Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009883.1 Corchorus capsularis cultivar CVL-1 contig09904, 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: 10277
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:235 original size:17 final size:18
Alignment explanation
Indices: 213--246 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
203 TCGAAAGTGA
213 ACCCGAACCCG-ACCCGG
1 ACCCGAACCCGAACCCGG
230 ACCCGAACCCGAACCCG
1 ACCCGAACCCGAACCCG
247 AAAATACTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.26, C:0.53, G:0.21, T:0.00
Consensus pattern (18 bp):
ACCCGAACCCGAACCCGG
Found at i:260 original size:16 final size:16
Alignment explanation
Indices: 236--326 Score: 134
Period size: 16 Copynumber: 5.8 Consensus size: 16
226 CCGGACCCGA
236 ACCCGAACCCGAAAAT
1 ACCCGAACCCGAAAAT
*
252 ACTCGAACCCG-AAAT
1 ACCCGAACCCGAAAAT
267 ACCCGAACCCG-AAAT
1 ACCCGAACCCGAAAAT
282 ACCCGAACCCGAAAA-
1 ACCCGAACCCGAAAAT
*
297 ATCCCGAACCTGAAAAT
1 A-CCCGAACCCGAAAAT
314 ACCCGAACCCGAA
1 ACCCGAACCCGAA
327 CCCGCCCAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
15 30 0.44
16 37 0.54
17 1 0.01
ACGTcount: A:0.42, C:0.37, G:0.13, T:0.08
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:264 original size:6 final size:6
Alignment explanation
Indices: 211--248 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
201 TATCGAAAGT
*
211 GAACCC GAACCC G-ACCC GGACCC GAACCC GAACCC GAA
1 GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAA
249 AATACTCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.32, C:0.47, G:0.21, T:0.00
Consensus pattern (6 bp):
GAACCC
Found at i:268 original size:15 final size:15
Alignment explanation
Indices: 236--326 Score: 128
Period size: 15 Copynumber: 5.9 Consensus size: 15
226 CCGGACCCGA
236 ACCCGAACCCGAAAAT
1 ACCCGAACCCG-AAAT
*
252 ACTCGAACCCGAAAT
1 ACCCGAACCCGAAAT
267 ACCCGAACCCGAAAT
1 ACCCGAACCCGAAAT
*
282 ACCCGAACCCGAAAA
1 ACCCGAACCCGAAAT
*
297 ATCCCGAACCTGAAAAT
1 A-CCCGAACCCG-AAAT
314 ACCCGAACCCGAA
1 ACCCGAACCCGAA
327 CCCGCCCAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
15 35 0.52
16 28 0.42
17 4 0.06
ACGTcount: A:0.42, C:0.37, G:0.13, T:0.08
Consensus pattern (15 bp):
ACCCGAACCCGAAAT
