Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010830.1 Corchorus capsularis cultivar CVL-1 contig10851, 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: 6559
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--49 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
* *
1 TA TA TA TA TA TA TA TA CA TA TA TN TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43 TA TA TA T
1 TA TA TA T
50 GCTCTTTACA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4369 original size:2 final size:2
Alignment explanation
Indices: 4356--4390 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
4346 GTTATTTTTA
* *
4356 AT AT AT AC AT AT AT AA AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4391 CACACACTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:5613 original size:332 final size:332
Alignment explanation
Indices: 5002--6559 Score: 2450
Period size: 331 Copynumber: 4.7 Consensus size: 332
4992 TTTTTTAGCG
*
5002 TATTTGAAGCGCGAAAAACCCTTCAAACATTTTGGCGTTGATTTGTATA-TTTTTATACGTATTT
1 TATTCGAAGCGCGAAAAACCCTTCAAACATTTTGGCGTTGATTTGTATATTTTTTATACGTATTT
* *
5066 TGGCCAAATATTGAGAAAAAAATTATTCGGGTCAATTTTTGCAAAATCTTGACCGAAACCGTGTG
66 TGGCCAAAAATTGAG-GAAAAATTATTCGGGTCAATTTTTGCAAAATCTTGACCGAAACCGTGTG
5131 CTAATCATCACGATTTTTGGCT-AAAACGCGTTCCGGGGTCCCGGCTCAGTTTTGTGTGATTTTT
130 CTAATCATCACGATTTTTGGCTAAAAACGCGTTCCGGGGTCCCGGCTCAGTTTTGTGTGATTTTT
* *
5195 GATGCCAAGAATCATTGTATTATCTATATTCATCTACCCAAATCTCATCCACATAGGATTTAAAG
195 GACGCCAAGAATCCTTG-ATTATCTATATTCATCTACCCAAATCTCATCCACATAGGATTTAAAG
*
5260 ATTTGTTTTTACGAGCATCAGAATCCAGTTTCAATTTAACTGGAAATTAATTCGGAAAAGCATAG
259 ATTTGTTTTTACGAGCATCAGAATCCAATTTCAATTTAACTGGAAATTAATTCGGAAAAGCATAG
5325 GAAAAACTA
324 GAAAAACTA
* *
5334 TATTCGAAGCGCGAAAAACCCTTCAAACATTTTGGTGTTGATTTGTATATTTTTTATACATATTT
1 TATTCGAAGCGCGAAAAACCCTTCAAACATTTTGGCGTTGATTTGTATATTTTTTATACGTATTT
*
5399 TGGCCAAATATTGA-GAAAAATTATTCGGGTCAATTTTTGCAAAATCTTGACCGAAACCGTGTGC
66 TGGCCAAAAATTGAGGAAAAATTATTCGGGTCAATTTTTGCAAAATCTTGACCGAAACCGTGTGC
*
5463 TAATCATCACGATTTTTGGCTAAAAACGCGTTCCGGGGTCCCGACTCAGTTTTGTGTGATTTTTG
131 TAATCATCACGATTTTTGGCTAAAAACGCGTTCCGGGGTCCCGGCTCAGTTTTGTGTGATTTTTG
* * * *
5528 GCGCCAAGAATCCTTGCTTTATCTATATTCATCTACACAGATCTCATCCACATAGGATTTAAAGA
196 ACGCCAAGAATCCTTG-ATTATCTATATTCATCTACCCAAATCTCATCCACATAGGATTTAAAGA
* *
5593 TTTGTTTTCACGAGCATCAGAATCCAAATTCAATTTAACTGGAAATTAATTCGGAAAAGCATAGG
260 TTTGTTTTTACGAGCATCAGAATCCAATTTCAATTTAACTGGAAATTAATTCGGAAAAGCATAGG
*
