Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010550.1 Corchorus capsularis cultivar CVL-1 contig10571, 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: 25758
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:3900 original size:13 final size:13
Alignment explanation
Indices: 3882--3906 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3872 ATTCAGTTAT
3882 ACTATACTATAAG
1 ACTATACTATAAG
3895 ACTATACTATAA
1 ACTATACTATAA
3907 TTTTTTTGTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.32
Consensus pattern (13 bp):
ACTATACTATAAG
Found at i:5944 original size:1 final size:1
Alignment explanation
Indices: 5938--5968 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
5928 ATTAGTCTAC
5938 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5969 CTGGTAAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:15663 original size:28 final size:29
Alignment explanation
Indices: 15631--15686 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
15621 ACCAGTAAGT
15631 AATTTGA-AAAGTA-ATACTAATAA-CTAGA
1 AATTTGATAAA-TATATACT-ATAAGCTAGA
15659 AATTTGATAAATATATACTATAAGCTAG
1 AATTTGATAAATATATACTATAAGCTAG
15687 TGGTTCCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.32
Consensus pattern (29 bp):
AATTTGATAAATATATACTATAAGCTAGA
Found at i:23429 original size:337 final size:331
Alignment explanation
Indices: 22809--24102 Score: 1571
Period size: 337 Copynumber: 3.9 Consensus size: 331
22799 AGGTTAGAGT
* * *
22809 GTACACGATTTCGGTTAAAATTTTGTAAAATATTGACTCGAAAAATTTTCTTCTCAGTTTTTGTC
1 GTACACGATTTCGGTTAAAATTTTGCAAAA-ATTGACCCGAAAAA-TTTCTCCTCAGTTTTTGTC
*
22874 TACAATACTCATAAAAAATATATAACTCAACGCCAAAAAGATTGAAGGGCTTCCCATGCTTCTAA
64 TACAATACTCATAAAAAATATATAACTCAACGCCAAAAAGATTGAAGGGCTTCCCACGCTTCTAA
* * * *
22939 TATTGTTTTTTTGCTATTTTTTTTCGAATTAATTTCTAATTAAATCGAAATCGGATTGAGATGCT
129 TATCG--TTTTTCCTATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACCGGATTGAGATGCT
* * *
23004 CGTAAAACCAAATCCTTAAATCCATTTTTGCTGATATTTTGTTAGATGAATAGAGATATTTCAAG
192 CGTAAAACCAAATCCTTAAATCCA-ATTTGCTGAGATTTTGTTAGATGAATATAGATATTTCAAG
* *
23069 GAGTCTCGGTGCCAAAAATCATGCAAAACTGAGTCGGAGCCCCGTACCGCGTTCTTAGTAAAAAA
256 GAGTCTCGGTGCCAAAAATCATGCAAAACTGAGTCGGAGCCCCGGACCGCGTTTTTAGTAAAAAA
23134 CTTTGATGATTA
321 C-TTGATGATTA
** * * *
23146 GTACACGATTTCACTTAAAATTTTGCAAAAATTGACCCGAAAAGTTTCTCTTCAGTTTTTTTGCT
1 GTACACGATTTCGGTTAAAATTTTGCAAAAATTGACCCGAAAAATTTCTCCTCAGTTTTTGT-CT
* * ** * *
23211 ACAATACTCATAAAAAAAAATATATTACTCAACGCCAAAAATATTGAAGGGCTTCCTGCGCATCC