Found at i:274 original size:31 final size:31
Alignment explanation
Indices: 235--326 Score: 141
Period size: 31 Copynumber: 3.0 Consensus size: 31
225 CCCGGACCCG
*
235 AACCCGAACCCGAAAATACTCGAACCCGAAA
1 AACCCGAACCCGAAAATACCCGAACCCGAAA
*
266 TACCCGAACCCG-AAATACCCGAACCCGAAA
1 AACCCGAACCCGAAAATACCCGAACCCGAAA
*
296 AATCCCGAACCTGAAAATACCCGAACCCGAA
1 AA-CCCGAACCCGAAAATACCCGAACCCGAA
327 CCCGCCCAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
30 18 0.33
31 20 0.36
32 17 0.31
ACGTcount: A:0.42, C:0.37, G:0.13, T:0.08
Consensus pattern (31 bp):
AACCCGAACCCGAAAATACCCGAACCCGAAA
Found at i:8597 original size:596 final size:594
Alignment explanation
Indices: 7138--10277 Score: 5190
Period size: 596 Copynumber: 5.3 Consensus size: 594
7128 AACGAATTAA
*
7138 AAAAAAAATCTAAAACAGAATCAAATATAAAATCCAATTATATTTATTTTACTAAACTTTAAATG
1 AAAAAAAA-CTAAAACAGAATCAAATATAAAATCCGATTATATTTATTTTACTAAACTTTAAATG
* *
7203 AAAAAACAACCTATATCTAAGCTCAGATGACATCTTGCATATTGATATCAGAAGTCTCAAATGTT
65 ATAAAACAACCTATATCTAAGCTCGGATGACATCTTGCATATTGATATCAGAAGTCTCAAATGTT
*
7268 TTCTTGCATCCTATCGGATCTGAACCAATCGCAATACCACCAACCTCATCAATTTTAATGGTATC
130 TTCTTGCATCCTATCGGATCTGAACCAATCGCAATACCACCAACCTCATCAATTTTGATGGTATC
* * * * *
7333 TACACCGAATACTCTAACATCTTGCACTCTGTATGATTCTCTCCCAAGTCGAATCACATCATTCA
195 TACACCCAATATTCTCACATCTTGCACCCTGTATGATTCTCTCCCGAGTCGAATCACATCATTCA
* *
7398 CTTGCACGAGATCTTTTAC-AAAATAGCCACCTAGGATTGACTGACGAAGCGAAACTGGGTGAAT
260 CTTGCACGAGATCTTTTACAAAAATAGCCACCTGGGATTGACTGACGAAGCAAAACTGGGTGAAT
7462 AATATGCTGTAGCTATTCCCAATGTTGAAAGTAC-GATAACAGCAATAGCAAAATATATCCA-CT
325 AATATGCTGTAGCTATTCCCAATGTTGAAAGTACGGA-AACAGCAATAGCAAAATATATCCACCT
* *
7525 CAGTAATTAATAACACACAACCCAGGACATATATGAAGGCTAATGCATTATAAAAAATATTCATC
389 -AGTAATTAATAACACACAACCCAGGACACATATGAAGGCTAATGCATTATAAAAAATGTTCATC
* * *
7590 TCCTGCACTTACGACCCCTTTCTACGATCTGTGGGTCGAATTA-TTTGTATAAGAAAAATTAATT
453 TCCTGCACTGACGACCCCTTTCTACGATTTGTGGGTCCAATTACTTT-TATAAGAAAAATTAA-T
*
7654 CTCATGCCAAGAAAACTGCAGGTATATAATCCGTGATGAGCTGTATCAGGCCCTGGTCAAGCACA
516 CTCATGCCAAGAAAACTGCGGGTATATAATCCGTGATGAGCTGTATCAGGCCCTGGTCAAGCACA
7719 ATTTCGGATCGAAT
581 ATTTCGGATCGAAT
*
7733 AAAAAAAACTAAAACAGAATCAAATATAAAATTCGATTATATTTATTTTACTAAACTTTAAATGA
