Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014360.1 Corchorus capsularis cultivar CVL-1 contig14381, 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: 43261
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:6187 original size:50 final size:50
Alignment explanation
Indices: 6099--6209 Score: 134
Period size: 50 Copynumber: 2.2 Consensus size: 50
6089 AGGAAAGTTC
* * * *
6099 TAGTTAAAGTTGGTATTTTTGTTTTGAGAAAACTGAAAAGTTTATTTTTT
1 TAGTTAAAGTTGGAATCTTTGTTTTGAGAAAACAGAAAAGTTTATATTTT
* * *
6149 TGGTTAAAGTTGGAATCTTTGTTTTGATATAAA-AGAAAAGTTTGTATTTT
1 TAGTTAAAGTTGGAATCTTTGTTTTGAGA-AAACAGAAAAGTTTATATTTT
*
6199 TAATTAAAGTT
1 TAGTTAAAGTT
6210 AGTTTTTTTT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
50 48 0.94
51 3 0.06
ACGTcount: A:0.32, C:0.02, G:0.18, T:0.48
Consensus pattern (50 bp):
TAGTTAAAGTTGGAATCTTTGTTTTGAGAAAACAGAAAAGTTTATATTTT
Found at i:10999 original size:21 final size:21
Alignment explanation
Indices: 10975--11044 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
10965 AGTCCCTAGC
10975 AAACTAATGTTAATCCTAAGA
1 AAACTAATGTTAATCCTAAGA
* * * *
10996 AAACAAAAAAGGTTAGTCCCT-AGC
1 AAAC---TAATGTTAAT-CCTAAGA
11020 AAACTAATGTTAATCCTAAGA
1 AAACTAATGTTAATCCTAAGA
11041 AAAC
1 AAAC
11045 AAAAAAGGTT
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
20 3 0.08
21 17 0.47
24 13 0.36
25 3 0.08
ACGTcount: A:0.49, C:0.17, G:0.11, T:0.23
Consensus pattern (21 bp):
AAACTAATGTTAATCCTAAGA
Found at i:11010 original size:24 final size:24
Alignment explanation
Indices: 10983--11055 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
10973 GCAAACTAAT
10983 GTTAATCCTAAGAAAACAAAAAAG
1 GTTAATCCTAAGAAAACAAAAAAG
* * * *
11007 GTTAGTCCCT-AGCAAAC---TAAT
1 GTTAAT-CCTAAGAAAACAAAAAAG
11028 GTTAATCCTAAGAAAACAAAAAAG
1 GTTAATCCTAAGAAAACAAAAAAG
11052 GTTA
1 GTTA
11056 GTGACTAAAC
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
20 3 0.08
21 13 0.36
24 17 0.47
25 3 0.08
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.22
Consensus pattern (24 bp):
GTTAATCCTAAGAAAACAAAAAAG
Found at i:11028 original size:45 final size:45
Alignment explanation
Indices: 10964--11057 Score: 188
Period size: 45 Copynumber: 2.1 Consensus size: 45
10954 TAAGCTTTGC
10964 TAGTCCCTAGCAAACTAATGTTAATCCTAAGAAAACAAAAAAGGT
1 TAGTCCCTAGCAAACTAATGTTAATCCTAAGAAAACAAAAAAGGT
11009 TAGTCCCTAGCAAACTAATGTTAATCCTAAGAAAACAAAAAAGGT
1 TAGTCCCTAGCAAACTAATGTTAATCCTAAGAAAACAAAAAAGGT
11054 TAGT
1 TAGT
11058 GACTAAACTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (45 bp):
TAGTCCCTAGCAAACTAATGTTAATCCTAAGAAAACAAAAAAGGT
Found at i:15015 original size:15 final size:15
Alignment explanation
Indices: 14976--15019 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
14966 ATTTAGCACT
*
14976 AAAACGAAAAATAAA
1 AAAACGAAAAAGAAA
**
14991 AAAAATAAAAAGAAA
1 AAAACGAAAAAGAAA
*
15006 ATAACGAAAAAGAA
1 AAAACGAAAAAGAA
15020 GAAGATAAGG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.80, C:0.05, G:0.09, T:0.07
Consensus pattern (15 bp):
AAAACGAAAAAGAAA
Found at i:18189 original size:104 final size:104
Alignment explanation
Indices: 18055--18258 Score: 408
Period size: 104 Copynumber: 2.0 Consensus size: 104
