Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005554.1 Corchorus capsularis cultivar CVL-1 contig05572, 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, 952
Length: 1588
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:623 original size:327 final size:327
Alignment explanation
Indices: 3--1519 Score: 1893
Period size: 327 Copynumber: 4.6 Consensus size: 327
1 GA
* * * * * *
3 TAGTCTTTGCAAAATTTTAGCAGAAATTGTGTACTAACCATCACGATATTTGGCTAAAAACACAT
1 TAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATATTTGGCCAAAAACGCGT
* * * * * * * * *
68 TACAGGGCTCCGGCTCAGTTTTGAATTATTTTGGGCGTCGGGACTCGCTGAAATATCTTTGTTTA
66 TCCGGGGCTCCGGCTCAGTTTTGAATGATTTTTGGCGTCGAGACTCGCCGAAATATC-ATATTCA
* * *
133 TCTGATAAAATCTCAGCCACTTTAGATTTAAGGATATGTTTTTACGAGCATCTGAATCTTGTTTC
130 TCTAATCAAATCTCAGCCACATTAGATTTAAGGATATGTTTTTACGAGCATCTGAATCTTGTTTC
* * * *
198 GAATTAATCAGAAATTACATTACAAAAATAAAAGAATAACGATATTAGAAGCATGAAAAGCCATT
195 GATTTAATAAGAAATTAAATTAC-AAAA-AAAAG---AACGATATTAGAAGCGTGAAAAGCCATT
** * *
263 CAATCTTTTTGTAGTTGAATTCTAAAATTTTTATAAGTGTTGTGGCGAAAAATTGAGGAAAAATC
255 CAATCTTTTTGGCGTTGAATTCTAAATTTTTTATAAGTGTTGTGGCAAAAAATTGAGGAAAAATC
*
328 TTTCGGGT
320 TTTCAGGT
* *
336 AAGTTTTTCCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATATTTGGCCAAAAACGCGT
1 TAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATATTTGGCCAAAAACGCGT
* * * *
401 TCCGGGGCTCCGACTCAGTTTTTGCATGATCTTTGGCGTCGAGACTCACCGAAATATC-TATTCA
66 TCCGGGGCTCCGGCTCAG-TTTTGAATGATTTTTGGCGTCGAGACTCGCCGAAATATCATATTCA
* * *
465 TCTAATCAAATCTCAGCCACATTAGATTTAAGGATATGTTTTTACGAGTATCTGTATCTTATTTC
130 TCTAATCAAATCTCAGCCACATTAGATTTAAGGATATGTTTTTACGAGCATCTGAATCTTGTTTC
*
530 GATTTAATAACAAATTAAATTACAAAAAAAAGAACGATATTAGAAGCGTGAAAAGCCATTCAATC
195 GATTTAATAAGAAATTAAATTACAAAAAAAAGAACGATATTAGAAGCGTGAAAAGCCATTCAATC
595 TTTTTGGCGTTGAATTCTAAATTTTTTATAAGTGTTGTGGCAAAAAATTGAGGAAAAATCTTTC-
260 TTTTTGGCGTTGAATTCTAAATTTTTTATAAGTGTTGTGGCAAAAAATTGAGGAAAAATCTTTCA
659 GAGT
325 G-GT
* * * * * * * *
663 TAG-TTTAGTATAACTTTAGCCGAATTCGAGTACTAACTATCACGATATTTGGCCAAAAACGCCT
1 TAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATATTTGGCCAAAAACGCGT
** *
727 TCCGGGGCTCCTTCTCAGTTTTGAATGATTTTTGGCGTCGAGACTTGCCGAAATATCAATATTCA
66 TCCGGGGCTCCGGCTCAGTTTTGAATGATTTTTGGCGTCGAGACTCGCCGAAATATC-ATATTCA
* *
792 TCTAATCAAATCTCAGCCACATTAGATTTAAGGATATGTTTTTACGAGCATTTAAATCTTGTTTC
130 TCTAATCAAATCTCAGCCACATTAGATTTAAGGATATGTTTTTACGAGCATCTGAATCTTGTTTC
