Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011086.1 Corchorus capsularis cultivar CVL-1 contig11107, 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: 37496
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:2291 original size:654 final size:642
Alignment explanation
Indices: 102--3471 Score: 3075
Period size: 652 Copynumber: 5.2 Consensus size: 642
92 TGGATTTAAT
* * * *
102 GATTTAATTAGAGATAAATTCAGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTTA
1 GATTTAATTAGAAATAAATTCAAAAAAAATGAAAAAACGATATTAGAAGCGTGAAAAACCCTTCA
* * * *
167 ATTTTTTTTGGCATTGAGTTATATATTTTTTCTGAGTATTGTGGCAAAAAACTGAG--AAAGAAA
66 A-TTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAAA
* * * * *
230 CTTTTCGGGTCAG-T----TTTTAGTCGAAATCGTG--CATCGC-AGCTTTTGGATAAAACCGCG
130 CTTTTCGGGTCAGTTCAAATTTTAGCCGAAATCGTGTACATCACGA-TTTTTGGCTAAAAACGCG
* * * * * *
287 TT-TCGGGGTCTCGGCTCAGTTTCGCATGATTTTTGGCAG-AAAGAGTCCTTTAAATTTCTATAT
194 TTCT-GGGGCCCCGGCTCAGTTTTGCATGATTTTTGG-AGCAAAGACTCCTTGAAATATCTATAT
350 TCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATATGAATCTTGT
257 TCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATATGAATCTTGT
* * * *
415 TTCGATTTAATTAGAAATAAATTCAGAAAAAAGTGG-AAAACGAAATTAGAAGTGTGAAAA-CCC
322 TTCGATTTAATTAGAAATTAATT-AGGAAAAA-TGGAAAAACGATATTAGAAGCGTGAAAAGCCC
* * * ** *
478 TTTAATTTTTTTTGGCGTTGAATTATATATTTTTT-TGAGTATTGCAGCAAAGAATTGAGGAAAA
385 TTCAA-TCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA-GAAAA
** * * *
542 ATTTTTCGGGTAAGTTTTTGCAAAATTTTAGCCGAAATCGTTTACT---CATCACGGTTTTTAGC
448 AAATTTC-GG---G----T--AAATTTTTAGCCGAAATCGTGTACTAAACATCACGGTTTTTGGC
** * * *
604 TAAAAACGTGTTTCGATTCCCCGGCTCATTTTTGCATGATTTTTGACATAAAGACTCCTTGAAAT
503 TAAAAACGTGTTTCG-GGCCCCGACTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAAT
* * *
669 ATCTATATTCATCGAACCAAATCTCAGTCACATTCGATTTAACGATTTGTTTTTACGAGCATCTG
567 ATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTG
*
734 AATCTTGTTTA
632 AATCTTGTTTC
* * * * *
745 TATTTAATTTGAAATTAATTCGAAAAAAAAAGAGGGAAAACGATATTAGAAGCGTGAAAAACCCT
1 GATTTAATTAGAAATAAATTC-AAAAAAAATGA--AAAAACGATATTAGAAGCGTGAAAAACCCT
* * * * *
810 TCAATCTTTTTGGTGTAGAATTATA-AGTTTTTTATGAGTATTGTGGCGAAAAATTGA-AAAAAA
63 TCAATTTTTTTGGCGTTGAATTATATA-TTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAA
* * * * * **
873 AAA---ATC--G--AGTT--ACTATTTAGCCAAAAACGTGTACTAACCATCACGGTTTTTTACTA
127 AAACTTTTCGGGTCAGTTCAAAT-TTTAGCCGAAATCGTG---T-A-CATCACGATTTTTGGCTA
* * * * *
929 AAAACGCGTTCTGGGGTCTCGACTCAGTTTTGCATCG-TTTTT-G-GCATAAAACTCCTTAAAAT
186 AAAACGCGTTCTGGGGCCCCGGCTCAGTTTTGCAT-GATTTTTGGAGCA-AAGACTCCTTGAAAT
* * * * * * *
991 ATTTATATTCATCTAACCAAATCTCAGCTACATTGGATATAAGGATTTGTTTTTATGAGGATTTT
