Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005559.1 Corchorus capsularis cultivar CVL-1 contig05577, 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: 6632
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Found at i:719 original size:332 final size:331
Alignment explanation
Indices: 1--2646 Score: 2199
Period size: 332 Copynumber: 8.0 Consensus size: 331
**
1 TATTGAAGGGA-TTTTCGTGCTTCTAATATCGTTTTTCTTTTTCTTTT-TGAATTAATTTCTAAT
1 TATTGAA-GGACTTTTCACGCTTCTAATATCGTTTTTCTTTTT-TTTTCTGAATTAATTTCTAAT
* * * * * * *
64 TAAATCAAAACTTGA-TCTGATGCTCGTAAAAACAAATCCTTATATCCACTATGGTTGAGATTTC
64 TAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTC
* * * *
128 GTTAGATGAATATTGATATTACAAGGAGTCTTGACGCCAAAAATCATGCAAAATTGAGTCGGGAC
129 GTTAGATGAATATAGATATTACAATGAGTCTTGACGCCAAAAATCATGCAAAACTGAGTCGGGGC
* * * * * * * *
193 CCTGTAACGCATTTTAAGCCAAAAATTGTGATGGTTAGTAGACAATTTCGGTTAAAATTTCGCAA
194 CCCGGAACGCGTTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTCGGTTAAAATTTCACAA
* * * * ** * * *
258 AACTTGACCTGAAAATTTTTTCCTCAATTTTTAGCCATGATACTTATAAAAAATATATAATTTAT
259 AAATTGACC-CAAAAATTTTTCCTTAATTTTTAGCCACAATACTCATAAAAAATATATAACTTAA
* *
323 CACAAAAAA
323 CGCCAAAAA
* * * * * * *
332 AATGGAAGGACTTTTCACGCTTGTAATATCGTTTTCCTTTTTTTTTCTAAATTAATTTTTAATAA
1 TATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCTTTTTTTTTCTGAATTAATTTCTAATTA
* * *
397 AACCGAAACATGATTCAGATGCTCGTAAAAGCAAATCCTTAAATCCAATGTGGCTGAGATTTGGT
66 AATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTCGT
** * * *
462 TAGATGAATATAGATATTTTAATGTGTCTTG-CTGCCAGAAATCATGCAAAACTGAGCCGGGGCC
131 TAGATGAATATAGATATTACAATGAGTCTTGAC-GCCAAAAATCATGCAAAACTGAGTCGGGGCC
* * * * *
526 CCGGAACGCTTTTTTATCCAAAAATCGTGATGGTTAGTACAAGATTTCGGCTAAAATTTTACAAA
195 CCGGAACGCGTTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTCGGTTAAAATTTCACAAA
* * *
591 AATTGA-CCATAAGATTTTTCCTTAATTTTTGGCCACAATACTCATATAAAATATATAACTTAAC
260 AATTGACCCA-AAAATTTTTCCTTAATTTTTAGCCACAATACTCATAAAAAATATATAACTTAAC
655 GCCAAAAA
324 GCCAAAAA
* * *
663 GATTGAATGACTTTTCA-GACTTCTAATATCGTTTTTCTTTTTGTTTTCTGAATTAATTTCTTAT
1 TATTGAAGGACTTTTCACG-CTTCTAATATCGTTTTTCTTTTT-TTTTCTGAATTAATTTCTAAT
* * * *
727 TAAATCGAAACAAGATTCTA-ATGCTAGTAAAAA-AAATCCTTAAATCCAATGTCGATGAGATTT
64 TAAATCGAAACATGATTC-AGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
* * * * * * * *** * *
790 GGATAGCTTAATATGGATATTTCAAAGAGTCTTGGTACCAAAAATCAAGCAAAACTGAG-CTGAG
128 CGTTAGATGAATATAGATATTACAATGAGTCTTGACGCCAAAAATCATGCAAAACTGAGTC-GGG
* * * ** * *