65 ACAATACTCAT---AAAAAATATATAACTCAACGCCAAAAAGATTGAAGGGCTTCCCACGCTTCT
** *
23276 AATATCGTTTTTCCTATTTTTTTCCGAAAGAATTTCTAATTAATTCGAAACCGGATTGAGATGCT
127 AATATCGTTTTTCCTATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACCGGATTGAGATGCT
* *
23341 CGTAAAACCAAATCGTTAAATCCAATTTGACTGAGATTTTGTTAGATTAATATAGATATTTCAAG
192 CGTAAAACCAAATCCTTAAATCCAATTTG-CTGAGATTTTGTTAGATGAATATAGATATTTCAAG
* * * * *
23406 GAGTCTCGGTGCCAAATATCATGCAGAACTGAGTCGGGGCCCCGGACTGCATTTTTAGTAAAAAA
256 GAGTCTCGGTGCCAAAAATCATGCAAAACTGAGTCGGAGCCCCGGACCGCGTTTTTAGTAAAAAA
23471 C-TG-TGA-T-
321 CTTGATGATTA
** * *
23478 GGCCTACGATTTCGGTTAAAATTTTGCTAAAATTGACCCGAAAAATTTCTCCTCAGTTTTGGTCT
1 GTAC-ACGATTTCGGTTAAAATTTTGCAAAAATTGACCCGAAAAATTTCTCCTCAGTTTTTGTCT
* * * * *
23543 ACGATACTCATAAGAAATATATAACTCAATGCCGAAAAGATTGAAGGCCTTCCCACGCTTCTAAT
65 ACAATACTCATAAAAAATATATAACTCAACGCCAAAAAGATTGAAGGGCTTCCCACGCTTCTAAT
* *** *
23608 ATCGTTTTCCCTATTTTTTTTGCCGAATTAATTTCTAAAGCAATCGAAATCGGATTGAGATGCTC
130 ATCGTTTTTCCTA-TTTTTTT-CCGAATTAATTTCTAATTAAATCGAAACCGGATTGAGATGCTC
* * *
23673 GTAAAACCAAATCCTTAAATCCAATTCGCCTGATATTTTGTTAGATTAATATAGATATTTCAAGG
193 GTAAAACCAAATCCTTAAATCCAATTTG-CTGAGATTTTGTTAGATGAATATAGATATTTCAAGG
* ** *
23738 AGTCTCGGTGCCAAAAATCATGCACAACTGAG-CCAAGGCCCCGGAACGCGTTTTTAGTAAAAAA
257 AGTCTCGGTGCCAAAAATCATGCAAAACTGAGTCGGA-GCCCCGGACCGCGTTTTTAGTAAAAAA
* *
23802 CTGTAATGGTTA
321 CT-TGATGATTA
* ** * *
23814 GTAC-CTGATTTCGGTTAAAATTTTGCAAAAAATGA-CTAAAAGAATTTTTCCTCAGTTTTTGAC
1 GTACAC-GATTTCGGTTAAAATTTTGCAAAAATTGACCCGAAA-AATTTCTCCTCAGTTTTTGTC
* * * *
23877 TACAATACTCATAAAAAATATATAAATAAATGCCAAAAAGGATTGAAGGGCTTCCCACGCTTTTA
64 TACAATACTCATAAAAAATATATAACTCAACGCCAAAAA-GATTGAAGGGCTTCCCACGCTTCTA
* * * * * *
23942 A-ATCATTTTT-CTTTTTTTTTCCTGAATTAATTTCTAATTAAATCAAAACTGGATTAAGATTCT
128 ATATCGTTTTTCCTATTTTTTTCC-GAATTAATTTCTAATTAAATCGAAACCGGATTGAGATGCT
* * * * * * * * *
24005 CGTAAAAACAAACCCTAAAATCCAGTGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCCAT
192 CGTAAAACCAAATCCTTAAATCCAAT-TTGCTGAGATTTTGTTAGATGAATATAGATATTTCAAG
* * *
24070 GACTCTCGGTGTCAAAAATCATGTAAAACTGAG
256 GAGTCTCGGTGCCAAAAATCATGCAAAACTGAG
24103 CCGGGAAACG
Statistics
Matches: 820, Mismatches: 118, Indels: 42
0.84 0.12 0.04
Matches are distributed among these distances:
329 56 0.07
330 8 0.01
331 152 0.19
332 16 0.02
333 172 0.21
334 14 0.02
335 104 0.13
336 55 0.07
337 193 0.24
339 50 0.06
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (331 bp):
