Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015126.1 Corchorus capsularis cultivar CVL-1 contig15147, 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: 19516
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Found at i:7393 original size:15 final size:15
Alignment explanation
Indices: 7373--7405 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
7363 GGGAGAGATC
7373 TTTCGAGTCAG-GGTT
1 TTTCGAG-CAGAGGTT
7388 TTTCGAGCAGAGGTT
1 TTTCGAGCAGAGGTT
7403 TTT
1 TTT
7406 GGGGTTTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.15, C:0.12, G:0.30, T:0.42
Consensus pattern (15 bp):
TTTCGAGCAGAGGTT
Found at i:8213 original size:14 final size:14
Alignment explanation
Indices: 8194--8221 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
8184 CTATCATCAA
8194 ATTTAGTAATTTAG
1 ATTTAGTAATTTAG
8208 ATTTAGTAATTTAG
1 ATTTAGTAATTTAG
8222 TTAGCTTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (14 bp):
ATTTAGTAATTTAG
Found at i:9063 original size:45 final size:45
Alignment explanation
Indices: 9013--9103 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
9003 AAGTAATTCC
9013 AACAAAAGTTTTTTTTTTTAACAAATCCAAAAGAAGATTTTGGAA
1 AACAAAAGTTTTTTTTTTTAACAAATCCAAAAGAAGATTTTGGAA
9058 AACAAAAGTTTTTTTTTTTAACAAATCCAAAAGAAGATTTTGGAA
1 AACAAAAGTTTTTTTTTTTAACAAATCCAAAAGAAGATTTTGGAA
9103 A
1 A
9104 TTAATAAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (45 bp):
AACAAAAGTTTTTTTTTTTAACAAATCCAAAAGAAGATTTTGGAA
Found at i:10735 original size:16 final size:16
Alignment explanation
Indices: 10714--10748 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
10704 GATCTACCCT
*
10714 TAACAATTATTACGGG
1 TAACAATCATTACGGG
10730 TAACAATCATTACGGG
1 TAACAATCATTACGGG
10746 TAA
1 TAA
10749 TCATTTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (16 bp):
TAACAATCATTACGGG
Found at i:11033 original size:16 final size:16
Alignment explanation
Indices: 11012--11072 Score: 70
Period size: 16 Copynumber: 3.8 Consensus size: 16
11002 ACCCGCCCGA
*
11012 ACCCGAACCCGAAATT
1 ACCCGAACCCGAAAAT
*
11028 ATCCGAACCCGAAAAT
1 ACCCGAACCCGAAAAT
* *
11044 ACCCAAACCCGAGACA-
1 ACCCGAACCCGA-AAAT
11060 ACCCGAACCCGAA
1 ACCCGAACCCGAA
11073 CCCGCCCGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
15 1 0.03
16 35 0.92
17 2 0.05
ACGTcount: A:0.41, C:0.39, G:0.13, T:0.07
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:11068 original size:6 final size:6
Alignment explanation
Indices: 11059--11098 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
11049 AACCCGAGAC
*
11059 AACCCG AACCCG AACCCG --CCCG AACCC- AACCCG AGCCCG A
1 AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG A
11099 GATCAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
4 4 0.13
5 5 0.17
6 21 0.70
ACGTcount: A:0.30, C:0.53, G:0.17, T:0.00
Consensus pattern (6 bp):
AACCCG
Found at i:11080 original size:16 final size:15
Alignment explanation
Indices: 11061--11091 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
11051 CCCGAGACAA
11061 CCCGAACCCGAACCCG
1 CCCGAACCC-AACCCG
11077 CCCGAACCCAACCCG
1 CCCGAACCCAACCCG
11092 AGCCCGAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.26, C:0.58, G:0.16, T:0.00
Consensus pattern (15 bp):
CCCGAACCCAACCCG
Found at i:11864 original size:17 final size:18
Alignment explanation
Indices: 11840--11900 Score: 90
Period size: 17 Copynumber: 3.5 Consensus size: 18
11830 TAACGAAAGT
11840 GAACCCGAACCCG-ACCC
1 GAACCCGAACCCGAACCC
*
11857 GGACCCGAACCCGAACCC
1 GAACCCGAACCCGAACCC
*
11875 GAACCCG-ATCCGAACCC
1 GAACCCGAACCCGAACCC
11892 GAACCCGAA
1 GAACCCGAA
11901 AATACCCGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
17 28 0.72
18 11 0.28
ACGTcount: A:0.31, C:0.48, G:0.20, T:0.02
Consensus pattern (18 bp):
GAACCCGAACCCGAACCC
Found at i:11875 original size:29 final size:29
Alignment explanation
