Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005401.1 Corchorus capsularis cultivar CVL-1 contig05419, 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: 6029
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Found at i:807 original size:75 final size:74
Alignment explanation
Indices: 675--832 Score: 228
Period size: 75 Copynumber: 2.1 Consensus size: 74
665 TTAAGGAAGA
* * *
675 GAAATGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATGAGGGTAACTCATAGAGGGGCTTTC
1 GAAAAGTGTAATTACGAAAAAAGGTAGAAGGAAAAGGAATGAGGGAAACTCATAGAGGGGCTTTC
*
740 TAGTCATCC
66 TAGTCACCC
* *
749 GAAAAGTGTAATTATGAAAAAAGGTAGAAGGAAAAAGGAAT-AGGGGAAACTCATAGAGGGGTTT
1 GAAAAGTGTAATTACGAAAAAAGGTAGAAGG-AAAAGGAATGA-GGGAAACTCATAGAGGGGCTT
*
813 TTTAGTCACCC
64 TCTAGTCACCC
824 GAAAAGTGT
1 GAAAAGTGT
833 GAAAAGACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
74 29 0.39
75 46 0.61
ACGTcount: A:0.41, C:0.09, G:0.29, T:0.22
Consensus pattern (74 bp):
GAAAAGTGTAATTACGAAAAAAGGTAGAAGGAAAAGGAATGAGGGAAACTCATAGAGGGGCTTTC
TAGTCACCC
Found at i:1511 original size:18 final size:18
Alignment explanation
Indices: 1460--1515 Score: 78
Period size: 18 Copynumber: 3.1 Consensus size: 18
1450 CGAAGATGGA
*
1460 GGTGGAGGAGGTGATGAT
1 GGTGGAGGAGGTGGTGAT
1478 GGTGG-GGATGGTGGTGAT
1 GGTGGAGGA-GGTGGTGAT
*
1496 GGTGGAGGAGGCGGTGAT
1 GGTGGAGGAGGTGGTGAT
1514 GG
1 GG
1516 CGGCAGCAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 3 0.09
18 28 0.82
19 3 0.09
ACGTcount: A:0.16, C:0.02, G:0.61, T:0.21
Consensus pattern (18 bp):
GGTGGAGGAGGTGGTGAT
Found at i:2554 original size:12 final size:12
Alignment explanation
Indices: 2539--2573 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2529 TGCAGGTTTT
*
2539 GGTGGCGGTGGC
1 GGTGGCGGCGGC
2551 GGTGGCGGCGGC
1 GGTGGCGGCGGC
*
2563 GGCGGCGGCGG
1 GGTGGCGGCGG
2574 TGGCTGTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.23, G:0.69, T:0.09
Consensus pattern (12 bp):
GGTGGCGGCGGC
Found at i:4929 original size:330 final size:330
Alignment explanation
Indices: 4212--5773 Score: 1503
Period size: 332 Copynumber: 4.6 Consensus size: 330
4202 CAATGATGGT
* * * * * *
4212 AAAAA-TGACCGGGAAGATTTTTCCTCAATTTTTGGCAAAAATACTCATAAGATATATATAATTC
1 AAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTC
* * * ** *
4276 AAC-TCCAAAAAATT-AGAGGACTTTTCAA-GTGTTTC-ATATCATTTTTCATATTTTTTTCTGA
66 AACAT-CAAAAAATTGAAAGG-CTTTT-AACG-CTTCCAATATTGTTTTTCCTA-TTTTTTCTGA
* * * * *