249 ATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATATG
* * * * *
1056 AATCATGTTTCTATTTAAATAGAAATTAATTTGAAAAATAATAGGAAAAACGATATTAGAAGCGT
314 AATCTTGTTTCGATTTAATTAGAAATTAATTAG-GAAA-AAT-GGAAAAACGATATTAGAAGCGT
* * * * * * * *
1121 GAGATGCCCTTCAATATGTTTGGCATTTAATTATATATTATTTATGAGTATTGTGGCTAAAAATT
376 GAAAAGCCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATT
* * * * * * *
1186 GAGAAAAAATATTTCGGGTCAGTTTTT--CCAAAATTTCTGTTGAAATCGTGTACCATCAGGGTT
441 GAGAAAAAA-ATTTCGGGTAAATTTTTAGCCGAAA--TC-G-TG-TA-C-T-AAACATCACGG-T
* * * * * * * **
1249 TTTTAGCAAAAAACGAGTTCCGGGACCCCGGA-TAATTTTTGCATGATTTTTGACGCAAAGACTC
496 TTTTGGCTAAAAACGTGTTTCGGG-CCCC-GACTCAGTTTTGCATGATTTTTGGCATAAAGACTC
1313 CTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGG-TTATAAGGATTTGTTTTTAC
559 CTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATT-TAAGGATTTGTTTTTAC
* *
1377 GAGCATCTAAATATTGTTTC
623 GAGCATCTGAATCTTGTTTC
* ** * ** * * * *
1397 GATTTAATTATAAATTGACTCGGAAAAAA-GGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCC
1 GATTTAATTAGAAATAAATTCAAAAAAAATGAAAAAACGATATTAGAAGCGTGAAAAACCCTTCA
* * *
1461 ATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGACAAAAAATT---CAAAAAAAA-
66 ATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAAAC
* * *
1522 --TTC-GG---G-TCAATTTTTAGCCAAAATCGTGTACGCATCACGATTTTTGGGCTAAAAACGT
131 TTTTCGGGTCAGTTCAAATTTTAGCCGAAATCGTGTA--CATCACGATTTTT-GGCTAAAAACGC
* ** * *
1580 GTT-TCGGGGCCCCGGCTCAGTTTTGCATGGTTTTTGGAATAAAGTCTACTTGAAATATCTATA-
193 GTTCT-GGGGCCCCGGCTCAGTTTTGCATGATTTTTGGAGCAAAGACTCCTTGAAATATCTATAT
* * * *
1643 TCTATCTAACCAAATCTCAGCCACATTGGATTTAAGAATTTATTTTTACGAGCATCTAAATCTTG
257 TC-ATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATATGAATCTTG
* * * *
1708 TTTCGATTTAATTATAAATTGATTAGGAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGTCCG
321 TTTCGATTTAATTAGAAATTAATTAGGAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCT
* * * * *
1773 TCCATCTTTTTAGCGTTGAATTATATATTTTTTTCTGAGTACTGTGGCAAAAAATTCA-AAAAAA
386 TCAATCTTTTTGGCATTGAATTATATA-TTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAA
* *
1837 AATTCGGGTAAATTTTTAGCCGAAATCGTGTACTAAACATCACGGTTTTTGGGCTAAAAACATGT
450 ATTTCGGGTAAATTTTTAGCCGAAATCGTGTACTAAACATCACGGTTTTT-GGCTAAAAACGTGT
* * * * *
1902 TTTGGGGCCCGACTCAGTTTTGCATGGTTTTTGGCATAAAGTCTCCTTGAAATATATCTATATCC
514 TTCGGGCCCCGACTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTG-AA-ATATCTATATTC
* * * *
1967 ATCTAACCAAATCTCAGCCACATTGGACTTAAAGGATTTGTTTTTATGAGCATCTGAATCTTATT
577 ATCGAACCAAATCTCAGCCACATTGGA-TTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTT
2032 TC
641 TC
* *
2034 GATTTAATTAGAAATAAATTCAGAAAAAATGAAAAAACGATATTAGAAGCGTGAAAATCCCTTCA