1 AAAAAAAACTAAAACAGAATCAAATATAAAATCCGATTATATTTATTTTACTAAACTTTAAATGA
* *
7798 -AAAAAAACCTATATCTAAGCTCGGATGACATCTTGCATCTTGATATCAGAAGTCTCAAATGTTT
66 TAAAACAACCTATATCTAAGCTCGGATGACATCTTGCATATTGATATCAGAAGTCTCAAATGTTT
*
7862 TCTTGTATCCTATCGGATCTGAACCAATCGCAATACCACCAACCTCATCAATTTTGATGGTATCT
131 TCTTGCATCCTATCGGATCTGAACCAATCGCAATACCACCAACCTCATCAATTTTGATGGTATCT
*
7927 ACACCCAATATTCTCACATCTTGCGCCCTGTATGATTCTCTCCCGAGTCGAATCACATCATTCAC
196 ACACCCAATATTCTCACATCTTGCACCCTGTATGATTCTCTCCCGAGTCGAATCACATCATTCAC
* * *
7992 TTGCACGAGATATTTTACAAAAATGGCCACCTGGGATTGACTGAACGAAGCAAAACTTGGTGAAT
261 TTGCACGAGATCTTTTACAAAAATAGCCACCTGGGATTGACTG-ACGAAGCAAAACTGGGTGAAT
8057 AATATGCTGTAGCTATTCCCAATGTTGAAAGTACGGAAACAGCAATAGCAAAATATATCCACCTA
325 AATATGCTGTAGCTATTCCCAATGTTGAAAGTACGGAAACAGCAATAGCAAAATATATCCACCTA
8122 GTAATTAATAACACACAACCCAGGACACATATGAAGGCTAATGCATTATAAAAAATGTTCATCTC
390 GTAATTAATAACACACAACCCAGGACACATATGAAGGCTAATGCATTATAAAAAATGTTCATCTC
*
8187 CTGCATTGACGACCCCTTTCTACGATTTGTGGGTCCAATTACTTTTATAAGAAAAATTAATTCCT
455 CTGCACTGACGACCCCTTTCTACGATTTGTGGGTCCAATTACTTTTATAAGAAAAATTAA-T-CT
* *
8252 CATGCCAAGAAAACTACGGGTATATAATCTGTGATGAGCTGTATCAGGCCCTGGTCAAGCACAAT
518 CATGCCAAGAAAACTGCGGGTATATAATCCGTGATGAGCTGTATCAGGCCCTGGTCAAGCACAAT
*
8317 TACGGATCGAAT
583 TTCGGATCGAAT
*
8329 -AAAAAAACTAAAACAGAATCAAATATAAAATTCGATTATATTTATTTTACTAAACTTTAAATGA
1 AAAAAAAACTAAAACAGAATCAAATATAAAATCCGATTATATTTATTTTACTAAACTTTAAATGA
* * * *
8393 TGAAACAACCTATATTTAAGCTCGGATGACATCTTGTATATTGACATCAGAAGTCTCAAATGTTT
66 TAAAACAACCTATATCTAAGCTCGGATGACATCTTGCATATTGATATCAGAAGTCTCAAATGTTT
* *
8458 TCTTGCATCATATCAGATCTGAACCAATCGCAATACCACCAACCTCATCAATTTTGATGGTATCT
131 TCTTGCATCCTATCGGATCTGAACCAATCGCAATACCACCAACCTCATCAATTTTGATGGTATCT
* *
8523 ACACCCAATATTCTCAAATATTGCACCCTGTATGATTCTCTCCCGAGTCGAATCACATCATTCAC
196 ACACCCAATATTCTCACATCTTGCACCCTGTATGATTCTCTCCCGAGTCGAATCACATCATTCAC
* *
8588 TTGCACGAGATCTTTTACAAAAATAACCATCTGGGATTGACTGGACGAAGCAAAACTGGGTGAAT
261 TTGCACGAGATCTTTTACAAAAATAGCCACCTGGGATTGACT-GACGAAGCAAAACTGGGTGAAT
8653 AATATGCTGTAGCTATTCCCAATGTTGAAAGTACGGAAACAGCAATAGCAAAATATATCCACCTA
325 AATATGCTGTAGCTATTCCCAATGTTGAAAGTACGGAAACAGCAATAGCAAAATATATCCACCTA
* * *
8718 GTAATTAATAACACACAACTCAGGACACATATGAAGGCTAATGCATTATAAAAAAAGTTCATTTC