4337 ACTAATTTCTAATTAAATCGAAACAAGATTTAGATACACGTAAAAACAAATACTTAAATCCAATG
126 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAAAAAATCCTTAAATCCAATG
* * ** * * *
4402 TAGCTGAGATTTAATTAGATGAATAAAGATATTTCAAGGAGTCTGGGCGCCAAAAATCATGCAAA
191 TGGCTGAGATTTGATTAGATGAATAAAGATATTAAAAGGAATCTTGGCACCAAAAATCATGCAAA
* * * * * * *
4467 ACAGAGTCGTGGCCCCGGAACGTGTTTTTAG-TGAAAACCCGTGATGGTTAGTGCACGATTTCAG
256 ACTGAGCCG-GGCCCCGAAACGCGTTTTTAGCCGAAAA-CCGTGATGGTTAGTACACGATTTCGG
4531 CTAAAATTTTGC
319 CTAAAATTTTGC
* * ** *
4543 AAAAATTGACCCAAAAGATATTTCCACAATTTTTGATTAAAATACTCAT-AAAAATATATAATTT
1 AAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTC
* * *
4607 TACATCAAAAAGATTGAAAGGCTTTTAACGCTTCCAATATTGGTTTTCCTA-TTTTTCTGTATTA
66 AACATCAAAAA-ATTGAAAGGCTTTTAACGCTTCCAATATTGTTTTTCCTATTTTTTCTGAATTA
* *
4671 ATTTCTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAAAAAATCCTTAAATCCAATGTGGC
130 ATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAAAAAATCCTTAAATCCAATGTGGC
* * * * *
4736 TGAGATTTGGTTAGATGAATAGAGATATAAAAAGGACTCTTGGAACCAAAAATCATGCAAAACTG
195 TGAGATTTGATTAGATGAATAAAGATATTAAAAGGAATCTTGGCACCAAAAATCATGCAAAACTG
* * *
4801 AGCCGGGCCCTGAAACGCGTTTTTAGCCGAAAACCGTGATGATTAGTACATGATTTCGGCTAAAA
260 AGCCGGGCCCCGAAACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAA
4866 TTTTGC
325 TTTTGC
4872 AAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTC
1 AAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTC
* * * * ** * * *
4937 AAAATCAAAAACATTGTAGGGCTTTTCACAG-TTGTAATATTGTTTTTCTTTTTTTTTTTCGAAT
66 AACATCAAAAA-ATTGAAAGGCTTTTAAC-GCTTCCAATATTGTTTTTCCTATTTTTTCT-GAAT
* * *
5001 TAATTTCTAATTAAATCGAAAAAAGATTCAGAAACTCGTAAAAACAAATCCTTAAATCCAATGTG
128 TAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAAAAAATCCTTAAATCCAATGTG
** * * ** ** *
5066 TTTGAAATTTGTTTAGATGAATATTGATATTGTAAGGAATCTTGGCACCAAAAATCTTGCAAAAC
193 GCTGAGATTTGATTAGATGAATAAAGATATTAAAAGGAATCTTGGCACCAAAAATCATGCAAAAC
* *
5131 TGAGCAGGGCCCCGAAACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGACTAA
258 TGAGCCGGGCCCCGAAACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAA
5196 AATTTTGC
323 AATTTTGC
* * *
5204 AAAAATTGACCCGAAAGATATTTCCCCAATTTTTGGCTAAACTACTCATAAAAAATATATAATTT
1 AAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTC
* * * * * *
5269 GACATAAAAAATATTGAAGGGCTTTTAATGCTTCTAATATTGTTTTTCCTATTTTTTCCGAATTA
66 AACATCAAAAA-ATTGAAAGGCTTTTAACGCTTCCAATATTGTTTTTCCTATTTTTTCTGAATTA
* *
5334 ATTTCTAATTAAATCGAAACAAAATTCAGATCCTCGTAAAAAAAATATCCTTAAATCCAATGTGG
