Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012063.1 Corchorus capsularis cultivar CVL-1 contig12084, 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: 34453
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Found at i:4127 original size:10 final size:10
Alignment explanation
Indices: 4112--4136 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4102 GATAAGCCAG
4112 AAAAGTACAA
1 AAAAGTACAA
4122 AAAAGTACAA
1 AAAAGTACAA
4132 AAAAG
1 AAAAG
4137 AACCGTAATT
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:0.72, C:0.08, G:0.12, T:0.08
Consensus pattern (10 bp):
AAAAGTACAA
Found at i:6223 original size:25 final size:25
Alignment explanation
Indices: 6195--6244 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
6185 CAAAAAATGA
* **
6195 CATGATATGAAAGTTAAACCCTAAC
1 CATGACATGAAAGGCAAACCCTAAC
6220 CATGACATGAAAGGCAAACCCTAAC
1 CATGACATGAAAGGCAAACCCTAAC
6245 ATGTCATCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.44, C:0.24, G:0.14, T:0.18
Consensus pattern (25 bp):
CATGACATGAAAGGCAAACCCTAAC
Found at i:6257 original size:25 final size:25
Alignment explanation
Indices: 6210--6257 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
6200 TATGAAAGTT
*
6210 AAACCCTAACCATGACATGAAAGGC
1 AAACCCTAACCATGACATCAAAGGC
*
6235 AAACCCTAA-CATGTCATCCAAAG
1 AAACCCTAACCATGACAT-CAAAG
6258 TGAAAGGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.44, C:0.29, G:0.12, T:0.15
Consensus pattern (25 bp):
AAACCCTAACCATGACATCAAAGGC
Found at i:6320 original size:31 final size:32
Alignment explanation
Indices: 6274--6335 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
6264 GTAAAAAAGA
* * *
6274 ATTGGAATGCCCAAATTATCCTTAAGTCTTAT
1 ATTGGAATGACCAAATTACCCTTAAGACTTAT
6306 ATTGG-ATGACCAAATTACCCTTAAGACTTA
1 ATTGGAATGACCAAATTACCCTTAAGACTTA
6336 CATGAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (32 bp):
ATTGGAATGACCAAATTACCCTTAAGACTTAT
Found at i:15261 original size:2 final size:2
Alignment explanation
Indices: 15254--15279 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15244 CACTGAACTT
15254 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
15280 ATAATTTGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18707 original size:14 final size:14
Alignment explanation
Indices: 18690--18720 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
18680 AACAAATTGG
18690 AGAAAAAATGAAAA
1 AGAAAAAATGAAAA
*
18704 AGAAAAAATGAGAA
1 AGAAAAAATGAAAA
18718 AGA
1 AGA
18721 GGAATATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.06
Consensus pattern (14 bp):
AGAAAAAATGAAAA
Found at i:22677 original size:6 final size:6
Alignment explanation
Indices: 22666--22690 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
22656 GTCTGGCAGC
22666 GGCGGT GGCGGT GGCGGT GGCGGT G
1 GGCGGT GGCGGT GGCGGT GGCGGT G
22691 TTCGTCAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.68, T:0.16
Consensus pattern (6 bp):
GGCGGT
Found at i:23583 original size:13 final size:13
Alignment explanation
Indices: 23545--23584 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
23535 TCTCCAGATA
* *
23545 ATCTTCAGTTGAA
1 ATCTTCTGTTGAT
*
23558 ATCTTCTGATGAT
1 ATCTTCTGTTGAT
23571 ATCTTCTGTTGAT
1 ATCTTCTGTTGAT
23584 A
1 A
23585 ATATTCTCTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (13 bp):
ATCTTCTGTTGAT
Found at i:26364 original size:200 final size:200