GTACACGATTTCGGTTAAAATTTTGCAAAAATTGACCCGAAAAATTTCTCCTCAGTTTTTGTCTA
CAATACTCATAAAAAATATATAACTCAACGCCAAAAAGATTGAAGGGCTTCCCACGCTTCTAATA
TCGTTTTTCCTATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACCGGATTGAGATGCTCGTA
AAACCAAATCCTTAAATCCAATTTGCTGAGATTTTGTTAGATGAATATAGATATTTCAAGGAGTC
TCGGTGCCAAAAATCATGCAAAACTGAGTCGGAGCCCCGGACCGCGTTTTTAGTAAAAAACTTGA
TGATTA
Found at i:24350 original size:292 final size:293
Alignment explanation
Indices: 23856--24398 Score: 795
Period size: 292 Copynumber: 1.8 Consensus size: 293
23846 TGACTAAAAG
23856 AATTTTTCCTCAGTTTTTGACTACAATACTCATAAAAAATATATAAATAAATGCCAAAAAGGATT
1 AATTTTTCCTCAGTTTTTGACTACAATACTCA-AAAAAATATATAAATAAATGCCAAAAAGGATT
*
23921 GAAGGGCTTCCCACGCTTTTAAATCATTTTTCTTTTTTTTTCCTGAATTAATTTCTAATTAAATC
65 GAAAGGCTTCCCA------TAAATCATTTTTCTTTTTTTTTCCTGAATTAATTTCTAATTAAATC
** * *
23986 AAAACTGGATTAAGATTCTCGTAAAAACAAACCCTAAAATCCAGTGTGGTTGAGATTTGGTTAGA
124 AAAACCCGATTAAGATGCTCGTAAAAACAAACCCTAAAATCCAGTGTGGCTGAGATTTGGTTAGA
* * * *
24051 TGAATATAGATATTTCCATGACTCTCGGTGTCAAAAATCATGTAAAACTGAGCCGGGAAACGTAC
189 TGAATATAGATATTTCAAGGACTCTCGGTGCCAAAAATCATGCAAAACTGAGCCGGGAAACGTAC
24116 ACGATTTCGATAAAAATTTTGTAAAAAAAATGACTCGTAA
254 ACGATTTCGATAAAAATTTTGTAAAAAAAATGACTCGTAA
* * *
24156 AATTTTTCCTCAGTTTTTGGCTACAATACTC-AAAAAATATATAAATCAATGCC-AAATGGATTG
1 AATTTTTCCTCAGTTTTTGACTACAATACTCAAAAAAATATATAAATAAATGCCAAAAAGGATTG
* * **
24219 AAAGGCTTCCCA-AAATCGTTTTTCCTTTTTTTTTTTCTGAATTAATTTCTAATTAAATTGAAAC
66 AAAGGCTTCCCATAAATCATTTTT-C-TTTTTTTTTCCTGAATTAATTTCTAATTAAATCAAAAC
* * * *
24283 CCGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAGTGTGGCTGAGATTTTGTTAGATGAAT
129 CCGATTAAGATGCTCGTAAAAACAAACCCTAAAATCCAGTGTGGCTGAGATTTGGTTAGATGAAT
*
24348 ATAGATATTTCAAGGAGTCTCGGTGCCAAAAATCATGCAAAACTGAGCCGG
194 ATAGATATTTCAAGGACTCTCGGTGCCAAAAATCATGCAAAACTGAGCCGG
24399 TGCCCCGGGA
Statistics
Matches: 220, Mismatches: 21, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
290 10 0.05
291 1 0.00
292 138 0.63
297 20 0.09
298 21 0.10
300 30 0.14
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Consensus pattern (293 bp):
AATTTTTCCTCAGTTTTTGACTACAATACTCAAAAAAATATATAAATAAATGCCAAAAAGGATTG
AAAGGCTTCCCATAAATCATTTTTCTTTTTTTTTCCTGAATTAATTTCTAATTAAATCAAAACCC
GATTAAGATGCTCGTAAAAACAAACCCTAAAATCCAGTGTGGCTGAGATTTGGTTAGATGAATAT
AGATATTTCAAGGACTCTCGGTGCCAAAAATCATGCAAAACTGAGCCGGGAAACGTACACGATTT
CGATAAAAATTTTGTAAAAAAAATGACTCGTAA
Found at i:24974 original size:334 final size:333
Alignment explanation
Indices: 24119--25758 Score: 1802
