Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011336.1 Corchorus capsularis cultivar CVL-1 contig11357, 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: 23348
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:1441 original size:29 final size:30
Alignment explanation
Indices: 1409--1485 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
1399 TCCAAATTGC
*
1409 AAGTTCAGGGGGTAAAATGTCCAAAAT-TA-
1 AAGTTAAGGGGGTAAAATGTCC-AAATCTAG
* * *
1438 AAGTTTAGGGAGCAAAATGTCCAAATCGTAG
1 AAGTTAAGGGGGTAAAATGTCCAAATC-TAG
1469 AAGTTAAGGGGGTAAAA
1 AAGTTAAGGGGGTAAAA
1486 AGGGCATTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 4 0.10
29 19 0.49
30 2 0.05
31 14 0.36
ACGTcount: A:0.42, C:0.09, G:0.27, T:0.22
Consensus pattern (30 bp):
AAGTTAAGGGGGTAAAATGTCCAAATCTAG
Found at i:6264 original size:13 final size:13
Alignment explanation
Indices: 6246--6270 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6236 AGCCAAGTCT
6246 CAGACTTGATTTA
1 CAGACTTGATTTA
6259 CAGACTTGATTT
1 CAGACTTGATTT
6271 GCTTTCATAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (13 bp):
CAGACTTGATTTA
Found at i:8961 original size:44 final size:44
Alignment explanation
Indices: 8882--8986 Score: 126
Period size: 44 Copynumber: 2.4 Consensus size: 44
8872 ATCATAGGAA
*
8882 AGTTA-CAAAATTTCATAGGAAGATTTATTAAAATTTCGTAGCT
1 AGTTATCAAAATTTCATAGGAAGATTTATCAAAATTTCGTAGCT
* * *
8925 AGGTTATCAAAGTTTCATATGG-AG-TTTATCAGAATTTCGTAGGT
1 A-GTTATCAAAATTTCATA-GGAAGATTTATCAAAATTTCGTAGCT
*
8969 AATTATCAAAATTTCATA
1 AGTTATCAAAATTTCATA
8987 AAAATATTCA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
43 16 0.30
44 22 0.42
45 13 0.25
46 2 0.04
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (44 bp):
AGTTATCAAAATTTCATAGGAAGATTTATCAAAATTTCGTAGCT
Found at i:11187 original size:26 final size:27
Alignment explanation
Indices: 11146--11197 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
11136 ACCCGACCGA
11146 CATATATTTTAATATATATA-ATATTT
1 CATATATTTTAATATATATATATATTT
11172 CATATA-TTTAATTATATATATATATT
1 CATATATTTTAA-TATATATATATATT
11198 ATGTTTTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 5 0.21
26 14 0.58
27 5 0.21
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (27 bp):
CATATATTTTAATATATATATATATTT
Found at i:13353 original size:23 final size:23
Alignment explanation
Indices: 13319--13365 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
13309 AACGGCTAAA
*
13319 TGCTCAATTTGGTCCTAAACCTT
1 TGCTCAAATTGGTCCTAAACCTT
*
13342 TGCTCAAATTGGTCTTAAACCTT
1 TGCTCAAATTGGTCCTAAACCTT
13365 T
1 T
13366 CAAAATCTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.40
Consensus pattern (23 bp):
TGCTCAAATTGGTCCTAAACCTT
Found at i:15017 original size:24 final size:24
Alignment explanation
Indices: 14970--15017 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
14960 TTTTAACTAG
* *
14970 CTGAATGATAGCTGAACCTTTCCC
1 CTGAATGATAGCTGAAACTATCCC
14994 CTGAATGATAGCTGAGAAC-ATCCC
1 CTGAATGATAGCTGA-AACTATCCC
15018 GACACTGGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (24 bp):
CTGAATGATAGCTGAAACTATCCC
Found at i:16691 original size:31 final size:31
Alignment explanation
Indices: 16651--16750 Score: 100
Period size: 31 Copynumber: 3.3 Consensus size: 31
16641 AATAGGACTG
* *
16651 AATTAAGCAGATTTCGATAGGTTTAGGACCA
1 AATTGAGCAGATTTCGAAAGGTTTAGGACCA
* * *
16682 ATTTGAGCAG--GTCTAAAGGTTTAGGACCA
1 AATTGAGCAGATTTCGAAAGGTTTAGGACCA
*
16711 AATTGAGC--ATTCCGTCAAAGGTTTAGGACCA
1 AATTGAGCAGATTTCG--AAAGGTTTAGGACCA
16742 AATTGAGCA
1 AATTGAGCA
16751 TATCCTCTTC
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
29 24 0.44
31 31 0.56
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (31 bp):
AATTGAGCAGATTTCGAAAGGTTTAGGACCA
Found at i:16751 original size:31 final size:30
Alignment explanation
Indices: 16669--16751 Score: 116
Period size: 31 Copynumber: 2.8 Consensus size: 30
16659 AGATTTCGAT
* *
16669 AGGTTTAGGACCAATTTGAGCA-GGTCTAA
1 AGGTTTAGGACCAAATTGAGCATCGTCTAA
16698 AGGTTTAGGACCAAATTGAGCATTCCGTC-AA
1 AGGTTTAGGACCAAATTGAGCA-T-CGTCTAA
16729 AGGTTTAGGACCAAATTGAGCAT
1 AGGTTTAGGACCAAATTGAGCAT
16752 ATCCTCTTCA
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
29 21 0.43
30 1 0.02
31 24 0.49
32 3 0.06
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.27
Consensus pattern (30 bp):
AGGTTTAGGACCAAATTGAGCATCGTCTAA
Done.