130 ATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAAAAA-ATCCTTAAATCCAATGTGG
* * * ***
5399 CTGAGATTATCGATAATCTAGTACTTCTAA-ACAA-ATCCTTAATATTGTTTAGATGAATATAAA
194 CTGAGATT-T-G---AT-TAG-A--T-GAATA-AAGAT-ATTAA-A------AG--GAATCTTGG
* * * * * * * *
5462 TATTTCAAGGAATCTTGCACAAAAATGAGGCACAACTGAGCTGGGCACCGGAATGCGTTTTTAGC
238 CA--CCAA-AAATCATG--CAAAACTGAG------C----C-GGGCCCCGAAACGCGTTTTTAGC
* * * *
5527 CGAAAACTGTGATGGTTAGTACACGGTTTCGGTTAAAATGTTGC
287 CGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGC
* * *
5571 AAAAATTGACCCGAATGATATTTCC-CTAATTTTTGACTAGAATACTCATAAAAAATATATAATT
1 AAAAATTGACCCGAAAGATATTTCCTC-AATTTTTGGCTAAAATACTCATAAAAAATATATAATT
* * * * * * **
5635 CGATATCAAAAAGATTG-AGGGCTTTTAATGCTTCTAATATTATTTTTCCTATTTTTTTCCAAAT
65 CAACATCAAAAA-ATTGAAAGGCTTTTAACGCTTCCAATATTGTTTTTCCTA-TTTTTTCTGAAT
* * *
5699 TAATTTCTAATTAAATCGAAACAAAACTCAGATACTTGTAAAAAATAAATCCTTAAATCCAATGT
128 TAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAAA-AAATCCTTAAATCCAATGT
*
5764 GGTTGAGATT
192 GGCTGAGATT
5774 ATGGATAATC
Statistics
Matches: 1029, Mismatches: 149, Indels: 70
0.82 0.12 0.06
Matches are distributed among these distances:
329 97 0.09
330 184 0.18
331 84 0.08
332 371 0.36
333 5 0.00
334 1 0.00
337 1 0.00
338 3 0.00
339 1 0.00
341 4 0.00
342 4 0.00
343 1 0.00
349 2 0.00
351 6 0.01
353 3 0.00
354 7 0.01
356 9 0.01
362 1 0.00
366 34 0.03
367 209 0.20
368 2 0.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (330 bp):
AAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTC
AACATCAAAAAATTGAAAGGCTTTTAACGCTTCCAATATTGTTTTTCCTATTTTTTCTGAATTAA
TTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAAAAAATCCTTAAATCCAATGTGGCT
GAGATTTGATTAGATGAATAAAGATATTAAAAGGAATCTTGGCACCAAAAATCATGCAAAACTGA
GCCGGGCCCCGAAACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAT
TTTGC
Found at i:5787 original size:367 final size:367
Alignment explanation
Indices: 5074--6029 Score: 1354
Period size: 367 Copynumber: 2.6 Consensus size: 367
5064 TGTTTGAAAT
* * ***
5074 TTGTTTAGATGAATATTGATATTGTAAGGAATCTTGGCACCAAAAATCTTGCAAAACTGAGCAGG
1 TTGTTTAGATGAATATAGATATT-TAAGGAATCTTAGCA-CAAAAATGAGGCAAAACTGAGCAGG
* * * *
5139 GCCCCGAAACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGACTAAAATTTTGC
64 GCCCCGGAATGCGTTTTTAGCCGAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGC
5204 AAAAATTGACCCGAAAGATATTTCCCCAATTTTTGGCTA-AACTACTCATAAAAAATATATAATT
129 AAAAATTGACCCGAAAGATATTTCCCCAATTTTTGGCTAGAACTACTCATAAAAAATATATAATT