* * *
857 GATTTAATCAGGAAA--AAATTTAAAAGAAAAATATGGAAAAACGATATTAGAAGCG-GGAAA-C
195 GATTTAAT-AAGAAATTAAA-TTACAA-AAAAA-A--G---AACGATATTAGAAGCGTGAAAAGC
* * * * ** *
918 CCTTAAATCTTTTTTTGCGTTGAA-T-TAAATCTTTTTATGAGTACTGTGG-AAAAATTTTG-GG
251 CATTCAATC-TTTTTGGCGTTGAATTCTAAAT-TTTTTATAAGTGTTGTGGCAAAAA-ATTGAGG
*
979 AAAAAAT-TTTTAGGT
313 -AAAAATCTTTCAGGT
* * * * *
994 CAGTTTTTGCAAAA-TTTAGTCGAAATCGTATACTAACCATTACGATATTCGGCCAAAAAC-CTG
1 TAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATATTTGGCCAAAAACGC-G
* * * *
1057 TTCCAGGGCTCCGGCTCAGTTATGAAT-ATTTTTTGCGTCGGGACTCGCCGAAATATCTATATTC
65 TTCCGGGGCTCCGGCTCAGTTTTGAATGATTTTTGGCGTCGAGACTCGCCGAAATATC-ATATTC
* * *
1121 ATCTAAACAAATCTCAGCCACATTAGATTTAAGGATATGTTTTTACGAGTATCTGAATCCTGTTT
129 ATCTAATCAAATCTCAGCCACATTAGATTTAAGGATATGTTTTTACGAGCATCTGAATCTTGTTT
* * * *
1186 CAATTTAATCAGAAATTAAATT---AAAAAAACAATGATATTAGAAGCGTGAAAAGCCATTCAAT
194 CGATTTAATAAGAAATTAAATTACAAAAAAAAGAACGATATTAGAAGCGTGAAAAGCCATTCAAT
* *
1248 CTTTTTGGCATTGAATTCTAAATTTTTTTTAAGTGTTGTGGCAAAAAATTGAGGAAAAATCTTTC
259 CTTTTTGGCGTTGAATTCTAAATTTTTTATAAGTGTTGTGGCAAAAAATTGAGGAAAAATCTTTC
*
1313 AGCT
324 AGGT
1317 TAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATATTT-GCCTAAAAACGCG
1 TAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATATTTGGCC-AAAAACGCG
* ** *
1381 TTACGGGGCTCCTTCTCAGTTTTGAATGATTTTTGGCGTCGAGACTTGCCGAAATATCAATATTC
65 TTCCGGGGCTCCGGCTCAGTTTTGAATGATTTTTGGCGTCGAGACTCGCCGAAATATC-ATATTC
* *
1446 ATCTAATCAAATCTCAGCCACATTAGATTTAAGGATATGTTTTTACGAGCATTTAAATCTTGTTT
129 ATCTAATCAAATCTCAGCCACATTAGATTTAAGGATATGTTTTTACGAGCATCTGAATCTTGTTT
1511 CGATTTAAT
194 CGATTTAAT
1520 CAGGAAAAGA
Statistics
Matches: 1021, Mismatches: 130, Indels: 74
0.83 0.11 0.06
Matches are distributed among these distances:
320 15 0.01
321 16 0.02
322 32 0.03
323 34 0.03
324 61 0.06
325 138 0.14
326 77 0.08
327 176 0.17
328 9 0.01
329 5 0.00
330 109 0.11
331 89 0.09
332 123 0.12
333 89 0.09
334 48 0.05
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (327 bp):
TAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATATTTGGCCAAAAACGCGT
TCCGGGGCTCCGGCTCAGTTTTGAATGATTTTTGGCGTCGAGACTCGCCGAAATATCATATTCAT
CTAATCAAATCTCAGCCACATTAGATTTAAGGATATGTTTTTACGAGCATCTGAATCTTGTTTCG
ATTTAATAAGAAATTAAATTACAAAAAAAAGAACGATATTAGAAGCGTGAAAAGCCATTCAATCT
TTTTGGCGTTGAATTCTAAATTTTTTATAAGTGTTGTGGCAAAAAATTGAGGAAAAATCTTTCAG
GT
Found at i:1461 original size:655 final size:658
Alignment explanation
