Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007597.1 Corchorus capsularis cultivar CVL-1 contig07618, 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: 31209
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:297 original size:37 final size:36
Alignment explanation
Indices: 221--297 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 36
211 AATTTAAGAC
221 CAAAGACAAAGCAAAATTAAATACAACGATTGGAAA
1 CAAAGACAAAGCAAAATTAAATACAACGATTGGAAA
*
257 CAAAGACAAAAGGTAAAATTAAATA-AGACG-TTGGAAA
1 CAAAGAC-AAA-GCAAAATTAAATACA-ACGATTGGAAA
294 CAAA
1 CAAA
298 AAGTCAAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 7 0.19
37 15 0.41
38 15 0.41
ACGTcount: A:0.58, C:0.12, G:0.16, T:0.14
Consensus pattern (36 bp):
CAAAGACAAAGCAAAATTAAATACAACGATTGGAAA
Found at i:432 original size:31 final size:31
Alignment explanation
Indices: 397--462 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
387 TGGTAATTTA
* * *
397 GAAATATGTTTTTTAAAA-AAGGGTACAATTG
1 GAAATAT-ATTTTAAAAATAAGGGTACAATCG
428 GAAATATATTTTAAAAATAAGGGTACAATCG
1 GAAATATATTTTAAAAATAAGGGTACAATCG
459 GAAA
1 GAAA
463 AAATAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.30
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGGTACAATCG
Found at i:3472 original size:27 final size:29
Alignment explanation
Indices: 3410--3470 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 29
3400 TAAAAGCACA
3410 AAATTGGTCCCTCAAGTGGAGTGAAAATAGC
1 AAATTGGTCCCTCAAGTGGA--GAAAATAGC
3441 AAATTGGTCCCTCAAGT-GA-AAAATATGC
1 AAATTGGTCCCTCAAGTGGAGAAAATA-GC
3469 AA
1 AA
3471 TTTAGTTCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
27 6 0.21
28 4 0.14
30 2 0.07
31 17 0.59
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.23
Consensus pattern (29 bp):
AAATTGGTCCCTCAAGTGGAGAAAATAGC
Found at i:4554 original size:30 final size:31
Alignment explanation
Indices: 4518--4581 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
4508 TGTAAATGGA
4518 TCCCTGAAGTGAACTT-AGTGAGCAATTGAG
1 TCCCTGAAGTGAACTTAAGTGAGCAATTGAG
* * * *
4548 TCCCTGAAGTGGAGTTAATTGAGCAATTGGG
1 TCCCTGAAGTGAACTTAAGTGAGCAATTGAG
4579 TCC
1 TCC
4582 GTAACTCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 14 0.48
31 15 0.52
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (31 bp):
TCCCTGAAGTGAACTTAAGTGAGCAATTGAG
Found at i:4884 original size:6 final size:6
Alignment explanation
Indices: 4875--4902 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
4865 TATATATGTA
4875 TTATCT TTATCT TTATCT TTATCT TTAT
1 TTATCT TTATCT TTATCT TTATCT TTAT
4903 ATTATATAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.00, T:0.68
Consensus pattern (6 bp):
TTATCT
Found at i:8828 original size:12 final size:12
Alignment explanation
Indices: 8791--8829 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
8781 ACATAATAAT
8791 AAGAAAGAGGAAA
1 AAGAAA-AGGAAA
**
8804 AAGAAAAAAAAA
1 AAGAAAAGGAAA
8816 AAGAAAAGGAAA
1 AAGAAAAGGAAA
8828 AA
1 AA
8830 CCTTCGTATC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 16 0.73
13 6 0.27
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AAGAAAAGGAAA
Found at i:9333 original size:34 final size:34
Alignment explanation
Indices: 9290--9354 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
9280 TAGTAGCAGT
*
9290 GGATTTAACCCAGATTAAATAGGATTTTCTTCCA
1 GGATTTAACCCAAATTAAATAGGATTTTCTTCCA
*
9324 GGATTTAACCCAAATTAAATAGGTTTTTCTT
1 GGATTTAACCCAAATTAAATAGGATTTTCTT
9355 TTTATGTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.38
Consensus pattern (34 bp):
GGATTTAACCCAAATTAAATAGGATTTTCTTCCA
Found at i:9476 original size:16 final size:16
Alignment explanation
Indices: 9451--9481 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9441 TAAATAGGAT
9451 TTTGAAAATTAATTAG
1 TTTGAAAATTAATTAG
*
9467 TTTGATAATTAATTA
1 TTTGAAAATTAATTA
9482 ATTAACTCCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTGAAAATTAATTAG
Found at i:9678 original size:2 final size:2
Alignment explanation
Indices: 9671--9706 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
9661 CTTTCACCAA
