Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008102.1 Corchorus capsularis cultivar CVL-1 contig08123, 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: 3586
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Found at i:912 original size:320 final size:322
Alignment explanation
Indices: 1--1965 Score: 1496
Period size: 320 Copynumber: 6.0 Consensus size: 322
1 CAAAACTGAGTCGAGGCCCCGAAACGCGTTATTAAGC-AAAAACCGTGA----T-GTACACGATT
1 CAAAACTGAGTCGAGGCCCCGAAACGCGTT-TTAAGCTAAAAACCGTGATGGTTAGTACACGATT
* *
60 TCGGCAAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCAGAATACTCAT
65 TCGGCAAAAATTTTGCAAAAACTGACCCGAAAAGATTTTCCTCAATTTTTTGCCACAATACTCAT
* *
125 GAA-AAATATATAATTCAATGCCAAAAAAATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTTC
130 -AAGAAATATATAATTCAACGCC------A---AAGGGTTTTTCACGCTTCTAATATCGTTTTTC
* * * * * *
189 CTTTTTTTATTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTAAGATGCTCATAAAAAC
185 C-ATTTTTA----T-CGAATTTATTTCTTATTAAATCGAAAGAAAATTAAGATGCTCGTAAAATC
* * * * * * *
254 AAATCCTTTAATCCATTGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAAGAGTCATTC
244 AAATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTTC
*
319 TACCAAAAATCATG
309 TGCCAAAAATCATG
* * *
333 CAAAACTGAGTCGATGCCCCAAAACGCG--TTAAG-TCAAAAACCGTGAAGGTTAGTACACGATT
1 CAAAACTGAGTCGAGGCCCCGAAACGCGTTTTAAGCT-AAAAACCGTGATGGTTAGTACACGATT
* * * * * *
395 TCGGCTAAAATTTTGCAAAAACAGAGCCGTAAAGTTTTTCCTCAAATTTTTT-ACACAATACTCA
65 TCGGCAAAAATTTTGCAAAAACTGACCCGAAAAGATTTTCCTC-AATTTTTTGCCACAATACTCA
* * *
459 TAAGAGATATATAATT-AGACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTCATATCGTTTTC
129 TAAGAAATATATAATTCA-ACGCC------A---AAGGGTTTTTCACGCTTCTAATATCGTTTTT
* *
523 CCATTTTTACCGAATTTATTTCTTATTAAATCGAAAGAAAATTCAA-ATGCTCGTAAAATCAAGT
184 CCATTTTTATCGAATTTATTTCTTATTAAATCGAAAGAAAATT-AAGATGCTCGTAAAATCAAAT
*
587 CCTTAAATTCAATGT-GATCGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTTCTGC
248 CCTTAAATTCAATGTGGCT-GAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTTCTGC
651 CAAAAATCATG
312 CAAAAATCATG
*
662 CAAAACTGAGTCGAGGCCCCGAAACGCGTTTTTAGCTAAAAACCGTGATGGTTAGTACACGATTT
1 CAAAACTGAGTCGAGGCCCCGAAACGCGTTTTAAGCTAAAAACCGTGATGGTTAGTACACGATTT
* * * *
727 TGGCTAAAATTTTGCAAAAACTGACCTGAAAAGATTTTCCTTAATTTTTTGCCACAATACTCATA
66 CGGCAAAAATTTTGCAAAAACTGACCCGAAAAGATTTTCCTCAATTTTTTGCCACAATACTCATA
* *** *
792 AGAAATATATATTTCAACG-C-AAGGGTTTTTTTTGCTTCTAATATCGTTTTTCCATTTTTATCA
131 AGAAATATATAATTCAACGCCAAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTATCG
* * *
855 AATTTATTTCTTATTAAATCGATAGAAAATTTAGATGCACGTAAAATCAAATCCTTAAATTCAAT