Indices: 3--1588 Score: 2204
Period size: 655 Copynumber: 2.4 Consensus size: 658
1 GA
* * * * *
3 TAGTCTTTGCAAAATTTTAGCAGAAATTGTGTACTAACCATCACGATATTTGGCTAAAAACACAT
1 TAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATATTTGCCTAAAAACGCAT
* ** * * * * * ** * *
68 TACAGGGCTCCGGCTCAGTTTTGAATTATTTTGGGCGTCGGGACTCGCTGAAATATCTTTGTTTA
66 TACGGGGCTCCTTCTCAGTTTTGAATGATTTTTGGCGTCGAGACTTGCCGAAATATCAATATTCA
* * * * *
133 TCTGATAAAATCTCAGCCACTTTAGATTTAAGGATATGTTTTTACGAGCATCTGAATCTTGTTTC
131 TCTAATCAAATCTCAGCCACATTAGATTTAAGGATATGTTTTTACGAGCATTTAAATCTTGTTTC
* * * * *
198 GAATTAATCA-GAAATTACA-TTACAAA-AATAAA-A--GAATAACGATATTAGAAGCATGAAAA
196 GATTTAATCAGGAAA--AAATTTA-AAAGAA-AAATATGGAAAAACGATATTAGAAGC-GGGAAA
* * * **
257 GCCATTCAATCTTTTTGTAGTTGAATTCTAAAATTTTTATAAGTGTTGTGGCGAAAAATTGAGGA
256 -CCCTTAAATCTTTTTTTAGTTGAATTCTAAAATTTTTATAAGTACTGTGGCGAAAAATTGAGGA
* * *
322 AAAATCTTTCGGGTAAGTTTTTCCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATATTT
320 AAAATCTTTCAGGTAAGTTTTTCCAAAATTTTAGCCGAAATCGTATACTAACCATCACGATATTC
* * *
387 GGCCAAAAACGCGTTCCGGGGCTCCGACTCAGTTTTTGCATGATCTTTGGCGTCGAGACTCACCG
385 GGCCAAAAACGCGTTCCAGGGCTCCGACTCAGTTTATGAATGATCTTTGGCGTCGAGACTCACCG
*
452 AAATATCTATTCATCTAATCAAATCTCAGCCACATTAGATTTAAGGATATGTTTTTACGAGTATC
450 AAATATCTATTCATCTAAACAAATCTCAGCCACATTAGATTTAAGGATATGTTTTTACGAGTATC
* * * *
517 TGTATCTTATTTCGATTTAATAACAAATTAAATTACAAAAAAAAGAACGATATTAGAAGCGTGAA
515 TGAATCCTATTTCAATTTAATAACAAATTAAATT--AAAAAAAACAACGATATTAGAAGCGTGAA
*
582 AAGCCATTCAATCTTTTTGGCGTTGAATTCTAAATTTTTTATAAGTGTTGTGGCAAAAAATTGAG
578 AAGCCATTCAATCTTTTTGGCATTGAATTCTAAATTTTTTATAAGTGTTGTGGCAAAAAATTGAG
647 GAAAAATCTTTCGAGT
643 GAAAAATCTTTCGAGT
* * * * * * * *
663 TAG-TTTAGTATAACTTTAGCCGAATTCGAGTACTAACTATCACGATATTTGGCC-AAAAACGCC
1 TAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATATTT-GCCTAAAAACGCA
*
726 TTCCGGGGCTCCTTCTCAGTTTTGAATGATTTTTGGCGTCGAGACTTGCCGAAATATCAATATTC
65 TTACGGGGCTCCTTCTCAGTTTTGAATGATTTTTGGCGTCGAGACTTGCCGAAATATCAATATTC
791 ATCTAATCAAATCTCAGCCACATTAGATTTAAGGATATGTTTTTACGAGCATTTAAATCTTGTTT
130 ATCTAATCAAATCTCAGCCACATTAGATTTAAGGATATGTTTTTACGAGCATTTAAATCTTGTTT
856 CGATTTAATCAGGAAAAAATTTAAAAGAAAAATATGGAAAAACGATATTAGAAGCGGGAAACCCT
195 CGATTTAATCAGGAAAAAATTTAAAAGAAAAATATGGAAAAACGATATTAGAAGCGGGAAACCCT
* * *
921 TAAATCTTTTTTTGCGTTGAA-T-TAAATCTTTTTATGAGTACTGT-G-GAAAAATTTTG-GGAA
260 TAAATCTTTTTTT-AGTTGAATTCTAAA-ATTTTTATAAGTACTGTGGCGAAAAA--TTGAGG-A
* * * * *
