
* * * * **
904 AAAAATGAAGGGTTTTTCATGCTTCTTATATCGTTTTTCCAGTTTTTTTTTCGAATTTATTTCTA
260 AAAAATTAAGGGTTCTTCACGCTTCTAATATCGTTTTTCCA-TTTTTTTCCCGAATTTATTTCTA
* * * *
969 ATTAAATCGAAACAAGATTCAGGTGCTCGTAAAAAGAAATCCTTAAATCGATGGTGGCTGAGATT
324 ATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCATTGTGGCTGAGATT
* * * *
1034 TCGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTTCCAAAAAATCATGAAAAATTGAGCTGG
389 TGGTTAGATGAATATAGATATTTCAAGGAGTCTTTC-TGCAAAAAATCATGCAAAATTGAGCCGG
1099 GTCTCCGGAACGCGTTTTTAGCCAAAAACGGTGATGTTTAGTACACGATTTCGGCTAAAAATTGA
453 GTCTCCGGAACGCGTTTTTAGCCAAAAACGGTGATGTTTAGTACACGATTTCGGCTAAAAATTGA
* * * *
1164 CCCGAAAA-TTTTTCCTCAATTTTTTGCCACAATACTAAGAAAAAATATATAAATCAATGCCCAA
518 CCCGAAAAGTATTTCATCAATTTTTTGCCACAATACTAAGAAAAAATATATAAATCAACGCCAAA
* * *
1228 AAAATGATGGATTTTTCACGCTTCTAATATCGTTTTTTCTTTTTTTTCTGAACTTTTATTTCA
583 AAAATGATGGATTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAACTTTTATTTCA
*
1291 AAATAAATCGAAAAAACATTCAGATGCTCGTAAATAGAAATCCTTAAATCCATTATGGATGAGAT
1 AAATAAATCGAAAAAACATTCAGATGCTCGTAAATAGAAATCCTTAAATCCATTGTGGATGAGAT
1356 TTGATTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCGAAAAAATCATGCAAAATTGAGCCA
66 TTGATTAGATGAATATAAATATTTCAAGGAGTCTTTCTGC-AAAAAATCATGCAAAATTGAGCCA
1421 GGTCTCCGGAATACGTTTTTAGCCAAAAAAACGTGATGGTTAGTACACGATTTCGGCTAAAAATT
130 GGTCTCCGGAATACGTTTTTAGCC-AAAAAACGTGATGGTTAGTACACGATTTCGGCTAAAAATT
1486 GACCCGAAATGATTTTCCTCAATTTTTTGCCACAACT-CTCAGAAAAAATATATAAATCAACGCC
194 GACCCGAAATGATTTTCCTCAATTTTTTGCCACAA-TACTCAGAAAAAATATATAAATCAACGCC
* *
1550 AAAAAAATTAAGGGTTCTTCACGCTTCTAATATCGTTTTTCCA-TATTTTCCCTAATTTATTTCT
258 AAAAAAATTAAGGGTTCTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCCGAATTTATTTCT
* * *
1614 AATTAAATCGAAACAAAATTAAGATGCTCGTAGAAAGAAATCCTTAAATCCATTGTGGCTAAGAT
323 AATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCATTGTGGCTGAGAT
* * * * *
1679 TTGGTGAGATTAATATAGATATTTCAAGGAGTCTTTCGGAAAAAAATCATGCTAAATTGAGCCGG
388 TTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCAAAAAATCATGCAAAATTGAGCCGG
** * *
1744 GTCTCCGGAATACGTTTTTAGCCAAAAAAC-GTGACG--GAGTACACGATTTCGGCTAAAAATTG
453 GTCTCCGGAACGCGTTTTTAGCC-AAAAACGGTGATGTTTAGTACACGATTTCGGCTAAAAATTG
Statistics
Matches: 1034, Mismatches: 114, Indels: 26
0.88 0.10 0.02
Matches are distributed among these distances:
643 25 0.02
645 490 0.47
646 363 0.35
647 117 0.11
648 39 0.04
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Consensus pattern (645 bp):
AAATAAATCGAAAAAACATTCAGATGCTCGTAAATAGAAATCCTTAAATCCATTGTGGATGAGAT
TTGATTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCAAAAAATCATGCAAAATTGAGCCAG
GTCTCCGGAATACGTTTTTAGCCAAAAAACGTGATGGTTAGTACACGATTTCGGCTAAAAATTGA
CCCGAAATGATTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAATCAACGCCAAA
AAAATTAAGGGTTCTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCCGAATTTATTTCTAAT
TAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCATTGTGGCTGAGATTTG
GTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCAAAAAATCATGCAAAATTGAGCCGGGTC
TCCGGAACGCGTTTTTAGCCAAAAACGGTGATGTTTAGTACACGATTTCGGCTAAAAATTGACCC
GAAAAGTATTTCATCAATTTTTTGCCACAATACTAAGAAAAAATATATAAATCAACGCCAAAAAA
ATGATGGATTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAACTTTTATTTCA
Done.