5658 AAAAACTG
325 AAAAACTA
* *
5666 TATTCGAAGCGCGAAAAACTCTTCAAACATTTTGGCGTTGATTTGTATATTTTTAATACGTATTT
1 TATTCGAAGCGCGAAAAACCCTTCAAACATTTTGGCGTTGATTTGTATATTTTTTATACGTATTT
* * *
5731 TGGCCAAAAATTGAGGAAAAATTATTCGGGTCCATTTCTGCAAAATCTTGACCGAAACTGTGTGC
66 TGGCCAAAAATTGAGGAAAAATTATTCGGGTCAATTTTTGCAAAATCTTGACCGAAACCGTGTGC
*
5796 TAATCATCACGATTTTAT-GCT-AAAATGCGTTCC-GGGTCCCGGCTCAGTTTTGTGTGATTTTT
131 TAATCATCACGATTTT-TGGCTAAAAACGCGTTCCGGGGTCCCGGCTCAGTTTTGTGTGATTTTT
* * * *
5858 TACGCCAAGAATCATTAGATTATCGATATTCATCTACCCAAATCTCATCCACATAGGAATTAAAG
195 GACGCCAAGAATCCTT-GATTATCTATATTCATCTACCCAAATCTCATCCACATAGGATTTAAAG
* ** **
5923 ATTTGTTTTTACGAGCATCATAATGGAATTTCAATTTAACTGGAAATTAATTTAGAAAAGCATAG
259 ATTTGTTTTTACGAGCATCAGAATCCAATTTCAATTTAACTGGAAATTAATTCGGAAAAGCATAG
*
5988 GAAAAACTG
324 GAAAAACTA
*
5997 TATTCGAAGCGCGAAAAACCCTTCAAACATTTTGGCGTTGGTTTGTATATTTTTTATACGTATTT
1 TATTCGAAGCGCGAAAAACCCTTCAAACATTTTGGCGTTGATTTGTATATTTTTTATACGTATTT
*
6062 TGGCCAAAAATTGAGGAAAAATTATTCGGGTCAATTTTTGCAAAATCTTGACCAAAACCGTGTGC
66 TGGCCAAAAATTGAGGAAAAATTATTCGGGTCAATTTTTGCAAAATCTTGACCGAAACCGTGTGC
** * ** *
6127 TAATTTTCACGATTTTTCGCTAAAAACGCGTT-CGGGAGTGTCGGCTCAGTTTTTTGTGATTTTT
131 TAATCATCACGATTTTTGGCTAAAAACGCGTTCCGGG-GTCCCGGCTCAGTTTTGTGTGATTTTT
** * *
6191 GACGCCAAGAATCCTTGGATTATCTATATTCATCTACGTATATCTCATCCACATAGGATTTAATG
195 GACGCCAAGAATCCTT-GATTATCTATATTCATCTACCCAAATCTCATCCACATAGGATTTAAAG
* *
6256 ATTTGTTTTTACAAGCATCAGAATCCAGTTTCAATTTAACTGGAAATTAATTCGGAAAAGCATAG
259 ATTTGTTTTTACGAGCATCAGAATCCAATTTCAATTTAACTGGAAATTAATTCGGAAAAGCATAG
*
6321 AAAAAACTA
324 GAAAAACTA
* * *
6330 TATTCGAAGCGCGAAAAAACCCTTCAAACATTTTGGCGTTGATTTATATATATTTTATAAGTATT
1 TATTCGAAGCGCG-AAAAACCCTTCAAACATTTTGGCGTTGATTTGTATATTTTTTATACGTATT
* *
6395 TTGGCCAAAAATTGAGGAAACATCATTCGGGTC-ATTATTTGCAAAATCTTGACCGAAACCGTGT
65 TTGGCCAAAAATTGAGGAAAAATTATTCGGGTCAATT-TTTGCAAAATCTTGACCGAAACCGTGT
*
6459 GCTAATCATCACGATTTTTGTCTAAAAACGCGTTCCGGGG-CACCGGCTCAGTTTTGTGTGATTT
129 GCTAATCATCACGATTTTTGGCTAAAAACGCGTTCCGGGGTC-CCGGCTCAGTTTTGTGTGATTT
* *
6523 TTGACGCCAAGAATCCTTGGATTACCTATATTGATCT
193 TTGACGCCAAGAATCCTT-GATTATCTATATTCATCT
Statistics
Matches: 1125, Mismatches: 88, Indels: 24
0.91 0.07 0.02
Matches are distributed among these distances:
330 1 0.00
331 361 0.32
332 313 0.28
333 255 0.23
334 191 0.17
335 4 0.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (332 bp):
TATTCGAAGCGCGAAAAACCCTTCAAACATTTTGGCGTTGATTTGTATATTTTTTATACGTATTT
