Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014507.1 Corchorus capsularis cultivar CVL-1 contig14528, 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: 6296
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Found at i:1468 original size:651 final size:648
Alignment explanation
Indices: 205--1824 Score: 2372
Period size: 651 Copynumber: 2.5 Consensus size: 648
195 TCTAATATCG
* * * *
205 TTTAGCTAAAAACTGACTTGAAAATATTTTTCTCATTTTTTTGCCATAATACTCAGAAAAGATAG
1 TTTAGCAAAAAACTGACCT-AAAATATTTTTCTCAATTTTTTGCCATAATACTCAGAAAAGATAC
*
270 ATAATTCAACACCAAAAAGGTTGACGGGCTTTTCACGGTTCTAATATCGTTTTCCAATTTTTTTT
65 ATAATTCAACACCAAAAAGGATGACGGGCTTTTCACGGTTCTAATATCGTTTTCC-A--TTTTTT
* *
335 TTCCGAATTAATTTTAATCAAATCGAAACAAGATGTCGTAACAACAAATCCTTATATCCAATGTG
127 TTCCGAATTAATTTTAATTAAATCGAAACAAGATGTCGTAAAAACAAATCCTTATATCCAATGTG
*
400 GCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCATAAATCATGCAAAAT
192 GCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACACCATAAATCATGCAAAAT
*
465 TGAGCCGGGGCTCCGGAACTCGTTTTTAGCAAAAAAACTGTGATGATTAGTACACGATTTCGGCT
257 TGAGCCGGGGCTCCGGAACTCGTTTTTAGCAAAAAAACTGTGATGGTTAGTACACGATTTCGGCT
*
530 AAAATTTTTGCAAAAATTGGCCTGAAAAGTTTTTCCTAAATTTTTTGCCCAAATTCTCAGAAAAA
322 AAAATTTTTGCAAAAATTGGCCTGAAAAGTTTTTCCTAAATTTTTTACCCAAATTCTCAGAAAAA
* * *
595 ATATATAATTCAACGCCAAAAAATTGAATAGTTTTTTCGCGCTTCTAATATCGTTTTACCATTTT
387 ATATATAATTCAACGCCAAAAAATTGAATAGTTTTTTCACCCTTCTAATATCATTTTACCATTTT
*
660 TTTTCTCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGAAGCCCGTAAAAACAAATCCTTA
452 TTTTCTCGAATTTATTTCTAATTAAATCGAAACAAGATTAAGAAGCCCGTAAAAACAAATCCTTA
* * * * *
725 ACCAATGTGGCTGAGATTTGGTTAGATGAATATAGTTATTTCAAGGAAAATTTCTTCTAAAAGTT
517 ACCAATGTGGCTAAAATTTGGTTAGATGAATATAGATATTTCAAGGAAAATCTCTTCCAAAAGTT
790 ATACAAAACTGAGACGGGGTCCTGAAACGTGTTTTTAGCCCAAAAACCGTGATGATTAGTACACG
582 ATACAAAACTGAGACGGGGTCCTGAAACGTGTTTTTAGCCCAAAAACCGTGATGATTAGTACACG
855 AT
647 AT
* *
857 TTTAGCAAAAAACTGACCTAAAATATTTTTCTCAATTTATTGCCATAATACTCAGAAAATATACA
1 TTTAGCAAAAAACTGACCTAAAATATTTTTCTCAATTTTTTGCCATAATACTCAGAAAAGATACA
* *
922 TAATTGAACACCAAAAAGGATGACGGGTTTTTCACGGTTCTAATATCGTTTTCCATTTTTTTTCC
66 TAATTCAACACCAAAAAGGATGACGGGCTTTTCACGGTTCTAATATCGTTTTCCATTTTTTTTCC
987 GAATTAATTTTAATTAAATCGAAACAAGATGTCGTAAAAACAAATCCTTATATCCAATGTGGCTG
131 GAATTAATTTTAATTAAATCGAAACAAGATGTCGTAAAAACAAATCCTTATATCCAATGTGGCTG
1052 AGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACACCATAAATCATGCAAAATTGAG
196 AGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACACCATAAATCATGCAAAATTGAG
* * * *
1117 CCGGGACTCCGAAACTCGTTTTTAACAAAAAAAACTGTGATGGTTAGTACACGATTTTGGCTAAA
261 CCGGGGCTCCGGAACTCGTTTTTAGC-AAAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAA
* * * *
1182 ATTTTTGCAAAATTTGGCCTGAAAAGTTTTTCCTCAATTTTTTACCTC-AATTGTGAGAAAAAAA
325 ATTTTTGCAAAAATTGGCCTGAAAAGTTTTTCCTAAATTTTTTACC-CAAATTCTCAG-AAAAAA
* ***
1246 TATATAATTCACCGCCAAAAAAATTGAATAGTTTTTTCACCCTTCTAATATCATTTTTGGA-TTT
388 TATATAATTCAACGCC-AAAAAATTGAATAGTTTTTTCACCCTTCTAATATCATTTTACCATTTT
* * *
1310 TTTT-TCGAATTTATTTTTAATTAAATCGAAATAAGATTAAGAAGCTCGTAAAAACAAATCCTTA
452 TTTTCTCGAATTTATTTCTAATTAAATCGAAACAAGATTAAGAAGCCCGTAAAAACAAATCCTT-
***
1374 AATCCAATGTGGCTAAAATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCTCTTCCAAAAG
516 AA-CCAATGTGGCTAAAATTTGGTTAGATGAATATAGATATTTCAAGGAAAATCTCTTCCAAAAG
* * * *
1439 TTATGCAAAACTGAGCCGGGGAT-CTGAAACGTGTTTTTAGCCCAAAACCCGTGATGGTTAGTAC
580 TTATACAAAACTGAGACGGGG-TCCTGAAACGTGTTTTTAGCCCAAAAACCGTGATGATTAGTAC
1503 ACGAT
644 ACGAT
* * * * * *
1508 TTCAG-ATAAAAACTGACCCGAAAATATTTTTTTTAATTTTTTGCCACAATACTAAGAAAAGATA
1 TTTAGCA-AAAAACTGA-CCTAAAATATTTTTCTCAATTTTTTGCCATAATACTCAGAAAAGATA
* * * * * * * *
1572 TATAATACAACGCCAAATA-GATTGACGGGCTTTTCATGGTTCTTAT-TCATTTTCCAATTTTTT
64 CATAATTCAACACCAAAAAGGA-TGACGGGCTTTTCACGGTTCTAATATCGTTTTCCATTTTTTT
*
1635 TCTGAATTAATTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCC
128 TCCGAATTAATTTTAATTAAATCGAAAC---A---AGATG-TCGTAAAAACAAATCCTTATATCC
* * * *
1700 AATGTGGCTGAGATTTGGTTCGATAAATATAGATATTTCAAGGAGTCATTACCCCAAAAATCATG
186 AATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACACCATAAATCATG
* * * * * *
1765 CAAAATTGATCCGGGGCACTGGAACTCGTTTTTAGCAAAAAAGCTATGATGGTTATTACA
251 CAAAATTGAGCCGGGGCTCCGGAACTCGTTTTTAGCAAAAAAACTGTGATGGTTAGTACA
1825 TGATCCTGAA
Statistics
Matches: 874, Mismatches: 77, Indels: 29
0.89 0.08 0.03
Matches are distributed among these distances:
648 160 0.18
649 141 0.16
650 33 0.04
651 305 0.35
652 93 0.11
654 1 0.00
657 26 0.03
658 115 0.13
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (648 bp):
TTTAGCAAAAAACTGACCTAAAATATTTTTCTCAATTTTTTGCCATAATACTCAGAAAAGATACA
TAATTCAACACCAAAAAGGATGACGGGCTTTTCACGGTTCTAATATCGTTTTCCATTTTTTTTCC
GAATTAATTTTAATTAAATCGAAACAAGATGTCGTAAAAACAAATCCTTATATCCAATGTGGCTG
AGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACACCATAAATCATGCAAAATTGAG
CCGGGGCTCCGGAACTCGTTTTTAGCAAAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAA
TTTTTGCAAAAATTGGCCTGAAAAGTTTTTCCTAAATTTTTTACCCAAATTCTCAGAAAAAATAT
ATAATTCAACGCCAAAAAATTGAATAGTTTTTTCACCCTTCTAATATCATTTTACCATTTTTTTT
CTCGAATTTATTTCTAATTAAATCGAAACAAGATTAAGAAGCCCGTAAAAACAAATCCTTAACCA
ATGTGGCTAAAATTTGGTTAGATGAATATAGATATTTCAAGGAAAATCTCTTCCAAAAGTTATAC
AAAACTGAGACGGGGTCCTGAAACGTGTTTTTAGCCCAAAAACCGTGATGATTAGTACACGAT
Found at i:3101 original size:661 final size:655
Alignment explanation
