Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009547.1 Corchorus capsularis cultivar CVL-1 contig09568, 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: 12214
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:1886 original size:19 final size:19
Alignment explanation
Indices: 1862--1904 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
1852 CTGTTTTTAT
*
1862 TCTCAAAGGAATATATAGA
1 TCTCAAAGGAATAAATAGA
*
1881 TCTCAAATGAATAAATAGA
1 TCTCAAAGGAATAAATAGA
1900 TCTCA
1 TCTCA
1905 TCCACTCCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.28
Consensus pattern (19 bp):
TCTCAAAGGAATAAATAGA
Found at i:9357 original size:21 final size:21
Alignment explanation
Indices: 9333--9372 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
9323 CTCGTAAAAG
9333 CAAATCTTTAAATCCAATAAA
1 CAAATCTTTAAATCCAATAAA
9354 CAAATCTTTAAATCCAATA
1 CAAATCTTTAAATCCAATA
9373 TGATTGAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (21 bp):
CAAATCTTTAAATCCAATAAA
Found at i:9862 original size:324 final size:331
Alignment explanation
Indices: 9480--10271 Score: 1036
Period size: 325 Copynumber: 2.4 Consensus size: 331
9470 TAAAAATTGT
* * * *
9480 TGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTAACCCGAAAGATTTTTCCTCAAT
1 TGATGGATAGTACACGATTTCGGCTAAAATTTTGCAAAAAATAACCCGAAATATTTTTCCTCAAT
* * *
9545 TTTTGGGCAAAATAC-CGGTAAAAAATATTTAATTCAAC-ACAAAAATATTGAAGGACTTTTCAC
66 TTTTGGCCAAAATACTC-GTAAAAAATATATAATTCAACTACAAAAAGATTGAAGGACTTTTCAC
*
9608 GCTTCTAATATCGATTTTCCTA-TTTTCCCGAATTAATTT-ACAAA-TAAATCGAACCGATTTCT
130 ACTTCTAATATCGATTTTCCTATTTTTCCCGAATTAATTTCA-AAATTAAATCGAACCGATTTCT
* *
9670 GATGCTCATAAAAACAAACCCCTAAATCCAATGTGACTGAGATTTGGTTAGATAAAATATACATA
194 GATGCTCATAAAAA-AAACCCCTAAATCCAATGCGACTGAGATATGGTTAGATAAAATATACATA
* *
9735 ATTCAACGAGTCTAGGCGGAAAAAATCAAGCAAAACTGAATCGGCG-CCGGAACGTGTTTTTAGC
258 ATTCAACGAGTCTAGGCGCAAAAAATCAAGCAAAACTGAATCGGCGCCCGGAACGTGTATTTAGC
9799 CAAAAA-C-
323 CAAAAACCA
*
9806 T-AT-GATAGTACACGATTTCGGCTAAAATTTGGCAAAAAATAACCCGAAATATTTTTCCTCAA-
1 TGATGGATAGTACACGATTTCGGCTAAAATTTTGCAAAAAATAACCCGAAATATTTTTCCTCAAT
* * * * * * *
9868 TTTTGACCACAACACTCGTAGAAAATATATAATTCAACTCCAAAAGGATTGAAGGGCTTTTCACA
66 TTTTGGCCAAAATACTCGTAAAAAATATATAATTCAACTACAAAAAGATTGAAGGACTTTTCACA
* *
9933 CTTCTAATATCGATTTTCCTATTTTTGCCGAATTAATTTCAAAATTAAATCGAACCGATTTTTGA
131 CTTCTAATATCGATTTTCCTATTTTTCCCGAATTAATTTCAAAATTAAATCGAACCGATTTCTGA
* * * **
9998 TGCTCGTAAAAAAAATCCTTAAATCCAATGCGGTTGAGATATGGTTAGATAAAATATACATAATT
196 TGCTCATAAAAAAAACCCCTAAATCCAATGCGACTGAGATATGGTTAGATAAAATATACATAATT
* * * * *