TGGCCAAAAATTGAGGAAAAATTATTCGGGTCAATTTTTGCAAAATCTTGACCGAAACCGTGTGC
TAATCATCACGATTTTTGGCTAAAAACGCGTTCCGGGGTCCCGGCTCAGTTTTGTGTGATTTTTG
ACGCCAAGAATCCTTGATTATCTATATTCATCTACCCAAATCTCATCCACATAGGATTTAAAGAT
TTGTTTTTACGAGCATCAGAATCCAATTTCAATTTAACTGGAAATTAATTCGGAAAAGCATAGGA
AAAACTA
Found at i:6275 original size:664 final size:660
Alignment explanation
Indices: 5001--6546 Score: 2484
Period size: 664 Copynumber: 2.3 Consensus size: 660
4991 TTTTTTTAGC
*
5001 GTATTTGAAGCGCGAAAAACCCTTCAAACATTTTGGCGTTGATTTGTATATTTTTATACGTATTT
1 GTATTCGAAGCGCGAAAAACCCTTCAAACATTTTGGCGTTGATTTGTATATTTTTATACGTATTT
* * *
5066 TGGCCAAATATTGAGAAAAAAATTATTCGGGTCAATTTTTGCAAAATCTTGACCGAAACCGTGTG
66 TGGCCAAAAATTGAG-GAAAAATTATTCGGGTCCATTTTTGCAAAATCTTGACCGAAACCGTGTG
5131 CTAATCATCACGATTTTTGGCTAAAACGCGTTCCGGGGTCCCGGCTCAGTTTTGTGTGATTTTTG
130 CTAATCATCACGATTTTT-GCTAAAACGCGTTCC-GGGTCCCGGCTCAGTTTTGTGTGATTTTTG
* * *
5196 ATGCCAAGAATCATTGTATTATCTATATTCATCTACCCAAATCTCATCCACATAGGATTTAAAGA
193 ACGCCAAGAATCATTG-ATTATCGATATTCATCTACCCAAATCTCATCCACATAGGAATTAAAGA
* *
5261 TTTGTTTTTACGAGCATCAGAATCCAGTTTCAATTTAACTGGAAATTAATTCGGAAAAGCATAGG
257 TTTGTTTTTACGAGCATCAGAATCCAATTTCAATTTAACTGGAAATTAATTCAGAAAAGCATAGG
*
5326 AAAAACTATATTCGAAGCGCGAAAAACCCTTCAAACATTTTGGTGTTGATTTGTATATTTTTTAT
322 AAAAACTATATTCGAAGCGCGAAAAACCCTTCAAACATTTTGGCGTTGATTTGTATATTTTTTAT
* *
5391 ACATATTTTGGCCAAATATTGAGAAAAATTATTCGGGTCAATTTTTGCAAAATCTTGACCGAAAC
387 ACATATTTTGGCCAAAAATTGAGAAAAATTATTCGGGTCAATTTTTGCAAAATCTTGACCAAAAC
*
5456 CGTGTGCTAATCATCACGATTTTTGGCTAAAAACGCGTTCCGGGGTCCCGACTCAGTTTTGTGTG
452 CGTGTGCTAATCATCACGATTTTTCGCTAAAAACGCGTTCCGGGGTCCCGACTCAGTTTTGTGTG
* *
5521 ATTTTTGGCGCCAAGAATCCTTGCTTTATCTATATTCATCTACACAGATCTCATCCACATAGGAT
517 ATTTTTGACGCCAAGAATCCTTGCATTATCTATATTCATCTACACAGATCTCATCCACATAGGAT
*
5586 TTAAAGATTTGTTTTCACGAGCATCAGAATCCAAATTCAATTTAACTGGAAATTAATTCGGAAAA
582 TTAAAGATTTGTTTTCACAAGCATCAGAATCCAAATTCAATTTAACTGGAAATTAATTCGGAAAA
*
5651 GCATAGGAAAAACT
647 GCATAGAAAAAACT
*
5665 GTATTCGAAGCGCGAAAAACTCTTCAAACATTTTGGCGTTGATTTGTATATTTTTAATACGTATT
1 GTATTCGAAGCGCGAAAAACCCTTCAAACATTTTGGCGTTGATTTGTATATTTTT-ATACGTATT
* *
5730 TTGGCCAAAAATTGAGGAAAAATTATTCGGGTCCATTTCTGCAAAATCTTGACCGAAACTGTGTG
65 TTGGCCAAAAATTGAGGAAAAATTATTCGGGTCCATTTTTGCAAAATCTTGACCGAAACCGTGTG
* *
5795 CTAATCATCACGATTTTATGCTAAAATGCGTTCCGGGTCCCGGCTCAGTTTTGTGTGATTTTTTA
130 CTAATCATCACGATTTT-TGCTAAAACGCGTTCCGGGTCCCGGCTCAGTTTTGTGTGATTTTTGA
5860 CGCCAAGAATCATTAGATTATCGATATTCATCTACCCAAATCTCATCCACATAGGAATTAAAGAT