* * * *
5268 TGACATAAAAAATATTGAAGGGCTTTTAATGCTTCTAATATTGTTTTTCCTATTTTTTCCGAATT
194 CGACAT-AAAAAGATTGAAGGGCTTTTAATGCTTCTAATATTATTTTTCCTATTTTTTCCAAATT
* *
5333 AATTTCTAATTAAATCGAAACAAAATTCAGATCCTCGTAAAAAAAATATCCTTAAATCCAATGTG
258 AATTTCTAATTAAATCGAAACAAAACTCAGATACTCGTAAAAAAAATATCCTTAAATCCAATGTG
5398 GCTGAGATTATCGATAATCTAGTACTTCTAAACAAATCCTTAATA
323 GCTGAGATTATCGATAATCTAGTACTTCTAAACAAATCCTTAATA
* * *
5443 TTGTTTAGATGAATATAAATATTTCAAGGAATCTT-GCACAAAAATGAGGCACAACTGAGCTGGG
1 TTGTTTAGATGAATATAGATATTT-AAGGAATCTTAGCACAAAAATGAGGCAAAACTGAGCAGGG
* * * *
5507 CACCGGAATGCGTTTTTAGCCGAAAACTGTGATGGTTAGTACACGGTTTCGGTTAAAATGTTGCA
65 CCCCGGAATGCGTTTTTAGCCGAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCA
* * *
5572 AAAATTGACCCGAATGATATTTCCCTAATTTTTGACTAGAA-TACTCATAAAAAATATATAATTC
130 AAAATTGACCCGAAAGATATTTCCCCAATTTTTGGCTAGAACTACTCATAAAAAATATATAATTC
*
5636 GATATCAAAAAGATTG-AGGGCTTTTAATGCTTCTAATATTATTTTTCCTATTTTTTTCCAAATT
195 GACAT-AAAAAGATTGAAGGGCTTTTAATGCTTCTAATATTATTTTTCCTA-TTTTTTCCAAATT
*
5700 AATTTCTAATTAAATCGAAACAAAACTCAGATACTTGTAAAAAATAA-ATCCTTAAATCCAATGT
258 AATTTCTAATTAAATCGAAACAAAACTCAGATACTCGTAAAAAA-AATATCCTTAAATCCAATGT
* *
5764 GGTTGAGATTATGGATAATCTAGTACTTCTAAACAAATCCTTAATA
322 GGCTGAGATTATCGATAATCTAGTACTTCTAAACAAATCCTTAATA
* *
5810 TTGGTTAGATGAATATAGATATTTTAAGGAATCTTAGCACAAAAAATGAGGCAAAACTGAGCCGG
1 TTGTTTAGATGAATATAGATA-TTTAAGGAATCTTAGCAC-AAAAATGAGGCAAAACTGAGCAGG
* * * *
5875 GCCCCGGAATGCGGTTTTAGCTGAAAA-TCGTGATGGTTAAGTATACGATTTCGGCGAAAATTTT
64 GCCCCGGAATGCGTTTTTAGCCGAAAACT-GTGATGGTT-AGTACACGATTTCGGCTAAAATTTT
* ** * * *
5939 GCAAAAAATGTTCCGAAAGATCTTTCCCCAATTTTTGGCT-GAAGTAGC-CATAAAAAA-ATTTA
127 GCAAAAATTGACCCGAAAGATATTTCCCCAATTTTTGGCTAGAACTA-CTCATAAAAAATATATA
* *
6001 ATTCAACATAAAAAGATTGAAGGTCTTTT
191 ATTCGACATAAAAAGATTGAAGGGCTTTT
Statistics
Matches: 523, Mismatches: 52, Indels: 24
0.87 0.09 0.04
Matches are distributed among these distances:
366 33 0.06
367 291 0.56
368 26 0.05
369 108 0.21
370 64 0.12
371 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33
Consensus pattern (367 bp):
TTGTTTAGATGAATATAGATATTTAAGGAATCTTAGCACAAAAATGAGGCAAAACTGAGCAGGGC
CCCGGAATGCGTTTTTAGCCGAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAA
AAATTGACCCGAAAGATATTTCCCCAATTTTTGGCTAGAACTACTCATAAAAAATATATAATTCG
ACATAAAAAGATTGAAGGGCTTTTAATGCTTCTAATATTATTTTTCCTATTTTTTCCAAATTAAT
TTCTAATTAAATCGAAACAAAACTCAGATACTCGTAAAAAAAATATCCTTAAATCCAATGTGGCT
GAGATTATCGATAATCTAGTACTTCTAAACAAATCCTTAATA
Done.