10063 CAACGAGTCTAGGCGCAAAAAATCATGCAAAACTGAGTCGGGGCCCTGAATGTGTATTTAGCCAA
261 CAACGAGTCTAGGCGCAAAAAATCAAGCAAAACTGAATCGGCGCCCGGAACGTGTATTTAGCCAA
10128 AAACCA
326 AAACCA
* * * *
10134 TGATGGTTAGTACACAATTTCGGCTAAAATTTTGC-AAATATGGACCCGAAATATTTTTCCTCAA
1 TGATGGATAGTACACGATTTCGGCTAAAATTTTGCAAAAAAT-AACCCGAAATATTTTTCCTCAA
* * * ** * * *
10198 TTTTTGGCCAAAATACTCAT-TAAATTATATAATTCAACGCCAAAAA-ATTTGATGGGCTTTTGA
65 TTTTTGGCCAAAATACTCGTAAAAAATATATAATTCAACTACAAAAAGA-TTGAAGGACTTTTCA
*
10261 CGCTTCTAATA
129 CACTTCTAATA
10272 ACGAACGTGT
Statistics
Matches: 405, Mismatches: 48, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
323 30 0.07
324 97 0.24
325 107 0.26
326 53 0.13
327 1 0.00
328 1 0.00
329 8 0.02
330 93 0.23
331 15 0.04
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.31
Consensus pattern (331 bp):
TGATGGATAGTACACGATTTCGGCTAAAATTTTGCAAAAAATAACCCGAAATATTTTTCCTCAAT
TTTTGGCCAAAATACTCGTAAAAAATATATAATTCAACTACAAAAAGATTGAAGGACTTTTCACA
CTTCTAATATCGATTTTCCTATTTTTCCCGAATTAATTTCAAAATTAAATCGAACCGATTTCTGA
TGCTCATAAAAAAAACCCCTAAATCCAATGCGACTGAGATATGGTTAGATAAAATATACATAATT
CAACGAGTCTAGGCGCAAAAAATCAAGCAAAACTGAATCGGCGCCCGGAACGTGTATTTAGCCAA
AAACCA
Found at i:10336 original size:166 final size:166
Alignment explanation
Indices: 10136--10441 Score: 420
Period size: 166 Copynumber: 1.8 Consensus size: 166
10126 AAAAACCATG
* * *
10136 ATGGTTAGTACACAATTTCGGCTAAAATTTTGCAAATATGGACCCGAAATATTTTTCCTCAATTT
1 ATGGTTAGTACACAATTTCGGCTAAAAGTTTGCAAAAATGGACCCGAAAGATTTTTCCTCAATTT
* * * * * *
10201 T-TGGCCAAAATACTCAT-TAAATTATATAATTCAACGCCAAAAA-ATTTGATGGGCTTTTGACG
66 TGT-G-CAAAATACTCATAAAAAATATATAATTAAACGCCAAAAAGA-TTGAAGGACTTTTCACG
10263 CTTCTAATAACGAACGTGTTTTTTTGCTAAAAACTGTTA
128 CTTCTAATAACGAACGTGTTTTTTTGCTAAAAACTGTTA
** * *
10302 ATGGTTAGTACACGGTTTCGGCTAAAAGTTTGCAAAAATTGACCCGAAGGATTTTTCCTCAATTT
1 ATGGTTAGTACACAATTTCGGCTAAAAGTTTGCAAAAATGGACCCGAAAGATTTTTCCTCAATTT
** *
10367 TGTGCAAAATACTGGTAAAAAATATATAATTAAACTCCAAAAAGATTGAAGGACTTTTCACGCTT
66 TGTGCAAAATACTCATAAAAAATATATAATTAAACGCCAAAAAGATTGAAGGACTTTTCACGCTT
10432 CTAATAACGA
131 CTAATAACGA
10442 TTTTCCTATT
Statistics
Matches: 121, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
165 10 0.08
166 109 0.90
167 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (166 bp):
ATGGTTAGTACACAATTTCGGCTAAAAGTTTGCAAAAATGGACCCGAAAGATTTTTCCTCAATTT
TGTGCAAAATACTCATAAAAAATATATAATTAAACGCCAAAAAGATTGAAGGACTTTTCACGCTT
CTAATAACGAACGTGTTTTTTTGCTAAAAACTGTTA
Found at i:10884 original size:306 final size:305
Alignment explanation
Indices: 10309--11233 Score: 776