390 GTAATTAATAACACACAACCCAGGACACATATGAAGGCTAATGCATTATAAAAAATGTTCATCTC
** *
8783 CTGCACTGACGACCCCTTTCTACGATTTGTGGGTAGAATTACTTTTATAAGAAGAATTAATCCTC
455 CTGCACTGACGACCCCTTTCTACGATTTGTGGGTCCAATTACTTTTATAAGAAAAATTAAT-CTC
*
8848 ATGCGAAGAAAACTGCGGGTATATAATCCGTGATGAGCTGTATCAGGCCCTGGTCAAGCACAATT
519 ATGCCAAGAAAACTGCGGGTATATAATCCGTGATGAGCTGTATCAGGCCCTGGTCAAGCACAATT
*
8913 ACGGATCGAAT
584 TCGGATCGAAT
*
8924 AAAAAAAACTAAAACAGAATCAAATATAAAATTCGATTATATTTATTTTACTAAACTTTAAATGA
1 AAAAAAAACTAAAACAGAATCAAATATAAAATCCGATTATATTTATTTTACTAAACTTTAAATG-
*
8989 AAAAAACAACCTATATCTAAGCTCGGATGACATCTTGCATATTGATATCAGAAGTCT-ATAATGT
65 ATAAAACAACCTATATCTAAGCTCGGATGACATCTTGCATATTGATATCAGAAGTCTCA-AATGT
*
9053 TTTCTTGTATCCTATCGGATCTGAACCAATCGCAATACCACCAACCTCATCAATTTTGATGGTAT
129 TTTCTTGCATCCTATCGGATCTGAACCAATCGCAATACCACCAACCTCATCAATTTTGATGGTAT
9118 CTACACCCAATATTCTCACATCTTGCACCCTGTATGATTCTCT-CCGAAGTCGAATCACATCATT
194 CTACACCCAATATTCTCACATCTTGCACCCTGTATGATTCTCTCCCG-AGTCGAATCACATCATT
9182 CACTTGCACGAGATCTTTTACAAAAATAGCCACCTGGGATTGACTGACGAAGCAAAACTGGGTGA
258 CACTTGCACGAGATCTTTTACAAAAATAGCCACCTGGGATTGACTGACGAAGCAAAACTGGGTGA
*
9247 ATAATATGCTGCAGCTATTCCCAATGTTGAAAGTACGGAAACAGCAATAGCAAAATATATCCACC
323 ATAATATGCTGTAGCTATTCCCAATGTTGAAAGTACGGAAACAGCAATAGCAAAATATATCCACC
*
9312 CAGTAATTAATAACACACAACCCAGGACACATATGAAGGCTAATGCATTATAAAAAATGTTCATC
388 TAGTAATTAATAACACACAACCCAGGACACATATGAAGGCTAATGCATTATAAAAAATGTTCATC
* * * * *
9377 TCCTGCACTGAAGACCCCTTTCTACGATTTGT-GGACCGAATTGCTTGTATAAGAAAAATAAATC
453 TCCTGCACTGACGACCCCTTTCTACGATTTGTGGGTCC-AATTACTTTTATAAGAAAAATTAATC
**
9441 TCCATGCCAAGAAAACTGCGGGTATATAATCCGTGATGAGCTGTATCAGGCCCTTCTCAAGCACA
517 T-CATGCCAAGAAAACTGCGGGTATATAATCCGTGATGAGCTGTATCAGGCCCTGGTCAAGCACA
9506 ATTTCGGATCGATTAT
581 ATTTCGGATCGA--AT
9522 AAAAAAAACTAAAACAGAATCAAATATAAAATCCGATTATATTTATTTTACTAAACTTTAAATGA
1 AAAAAAAACTAAAACAGAATCAAATATAAAATCCGATTATATTTATTTTACTAAACTTTAAATGA
* * *
9587 TAAAACAACCTATATTTAAGCTCGGATGACATCTTGTATCTTGATATCAGAAGTCTCAAATGTTT
66 TAAAACAACCTATATCTAAGCTCGGATGACATCTTGCATATTGATATCAGAAGTCTCAAATGTTT
* * *
9652 TCTTGCATCCTATCGGATCTGAACCAATTGCAATACTACTAACCTCATCAATTTTGATGGTATCT
131 TCTTGCATCCTATCGGATCTGAACCAATCGCAATACCACCAACCTCATCAATTTTGATGGTATCT