981 AAAAT-TTTTAGGTCAGTTTTTGCAAAA-TTTAGTCGAAATCGTATACTAACCATTACGATATTC
320 AAAATCTTTCAGGTAAGTTTTTCCAAAATTTTAGCCGAAATCGTATACTAACCATCACGATATTC
* * * * *
1044 GGCCAAAAAC-CTGTTCCAGGGCTCCGGCTCAG-TTATGAAT-ATTTTTTGCGTCGGGACTCGCC
385 GGCCAAAAACGC-GTTCCAGGGCTCCGACTCAGTTTATGAATGATCTTTGGCGTCGAGACTCACC
1106 GAAATATCTATATTCATCTAAACAAATCTCAGCCACATTAGATTTAAGGATATGTTTTTACGAGT
449 GAAATATC--TATTCATCTAAACAAATCTCAGCCACATTAGATTTAAGGATATGTTTTTACGAGT
* * * *
1171 ATCTGAATCCTGTTTCAATTTAATCAGAAATTAAATT-AAAAAAACAATGATATTAGAAGCGTGA
512 ATCTGAATCCTATTTCAATTTAATAACAAATTAAATTAAAAAAAACAACGATATTAGAAGCGTGA
*
1235 AAAGCCATTCAATCTTTTTGGCATTGAATTCTAAATTTTTTTTAAGTGTTGTGGCAAAAAATTGA
577 AAAGCCATTCAATCTTTTTGGCATTGAATTCTAAATTTTTTATAAGTGTTGTGGCAAAAAATTGA
1300 GGAAAAATCTTTC-AGCT
642 GGAAAAATCTTTCGAG-T
*
1317 TAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATATTTGCCTAAAAACGCGT
1 TAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATATTTGCCTAAAAACGCAT
1382 TACGGGGCTCCTTCTCAGTTTTGAATGATTTTTGGCGTCGAGACTTGCCGAAATATCAATATTCA
66 TACGGGGCTCCTTCTCAGTTTTGAATGATTTTTGGCGTCGAGACTTGCCGAAATATCAATATTCA
1447 TCTAATCAAATCTCAGCCACATTAGATTTAAGGATATGTTTTTACGAGCATTTAAATCTTGTTTC
131 TCTAATCAAATCTCAGCCACATTAGATTTAAGGATATGTTTTTACGAGCATTTAAATCTTGTTTC
* *
1512 GATTTAATCAGGAAAAGATTTAAAAGAAAAATATGGAAAAACGATATTAGAAACGGGAAACCCTT
196 GATTTAATCAGGAAAAAATTTAAAAGAAAAATATGGAAAAACGATATTAGAAGCGGGAAACCCTT
1577 AAATCTTTTTTT
261 AAATCTTTTTTT
Statistics
Matches: 826, Mismatches: 82, Indels: 41
0.87 0.09 0.04
Matches are distributed among these distances:
653 2 0.00
654 108 0.13
655 279 0.34
656 7 0.01
657 151 0.18
658 33 0.04
659 209 0.25
660 19 0.02
661 18 0.02
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Consensus pattern (658 bp):
TAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATATTTGCCTAAAAACGCAT
TACGGGGCTCCTTCTCAGTTTTGAATGATTTTTGGCGTCGAGACTTGCCGAAATATCAATATTCA
TCTAATCAAATCTCAGCCACATTAGATTTAAGGATATGTTTTTACGAGCATTTAAATCTTGTTTC
GATTTAATCAGGAAAAAATTTAAAAGAAAAATATGGAAAAACGATATTAGAAGCGGGAAACCCTT
AAATCTTTTTTTAGTTGAATTCTAAAATTTTTATAAGTACTGTGGCGAAAAATTGAGGAAAAATC
TTTCAGGTAAGTTTTTCCAAAATTTTAGCCGAAATCGTATACTAACCATCACGATATTCGGCCAA
AAACGCGTTCCAGGGCTCCGACTCAGTTTATGAATGATCTTTGGCGTCGAGACTCACCGAAATAT
CTATTCATCTAAACAAATCTCAGCCACATTAGATTTAAGGATATGTTTTTACGAGTATCTGAATC
CTATTTCAATTTAATAACAAATTAAATTAAAAAAAACAACGATATTAGAAGCGTGAAAAGCCATT
CAATCTTTTTGGCATTGAATTCTAAATTTTTTATAAGTGTTGTGGCAAAAAATTGAGGAAAAATC
TTTCGAGT
Done.