194 CGCCAAGAATCATT-GATTATCGATATTCATCTACCCAAATCTCATCCACATAGGAATTAAAGAT
* ** *
5925 TTGTTTTTACGAGCATCATAATGGAATTTCAATTTAACTGGAAATTAATTTAGAAAAGCATAGGA
258 TTGTTTTTACGAGCATCAGAATCCAATTTCAATTTAACTGGAAATTAATTCAGAAAAGCATAGGA
* *
5990 AAAACTGTATTCGAAGCGCGAAAAACCCTTCAAACATTTTGGCGTTGGTTTGTATATTTTTTATA
323 AAAACTATATTCGAAGCGCGAAAAACCCTTCAAACATTTTGGCGTTGATTTGTATATTTTTTATA
*
6055 CGTATTTTGGCCAAAAATTGAGGAAAAATTATTCGGGTCAATTTTTGCAAAATCTTGACCAAAAC
388 CATATTTTGGCCAAAAATTGA-GAAAAATTATTCGGGTCAATTTTTGCAAAATCTTGACCAAAAC
** ** * *
6120 CGTGTGCTAATTTTCACGATTTTTCGCTAAAAACGCGTT-CGGGAGTGTCGGCTCAGTTTTTTGT
452 CGTGTGCTAATCATCACGATTTTTCGCTAAAAACGCGTTCCGGG-GTCCCGACTCAGTTTTGTGT
* ** *
6184 GATTTTTGACGCCAAGAATCCTTGGATTATCTATATTCATCTACGTATATCTCATCCACATAGGA
516 GATTTTTGACGCCAAGAATCCTTGCATTATCTATATTCATCTACACAGATCTCATCCACATAGGA
* * **
6249 TTTAATGATTTGTTTTTACAAGCATCAGAATCCAGTTTCAATTTAACTGGAAATTAATTCGGAAA
581 TTTAAAGATTTGTTTTCACAAGCATCAGAATCCAAATTCAATTTAACTGGAAATTAATTCGGAAA
6314 AGCATAGAAAAAACT
646 AGCATAGAAAAAACT
* * *
6329 ATATTCGAAGCGCGAAAAAACCCTTCAAACATTTTGGCGTTGATTTATATATATTTTATAAGTAT
1 GTATTCGAAGCGCG-AAAAACCCTTCAAACATTTTGGCGTTGATTTGTATAT-TTTTATACGTAT
* *
6394 TTTGGCCAAAAATTGAGGAAACATCATTCGGGT-CATTATTTGCAAAATCTTGACCGAAACCGTG
64 TTTGGCCAAAAATTGAGGAAAAATTATTCGGGTCCATT-TTTGCAAAATCTTGACCGAAACCGTG
*
6458 TGCTAATCATCACGATTTTTGTCTAAAAACGCGTTCCGGGGCACCGGCTCAGTTTTGTGTGATTT
128 TGCTAATCATCACGATTTTTG-CT-AAAACGCGTTCCGGGTC-CCGGCTCAGTTTTGTGTGATTT
*
6523 TTGACGCCAAGAATCCTTGGATTA
190 TTGACGCCAAGAATCATT-GATTA
6547 CCTATATTGA
Statistics
Matches: 815, Mismatches: 56, Indels: 19
0.92 0.06 0.02
Matches are distributed among these distances:
663 234 0.29
664 376 0.46
665 143 0.18
666 19 0.02
667 43 0.05
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (660 bp):
GTATTCGAAGCGCGAAAAACCCTTCAAACATTTTGGCGTTGATTTGTATATTTTTATACGTATTT
TGGCCAAAAATTGAGGAAAAATTATTCGGGTCCATTTTTGCAAAATCTTGACCGAAACCGTGTGC
TAATCATCACGATTTTTGCTAAAACGCGTTCCGGGTCCCGGCTCAGTTTTGTGTGATTTTTGACG
CCAAGAATCATTGATTATCGATATTCATCTACCCAAATCTCATCCACATAGGAATTAAAGATTTG
TTTTTACGAGCATCAGAATCCAATTTCAATTTAACTGGAAATTAATTCAGAAAAGCATAGGAAAA
ACTATATTCGAAGCGCGAAAAACCCTTCAAACATTTTGGCGTTGATTTGTATATTTTTTATACAT
ATTTTGGCCAAAAATTGAGAAAAATTATTCGGGTCAATTTTTGCAAAATCTTGACCAAAACCGTG
TGCTAATCATCACGATTTTTCGCTAAAAACGCGTTCCGGGGTCCCGACTCAGTTTTGTGTGATTT
TTGACGCCAAGAATCCTTGCATTATCTATATTCATCTACACAGATCTCATCCACATAGGATTTAA
AGATTTGTTTTCACAAGCATCAGAATCCAAATTCAATTTAACTGGAAATTAATTCGGAAAAGCAT
AGAAAAAACT
Done.