Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011906.1 Corchorus capsularis cultivar CVL-1 contig11927, 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: 28785
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Found at i:981 original size:11 final size:11
Alignment explanation
Indices: 965--993 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
955 GAATTTGAAG
965 TTATTAATATA
1 TTATTAATATA
976 TTATTAATATA
1 TTATTAATATA
987 -TATTAAT
1 TTATTAAT
994 TGGAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TTATTAATATA
Found at i:5610 original size:26 final size:26
Alignment explanation
Indices: 5574--5626 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
5564 GCATCCCTCG
5574 AAAAAAATATCTCTTACACTCAACTA
1 AAAAAAATATCTCTTACACTCAACTA
*
5600 AAAAAAATATCTCTTACCCTCAACTA
1 AAAAAAATATCTCTTACACTCAACTA
5626 A
1 A
5627 CAATTGCTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (26 bp):
AAAAAAATATCTCTTACACTCAACTA
Found at i:8550 original size:15 final size:16
Alignment explanation
Indices: 8530--8563 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
8520 GTTTTCAAAG
*
8530 ATTATATGTATTAT-A
1 ATTATATGAATTATGA
8545 ATTATATGAATTATGA
1 ATTATATGAATTATGA
8561 ATT
1 ATT
8564 GTTTTATGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (16 bp):
ATTATATGAATTATGA
Found at i:8782 original size:38 final size:38
Alignment explanation
Indices: 8740--8967 Score: 350
Period size: 38 Copynumber: 6.0 Consensus size: 38
8730 GGCTGTGCAT
*
8740 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATGGTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG
* *
8778 AGTGGACCCGTGTCTTAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG
* *
8816 AGTGGACCCGTGCCTCAGGGGGTTAAACTCTTAGTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG
* *
8854 AGTGGACCCATGCCTCAGGGGGTTAAACTGATGGTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG
*
8892 AGTGGAACCGTGCCTCAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG
* * *
8930 AGTGGACCCGTACCTCAGGGGGCT-AACTGTTGGCAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG
8967 A
1 A
8968 TTGTGATTGT
Statistics
Matches: 172, Mismatches: 18, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
37 13 0.08
38 159 0.92
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (38 bp):
AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG
Found at i:8977 original size:6 final size:6
Alignment explanation
Indices: 8966--8990 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
8956 CTGTTGGCAA
8966 GATTGT GATTGT GATTGT GATTGT G
1 GATTGT GATTGT GATTGT GATTGT G
8991 GTGCAACCTG
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:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (6 bp):
GATTGT
Found at i:13724 original size:59 final size:59
Alignment explanation
Indices: 13632--13792 Score: 218
Period size: 60 Copynumber: 2.7 Consensus size: 59
13622 GCCTAATTGC
*
13632 TCAAATAAGGGTCTAACGTTTGTC-AAAATGCTCAAATAAGGGTCCGATC-TTTAATTTGG
1 TCAAATAA-GGTCTAACG-TTATCGAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGG
* * *
13691 TCAAATAAGAGTCTAACGTTATCGAAAATGCTCAAATAAGGATTCGGTCTTTTAATTTGG
1 TCAAATAAG-GTCTAACGTTATCGAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGG
* *
13751 CCAAATAAGGACCTAACGTTATCGAAAATGCTCAAATAAGGG
1 TCAAATAAGG-TCTAACGTTATCGAAAATGCTCAAATAAGGG
13793 CCCGGCGTCA
Statistics
Matches: 91, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
58 5 0.05
59 39 0.43
60 47 0.52
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (59 bp):
TCAAATAAGGTCTAACGTTATCGAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGG
Found at i:13933 original size:60 final size:60
Alignment explanation
Indices: 13834--13996 Score: 211
Period size: 60 Copynumber: 2.7 Consensus size: 60
13824 TTTCGACACA
* * * * *
13834 AGGCCTTTATTTGAACATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGCTC
1 AGGCCCTTATTTGAGCATTTTGGCAAACATTAGACCCTTATTTGGCCAAATTAAAAGATC
* * **
13894 GGGCCCTTATTTGAGCTTTTTGGCAAACATTAGACCCTTATTTGGTTAAATTAAAAGATC
1 AGGCCCTTATTTGAGCATTTTGGCAAACATTAGACCCTTATTTGGCCAAATTAAAAGATC
** *
13954 AACCCCTTATTTGAGCATTTT-GCAAACATTAGTCCCTTATTTG
1 AGGCCCTTATTTGAGCATTTTGGCAAACATTAGACCCTTATTTG
13997 AGCAATTAGG
Statistics
Matches: 89, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
59 21 0.24
60 68 0.76
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.36
Consensus pattern (60 bp):
AGGCCCTTATTTGAGCATTTTGGCAAACATTAGACCCTTATTTGGCCAAATTAAAAGATC
Found at i:15443 original size:132 final size:131
Alignment explanation
Indices: 15315--15567 Score: 389
Period size: 132 Copynumber: 1.9 Consensus size: 131
15305 AAATATTTTT
* * **
15315 AAAATTATAATATATCTAAGTTTTTTAATTAAGTTAGTAAAATGGTAAAAATAAAATAGGTATAA
1 AAAATTATAATATATATAAGTTTTTTAACTAAAATAGTAAAATGGTAAAAATAAAATAGGTATAA
* *
15380 GGATATTAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGCATATTT
66 GGATATTACATTTAATTAAAT-AAAAATAGAGTGTTTAGTTGAGTAAAACTATAAAAGCATATTT
15445 AA
130 AA
* * * *
15447 AAAATTCTATTATATATAAGTTTTTTAACTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAA
1 AAAATTATAATATATATAAGTTTTTTAACTAAAATAGTAAAATGGTAAAAATAAAATAGGTATAA
* *
15512 GGATATTACATTTAATTAAATAAAAATGGAGTGTTTAGTTGAGTAAAATTATAAAA
66 GGATATTACATTTAATTAAATAAAAATAGAGTGTTTAGTTGAGTAAAACTATAAAA
15568 ATTTTAAACT
Statistics
Matches: 109, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
131 32 0.29
132 77 0.71
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.37
Consensus pattern (131 bp):
AAAATTATAATATATATAAGTTTTTTAACTAAAATAGTAAAATGGTAAAAATAAAATAGGTATAA
GGATATTACATTTAATTAAATAAAAATAGAGTGTTTAGTTGAGTAAAACTATAAAAGCATATTTA
A
Found at i:16070 original size:21 final size:21
Alignment explanation
Indices: 16046--16087 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
16036 CTAACAACTT
16046 GATTTGAAAGCCAAAGCAGCA
1 GATTTGAAAGCCAAAGCAGCA
*
16067 GATTTGAAAGCCAAGGCAGCA
1 GATTTGAAAGCCAAAGCAGCA
16088 AATTAGCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.14
Consensus pattern (21 bp):
GATTTGAAAGCCAAAGCAGCA
Found at i:17201 original size:23 final size:25
Alignment explanation
Indices: 17169--17227 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 25
17159 ATTTTGATTA
17169 TTTTAGATTTTTGAAA-AC-C-TTTT
1 TTTTA-ATTTTTGAAAGACTCATTTT
17192 TATTTAA-TTTTGAAAGACTCATTTT
1 T-TTTAATTTTTGAAAGACTCATTTT
17217 TTTTAATTTTT
1 TTTTAATTTTT
17228 ATTTTGGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
22 8 0.26
23 4 0.13
24 10 0.32
25 9 0.29
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.59
Consensus pattern (25 bp):
TTTTAATTTTTGAAAGACTCATTTT
Found at i:22604 original size:31 final size:32
Alignment explanation
Indices: 22569--22631 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
22559 TATATTAAAA
22569 AAATAA-GGATATAAT-GGACGTTTCAAAAGTT
1 AAATAAGGGATATAATAGG-CGTTTCAAAAGTT
*
22600 AAATAAGGGGTATAATAGGCGTTTCAAAAGTT
1 AAATAAGGGATATAATAGGCGTTTCAAAAGTT
22632 TCTCAAAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 6 0.21
32 21 0.72
33 2 0.07
ACGTcount: A:0.43, C:0.06, G:0.22, T:0.29
Consensus pattern (32 bp):
AAATAAGGGATATAATAGGCGTTTCAAAAGTT
Done.