854 ACCCTGGAACGCATTTTTTTTTTCCAAAAATCGTGATGGTTAGTACACGATTTTGGCTAAAATTT
192 GCCCCGGAACGC---GTTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTCGGTTAAAATTT
** * * * * *
919 TGCAAAAATTGA-CCAGAAAGATTTTTCCTTAATTTTTGGTCACAAGAATCATATAAAATATATA
254 CACAAAAATTGACCCA-AAA-ATTTTTCCTTAATTTTTAGCCACAATACTCATAAAAAATATATA
* *
983 ACTCATCGCCAAAAA
317 ACTTAACGCCAAAAA
* * *
998 TATTGAAGGGA-TTTTCATGCTTTTAATATCGTTTTTCTTTTCATTTTC-GAATTAATTTCTAAT
1 TATTGAA-GGACTTTTCACGCTTCTAATATCGTTTTTCTTTT-TTTTTCTGAATTAATTTCTAAT
* * * * * * *
1061 TAAATCAAAACTTGATTCTGATGCTCGTAAAAGCAAATCCTTATATCCACTATGGCTGAGATTTC
64 TAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTC
* * * * *
1126 GTTAGATGAATATTGATATTATAAGGAGTCTTGACGCCAAATATCATGCAAAACTGAGCCGGGGC
129 GTTAGATGAATATAGATATTACAATGAGTCTTGACGCCAAAAATCATGCAAAACTGAGTCGGGGC
* * *
1191 CCCGTAACGCGTTTTAAGCCAAAAA-CTGTGATGGTTAATACACGATTTCGGTTAAAATTTCACA
194 CCCGGAACGCGTTTTTAGCCAAAAATC-GTGATGGTTAGTACACGATTTCGGTTAAAATTTCACA
* * * ** *
1255 AAATTTGACCCAAAATTTTTTTCTTCAATTTTTAGTTACAATAGTCATAAAAAA-ATATATACTT
258 AAAATTGACCCAAAAATTTTTCCTT-AATTTTTAGCCACAATACTCATAAAAAATATATA-AC-T
1319 TAACG-CAAAAGA
320 TAACGCCAAAA-A
* * * * ** * * *
1331 GAATG-TGGGCTTTTCACTATTCTTATAT-TTTCTTTC-TTTTTTTTCCGAATTAATTTCTAATT
1 TATTGAAGGACTTTTCACGCTTCTAATATCGTT-TTTCTTTTTTTTTCTGAATTAATTTCTAATT
* * * * ** *
1393 AAAAT-GAAA-TTAGATTCTGATGCTCGTAAAAACAAATCCTTATATACAACATGGTTGAG-TTT
65 -AAATCGAAACAT-GATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
* * * *
1455 CGTTAGATGAAAATTGATATTACAAGGAGTCTTGACGCAAAAAATCATGCAAAACTGAGTCGGGG
128 CGTTAGATGAATATAGATATTACAATGAGTCTTGACGCCAAAAATCATGCAAAACTGAGTCGGGG
* * * *
1520 CCCCGTAATGCGTTTTAAGCCAAAAA-CTGTGATGGTTAGTACACGATTTCGGTTAAAATTTCGC
193 CCCCGGAACGCGTTTTTAGCCAAAAATC-GTGATGGTTAGTACACGATTTCGGTTAAAATTTCAC
* * * *
1584 AAAACTTGACTCAAAAATTTTTTTTCCTCAATTTTTAGCCACGATACTCATAAAAAATATATAA-
257 AAAAATTGACCCAAAAA---TTTTTCCTTAATTTTTAGCCACAATACTCATAAAAAATATATAAC
*
1648 TTGAAC-ACAAAAA
319 TT-AACGCCAAAAA
* ** *
1661 TATGGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCTTTTTTTTTTCTAATTTTTTTTCTAAAT
1 TATTGAAGGACTTTTCACGCTTCTAATATCG-----------TTTTTCT--TTTTTTTTCTGAAT
* * *
1726 TAATTTCTAATTAAACCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCAAATGTA
53 TAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * ** *
1791 GCTGAGATTTGGTTAGATTAATATAGATATTACAATGAGTCTTGACGGAAAAAATCATGCAAAAT
118 GCTGAGATTTCGTTAGATGAATATAGATATTACAATGAGTCTTGACGCCAAAAATCATGCAAAAC
* * ***
1856 TGAGTCGGGGCCCCGTAACGCGTTTTTAG-CAAAAAACTGTGATGGTTACG--C-C-ATTAAAGT