Period size: 330 Copynumber: 2.9 Consensus size: 305
10299 TTAATGGTTA
* * * *
10309 GTACACGGTTTCGGCTAAAAGTTTGCAAAAATTGACCCGAAGGATTTTTCCTCAATTTTGTGCAA
1 GTACACGATTTCGGCAAAAAGTTTGCAAAAAATGACCCGAAAGATTTTTCCTCAATTTTGTGCAA
* * *
10374 AATACTGGTAAAAAATATATAATTAAACTCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATAA
66 AACACTCGTAAAAAATATATAATTAAACTCCAAAAAGATTGAAGGACTTTTCACACTTCTAATAA
* * *
10439 CGATTTTCCTATTTTTGCCGAATTAATTTGTAATTAAAAGAACCGATTTCTGATGCTCGTAAAAA
131 CGATTTTCCTAATTTTGCCGAATTAATTTCTAATTAAAAGAACCGATTTCTGAAGCTCGTAAAAA
* *
10504 CAAACTCTTAAATCCAATGTGGCTGAGATTTGGTTAAATAAAATATACATAAATCAACGTGTCTA
196 CAAACTCTTAAATCCAATATGACTGAGATTTGGTTAAATAAAATATACATAAATCAACGTGTCTA
* *
10569 GGCGCCAAAAATCATGCAAAACTAAGTCGGGGCTCCGGAACGAAC
261 GGCGCCAAAAATCATGCAAAACTAAGTCGAGGCCCCGGAACGAAC
* ** *
10614 GTACACGATTTCGGCAAAAATTTTGCAAAAAATGACTTGAAAGATTTTTCGTCAATTTT-TGACC
1 GTACACGATTTCGGCAAAAAGTTTGCAAAAAATGACCCGAAAGATTTTTCCTCAATTTTGTG--C
* * * * * *
10678 ACAACACTCGTAGAAAATATATAATTCAACTCCAAAAATATTGAAGGGCTTTTCACACTTTTAAT
64 AAAACACTCGTAAAAAATATATAATTAAACTCCAAAAAGATTGAAGGACTTTTCACACTTCTAAT
*
10743 ATA-GATTTTCCTAATTTTGCCGAATTAATTTCTAATTAAATCGAACCGATTTCTGAAGCTCGTA
129 A-ACGATTTTCCTAATTTTGCCGAATTAATTTCTAATTAAA-AGAACCGATTTCTGAAGCTCGTA
* * * * * * * * * *
10807 ACACCAAA-TCCTTAAATTCAATATGACTTAGATTTGGTTACAT-GAGTATAGAT-ATTCTAAGG
192 AAAACAAACT-CTTAAATCCAATATGACTGAGATTTGGTTAAATAAAATATACATAAATC-AACG
* * *
10869 AT-TCTTGTG-GCCAAAAATCATGCAAAATTGAGTCGAGGCCCCGGAACG--C
255 -TGTCTAG-GCGCCAAAAATCATGCAAAACTAAGTCGAGGCCCCGGAACGAAC
* ** * * * *
10918 GTTTTTTGCTAAAAATTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCC
1 G-----TAC--ACGATT-T--CGG-CA--AAAAG-TTT--GC---AA-------AAAA-TGACCC
* * * * * *
10983 GTAGGATTTTTCCTCAATTTT-TGACACAACACTCGTAGAAAATATATAACTCAACTCCAAAAAG
39 GAAAGATTTTTCCTCAATTTTGTG-CAAAACACTCGTAAAAAATATATAATTAAACTCCAAAAAG
* * ** * * * *
11047 ACTAAAGGGTTTTTCACACATCTAATATCGATTTTCCTATTTTTGTCGAATTAATTTCTAATTAA
103 ATTGAAGGACTTTTCACACTTCTAATAACGATTTTCCTAATTTTGCCGAATTAATTTCTAATTAA
* * ** **
11112 ATCGAACCGATTTTTGAAGCTCGTAAAAA-AAA-TCCTTAAATCCAATGCGGTTGAGATTTGGTT
168 A-AGAACCGATTTCTGAAGCTCGTAAAAACAAACT-CTTAAATCCAATATGACTGAGATTTGGTT
* * * ** * *
11175 AGATAAAATATACATAATTCAACGAGTCTAGGCGTAAAAAATCATGTAAAACTGAGTCG
231 AAATAAAATATACATAAATCAACGTGTCTAGGCGCCAAAAATCATGCAAAACTAAGTCG
11234 GCGTCCCGAA
Statistics
Matches: 498, Mismatches: 82, Indels: 55
0.78 0.13 0.09
Matches are distributed among these distances:
304 4 0.01
305 54 0.11
306 143 0.29
307 58 0.12
309 2 0.00
311 4 0.01
312 1 0.00
314 2 0.00
