Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013761.1 Corchorus capsularis cultivar CVL-1 contig13782, 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: 35156
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:8466 original size:6 final size:6
Alignment explanation
Indices: 8455--8481 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
8445 AAAGCAAAGC
8455 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
8482 GCAAATTAAT
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:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:9427 original size:10 final size:10
Alignment explanation
Indices: 9412--9436 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
9402 GAGGACTCTA
9412 GAATTTTCTG
1 GAATTTTCTG
9422 GAATTTTCTG
1 GAATTTTCTG
9432 GAATT
1 GAATT
9437 GAGCAGGGAC
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:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:10644 original size:31 final size:31
Alignment explanation
Indices: 10603--10666 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
10593 TAATGATGTT
*
10603 AAATTCATAAAAATGGAGGGGTAAATTGGAG
1 AAATTAATAAAAATGGAGGGGTAAATTGGAG
10634 AAATTAATAAAAATGGAGGGGTAAATTGGAG
1 AAATTAATAAAAATGGAGGGGTAAATTGGAG
10665 AA
1 AA
10667 GTTGAGTGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.48, C:0.02, G:0.28, T:0.22
Consensus pattern (31 bp):
AAATTAATAAAAATGGAGGGGTAAATTGGAG
Found at i:10772 original size:2 final size:2
Alignment explanation
Indices: 10765--10796 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
10755 GAGGGAGTAC
10765 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10797 GTAGTAAGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11818 original size:19 final size:18
Alignment explanation
Indices: 11794--11829 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
11784 TGAAGATTTC
11794 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
11813 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
11830 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:14386 original size:78 final size:78
Alignment explanation
Indices: 14273--14429 Score: 305
Period size: 78 Copynumber: 2.0 Consensus size: 78
14263 ATTTTGTTTA
*
14273 TAATTTGAGGGTTTTCTTAAAATTGATAACCGAAACCGAAATTTAGGATTTTTCAATTGGGAATT
1 TAATTTGAGGGTTTTCTTAAAAATGATAACCGAAACCGAAATTTAGGATTTTTCAATTGGGAATT
14338 TTGTGAATTTTGT
66 TTGTGAATTTTGT
14351 TAATTTGAGGGTTTTCTTAAAAATGATAACCGAAACCGAAATTTAGGATTTTTCAATTGGGAATT
1 TAATTTGAGGGTTTTCTTAAAAATGATAACCGAAACCGAAATTTAGGATTTTTCAATTGGGAATT
14416 TTGTGAATTTTGT
66 TTGTGAATTTTGT
14429 T
1 T
14430 TCCAATTGGA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (78 bp):
TAATTTGAGGGTTTTCTTAAAAATGATAACCGAAACCGAAATTTAGGATTTTTCAATTGGGAATT
TTGTGAATTTTGT
Found at i:17303 original size:15 final size:15
Alignment explanation
Indices: 17283--17315 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
17273 GTAGAGTTTT
17283 GGAGGATATTGAAGA
1 GGAGGATATTGAAGA
*
17298 GGAGGATATTGAGGA
1 GGAGGATATTGAAGA
17313 GGA
1 GGA
17316 TTGGTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.45, T:0.18
Consensus pattern (15 bp):
GGAGGATATTGAAGA
Found at i:21970 original size:15 final size:16
Alignment explanation
Indices: 21950--22012 Score: 76
Period size: 15 Copynumber: 4.0 Consensus size: 16
21940 GTGAATTCTT
*
21950 TTTCC-TTCGTTCCTA
1 TTTCCTTTCCTTCCTA
*
21965 TTTCCTTTCCCTTGCTA
1 TTTCCTTT-CCTTCCTA
*
21982 TTTCCTTTCCTTTCTA
1 TTTCCTTTCCTTCCTA
21998 TTT-CTTTCCTTCCTA
1 TTTCCTTTCCTTCCTA
22013 CCAAACAAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
15 16 0.38
16 12 0.29
17 14 0.33
ACGTcount: A:0.06, C:0.33, G:0.03, T:0.57
Consensus pattern (16 bp):
TTTCCTTTCCTTCCTA
Found at i:21984 original size:17 final size:17
Alignment explanation
Indices: 21962--22006 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 17
21952 TCCTTCGTTC
21962 CTATTTCCTTTCCCTTG
1 CTATTTCCTTTCCCTTG
*
21979 CTATTTCCTTT-CCTTT
1 CTATTTCCTTTCCCTTG
21995 CTATTT-CTTTCC
1 CTATTTCCTTTCC
22007 TTCCTACCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 4 0.15
16 11 0.42
17 11 0.42
ACGTcount: A:0.07, C:0.33, G:0.02, T:0.58
Consensus pattern (17 bp):
CTATTTCCTTTCCCTTG
Found at i:21998 original size:16 final size:16
Alignment explanation
Indices: 21962--22008 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 16
21952 TCCTTCGTTC
21962 CTATTTCCTTTCCCTTG
1 CTATTTCCTTT-CCTTG
*
21979 CTATTTCCTTTCCTTT
1 CTATTTCCTTTCCTTG
21995 CTATTT-CTTTCCTT
1 CTATTTCCTTTCCTT
22009 CCTACCAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.28
16 10 0.34
17 11 0.38
ACGTcount: A:0.06, C:0.32, G:0.02, T:0.60
Consensus pattern (16 bp):
CTATTTCCTTTCCTTG
Found at i:29994 original size:19 final size:19
Alignment explanation
Indices: 29970--30011 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
29960 GCACACGTGG
29970 CACACGAGTTGCCGCATGT
1 CACACGAGTTGCCGCATGT
29989 CACACGAGTTGCCGCATGT
1 CACACGAGTTGCCGCATGT
30008 CACA
1 CACA
30012 GAAGAAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.19
Consensus pattern (19 bp):
CACACGAGTTGCCGCATGT
Found at i:32599 original size:35 final size:35
Alignment explanation
Indices: 32568--32635 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
32558 CCCTTGTTCC
*
32568 TTTTTTTTCTTTT-C-A-AAAAGCATAATTCTTGT
1 TTTTTTTTTTTTTGCTACAAAAGCATAATTCTTGT
32600 TTTTTTTTTTTTTGCTACAAAAGCATAATTCTTGT
1 TTTTTTTTTTTTTGCTACAAAAGCATAATTCTTGT
32635 T
1 T
32636 GAATCTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 12 0.38
33 1 0.03
34 1 0.03
35 18 0.56
ACGTcount: A:0.24, C:0.12, G:0.07, T:0.57
Consensus pattern (35 bp):
TTTTTTTTTTTTTGCTACAAAAGCATAATTCTTGT
Done.