Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006957.1 Corchorus capsularis cultivar CVL-1 contig06978, 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: 23912
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5760 original size:18 final size:18
Alignment explanation
Indices: 5737--5775 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
5727 ATTGGTCCCT
5737 CAAGTGATGCGACTATAG
1 CAAGTGATGCGACTATAG
5755 CAAGTGATGCGACTATAG
1 CAAGTGATGCGACTATAG
5773 CAA
1 CAA
5776 ATTGGTCCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.21
Consensus pattern (18 bp):
CAAGTGATGCGACTATAG
Found at i:6149 original size:24 final size:24
Alignment explanation
Indices: 6121--6166 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
6111 AAAAAAATCA
* *
6121 ATTTTTCTGTTTTTTTTAAGAACC
1 ATTTTTCTCTTTTTTTAAAGAACC
*
6145 ATTTTTTTCTTTTTTTAAAGAA
1 ATTTTTCTCTTTTTTTAAAGAA
6167 GAAAATGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.07, T:0.61
Consensus pattern (24 bp):
ATTTTTCTCTTTTTTTAAAGAACC
Found at i:6196 original size:21 final size:21
Alignment explanation
Indices: 6154--6191 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6144 CATTTTTTTC
6154 TTTTTTTAAAGAAGAAAATGA
1 TTTTTTTAAAGAAGAAAATGA
6175 TTTTTTTAAA-AA-AAAAT
1 TTTTTTTAAAGAAGAAAAT
6192 TTGATACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (21 bp):
TTTTTTTAAAGAAGAAAATGA
Found at i:11261 original size:23 final size:22
Alignment explanation
Indices: 11211--11263 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
11201 TTATTAAAAC
11211 ATTATATAATTAAATAATATAT
1 ATTATATAATTAAATAATATAT
*
11233 AATATAGTAA-TAAACTAATA-ATT
1 ATTATA-TAATTAAA-TAATATA-T
11256 ATTATATA
1 ATTATATA
11264 CTGTTATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 12 0.46
23 14 0.54
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
ATTATATAATTAAATAATATAT
Found at i:11948 original size:19 final size:19
Alignment explanation
Indices: 11921--11972 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
11911 AAATCTATTA
11921 CTTTATTTTTCTT-TTTTCT
1 CTTTA-TTTTCTTATTTTCT
*
11940 CTTTCTTTTCTTATTTTCTT
1 CTTTATTTTCTTATTTTC-T
11960 CCTCTTATTTTCT
1 -CT-TTATTTTCT
11973 GTTTCCTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 7 0.26
19 9 0.33
20 1 0.04
21 2 0.07
22 8 0.30
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.73
Consensus pattern (19 bp):
CTTTATTTTCTTATTTTCT
Found at i:13171 original size:18 final size:19
Alignment explanation
Indices: 13148--13189 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
13138 TATTAAATTT
13148 ATAAAATATTAAAA-AATA
1 ATAAAATATTAAAATAATA
13166 ATAAAATATTAAAATAATA
1 ATAAAATATTAAAATAATA
13185 A-AAAA
1 ATAAAA
13190 AGCCATATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (19 bp):
ATAAAATATTAAAATAATA
Found at i:13179 original size:16 final size:16
Alignment explanation
Indices: 13138--13187 Score: 64
Period size: 16 Copynumber: 3.0 Consensus size: 16
13128 GGAATGAAAT
* *
13138 TATTAAATTTATAAAA
1 TATTAAAATAATAAAA
13154 TATTAAAAAATAATAAAA
1 TATT--AAAATAATAAAA
13172 TATTAAAATAATAAAA
1 TATTAAAATAATAAAA
13188 AAAGCCATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 16 0.53
18 14 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TATTAAAATAATAAAA
Found at i:14789 original size:15 final size:16
Alignment explanation
Indices: 14759--14793 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
14749 GCAGGCAGAA
14759 AAAACTAAAAAACAAC
1 AAAACTAAAAAACAAC
*
14775 AAAAC-AAATAACAAC
1 AAAACTAAAAAACAAC
14790 AAAA
1 AAAA
14794 ACCAAACCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.77, C:0.17, G:0.00, T:0.06
Consensus pattern (16 bp):
AAAACTAAAAAACAAC
Found at i:14794 original size:16 final size:17
Alignment explanation
Indices: 14758--14795 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
14748 CGCAGGCAGA
14758 AAAAACTAAAAAACAAC
1 AAAAACTAAAAAACAAC
*
14775 -AAAAC-AAATAACAAC
1 AAAAACTAAAAAACAAC
14790 AAAAAC
1 AAAAAC
14796 CAAACCATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.76, C:0.18, G:0.00, T:0.05
Consensus pattern (17 bp):
AAAAACTAAAAAACAAC
Found at i:16942 original size:1 final size:1
Alignment explanation
Indices: 16899--16923 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
16889 AGGGGGAAGG
16899 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
16924 CATTTTGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:17306 original size:33 final size:33
Alignment explanation
Indices: 17264--17346 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 33
17254 CCGGTGTTGG
* *
17264 CCGGCCAACACCGGCCACGTGAC-TCGGAGATGC
1 CCGGCCAACACCGGCCACGCGACAT-GGACATGC
*
17297 CCGGCCAACACCGGCCACGCGACATGGACATGT
1 CCGGCCAACACCGGCCACGCGACATGGACATGC
17330 CCGGCC-ACAACCGGCCA
1 CCGGCCAAC-ACCGGCCA
17347 TCGCTAAGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
32 2 0.04
33 42 0.93
34 1 0.02
ACGTcount: A:0.23, C:0.42, G:0.28, T:0.07
Consensus pattern (33 bp):
CCGGCCAACACCGGCCACGCGACATGGACATGC
Found at i:23839 original size:33 final size:33
Alignment explanation
Indices: 23799--23905 Score: 126
Period size: 33 Copynumber: 3.2 Consensus size: 33
23789 AGCACTCGTG
* *
23799 ACCGGCCATGCGACTTGGAGAAGTCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
* * * *
23832 ACTGGCCACGTGACTCGGAGATGCCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
* *
23865 ACCGGCCACGCGACATGGACATGTCCGGCC-AC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
23897 AACCGGCCA
1 -ACCGGCCA
23906 TCGCTAG
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
32 2 0.03
33 59 0.97
ACGTcount: A:0.23, C:0.37, G:0.29, T:0.10
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
Done.