9671 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9707 TCTCAAATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10495 original size:299 final size:299
Alignment explanation
Indices: 9957--10555 Score: 1198
Period size: 299 Copynumber: 2.0 Consensus size: 299
9947 AACTTGGCCG
9957 TAGCATGTTTGAAGGGTAAATCACTTTTTACTACTCTTCTCAAATTAGCATGGACTACTTATTGT
1 TAGCATGTTTGAAGGGTAAATCACTTTTTACTACTCTTCTCAAATTAGCATGGACTACTTATTGT
10022 TATCACATTTGGATTGAGAGAAATGACAGACTATTTGGCAAGCAGCAGAATACTACTGATGGTGT
66 TATCACATTTGGATTGAGAGAAATGACAGACTATTTGGCAAGCAGCAGAATACTACTGATGGTGT
10087 TTTCCAGCAGATTAGTTATGTCCTTAGGCTCAAATTGCATGGATTAATTCATGTTAAGGCAGATT
131 TTTCCAGCAGATTAGTTATGTCCTTAGGCTCAAATTGCATGGATTAATTCATGTTAAGGCAGATT
10152 ATGTAAACAAGTGTCTTTGTGCTAGATAGAACTTAAAGATTTCTGGTCTTAGTTGCTAAGATTTG
196 ATGTAAACAAGTGTCTTTGTGCTAGATAGAACTTAAAGATTTCTGGTCTTAGTTGCTAAGATTTG
10217 ATTTGGTTGTAATGTCTTTTTGTAAGTACTTTTGTTGCT
261 ATTTGGTTGTAATGTCTTTTTGTAAGTACTTTTGTTGCT
10256 TAGCATGTTTGAAGGGTAAATCACTTTTTACTACTCTTCTCAAATTAGCATGGACTACTTATTGT
1 TAGCATGTTTGAAGGGTAAATCACTTTTTACTACTCTTCTCAAATTAGCATGGACTACTTATTGT
10321 TATCACATTTGGATTGAGAGAAATGACAGACTATTTGGCAAGCAGCAGAATACTACTGATGGTGT
66 TATCACATTTGGATTGAGAGAAATGACAGACTATTTGGCAAGCAGCAGAATACTACTGATGGTGT
10386 TTTCCAGCAGATTAGTTATGTCCTTAGGCTCAAATTGCATGGATTAATTCATGTTAAGGCAGATT
131 TTTCCAGCAGATTAGTTATGTCCTTAGGCTCAAATTGCATGGATTAATTCATGTTAAGGCAGATT
10451 ATGTAAACAAGTGTCTTTGTGCTAGATAGAACTTAAAGATTTCTGGTCTTAGTTGCTAAGATTTG
196 ATGTAAACAAGTGTCTTTGTGCTAGATAGAACTTAAAGATTTCTGGTCTTAGTTGCTAAGATTTG
10516 ATTTGGTTGTAATGTCTTTTTGTAAGTACTTTTGTTGCT
261 ATTTGGTTGTAATGTCTTTTTGTAAGTACTTTTGTTGCT
10555 T
1 T
10556 CCTTTGGATA
Statistics
Matches: 300, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
299 300 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (299 bp):
TAGCATGTTTGAAGGGTAAATCACTTTTTACTACTCTTCTCAAATTAGCATGGACTACTTATTGT
TATCACATTTGGATTGAGAGAAATGACAGACTATTTGGCAAGCAGCAGAATACTACTGATGGTGT
TTTCCAGCAGATTAGTTATGTCCTTAGGCTCAAATTGCATGGATTAATTCATGTTAAGGCAGATT
ATGTAAACAAGTGTCTTTGTGCTAGATAGAACTTAAAGATTTCTGGTCTTAGTTGCTAAGATTTG
ATTTGGTTGTAATGTCTTTTTGTAAGTACTTTTGTTGCT
Found at i:15425 original size:28 final size:28
Alignment explanation
Indices: 15386--15447 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
15376 AAAGAGGCTT
15386 TCAA-CAAACAATGGTACTATTTAGTTA
1 TCAATCAAACAATGGTACTATTTAGTTA
15413 TCAATCAAACAATGGTACTATTTAGTTA
1 TCAATCAAACAATGGTACTATTTAGTTA
15441 TCAATCA
1 TCAATCA
15448 TATTAAGTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 4 0.12
28 30 0.88
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (28 bp):
TCAATCAAACAATGGTACTATTTAGTTA
Found at i:17382 original size:13 final size:13
Alignment explanation
Indices: 17364--17398 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
17354 ATAATTATTG
17364 TTTGCTTTATTAA
1 TTTGCTTTATTAA
17377 TTTGCTTTATTAA
1 TTTGCTTTATTAA
*
17390 TCTGCTTTA
1 TTTGCTTTA
17399 GATTTAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.60
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:17406 original size:6 final size:6
Alignment explanation
Indices: 17395--17421 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
17385 ATTAATCTGC
17395 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
17422 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:23597 original size:10 final size:10
Alignment explanation
Indices: 23582--23606 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
23572 GTCCCTGCTC
23582 AATTCCAGAA
1 AATTCCAGAA
23592 AATTCCAGAA
1 AATTCCAGAA
23602 AATTC
1 AATTC
23607 TAGAGTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:24540 original size:13 final size:13
Alignment explanation
Indices: 24522--24556 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
24512 ATAATTATTG
*
24522 TTTGCTTTATTAA
1 TTTGCTTTATCAA
24535 TTTGCTTTATCAA
1 TTTGCTTTATCAA
*
24548 TCTGCTTTA
1 TTTGCTTTA
24557 GATTTAGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.20, C:0.14, G:0.09, T:0.57
Consensus pattern (13 bp):
TTTGCTTTATCAA
Done.