315 1 0.00
317 2 0.00
318 3 0.01
320 2 0.00
323 2 0.00
329 32 0.06
330 160 0.32
331 28 0.06
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (305 bp):
GTACACGATTTCGGCAAAAAGTTTGCAAAAAATGACCCGAAAGATTTTTCCTCAATTTTGTGCAA
AACACTCGTAAAAAATATATAATTAAACTCCAAAAAGATTGAAGGACTTTTCACACTTCTAATAA
CGATTTTCCTAATTTTGCCGAATTAATTTCTAATTAAAAGAACCGATTTCTGAAGCTCGTAAAAA
CAAACTCTTAAATCCAATATGACTGAGATTTGGTTAAATAAAATATACATAAATCAACGTGTCTA
GGCGCCAAAAATCATGCAAAACTAAGTCGAGGCCCCGGAACGAAC
Found at i:11431 original size:332 final size:331
Alignment explanation
Indices: 10614--12214 Score: 2030
Period size: 332 Copynumber: 4.8 Consensus size: 331
10604 CGGAACGAAC
* * * *
10614 GTACACGATTTCGGCAAAAATTTTGCAAAAAATGA-CTTGAAAGATTTTTCGTCAATTTTTGACC
1 GTACACGATTTCGGCTAAAATTTGGCAAAAAATGATC-CGAAAGATTTTTCCTCAATTTTTGACC
* *
10678 ACAACACTCGTAGAAAATATATAATTCAACTCCAAAAA-TATTGAAGGGCTTTTCACACTTTTAA
65 ACAACACTCGTAGAAAATATATAACTCAACTCCAAAAAGT-TTGAAGGGCTTTTCACACTTCTAA
* * *
10742 TATAGATTTTCCTAATTTTGCCGAATTAATTTCTAATTAAATCGAACCGATTTCTGAAGCTCGTA
129 TATCGATTTTCCTATTTTTGCCGAATTAATTTCTAATTAAATCGAACCGATTTTTGAAGCTCGTA
** * * * * * * *
10807 ACACCAAATCCTTAAATTCAATATGACTT-AGATTTGGTTACAT-GAGTATAGAT-ATTCTAAGG
194 A-AAAAAATCCTTAAATCCAATACG-GTTGAGATTTGGTTAGATAAAATATACATAATTC-AAGG
* * ** * * *
10869 ATTCTTGTG-GCCAAAAATCATGCAAAATTGAGTCGAG-GCCCCGGAACGCGTTTTTTGCTAAAA
256 AGTCTAG-GCGTAAAAAATCATGCAAAACTGAGTCG-GCGTCCCGAAACGCGTTTTTTGCTAAAA
*
10932 ATTGTGATGGTTA
319 ACTGTGATGGTTA
* * * * *
10945 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGTAGGATTTTTCCTCAATTTTTGA-CA
1 GTACACGATTTCGGCTAAAATTTGGCAAAAAATGATCCGAAAGATTTTTCCTCAATTTTTGACCA
** * * *
11009 CAACACTCGTAGAAAATATATAACTCAACTCCAAAAAGACTAAAGGGTTTTTCACACATCTAATA
66 CAACACTCGTAGAAAATATATAACTCAACTCCAAAAAGTTTGAAGGGCTTTTCACACTTCTAATA
*
11074 TCGATTTTCCTATTTTTGTCGAATTAATTTCTAATTAAATCGAACCGATTTTTGAAGCTCGTAAA
131 TCGATTTTCCTATTTTTGCCGAATTAATTTCTAATTAAATCGAACCGATTTTTGAAGCTCGTAAA
* *
11139 AAAAATCCTTAAATCCAATGCGGTTGAGATTTGGTTAGATAAAATATACATAATTCAACGAGTCT
196 AAAAATCCTTAAATCCAATACGGTTGAGATTTGGTTAGATAAAATATACATAATTCAAGGAGTCT
*
11204 AGGCGTAAAAAATCATGTAAAACTGAGTCGGCGTCCCGAAACGCGTTTTTTTGCTAAAAACTGTG
261 AGGCGTAAAAAATCATGCAAAACTGAGTCGGCGTCCCGAAACGCG-TTTTTTGCTAAAAACTGTG
11269 ATGGTTA
325 ATGGTTA
** *
11276 GTACACGATTTCAACTAAAATTTGGCAAAAAATGATTCGAAAGATTTTTCCTCAATTTTTGACCA
1 GTACACGATTTCGGCTAAAATTTGGCAAAAAATGATCCGAAAGATTTTTCCTCAATTTTTGACCA
*
11341 CAACACTCGTAGAAAATATATAACTCAACTCCAAAAAGTTTGAAGGGCTTTTCACGCTTCTAATA
66 CAACACTCGTAGAAAATATATAACTCAACTCCAAAAAGTTTGAAGGGCTTTTCACACTTCTAATA
* *
