Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011028.1 Corchorus capsularis cultivar CVL-1 contig11049, 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: 41575
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2522 original size:2 final size:2
Alignment explanation
Indices: 2515--2547 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2505 GGGGAGGAAT
2515 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2548 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2552 original size:2 final size:2
Alignment explanation
Indices: 2547--2580 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2537 ACACACACAC
2547 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
2581 CAATCCAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5727 original size:40 final size:39
Alignment explanation
Indices: 5676--5751 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 39
5666 AAATATTGGT
5676 TATATATGTTCATGTCAAAAAATATTGGTTTATATATATA
1 TATATATGTTCATGTCAAAAAATATTGG-TTATATATATA
5716 TATATATGTTCATGTCAAAAAATATTGGTTATATAT
1 TATATATGTTCATGTCAAAAAATATTGGTTATATAT
5752 GTTGTCCCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
39 8 0.22
40 28 0.78
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (39 bp):
TATATATGTTCATGTCAAAAAATATTGGTTATATATATA
Found at i:5936 original size:3 final size:3
Alignment explanation
Indices: 5930--5972 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
5920 TCGGTGGAAA
5930 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5973 AACCTACTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:6537 original size:65 final size:65
Alignment explanation
Indices: 6457--6588 Score: 237
Period size: 65 Copynumber: 2.0 Consensus size: 65
6447 TGTTATGTTA
* * *
6457 TCATTTCATAACAAAATTTCATTTTTTAATTGAATTTTCTTAAAAGAATTTATAAAATAAAATAG
1 TCATTTCATAACAAAATTTCATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAATAAAACAG
6522 TCATTTCATAACAAAATTTCATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAATAAAACAG
1 TCATTTCATAACAAAATTTCATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAATAAAACAG
6587 TC
1 TC
6589 GCACGCGAAG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.41
Consensus pattern (65 bp):
TCATTTCATAACAAAATTTCATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAATAAAACAG
Found at i:8201 original size:38 final size:38
Alignment explanation
Indices: 8150--8227 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
8140 TCCGCTTCCA
8150 TTGTAAATGAGAATAAAGAAACACGGTGATAATTCGAC
1 TTGTAAATGAGAATAAAGAAACACGGTGATAATTCGAC
8188 TTGTAAATGAGAATAAAGAAACACGGTGATAATTCGAC
1 TTGTAAATGAGAATAAAGAAACACGGTGATAATTCGAC
8226 TT
1 TT
8228 TATGTTGGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.26
Consensus pattern (38 bp):
TTGTAAATGAGAATAAAGAAACACGGTGATAATTCGAC
Found at i:12030 original size:11 final size:11
Alignment explanation
Indices: 12006--12040 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
11996 TTGACAGCAC
12006 AACAAAAACAA
1 AACAAAAACAA
* *
12017 AACGAAAACGA
1 AACAAAAACAA
12028 AACAAAAACAA
1 AACAAAAACAA
12039 AA
1 AA
12041 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:33548 original size:34 final size:34
Alignment explanation
Indices: 33505--33569 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
33495 AATAATTTAC
*
33505 AATGAGGTATTGAACTCATCTCACTACGTTTGTA
1 AATGAGGTATTGAACTCATCCCACTACGTTTGTA
*
33539 AATGAGGTATTGAACTCATCCCACTGCGTTT
1 AATGAGGTATTGAACTCATCCCACTACGTTT
33570 CTTTGTTCAA
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:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (34 bp):
AATGAGGTATTGAACTCATCCCACTACGTTTGTA
Found at i:34289 original size:17 final size:17
Alignment explanation
Indices: 34257--34290 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
34247 TTTTGTTTGT
* *
34257 AATAATAATAATAATAA
1 AATAATAAGAAGAATAA
34274 AATAATAAGAAGAATAA
1 AATAATAAGAAGAATAA
34291 TTATATCAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (17 bp):
AATAATAAGAAGAATAA
Found at i:35593 original size:16 final size:17
Alignment explanation
Indices: 35549--35598 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
35539 TCACAATTAC
35549 AAGAGATCTAAAAAATA
1 AAGAGATCTAAAAAATA
*
35566 AATGA-A-C-AAAAAAAA
1 AA-GAGATCTAAAAAATA
35581 AAGAGATCTAAAAAATA
1 AAGAGATCTAAAAAATA
35598 A
1 A
35599 TGAAAAATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 2 0.07
15 10 0.37
16 2 0.07
17 11 0.41
18 2 0.07
ACGTcount: A:0.70, C:0.06, G:0.10, T:0.14
Consensus pattern (17 bp):
AAGAGATCTAAAAAATA
Found at i:40701 original size:56 final size:56
Alignment explanation
Indices: 40623--40731 Score: 157
Period size: 56 Copynumber: 1.9 Consensus size: 56
40613 TATTGTATCA
** * *
40623 TAACCAATTCGTTCGTAATTAACTTGATCGGGTAATATAAATATTTAATTTGATCC
1 TAACCAATTCGTTAATAATTAACTTAATCAGGTAATATAAATATTTAATTTGATCC
*
40679 TAACCAATTCG-TAATAATTTAACTTAATCAGGTAATATAAATGTTTAATTTGA
1 TAACCAATTCGTTAATAA-TTAACTTAATCAGGTAATATAAATATTTAATTTGA
40732 AAACCGAATG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
55 4 0.09
56 43 0.91
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (56 bp):
TAACCAATTCGTTAATAATTAACTTAATCAGGTAATATAAATATTTAATTTGATCC
Done.