196 AATTTATTTCTTATTAAATCGAAAGAAAATTAAGATGCTCGTAAAATCAAATCCTTAAATTCAAT
920 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATG
261 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATG
* * * * * *
982 CAAAACTGAGTCGAGGCTCCGAAACGTGTTTTTAGCCAAAAACCGTGATAGTTATTACACGATTT
1 CAAAACTGAGTCGAGGCCCCGAAACGCGTTTTAAGCTAAAAACCGTGATGGTTAGTACACGATTT
** *
1047 CGGCAAAAATTTTGCAAAAACTGACCCGATCAGATTTTCCTCAACTTTTTGCCACAATACTCATA
66 CGGCAAAAATTTTGCAAAAACTGACCCGAAAAGATTTTCCTCAATTTTTTGCCACAATACTCATA
* *
1112 AGAAATATCTAATTC-ACTGCCAAAAAATTTGAAGGGTTTTTCACGTTTCTAATATCGTTTTTCC
131 AGAAATATATAATTCAAC-GCC-----A----AAGGGTTTTTCACGCTTCTAATATCGTTTTTCC
* * * * * * *
1176 TTTTTTTTTTCCGAATTTATTTCTAATTAAATCGAAATAAGATTCAA-ATGCTCATAACAA-AAA
186 --ATTTTTAT-CGAATTTATTTCTTATTAAATCGAAAGAAAATT-AAGATGCTCGTAA-AATCAA
* * * * * * * * * *
1239 AACCTTTAGTCCATTGTGGCTGAGATTTGGTTAGATGAATATGGATATTTCAAAGAGTCATTCTA
246 ATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTTCTG
*
1304 CAAAAAATCATG
311 CCAAAAATCATG
* * * * * *
1316 CAAAACTGAGTCGATGCCCCAAAACACG------G-T--ACA-C--GAT--TTCGGCTA-A-AAT
1 CAAAACTGAGTCGAGGCCCCGAAACGCGTTTTAAGCTAAAAACCGTGATGGTT-AG-TACACGAT
* * *** * *** ** ** * * * ** *
1365 TT-TGCAAAAACTGACCGAAAAAGTTTTTCC-TCAATTTTTTGCCACAATACTCATTAGAGATAT
64 TTCGGCAAAAATTTTGC-AAAAA-CTGACCCGAAAAGATTTT-CCTCAAT--T-TTTTGCCACA-
* * * * *
1428 ATAATTCA-ACGCCAAA-A-A-AATT----G---AAGGGTTTGTCACGCTTTTAATATCATTTTT
122 AT-ACTCATAAG--AAATATATAATTCAACGCCAAAGGGTTTTTCACGCTTCTAATATCGTTTTT
** * * * * * * * *
1482 CTTTTTTTTTTCCTAATTTATTTCTAAATAAATCGAAAGAAGATTCAA-ATGATCATAAAAACAA
184 C-CATTTTTAT-CGAATTTATTTCTTATTAAATCGAAAGAAAATT-AAGATGCTCGTAAAATCAA
* * * * * * * * *
1546 ATTCTTTAATCCAATGTGGCTAAGATTTGGTTAGATAAATATAGATATTTCAAAGAGTCATTCTA
246 ATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTTCTG
1611 CCAAAAATCATG
311 CCAAAAATCATG
* * ** * *
1623 CAAAACTGAGTCGATGCCCCAAAACGCGTTTTTCGCCAAAAACCGTGATGGTTAGTACCCGATTT
1 CAAAACTGAGTCGAGGCCCCGAAACGCGTTTTAAGCTAAAAACCGTGATGGTTAGTACACGATTT
* * * *
1688 CGGCTAAAATTTTGCAAAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTCCCACAATACTTAT
66 CGGCAAAAATTTTGC-AAAAACTGACCCGAAAAGATTTTCCTCAATTTTTTGCCACAATACTCAT
* * *
1753 AAGAGATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTATTATCATTTTT-C
130 AAGAAATATATAATTCAACGCC------A---AAGGGTTTTTCACGCTTCTAATATCGTTTTTCC
* * ** ** * * * * * *
1817 TTTTTTTTCCTTATTTATTTCCAATTAAATCGAAACAAGATTTAGAAGCTCATAAAAACAAATCC
186 ATTTTTAT-CGAATTTATTTCTTATTAAATCGAAAGAAAATTAAGATGCTCGTAAAATCAAATCC
* * * * * *
1882 TTTAATCCATTGTGGCTGAGATTTCG-TTAGAT-ATATATAGATATTTCAAAGAGTCATTCTACC