Period size: 331 Copynumber: 5.0 Consensus size: 333
24109 AACGTACACG
* * * *
24119 ATTTCGATAAAAATTTTGTAAAAAAAATGACTCGTAAAA-TTTTTCCTCAGTTTTTGGCTACAAT
1 ATTTCGGTTAAAATTTTGT-AAAAAAATGACCCG-AAAATTTTTTCCTCAGATTTTGGCTACAAT
* * *
24183 ACTC--AAAAAATATATAAATCAATGCCAAATGGATTGAAAGGCTT----C-C---CAAAATCGT
64 ACTCATAAAAAATATATAAATCAATACCAAAAGGATTGAAGGGCTTCCCACGCTTTCAAAATCGT
* *
24238 TTTTCCTTTTTTTTTTTCTGAATTAATTTCTAATTAAATTGAAACCCGATTGAGATGCTCGTAAA
129 TTTTCCTTTTTTTTTTTCTGAATTAATTTCTAATTAAATCGAAACCGGATTGAGATGCTCGTAAA
24303 AACAAATCCTTAAATCCAGTGTGGCTGAGATTTTGTTAGATGAATATAGATATTTCAAGGAGTCT
194 AACAAATCCTTAAATCCAGTGTGGCTGAGATTTTGTTAGATGAATATAGATATTTCAAGGAGTCT
* * *
24368 CGGTGCCAAAAATCATGCAAAACTGAGCCGGTGCCCCGGGACA-CGTTTTTAGTAAAAAACTGTG
259 CGGTGCCAAAAATCATGCAAAACTGAGCCGG-GACCC-GGAAAGCGGTTTTAGTAAAAAACTGTG
* *
24432 A---CA-TACATG
322 ATGTTAGTACA-A
* * *
24441 ATTTCGG-TACAAATTTTGTAAAAAAATGACTCGAAAACTTTTTCCTCAGTTTTTGGCTACAATA
1 ATTTCGGTTA-AAATTTTGTAAAAAAATGACCCGAAAATTTTTTCCTCAGATTTTGGCTACAATA
* * *
24505 CT-A-AAAAAAAATATAAATCAATTCCAAAAGGATTGAAGGGCTTCCCACGCTTT-AATATCGTT
65 CTCATAAAAAATATATAAATCAATACCAAAAGGATTGAAGGGCTTCCCACGCTTTCAAAATCGTT
* * *
24567 TTTCTTTTCTTTTTTTTATGAATTAATTTCTAATTAAATCGAAACCGGATTGAGATACTCGTAAA
130 TTTCCTTT-TTTTTTTTCTGAATTAATTTCTAATTAAATCGAAACCGGATTGAGATGCTCGTAAA
* * * * * * * * * *
24632 ACCAAATCCTTAAATCCAATGTTGCTGAGAATTCGATAGATTAACATAAATATTTCAAGGGGTCT
194 AACAAATCCTTAAATCCAGTGTGGCTGAGATTTTGTTAGATGAATATAGATATTTCAAGGAGTCT
* * *
24697 CAGTTCCAAAAATAATGCAAAACTGAGCCGGG-CCCTGGAAAGCGGTTTTAGTAAAAAACTGTGA
259 CGGTGCCAAAAATCATGCAAAACTGAGCCGGGACCC-GGAAAGCGGTTTTAGTAAAAAACTGTGA
*
24761 TGGTTAGCACACA
323 T-GTTAGTACA-A
* * * * *
24774 ATTTCGGTTAAAATTTTG-CAAAAATTGGCCCCAAATTTTTTTCC-CTA-ATTTTGGCTACAATA
1 ATTTCGGTTAAAATTTTGTAAAAAAATGACCCGAAAATTTTTTCCTC-AGATTTTGGCTACAATA
* * * *
24836 CTCATAAAAAATATATAACTCAATACCAAAAGGATTGATGGTCTTCCCACGCTTTCAAAATCATT
65 CTCATAAAAAATATATAAATCAATACCAAAAGGATTGAAGGGCTTCCCACGCTTTCAAAATCGTT
24901 TTTCCTTTTTTTTTTTCCTGAATTAATTTCTAATTAAATCGAAACCGGATTGAGATGCTCGTAAA
130 TTTCCTTTTTTTTTTT-CTGAATTAATTTCTAATTAAATCGAAACCGGATTGAGATGCTCGTAAA
* *
24966 AACAAATCCTTAAATCCAGTGTGGCTGAGATTTTTTTAGATGAATATAGATATTTCAAGGAGTCA
194 AACAAATCCTTAAATCCAGTGTGGCTGAGATTTTGTTAGATGAATATAGATATTTCAAGGAGTCT
** *
25031 CGGTGCCAAAAATCATGCAAAACTGAGCC-GGAGCCCTGGAGCGCGTTTTTAGTAAAAAA-TAGT
259 CGGTGCCAAAAATCATGCAAAACTGAGCCGGGA-CCC-GGAAAGCGGTTTTAGTAAAAAACT-GT
* *
25094 GATTATTAGTACATG
321 GA-TGTTAGTACA-A