11406 TCGATTTTCCTATTTTTGCCGAATTAATTTCTAATAAAATCGAACTGATTTTTGAAGCTCGTAAA
131 TCGATTTTCCTATTTTTGCCGAATTAATTTCTAATTAAATCGAACCGATTTTTGAAGCTCGT-AA
* * * *
11471 AAAAAATCTTTAAATCCAATACGGTTGTGATTTGGTTAGATAAAATATACA-AAATCCAGTGAGT
195 AAAAAATCCTTAAATCCAATACGGTTGAGATTTGGTTAGATAAAATATACATAATTCAAG-GAGT
* * *
11535 CTAGGCGTAAAAAAT-ATGCAAAACTAAGCCGGCG-CCTCGAAACGCGTTTTTTTGCTAAAACCT
259 CTAGGCGTAAAAAATCATGCAAAACTGAGTCGGCGTCC-CGAAACGCG-TTTTTTGCTAAAAACT
*
11598 GTGATGATTA
322 GTGATGGTTA
* * *
11608 GAACACGATTTCGGCTAAAATTTGGCAAAAAATGACCCGAAAGATTTTTCCACAATTTTTGACCA
1 GTACACGATTTCGGCTAAAATTTGGCAAAAAATGATCCGAAAGATTTTTCCTCAATTTTTGACCA
** * *
11673 CAACACTCGTAGAAAATATATAGTTCAACTCCAAAAAGATCGAAGGGCTTTTCACACTTCTAATA
66 CAACACTCGTAGAAAATATATAACTCAACTCCAAAAAGTTTGAAGGGCTTTTCACACTTCTAATA
* * * * *
11738 TAGATTTTCATAATTTTGCCGAATTAATTTCTAATTAAAACGAACCGATTTCTGAAGCTCGTAAA
131 TCGATTTTCCTATTTTTGCCGAATTAATTTCTAATTAAATCGAACCGATTTTTGAAGCTCGTAAA
* * * * ** * * * * * * *
11803 ACCAAACCCTTAAATCCAAAATGACTGAGATTTGGTTATAT-GATTATAGAT-TTTCTGAGGATT
196 A-AAAATCCTTAAATCCAATACGGTTGAGATTTGGTTAGATAAAATATACATAATTC-AAGGAGT
* * ** * * *
11866 CTTGACGCCAAAAGTCATGCAAAACTGAGTCGGCGTCCCGGAACACGTTTTTTGCTAAAAACTGT
259 CTAGGCGTAAAAAATCATGCAAAACTGAGTCGGCGTCCCGAAACGCGTTTTTTGCTAAAAACTGT
*
11931 GA---TAA
324 GATGGTTA
*
11936 CGTACACGATTTCGGCTAAAATTTGGCAAAACATGATCCGAAAGATTTTTCCTCAATTTTTGACC
1 -GTACACGATTTCGGCTAAAATTTGGCAAAAAATGATCCGAAAGATTTTTCCTCAATTTTTGACC
* * *
12001 ACAACAATCGTAGAAAATATATAACTCAACTCCAAAAAGTTTGAAGGGTTTTTCACGCTTCTAAT
65 ACAACACTCGTAGAAAATATATAACTCAACTCCAAAAAGTTTGAAGGGCTTTTCACACTTCTAAT
* * * **
12066 ATCGATATTT-CTATTTTTTCCGAATTAATTTCAAATTACATCGAACTAATTTTTGAAGCTCGTA
130 ATCGAT-TTTCCTATTTTTGCCGAATTAATTTCTAATTAAATCGAACCGATTTTTGAAGCTCGT-
* * *
12130 AAAAAAAATCTTTAAATCCAGTACGGTTGAGATTTGGTTAGATAAAATATACATAATTCAATAGA
193 AAAAAAAATCCTTAAATCCAATACGGTTGAGATTTGGTTAGATAAAATATACATAATTCAA-GGA
12195 GTCTAGGCGTAAAAAATCAT
257 GTCTAGGCGTAAAAAATCAT
Statistics
Matches: 1095, Mismatches: 152, Indels: 46
0.85 0.12 0.04
Matches are distributed among these distances:
328 4 0.00
329 230 0.21
330 182 0.17
331 202 0.18
332 406 0.37
333 71 0.06
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (331 bp):
GTACACGATTTCGGCTAAAATTTGGCAAAAAATGATCCGAAAGATTTTTCCTCAATTTTTGACCA
CAACACTCGTAGAAAATATATAACTCAACTCCAAAAAGTTTGAAGGGCTTTTCACACTTCTAATA
TCGATTTTCCTATTTTTGCCGAATTAATTTCTAATTAAATCGAACCGATTTTTGAAGCTCGTAAA
AAAAATCCTTAAATCCAATACGGTTGAGATTTGGTTAGATAAAATATACATAATTCAAGGAGTCT
AGGCGTAAAAAATCATGCAAAACTGAGTCGGCGTCCCGAAACGCGTTTTTTGCTAAAAACTGTGA
TGGTTA
Done.