Indices: 11840--11900 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
11830 TAACGAAAGT
*
11840 GAACCCGAACCCGACCCGGACCCGAACCC
1 GAACCCGAACCCGACCCGAACCCGAACCC
*
11869 GAACCCGAACCCGATCCGAACCCGAACCC
1 GAACCCGAACCCGACCCGAACCCGAACCC
11898 GAA
1 GAA
11901 AATACCCGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.48, G:0.20, T:0.02
Consensus pattern (29 bp):
GAACCCGAACCCGACCCGAACCCGAACCC
Found at i:11900 original size:23 final size:24
Alignment explanation
Indices: 11840--11900 Score: 99
Period size: 23 Copynumber: 2.6 Consensus size: 24
11830 TAACGAAAGT
11840 GAACCCGAACCCG-ACCCGGACCC
1 GAACCCGAACCCGAACCCGGACCC
*
11863 GAACCCGAACCCGAACCC-GATCC
1 GAACCCGAACCCGAACCCGGACCC
11886 GAACCCGAACCCGAA
1 GAACCCGAACCCGAA
11901 AATACCCGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
23 32 0.89
24 4 0.11
ACGTcount: A:0.31, C:0.48, G:0.20, T:0.02
Consensus pattern (24 bp):
GAACCCGAACCCGAACCCGGACCC
Found at i:11909 original size:16 final size:16
Alignment explanation
Indices: 11888--11931 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
11878 CCCGATCCGA
11888 ACCCGAACCCGAAAAT
1 ACCCGAACCCGAAAAT
*
11904 ACCCGAACCCG-AAGT
1 ACCCGAACCCGAAAAT
*
11919 ACCCGAGCCCGAA
1 ACCCGAACCCGAA
11932 CCCCCCCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.36, C:0.41, G:0.18, T:0.05
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:11916 original size:6 final size:6
Alignment explanation
Indices: 11840--11900 Score: 90
Period size: 6 Copynumber: 10.5 Consensus size: 6
11830 TAACGAAAGT
* *
11840 GAACCC GAACCC G-ACCC GGACCC GAACCC GAACCC GAACCC G-ATCC
1 GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC
11886 GAACCC GAACCC GAA
1 GAACCC GAACCC GAA
11901 AATACCCGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
5 9 0.18
6 41 0.82
ACGTcount: A:0.31, C:0.48, G:0.20, T:0.02
Consensus pattern (6 bp):
GAACCC
Found at i:12443 original size:23 final size:22
Alignment explanation
Indices: 12408--12450 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
12398 GTCATTTTCT
*
12408 AATTTACTTTTGGCATTTAGTA
1 AATTCACTTTTGGCATTTAGTA
*
12430 AATTCACTCTTTGGCCTTTAG
1 AATTCACT-TTTGGCATTTAG
12451 CATAGCATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.47
Consensus pattern (22 bp):
AATTCACTTTTGGCATTTAGTA
Found at i:12903 original size:24 final size:25
Alignment explanation
Indices: 12858--12904 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
12848 CCTAGTCTAC
* *
12858 AAATCCAAAAACAGGAATTAAAAGA
1 AAATACAAAAACAGGAACTAAAAGA
*
12883 AAATACAAAAA-ATGAACTAAAA
1 AAATACAAAAACAGGAACTAAAA
12905 AGCAAGAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 9 0.47
25 10 0.53
ACGTcount: A:0.68, C:0.11, G:0.09, T:0.13
Consensus pattern (25 bp):
AAATACAAAAACAGGAACTAAAAGA
Found at i:15787 original size:21 final size:21
Alignment explanation
Indices: 15709--15787 Score: 73
Period size: 21 Copynumber: 4.1 Consensus size: 21
15699 AAGTATGAAA
15709 AAGTAATTTGGTAATCAAC-T
1 AAGTAATTTGGTAATCAACTT
*
15729 ---TAATTTGGT--GCAA-TT
1 AAGTAATTTGGTAATCAACTT
* * *
15744 AAGTAAATTGGTAATTAAATT
1 AAGTAATTTGGTAATCAACTT
15765 AAGTAATTTGGTAATCAACTT
1 AAGTAATTTGGTAATCAACTT
15786 AA
1 AA
15788 TTCGCTGTAC
Statistics
Matches: 45, Mismatches: 7, Indels: 13
0.69 0.11 0.20
Matches are distributed among these distances:
15 4 0.09
17 9 0.20
18 8 0.18
20 2 0.04
21 22 0.49
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.38
Consensus pattern (21 bp):
AAGTAATTTGGTAATCAACTT
Found at i:16838 original size:20 final size:21
Alignment explanation
Indices: 16813--16852 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
16803 TATTTTTTTA
16813 AAATATATTTATA-AAAGAAT
1 AAATATATTTATATAAAGAAT
* *
16833 AAATATTTTTTTATAAAGAA
1 AAATATATTTATATAAAGAA
16853 AATTTGTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
AAATATATTTATATAAAGAAT
Done.