183 TGAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAATC-GTGATGGTTA-GTACACGATTTCGGT
* * * *
1916 TAAAATTTCACAAAACTTGACCCGAAAATTTTTTTCCCTCAATTTTTAGCCACAATATTCATAAA
246 TAAAATTTCACAAAAATTGACCC-AAAA-ATTTTT-CCTTAATTTTTAGCCACAATACTCATAAA
* *
1981 AAATATATAATTTAAC-ACAAAAGA
308 AAATATATAACTTAACGCCAAAA-A
* * * * * *
2005 TATTGAAGGCCTTTTCACGCTTCTAATATCATCTTTCTTTCTTTTTTCCGAATTAATTACTATTT
1 TATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCTTT-TTTTTTCTGAATTAATTTCTAATT
* ** * * * *
2070 AAAACGAAAC-TGGATTTTGATGCTCGTTAAAACAAATTCTTAAATCTAATGTGGCTGATATTTC
65 AAATCGAAACAT-GATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTC
* * * * * * * * * * * * * *
2134 ATCAGATAAATATAGATATTTCAATCAATCTTCATGTCAGAAATTCAT-AAAAACTTAAATCAGG
129 GTTAGATGAATATAGATATTACAATGAGTCTTGACGCCA-AAAATCATGCAAAAC-TGAGTCGGG
* * * * * *** * *
2198 ACACCGGAACGAGTTTTTAGCCAAAAAT--TG-T-GAT-GTACACAATTTCAACTAAAATTTTAT
192 GCCCCGGAACGCGTTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTCGGTTAAAATTTCAC
* * * * * *
2258 AAAAACTGACCCAAAAAATTTTCCTTGATTTTTAGCCACCATACTCATACAAAATAAATAA-TTC
257 AAAAATTGACCCAAAAATTTTTCCTTAATTTTTAGCCACAATACTCATAAAAAATATATAACTT-
* *
2322 AATGCAAAAAAAA
321 AACGC--CAAAAA
* * *
2335 AATTGAATGG-TTTTTCACGCTTCTAATA-------TC-ATTTTTTT-T-AATTAATTTCTAATT
1 TATTGAA-GGACTTTTCACGCTTCTAATATCGTTTTTCTTTTTTTTTCTGAATTAATTTCTAATT
* * * * * * *
2389 AGATTGAAACATGATTAAGATACTCGTAAAAACAAAACCTTAAATCCAATGTAGCTGAGATTTGG
65 AAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTCG
* * * * * *
2454 TTAGATGAATATAGACATTTCAATGTGTCTTGACGCAAAAAAAAAATCATGCAAAACTAAGTTGG
130 TTAGATGAATATAGATATTACAATGAGTCTTGACGC----CAAAAATCATGCAAAACTGAGTCGG
* * * * * * * *
2519 TGCCCTGGAAAGCG-TTTTAGCCAAAAAACCGAGATGGTTGGTATACGATTTCGGTTAAAATTTT
191 GGCCCCGGAACGCGTTTTTAGCC-AAAAATCGTGATGGTTAGTACACGATTTCGGTTAAAATTTC
** * ** *
2583 ACAAAAATTGACCCGAAAGGTTTTT-CTTAATTTTTTTGCCACAATACTGGTAACAAATATATAA
255 ACAAAAATTGACCC-AAAAATTTTTCCTTAA-TTTTTAGCCACAATACTCATAAAAAATATATAA
2647 TTCAAAGCTA
Statistics
Matches: 1885, Mismatches: 339, Indels: 185
0.78 0.14 0.08
Matches are distributed among these distances:
319 89 0.05
320 1 0.00
321 14 0.01
322 26 0.01
323 8 0.00
324 1 0.00
325 1 0.00
326 2 0.00
327 38 0.02
328 68 0.04
329 7 0.00
330 190 0.10
331 373 0.20
332 434 0.23
333 59 0.03
334 109 0.06
335 174 0.09
336 4 0.00
342 9 0.00
343 74 0.04
344 38 0.02
345 74 0.04
346 91 0.05
347 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (331 bp):
TATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCTTTTTTTTTCTGAATTAATTTCTAATTA
AATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTCGT
TAGATGAATATAGATATTACAATGAGTCTTGACGCCAAAAATCATGCAAAACTGAGTCGGGGCCC
CGGAACGCGTTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTCGGTTAAAATTTCACAAAA
ATTGACCCAAAAATTTTTCCTTAATTTTTAGCCACAATACTCATAAAAAATATATAACTTAACGC
CAAAAA
Found at i:2975 original size:53 final size:52
Alignment explanation
Indices: 2911--3020 Score: 211
Period size: 53 Copynumber: 2.1 Consensus size: 52
2901 ATTGTATCTC
2911 CATCCAATCACAAACAACACACAATTTGGGGTAATTTATTGGAAAGGAGATA
1 CATCCAATCACAAACAACACACAATTTGGGGTAATTTATTGGAAAGGAGATA
2963 CATCGCAATCACAAACAACACACAATTTGGGGTAATTTATTGGAAAGGAGATA
1 CATC-CAATCACAAACAACACACAATTTGGGGTAATTTATTGGAAAGGAGATA
3016 CATCC
1 CATCC
3021 CAGCAACTCA
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
52 5 0.09
53 52 0.91
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (52 bp):
CATCCAATCACAAACAACACACAATTTGGGGTAATTTATTGGAAAGGAGATA
Found at i:3291 original size:17 final size:17
Alignment explanation
Indices: 3265--3303 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
3255 GAACTAACTT
* * *
3265 CATTTTCAGCTGCCGAC
1 CATTTCCAGCAGCCAAC
3282 CATTTCCAGCAGCCAAC
1 CATTTCCAGCAGCCAAC
3299 CATTT
1 CATTT
3304 ACAACTTCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.23, C:0.36, G:0.13, T:0.28
Consensus pattern (17 bp):
CATTTCCAGCAGCCAAC
Found at i:3478 original size:85 final size:85
Alignment explanation
Indices: 3333--3492 Score: 284
Period size: 85 Copynumber: 1.9 Consensus size: 85
3323 GAGCTACACG
* * *
3333 AGGACAGCGGCTCTCAGCAGTGAGGCTCTCAACACGGCCGCCGACTATGAGGCTCGCGACACGAC
1 AGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTACGAGGCTCACGACACGAC
3398 ACACACGAAGGTACACGAGA
66 ACACACGAAGGTACACGAGA
*
3418 AGGACAGTGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTACGAGGCTCACGACACGAC
1 AGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTACGAGGCTCACGACACGAC
3483 ACACACGAAG
66 ACACACGAAG
3493 ACACAGGTGC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 71 1.00
ACGTcount: A:0.29, C:0.32, G:0.29, T:0.11
Consensus pattern (85 bp):
AGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTACGAGGCTCACGACACGAC
ACACACGAAGGTACACGAGA
Found at i:6556 original size:2 final size:2
Alignment explanation
Indices: 6551--6632 Score: 164
Period size: 2 Copynumber: 41.0 Consensus size: 2
6541 AAGCCAGGGA
6551 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
6593 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.