* * *
25109 ATTTCGG-TAAAATTTTGTAAAAAAATGA-CCAAAAGAATTTTTCCTCAGTTTTTGGCTACAATA
1 ATTTCGGTTAAAATTTTGTAAAAAAATGACCCGAAA-ATTTTTTCCTCAGATTTTGGCTACAATA
* * *
25172 CTCATAAAATATATATAAATCAATTCCAAAAGGATTAAAGGGCTTCCCACGCTTTCAAAATCGTT
65 CTCATAAAAAATATATAAATCAATACCAAAAGGATTGAAGGGCTTCCCACGCTTTCAAAATCGTT
*
25237 TTT-C---TTTTTTTTCTGAATTAATTTCTAATTAAATTGAAACCGGATTGAGATGCTCGTAAAA
130 TTTCCTTTTTTTTTTTCTGAATTAATTTCTAATTAAATCGAAACCGGATTGAGATGCTCGTAAAA
25298 ACAAATCCTTAAATCCAGTGTGGCTGAGATTTTGTTAGATGAATATAGATATTTCAAGGAGTCTC
195 ACAAATCCTTAAATCCAGTGTGGCTGAGATTTTGTTAGATGAATATAGATATTTCAAGGAGTCTC
* * * * *
25363 GTTGCCGAAAATCATGCAAAACTAAGCCGGGGTCCCGGAACGC-GTTTTAAGTAAAAAAC-----
260 GGTGCCAAAAATCATGCAAAACTGAGCC-GGGACCCGGAAAGCGGTTTT-AGTAAAAAACTGTGA
25422 TG-T-G-----
323 TGTTAGTACAA
* *
25426 A--T-GGTTAAAATTTTGT-AAAAATTGACCCGAAAATTTTTTCGC-CA-ATTTTTGGCTGCAAT
1 ATTTCGGTTAAAATTTTGTAAAAAAATGACCCGAAAATTTTTTC-CTCAGA-TTTTGGCTACAAT
* * * * *
25485 ACTCATAAAAAATATATAACTCAA-AGCCAAAAGGATTGATGGTCTTCCCA-GACTTTTAATATC
64 ACTCATAAAAAATATATAAATCAATA-CCAAAAGGATTGAAGGGCTTCCCACG-CTTTCAAAATC
* * * * *
25548 G----T-C--TTTTTTTTTCTAAATTAATTTTTAATTAAATCGAAAACGAATTGAGATGTTCGTA
127 GTTTTTCCTTTTTTTTTTTCTGAATTAATTTCTAATTAAATCGAAACCGGATTGAGATGCTCGTA
* * * * * * *
25606 AAAACAAATCTTTGAATCCAGTGTGGCTGAGATTTGGTTACATGAACATATATATTT-ATATGAG
192 AAAACAAATCCTTAAATCCAGTGTGGCTGAGATTTTGTTAGATGAATATAGATATTTCA-AGGAG
* * *
25670 TCTCGGTGCCCAAAATCATGCAAAACTGAGCCGGGACCCCGAAATGCGATTTTAGT-AAAAACTG
256 TCTCGGTGCCAAAAATCATGCAAAACTGAGCCGGGACCCGGAAA-GCGGTTTTAGTAAAAAACTG
*
25734 TAATGGTTAGTACAA
320 TGAT-GTTAGTACAA
25749 GATTTCGGTT
1 -ATTTCGGTT
Statistics
Matches: 1126, Mismatches: 129, Indels: 121
0.82 0.09 0.09
Matches are distributed among these distances:
310 18 0.02
311 137 0.12
312 4 0.00
313 1 0.00
314 84 0.07
315 19 0.02
316 1 0.00
317 2 0.00
318 1 0.00
320 4 0.00
321 79 0.07
322 15 0.01
323 1 0.00
324 2 0.00
325 2 0.00
326 2 0.00
327 11 0.01
328 37 0.03
329 135 0.12
330 4 0.00
331 168 0.15
332 33 0.03
333 75 0.07
334 157 0.14
335 57 0.05
336 77 0.07
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (333 bp):
ATTTCGGTTAAAATTTTGTAAAAAAATGACCCGAAAATTTTTTCCTCAGATTTTGGCTACAATAC
TCATAAAAAATATATAAATCAATACCAAAAGGATTGAAGGGCTTCCCACGCTTTCAAAATCGTTT
TTCCTTTTTTTTTTTCTGAATTAATTTCTAATTAAATCGAAACCGGATTGAGATGCTCGTAAAAA
CAAATCCTTAAATCCAGTGTGGCTGAGATTTTGTTAGATGAATATAGATATTTCAAGGAGTCTCG
GTGCCAAAAATCATGCAAAACTGAGCCGGGACCCGGAAAGCGGTTTTAGTAAAAAACTGTGATGT
TAGTACAA
Done.