250 TTAAATTCAATGTGGCTGAGATTT-GATTAGATGA-ATATAGATATTTCAAGGAGTCTTTCTGCC
1945 AAAAATCATG
313 AAAAATCATG
*
1955 CAAAATTGAGT
1 CAAAACTGAGT
1966 ATCATTCTAC
Statistics
Matches: 1348, Mismatches: 194, Indels: 182
0.78 0.11 0.11
Matches are distributed among these distances:
306 2 0.00
307 149 0.11
308 28 0.02
313 1 0.00
315 2 0.00
316 6 0.00
317 6 0.00
318 8 0.01
319 18 0.01
320 303 0.22
321 27 0.02
322 26 0.02
323 1 0.00
324 10 0.01
325 6 0.00
326 5 0.00
327 3 0.00
328 3 0.00
329 139 0.10
330 22 0.02
331 125 0.09
332 160 0.12
333 7 0.01
334 165 0.12
335 118 0.09
336 8 0.01
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (322 bp):
CAAAACTGAGTCGAGGCCCCGAAACGCGTTTTAAGCTAAAAACCGTGATGGTTAGTACACGATTT
CGGCAAAAATTTTGCAAAAACTGACCCGAAAAGATTTTCCTCAATTTTTTGCCACAATACTCATA
AGAAATATATAATTCAACGCCAAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTATCG
AATTTATTTCTTATTAAATCGAAAGAAAATTAAGATGCTCGTAAAATCAAATCCTTAAATTCAAT
GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATG
Found at i:2721 original size:332 final size:331
Alignment explanation
Indices: 1344--3586 Score: 2890
Period size: 333 Copynumber: 6.7 Consensus size: 331
1334 CCAAAACACG
1344 GTACACGATTTCGGCTAAAATTTTGCAAAAACTGA-CCGAAAAAGTTTTTCCTCAATTTTTTGCC
1 GTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCG-AAAAGTTTTTCCTCAATTTTTTGCC
* * *
1408 ACAATACTCATTAGAGATATATAATTCAACGCCAAAAAAATTGAAGGGTTTGTCACGCTTTTAAT
65 ACAATACTCATAAGAGATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAAT
* * * *
1473 ATCATTTTTCTTTTTTTTTTCCTAATTTATTTCTAAATAAATCGAAAGAAGATTCAAATGATCAT
130 ATCATTTTTC--CTTTTTTTCCTAATTTATTTCTAATTAAATCGAAACAAGATTCAAATGCTCAT
* * *
1538 AAAAACAAATTCTTTAATCCAATGTGGCTAAGATTTGGTTAGATAAATATAGATATTTCAAAGAG
193 AAAAACAAATCCTTTAATCCATTGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAAGAG
*
1603 TCATTCTACCAAAAATCATGCAAAACTGAGTCGATGCCCCAAAACGCGTTTTTCGCCAAAAACCG
258 TCATTCTACCAAAAATCATGCAAAACTGAGTCGATGCCCCAAAACGCGTTTTTAGCCAAAAACCG
1668 TGATGGTTA
323 TGATGGTTA
* *
1677 GTACCCGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTCCC
1 GTACACGATTTCGGCTAAAATTTTGC-AAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTGCC
* *
1742 ACAATACTTATAAGAGATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTATT
65 ACAATACTCATAAGAGATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAAT
* * * *
1807 ATCATTTTTCTTTTTTTTCCTTATTTATTTCCAATTAAATCGAAACAAGATTTAGAA-GCTCATA
130 ATCATTTTTCCTTTTTTTCCTAATTTATTTCTAATTAAATCGAAACAAGATTCA-AATGCTCATA
* *
1871 AAAACAAATCCTTTAATCCATTGTGGCTGAGATTTCGTTAGATATATATAGATATTTCAAAGAGT
194 AAAACAAATCCTTTAATCCATTGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAAGAGT
* * * ** **
1936 CATTCTACCAAAAATCATGCAAAATTGAGTATC-ATTCTACCAAAAATCATGCAAAACTGAATCG
259 CATTCTACCAAAAATCATGCAAAACTGAG--TCGATGC--CCCAAAA-C--G-----C-GTTTTT
* *
2000 ATGCCCCAAAACGCGT--T-TTTA
311 A-G-CCAAAAAC-CGTGATGGTTA
* * * ** * ** **** * ** *** **
2021 GCCAAAAACCGTGATGGTT-AG-TACCCGATTTCGGTTAAAA-TTTTGCAAAAAACTGACCCGAA
1 G---TACA-C--GAT--TTCGGCTA--AAATTT-TGCAAAAACTGACCCGAAAAGTTTTTCC-TC
* *
2083 AAGTTTTTCCT-CAATTTTTTTGCCACAATACTCATAAGAGATATATCATT-AGACGCCAACAAA
54 AA-TTTTT--TGC-----------CACAATACTCATAAGAGATATATAATTCA-ACGCCAAAAAA
* *
2146 TTTGAAGGGTTTTTCACGCTTCTAATATCATTTTTCC-TTTTTTCCT--TTTATTTCTAGTTAAA
104 ATTGAAGGGTTTTTCACGCTTCTAATATCATTTTTCCTTTTTTTCCTAATTTATTTCTAATTAAA
* * *
2208 TCGAAACAAGATTGAGATGCTTATAAAAACAAATCCTTTAATCCATTGTGGCTGAGATTTGGTTA
169 TCGAAACAAGATTCAAATGCTCATAAAAACAAATCCTTTAATCCATTGTGGCTGAGATTTGGTTA
2273 GATAAATATAGATATTTCAAAGAGTCATTCT-CCAAAAATCATGCAAAACTGAGTCGATGCCCCA
234 GATAAATATAGATATTTCAAAGAGTCATTCTACCAAAAATCATGCAAAACTGAGTCGATGCCCCA
*
2337 AAACGCGTTTTAAGCCAAAAACCGTGATGGTTA
299 AAACGCGTTTTTAGCCAAAAACCGTGATGGTTA
* *
2370 GTACCCGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTCCC
1 GTACACGATTTCGGCTAAAATTTTGC-AAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTGCC
* *
2435 ACAATACTAATAAGAGATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTATT
65 ACAATACTCATAAGAGATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAAT
* * * *
2500 ATCATTTGTCCTTTTTTTCCTAATTTATTTCTAAATAAATCGAAAGAAGATTCAAATGATCATAA
130 ATCATTTTTCCTTTTTTTCCTAATTTATTTCTAATTAAATCGAAACAAGATTCAAATGCTCATAA
* * * * *
2565 AAACAAATTCTTTAATCCAATGTGGCTAAGATTTGGTTAGATAAATATAGATATTTCAAAGGGTT
195 AAACAAATCCTTTAATCCATTGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAAGAGTC
*
2630 ATTCTACCAAAAATCATGCAAAACTGAGTCGATGCCCCAAAATGCGTTTTTAGCCAAAAACCGTG
260 ATTCTACCAAAAATCATGCAAAACTGAGTCGATGCCCCAAAACGCGTTTTTAGCCAAAAACCGTG
*
2695 ACGGTTA
325 ATGGTTA
2702 GTACACGATTTCGGCTAAAATTTTGCAGAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTGCC
1 GTACACGATTTCGGCTAAAATTTTGCA-AAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTGCC
* * *
2767 ACAATACTAATAAGAGATATATAATT-AGACGCCAACAAATTTGAAGGGTTTTTCACGCTTCTAA
65 ACAATACTCATAAGAGATATATAATTCA-ACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAA
* * * *
2831 TATTATTTTTCCTTTTTTATTCTAATTTATTTCTAATTAAATCGAAACAAGATTGAGATGCTCAT
129 TATCATTTTTCCTTTTTT-TCCTAATTTATTTCTAATTAAATCGAAACAAGATTCAAATGCTCAT
2896 AAAAACAAATCCTTTAATCCATTGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAAGAG
193 AAAAACAAATCCTTTAATCCATTGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAAGAG
* *
2961 TCATTCTACCAAAAATCATGCAAAACTGAGTCGATGCCCCAAAATGCGTTTTAAGCCAAAAACCG
258 TCATTCTACCAAAAATCATGCAAAACTGAGTCGATGCCCCAAAACGCGTTTTTAGCCAAAAACCG
3026 TGATGGTTA
323 TGATGGTTA
* * *
3035 GTACACGATTTCGGCTAAATTTTTGCAAAAAACTAGGCCCGAAAAGTTTTTCCTCAATTTTTTCC
1 GTACACGATTTCGGCTAAAATTTTGC-AAAAACT-GACCCGAAAAGTTTTTCCTCAATTTTTTGC
* *
3100 CACAATACTTATAAGAGATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTTTAA
64 CACAATACTCATAAGAGATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAA
* * * *
3165 TATCATTTTTCCTTTTTTTCCTAATTTAATTATAATTAAATCGAAACAAGATTCAGATGCGCATA
129 TATCATTTTTCCTTTTTTTCCTAATTTATTTCTAATTAAATCGAAACAAGATTCAAATGCTCATA
* *
3230 AAAACAAATCTTTTAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAAGAGT
194 AAAACAAATCCTTTAATCCATTGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAAGAGT
* * * * * *
3295 CATTCCACCAAAATTCATGCAAAACTGAGTCAACGCCCCAAAACGCGTTTTTAGCCAATAACCAT
259 CATTCTACCAAAAATCATGCAAAACTGAGTCGATGCCCCAAAACGCGTTTTTAGCCAAAAACCGT
3360 GATGGTTA
324 GATGGTTA
*
3368 GTACCCGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAG-TTTTCCTCAA-TTTTTGCCA
1 GTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCA
* * *
3431 CAATACTCATAAGAGATATATCATT-AGACGCCAACAAATTTGAAGGGTTTTTCACGCTTCTAAT
66 CAATACTCATAAGAGATATATAATTCA-ACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAAT
* * *
3495 ATCATTTTTCCTTTTTTTCCT--TTTATTTCTAATTAAATCGAAACAAGATTGAGATGCTTATAA
130 ATCATTTTTCCTTTTTTTCCTAATTTATTTCTAATTAAATCGAAACAAGATTCAAATGCTCATAA
3558 AAACAAATCCTTTAATCCATTGTGGCTGA
195 AAACAAATCCTTTAATCCATTGTGGCTGA
Statistics
Matches: 1671, Mismatches: 171, Indels: 142
0.84 0.09 0.07
Matches are distributed among these distances:
327 65 0.04
328 70 0.04
329 96 0.06
330 10 0.01
331 112 0.07
332 339 0.20
333 427 0.26
334 210 0.13
335 10 0.01
336 1 0.00
338 2 0.00
339 1 0.00
340 6 0.00
341 12 0.01
342 10 0.01
343 6 0.00
344 6 0.00
345 3 0.00
346 11 0.01
347 11 0.01
348 3 0.00
349 7 0.00
350 6 0.00
351 10 0.01
352 12 0.01
353 6 0.00
354 1 0.00
355 2 0.00
357 1 0.00
358 6 0.00
359 2 0.00
360 3 0.00
361 22 0.01
362 103 0.06
364 10 0.01
365 69 0.04
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (331 bp):
GTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCA
CAATACTCATAAGAGATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATA
TCATTTTTCCTTTTTTTCCTAATTTATTTCTAATTAAATCGAAACAAGATTCAAATGCTCATAAA
AACAAATCCTTTAATCCATTGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAAGAGTCA
TTCTACCAAAAATCATGCAAAACTGAGTCGATGCCCCAAAACGCGTTTTTAGCCAAAAACCGTGA
TGGTTA
Done.