Alignment explanation
Indices: 26015--26397 Score: 730
Period size: 200 Copynumber: 1.9 Consensus size: 200
26005 AATAATGGGA
* *
26015 GTAAAGTCTCAAAATAATCCGCGAATCTTGCGGTAAATAAATCACTCGTCAATGGTTCAAATAAC
1 GTAAAATCTCAAAATAATCCGCGAATCTTGCAGTAAATAAATCACTCGTCAATGGTTCAAATAAC
26080 CTAATAATGGACGGTGAATCAAGCCCAACATAAATGCCCATATGTCGTTGGGGACCCATTTTAAT
66 CTAATAATGGACGGTGAATCAAGCCCAACATAAATGCCCATATGTCGTTGGGGACCCATTTTAAT
**
26145 CATTTGCGGTGGTGCTACAGGTACTTGAACAACGCAAACAAGAGTGCAAACATAATCCGCGAATC
131 CATTTGCGGTGGTGCTACAGACACTTGAACAACGCAAACAAGAGTGCAAACATAATCCGCGAATC
26210 TTGCG
196 TTGCG
26215 GTAAAATCTCAAAATAATCCGCGAATCTTGCAGTAAATAAATCACTCGTCAATGGTTCAAATAAC
1 GTAAAATCTCAAAATAATCCGCGAATCTTGCAGTAAATAAATCACTCGTCAATGGTTCAAATAAC
26280 CTAATAATGGACGGTGAATCAAGCCCAACATAAATGCCCATATGTCGTTGGGGACCCATTTTAAT
66 CTAATAATGGACGGTGAATCAAGCCCAACATAAATGCCCATATGTCGTTGGGGACCCATTTTAAT
26345 CATTTGCGGTGGTGCTACAGACACTTGAACAACGCAAACAAGAGTGCAAACAT
131 CATTTGCGGTGGTGCTACAGACACTTGAACAACGCAAACAAGAGTGCAAACAT
26398 GTGAAATGTC
Statistics
Matches: 179, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
200 179 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.24
Consensus pattern (200 bp):
GTAAAATCTCAAAATAATCCGCGAATCTTGCAGTAAATAAATCACTCGTCAATGGTTCAAATAAC
CTAATAATGGACGGTGAATCAAGCCCAACATAAATGCCCATATGTCGTTGGGGACCCATTTTAAT
CATTTGCGGTGGTGCTACAGACACTTGAACAACGCAAACAAGAGTGCAAACATAATCCGCGAATC
TTGCG
Found at i:28401 original size:42 final size:41
Alignment explanation
Indices: 28277--28416 Score: 194
Period size: 41 Copynumber: 3.4 Consensus size: 41
28267 AATTTCTGGT
* ***
28277 GTGTCAACA-GTAATTATAATTTACTGGAGTAAC-ACTTCTG
1 GTGTCAA-AGGTAATTTTAATTTACCAAAGTAACAACTTCTG
28317 GTGTCAAAGGTAATTTTAATTTACCAAAGTAACAACTTCTG
1 GTGTCAAAGGTAATTTTAATTTACCAAAGTAACAACTTCTG
* *
28358 GTGTCAAAGATAATTTTAATTTACCAAAAGTGACAACTTCTG
1 GTGTCAAAGGTAATTTTAATTTACC-AAAGTAACAACTTCTG
28400 GTGTCAAAGGTAATTTT
1 GTGTCAAAGGTAATTTT
28417 CAATATTATA
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
39 1 0.01
40 27 0.30
41 31 0.34
42 31 0.34
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (41 bp):
GTGTCAAAGGTAATTTTAATTTACCAAAGTAACAACTTCTG
Found at i:30350 original size:20 final size:20
Alignment explanation
Indices: 30327--30365 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
30317 AACGAATTTC
30327 ACAAGAAACCC-AAGCAAATA
1 ACAA-AAACCCAAAGCAAATA
*
30347 ACAACAACCCAAAGCAAAT
1 ACAAAAACCCAAAGCAAAT
30366 GAAAGAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.59, C:0.28, G:0.08, T:0.05
Consensus pattern (20 bp):
ACAAAAACCCAAAGCAAATA
Found at i:30627 original size:16 final size:18
Alignment explanation
Indices: 30596--30633 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
30586 TGGAGAGAAA
30596 AAAAAAGAAAAGAAAT-G
1 AAAAAAGAAAAGAAATGG
*
30613 AAAAAAGAATA-AAATGG
1 AAAAAAGAAAAGAAATGG
30630 AAAA
1 AAAA
30634 GTCAGTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (18 bp):
AAAAAAGAAAAGAAATGG
Found at i:31541 original size:15 final size:16
Alignment explanation
Indices: 31515--31544 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
31505 AGATAACAAT
31515 ATAAACAACTTAAGAA
1 ATAAACAACTTAAGAA
31531 ATAAA-AACTTAAGA
1 ATAAACAACTTAAGA
31545 TTGGAAGATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.63, C:0.10, G:0.07, T:0.20
Consensus pattern (16 bp):
ATAAACAACTTAAGAA
Done.