1 GATTTAATTAGAAATAAATTCAAAAAAAATGAAAAAACGATATTAGAAGCGTGAAAAACCCTTCA
2099 ATTTTTTTGGCGTTGAATTATATATTTTTTTCTGAGTATTGTGGC-AAAAATTGAGAAAAAAAAA
66 ATTTTTTTGGCGTTGAATTATATA-TTTTTTCTGAGTATTGTGGCAAAAAATTGAG-AAAAAAAA
*
2163 ACTTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACATCACGATTTTTGGTTAAA
129 AC-TTTTCGGGTCAG---TT-C-AAATTTTAGCCGAAATCGTGTACATCACGATTTTTGGCT-AA
* * *
2228 AAACGCGTTCTGGAGCCCCGGCTCAATTTTGCATGATTTTTGGTGCAAAGACTCCTTGAAATATC
187 AAACGCGTTCTGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGAGCAAAGACTCCTTGAAATATC
* * * * * *
2293 TATATTCTTCGAATCAAATCTCAGCCAGATTGG-TTATAAGGATTTGTTTTTACAAGCATCTGAA
252 TATATTCATCTAACCAAATCTCAGCCACATTGGATT-TAAGGATTTGTTTTTACGAGCATATGAA
* * * *
2357 TCTTGTTTCGATTTAATTATAAATTAATTCGGGAAAATGGGAAAACGATATTAGAAGCGTGAAAA
316 TCTTGTTTCGATTTAATTAGAAATTAATTAGGAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
* * * * *
2422 GCCCATCAATC-TTTTGACATTGAATTATATATTTTTTCTGAATATTGTGACAAAAAATTCAGAA
381 GCCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAA
** * ** * *
2486 AAAAAAATCGGGTCAATTTTTAGCC-AATATCGCATACTAACCATCAGGGTTTTTAGGCTAAAAA
446 AAAAATTTCGGGTAAATTTTTAGCCGAA-ATCGTGTACTAAACATCACGGTTTTT-GGCTAAAAA
* * * * * *
2550 CGCGTTTCGGGACCCCGGCTCAGTTTTGCATTATTTTAT-GCAGAAAAACTCATTGAAATATCTA
509 CGTGTTTCGGG-CCCCGACTCAGTTTTGCATGATTTT-TGGCATAAAGACTCCTTGAAATATCTA
* * * *
2614 TATTCATCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTTTTTTTTACGAGCATATGAATC
572 TATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGA-TTTGTTTTTACGAGCATCTGAATC
2679 TTGTTTC
636 TTGTTTC
* * *
2686 GATTTAATTAGAAATAAATTCGGAAAAAAAAATGGAAAAACAATATTAGAAGCATGAAAAAACCC
1 GATTTAATTAGAAATAAATTC---AAAAAAAATGAAAAAACGATATTAGAAGCGTG-AAAAACCC
* * **
2751 TTCAATTTTTTTGGTGTTTAATTATATAATTTTTT-TGAGTATTGTCACAAAAAAAATTGAG--A
62 TTCAATTTTTTTGGCGTTGAATTATAT-ATTTTTTCTGAGTATTGTGGC--AAAAAATTGAGAAA
* * * * * * * * *
2813 TAAACA-TTTTCGGTTCAGTTTTTGCAAATATTTAGGCGAAATCATGTACGTTAC-AGTTTTGAC
124 AAAAAACTTTTCGGGTCAG---TT-CAAAT-TTTAGCCGAAATCGTGTACATCACGATTTTTGGC
* * * * * *
2876 TAAAAAAGCGTTCTAGAG-CCCAGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAAT
184 TAAAAACGCGTTCTGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGAGCAAAGACTCCTTGAAAT
* * * *
2940 ATCT-TATTCATCGAACAAAATCTTAGCTACATTGGATTTAAGGATTTGTTTTTACGAGCATATG
249 ATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATATG
* *
3004 AATCTTATTTCGATTTAATTAG-AATTAAATTCAGG-AAAA---AAAAACGATATTAGAAACGTG
314 AATCTTGTTTCGATTTAATTAGAAATT-AATT-AGGAAAAATGGAAAAACGATATTAGAAGCGTG
* * * * * *
3064 AAAAACCCTTTAATTTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTAGCGAAGAATTG
377 AAAAGCCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTG
* * * ** * *
3129 AGGAAAAAATTTTCGGGTAAGTTTTTACAAAATTTTAGCCGAAATCGTTTA-TTCATATCACAGT
442 A-GAAAAAAATTTC-GG---G----T--AAATTTTTAGCCGAAATCGTGTACTAAACATCACGGT
* * * *
3193 TTTTGGCTAAAAACGTGTTTCGGGGTCCCCG-CTTAGTTTTGCATGATTCTTGGCGTAAAAACTC
496 TTTTGGCTAAAAACGTGTTTC-GGG-CCCCGACTCAGTTTTGCATGATTTTTGGCATAAAGACTC
* * ** ** *
3257 CTTGAAATATCTATATTCATCGAATCAAATCCCAGCCACATTCAATTTAACTATTTGTTTTTACA
559 CTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACG
*
3322 AGAATCTGAATCTTGTTTC
624 AGCATCTGAATCTTGTTTC
* * *
3341 GATTTAATTAGAAATTAATT-AAAAATAAAAGAGTAAAAACGATATTATAGAAGCATGAAAAACC
1 GATTTAATTAGAAATAAATTCAAAAA-AAATGA--AAAAACGATA-T-TAGAAGCGTGAAAAACC
* *** * *
3405 CTTCAATATTTTTGATATTGAATTATATATTTTTTATGAGTATTGTGGGAAAAAATTGAGAAAAA
61 CTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAA
3470 AA
126 AA
3472 TTTTCAGTTC
Statistics
Matches: 2258, Mismatches: 341, Indels: 244
0.79 0.12 0.09
Matches are distributed among these distances:
633 2 0.00
634 37 0.02
635 24 0.01
636 37 0.02
637 57 0.03
638 64 0.03
639 23 0.01
640 7 0.00
641 17 0.01
642 72 0.03
643 81 0.04
644 53 0.02
645 137 0.06
646 99 0.04
647 50 0.02
648 90 0.04
649 182 0.08
650 104 0.05
651 96 0.04
652 304 0.13
653 138 0.06
654 238 0.11
655 142 0.06
656 156 0.07
657 20 0.01
658 26 0.01
659 2 0.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (642 bp):
GATTTAATTAGAAATAAATTCAAAAAAAATGAAAAAACGATATTAGAAGCGTGAAAAACCCTTCA
ATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAAAC
TTTTCGGGTCAGTTCAAATTTTAGCCGAAATCGTGTACATCACGATTTTTGGCTAAAAACGCGTT
CTGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGAGCAAAGACTCCTTGAAATATCTATATTCAT
CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATATGAATCTTGTTTCG
ATTTAATTAGAAATTAATTAGGAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAAT
CTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTCG
GGTAAATTTTTAGCCGAAATCGTGTACTAAACATCACGGTTTTTGGCTAAAAACGTGTTTCGGGC
CCCGACTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCGAACCA
AATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTC
Found at i:13192 original size:1 final size:1
Alignment explanation
Indices: 13188--13222 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
13178 AGGGATTAAG
13188 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
13223 GCACCCAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:33997 original size:3 final size:3
Alignment explanation
Indices: 33991--34024 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
33981 AAAAAAAAGA
33991 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
34025 GTTATAGAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Done.