Indices: 1832--3623 Score: 2688
Period size: 661 Copynumber: 2.7 Consensus size: 655
1822 ACATGATCCT
* * *
1832 GAAAATATTTTTCTCAATTTTTTGCCATAATACTCAGAAAATAAATATAATTCAAAACCAAAAAG
1 GAAAATATTTTTCTCAATTTTTTGCCATAATACTCAGAAAAGATATATAATTCAACACCAAAAAG
*
1897 GTTGACGGGCTTTTCACGGTTCTAATATCGTTTTCCAATTTTTTTCCGAATTAATTTTAATCAAA
66 GTTGACGGGCTTTTCACGGTTCTAATATCGTTTTCCAATTTTTTTCCGAATTAATTTTAATTAAA
*
1962 TCGAAACAAGA-T--G-TC--GTAACAACAATTCCTTATATCCAATGTGGCTGAGATTTGGCTCG
131 TCGAAACAAGATTCAGATCTTGTAACAACAAATCCTTATATCCAATGTGGCTGAGATTTGGCTCG
** * * *
2021 ATGAATATAGATATTTCAAGGAGT-TATTCCGCCAAAAATCATGCAAAATTGATTCGGGCACTGG
196 ATGAATATAGATATTTCAAGGAGTCT-TTATGCCAAAAATCATGCAAAATTAACTGGGGCACTGG
*
2085 AACTCGTTTTTAGCAAAAAAGCTAAGATGGTTATTACATGATTTTCGGCTAAAATTTTTGCAAAA
260 AACTCGTTTTTAGCAAAAAAGCTATGATGGTTATTACATGA-TTTCGGCTAAAATTTTTGCAAAA
* * * * *
2150 ACTAGCCTGATAAGTTTTTCCTCAACTTTCTGCCCCAATACTCATAAAAAATATATAATTTAACG
324 ACTAGCCTGAAAAGTTTTTCCTCAATTTTTTGCCCCTATACTCA-AAAAAATATATAATTCAACG
**
2215 CCAAAAAAATTGAATAGTTTTTTCGCGCTTCTAATATCGTTTTATCGTTTTTTTTCTCGAATTTA
388 CCAAAAAAATTGAATAGTTTTTTCGCGCTTCTAATATCGTTTT-TCAATTTTTTTCTCGAATTTA
*
2280 TTTCTAATTAAATCGAAACAAGATTCAGAAGCCCGTAAAAACAAATCCTTAAAACCAATGTGGTT
452 TTTCTAATTAAATCGAAACAAGATTCAGAAGCCCGTAAAAACAAATCCTTAAAACCAATGTGGCT
* * * *
2345 AAGATTTGGTTAGATGAATATTGATATTTCAAGGAAAATTTCTTATAAAAGTTATACAAAACTGA
517 AAGATTTGGTTAGATAAATATAGATATATCAAGGAAAATTTCTTACAAAAGTTATACAAAACTGA
* *
2410 GCCGGAGTCCTGAAACTTGTTTTTAGCCCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAA
582 GCCGGAGTCCTGAAACGTGTTTTTAGCCCAAAAACCGTGATGATTAGTACACGATTTCAGCTAAA
*
2475 AACTGACCC
647 AACCGACCC
*
2484 GAAAATATTTTTCTCAATTTTTTTGCCACAATACTCAGAAAAGATATATAATTCAACACCAAAAA
1 GAAAATATTTTTCTCAA-TTTTTTGCCATAATACTCAGAAAAGATATATAATTCAACACCAAAAA
2549 GGTTGACGGGCTTTTCACGGTTCTAATATCGTTTTCCAATTTTTTTTCCGAATTAATTTTAATTA
65 GGTTGACGGGCTTTTCACGGTTCTAATATCGTTTTCCAA-TTTTTTTCCGAATTAATTTTAATTA
* * *
2614 AATCGAAATAAGATTCAGATTCTTGTAACAACAAATCCTTATATCCAATGTGGTTGAGATTCAGG
129 AATCGAAACAAGATTCAGA-TCTTGTAACAACAAATCCTTATATCCAATGTGGCTGAGATT-TGG
* *
2679 -TCAATGAATATAGATACTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAATTAAGCTGGGGC-
192 CTCGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAATTAA-CTGGGGCA
* * * * * *
2742 TTCGGAACTCGTTTTCAGCAAAAAAAACTATGATGGTTAGTACACGATTTCGACTAAAATTTTTG
256 CT-GGAACTCGTTTTTAGC-AAAAAAGCTATGATGGTTATTACATGATTTCGGCTAAAATTTTTG
* * * * *
2807 CAAAAACTGGCCTGAAAAGTTTATCCTTAGTTTTTTGCCCCTTTACTCAGAAAAAATATATAATT
319 CAAAAACTAGCCTGAAAAGTTTTTCCTCAATTTTTTGCCCCTATACTCA-AAAAAATATATAATT
* * * * *
2872 CAAGGCCAAAAAGAGTGAATAGTTTTTTCACCCTTCTAATATCGTTTTTCAATTTTTTTCTCGAA
383 CAACGCCAAAAAAATTGAATAGTTTTTTCGCGCTTCTAATATCGTTTTTCAATTTTTTTCTCGAA