18045 TTTCGACCCC
18055 GCAGCGAAGCGCAGGTCAAAAAACTAGTATATGTGTATAAAGAAAGAGGGTTAATTGAGATTATA
1 GCAGCGAAGCGCAGGTCAAAAAACTAGTATATGTGTATAAAGAAAGAGGGTTAATTGAGATTATA
18120 TATCTTTTAATGAGACTCATTGGTGTGTCCTTTAAAAAA
66 TATCTTTTAATGAGACTCATTGGTGTGTCCTTTAAAAAA
18159 GCAGCGAAGCGCAGGTCAAAAAACTAGTATATGTGTATAAAGAAAGAGGGTTAATTGAGATTATA
1 GCAGCGAAGCGCAGGTCAAAAAACTAGTATATGTGTATAAAGAAAGAGGGTTAATTGAGATTATA
18224 TATCTTTTAATGAGACTCATTGGTGTGTCCTTTAA
66 TATCTTTTAATGAGACTCATTGGTGTGTCCTTTAA
18259 TTTTTTAACT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 100 1.00
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (104 bp):
GCAGCGAAGCGCAGGTCAAAAAACTAGTATATGTGTATAAAGAAAGAGGGTTAATTGAGATTATA
TATCTTTTAATGAGACTCATTGGTGTGTCCTTTAAAAAA
Found at i:18330 original size:7 final size:7
Alignment explanation
Indices: 18318--18343 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
18308 TATCTGTTTG
18318 CTCTTGC
1 CTCTTGC
18325 CTCTTGC
1 CTCTTGC
18332 CTCTTGC
1 CTCTTGC
18339 CTCTT
1 CTCTT
18344 TGTTCTTGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.42, G:0.12, T:0.46
Consensus pattern (7 bp):
CTCTTGC
Found at i:18350 original size:14 final size:14
Alignment explanation
Indices: 18314--18353 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
18304 TTCATATCTG
18314 TTTGCTCTTGCCTC
1 TTTGCTCTTGCCTC
18328 -TTGCCTCTTGCCTC
1 TTTG-CTCTTGCCTC
*
18342 TTTGTTCTTGCC
1 TTTGCTCTTGCC
18354 ACCAAAGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 3 0.13
14 17 0.74
15 3 0.13
ACGTcount: A:0.00, C:0.35, G:0.15, T:0.50
Consensus pattern (14 bp):
TTTGCTCTTGCCTC
Found at i:19362 original size:31 final size:31
Alignment explanation
Indices: 19327--19388 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
19317 CACAAGAGAA
*
19327 CTCTTGATTCATGAATAATTACAATATTCAT
1 CTCTTGATTCATGAATAATCACAATATTCAT
19358 CTCTTGATTCATGAATAATCACAATATTCAT
1 CTCTTGATTCATGAATAATCACAATATTCAT
19389 TAATGACTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.40
Consensus pattern (31 bp):
CTCTTGATTCATGAATAATCACAATATTCAT
Found at i:29759 original size:20 final size:21
Alignment explanation
Indices: 29734--29781 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
29724 TAAAATTATC
* *
29734 AATTAAAAAGAAAGC-AATTA
1 AATTAAAAACAAAGCAAAGTA
29754 AATTAAAAACAAAGCAAAGTA
1 AATTAAAAACAAAGCAAAGTA
29775 AATTAAA
1 AATTAAA
29782 TCTAAATCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.19
Consensus pattern (21 bp):
AATTAAAAACAAAGCAAAGTA
Found at i:32713 original size:6 final size:6
Alignment explanation
Indices: 32697--32727 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
32687 CTAAGCAAAG
32697 TAAAT- TAAATC TAAATC TAAATC TAAATC TA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TA
32728 TAGCAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATC
Found at i:41054 original size:16 final size:18
Alignment explanation
Indices: 41026--41059 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
41016 ATTTTTTCCA
41026 TCAAATCCATCAA-TTTT
1 TCAAATCCATCAAGTTTT
41043 TCAAAT-CATCAAGTTTT
1 TCAAATCCATCAAGTTTT
41060 GGGAAAGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (18 bp):
TCAAATCCATCAAGTTTT
Done.