*
9717 ACACCCAATATTCTCACATCTTGCACCCTGTATGATTCTCTCCGGAGTCGAATCACATCATTCAC
196 ACACCCAATATTCTCACATCTTGCACCCTGTATGATTCTCTCCCGAGTCGAATCACATCATTCAC
*
9782 TTGCACGAGATCTTTTAC-AAAATGGCCACCTGGGATTGACTGAACGAAGCAAAACTGGGTGAAT
261 TTGCACGAGATCTTTTACAAAAATAGCCACCTGGGATTGACTG-ACGAAGCAAAACTGGGTGAAT
* * *
9846 AATATGCTGCAGCTATTTCCAATGTTGAAAGTACGGAAACAGCAATAGCAAAATATATCCACCCA
325 AATATGCTGTAGCTATTCCCAATGTTGAAAGTACGGAAACAGCAATAGCAAAATATATCCACCTA
* *
9911 GTAATTAATATCACACAAGCCAGGACACATATGAAGGCTAATGCATTATAAAAAATGTTCATCTC
390 GTAATTAATAACACACAACCCAGGACACATATGAAGGCTAATGCATTATAAAAAATGTTCATCTC
* * *
9976 CTGCACCGACGACCCCTTTCTACGATATGTGGG-CCAAATTACTTGTATAAGAAAAATTAATCTC
455 CTGCACTGACGACCCCTTTCTACGATTTGTGGGTCC-AATTACTTTTATAAGAAAAATTAATCT-
* * *
10040 CATGCCATGAAAACTGCGGGTATATAATCTGTGATGAGCTGTATCAGGCCCTGCTCAAGCACAAT
518 CATGCCAAGAAAACTGCGGGTATATAATCCGTGATGAGCTGTATCAGGCCCTGGTCAAGCACAAT
*
10105 TTGGGATCGAAT
583 TTCGGATCGAAT
* *
10117 ATAAAAAAA-TAAAACAGAATCAAATATAAAATCCGATTATATTTGTTTTACTAAACTTTATATG
1 A-AAAAAAACTAAAACAGAATCAAATATAAAATCCGATTATATTTATTTTACTAAACTTTAAATG
** * *
10181 ATAATTCAACCTATAAT-TAAGCTCGGATGACATCTTGTATCTTGATATCAGAAGTCTCAAATGT
65 ATAAAACAACCTAT-ATCTAAGCTCGGATGACATCTTGCATATTGATATCAGAAGTCTCAAATGT
* * *
10245 TTTCCTACATCCTATCAGATCTGAACCAATCGC
129 TTTCTTGCATCCTATCGGATCTGAACCAATCGC
Statistics
Matches: 2407, Mismatches: 116, Indels: 44
0.94 0.05 0.02
Matches are distributed among these distances:
593 200 0.08
594 77 0.03
595 493 0.20
596 872 0.36
597 695 0.29
598 70 0.03
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (594 bp):
AAAAAAAACTAAAACAGAATCAAATATAAAATCCGATTATATTTATTTTACTAAACTTTAAATGA
TAAAACAACCTATATCTAAGCTCGGATGACATCTTGCATATTGATATCAGAAGTCTCAAATGTTT
TCTTGCATCCTATCGGATCTGAACCAATCGCAATACCACCAACCTCATCAATTTTGATGGTATCT
ACACCCAATATTCTCACATCTTGCACCCTGTATGATTCTCTCCCGAGTCGAATCACATCATTCAC
TTGCACGAGATCTTTTACAAAAATAGCCACCTGGGATTGACTGACGAAGCAAAACTGGGTGAATA
ATATGCTGTAGCTATTCCCAATGTTGAAAGTACGGAAACAGCAATAGCAAAATATATCCACCTAG
TAATTAATAACACACAACCCAGGACACATATGAAGGCTAATGCATTATAAAAAATGTTCATCTCC
TGCACTGACGACCCCTTTCTACGATTTGTGGGTCCAATTACTTTTATAAGAAAAATTAATCTCAT
GCCAAGAAAACTGCGGGTATATAATCCGTGATGAGCTGTATCAGGCCCTGGTCAAGCACAATTTC
GGATCGAAT
Done.