*
2937 TTTATTTCTAATTAAATCGAAACAAGATTCAGAAGCCCGTAAAAACAAATCCTTAAAACTAATGT
448 TTTATTTCTAATTAAATCGAAACAAGATTCAGAAGCCCGTAAAAACAAATCCTTAAAACCAATGT
* * * *
3002 GGCTGAGATTTGGTTAGATAAATATAGATATATCGAGGGAAATTTCTTCCAAAAGTTATACAAAA
513 GGCTAAGATTTGGTTAGATAAATATAGATATATCAAGGAAAATTTCTTACAAAAGTTATACAAAA
*
3067 CTGAGCCGGGGTCCTGAAACGTGTTTTTAGCCCAAAAACCGTGATGATTAGTACACGATTTCAGC
578 CTGAGCCGGAGTCCTGAAACGTGTTTTTAGCCCAAAAACCGTGATGATTAGTACACGATTTCAGC
* *
3132 TAAAATCCGACCT
643 TAAAAACCGACCC
* * *
3145 GAAAATATTTTTCTCAATTTTTTGCTATAATACTCAGAAAAGATATACAATTGAACACCAAAAAG
1 GAAAATATTTTTCTCAATTTTTTGCCATAATACTCAGAAAAGATATATAATTCAACACCAAAAAG
3210 GTTGACGGGCTTTTCACGGTTCTAATATCGTTTTCCAATTTTTTTCCGAATTAATTTTAATTAAA
66 GTTGACGGGCTTTTCACGGTTCTAATATCGTTTTCCAATTTTTTTCCGAATTAATTTTAATTAAA
* * * * * * *
3275 TCGAAACAGGATTCAGATGTTCTAAAAAATAAATCCTTATATCTAATGTGGCTGAGATTTGGTTC
131 TCGAAACAAGATTCAGATCTTGT-AACAACAAATCCTTATATCCAATGTGGCTGAGATTTGGCTC
* * *
3340 GATGAATATAGATATTTCAAGGAGTCATTATGCCAAAAA-CATGCAAAATTCATCCGGGGCACTG
195 GATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAATT-AACTGGGGCACTG
3404 GAACTCGTTTTTAGCAAAAAAGCTATGATGGTTATTACATGATTTCGGCTAAAATTTTTGCAAAA
259 GAACTCGTTTTTAGCAAAAAAGCTATGATGGTTATTACATGATTTCGGCTAAAATTTTTGCAAAA
* * * *
3469 ACTTGCTTGAAAAGTTTTTCCTCAATTTTTTG-CCCTAATACTCATAAAAATATATAGTTCAACG
324 ACTAGCCTGAAAAGTTTTTCCTCAATTTTTTGCCCCT-ATACTCAAAAAAATATATAATTCAACG
* * *
3533 CCAAAAAAATTGAATAGTTTTTTCGCGCTTCTAATATCGTTTTACCATTTTTTTCTCGAATTTAA
388 CCAAAAAAATTGAATAGTTTTTTCGCGCTTCTAATATCGTTTTTCAATTTTTTTCTCGAATTTAT
3598 TTCTAATTAAATCGAAACAAGATTCA
453 TTCTAATTAAATCGAAACAAGATTCA
3624 ACACCAAAAA
Statistics
Matches: 1024, Mismatches: 97, Indels: 34
0.89 0.08 0.03
Matches are distributed among these distances:
652 17 0.02
653 82 0.08
654 36 0.04
655 1 0.00
656 105 0.10
657 80 0.08
658 38 0.04
659 115 0.11
660 82 0.08
661 308 0.30
662 137 0.13
663 23 0.02
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (655 bp):
GAAAATATTTTTCTCAATTTTTTGCCATAATACTCAGAAAAGATATATAATTCAACACCAAAAAG
GTTGACGGGCTTTTCACGGTTCTAATATCGTTTTCCAATTTTTTTCCGAATTAATTTTAATTAAA
TCGAAACAAGATTCAGATCTTGTAACAACAAATCCTTATATCCAATGTGGCTGAGATTTGGCTCG
ATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAATTAACTGGGGCACTGGA
ACTCGTTTTTAGCAAAAAAGCTATGATGGTTATTACATGATTTCGGCTAAAATTTTTGCAAAAAC
TAGCCTGAAAAGTTTTTCCTCAATTTTTTGCCCCTATACTCAAAAAAATATATAATTCAACGCCA
AAAAAATTGAATAGTTTTTTCGCGCTTCTAATATCGTTTTTCAATTTTTTTCTCGAATTTATTTC
TAATTAAATCGAAACAAGATTCAGAAGCCCGTAAAAACAAATCCTTAAAACCAATGTGGCTAAGA
TTTGGTTAGATAAATATAGATATATCAAGGAAAATTTCTTACAAAAGTTATACAAAACTGAGCCG
GAGTCCTGAAACGTGTTTTTAGCCCAAAAACCGTGATGATTAGTACACGATTTCAGCTAAAAACC
GACCC
Done.