Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013708.1 Corchorus capsularis cultivar CVL-1 contig13729, 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: 13439
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:3128 original size:12 final size:13
Alignment explanation
Indices: 3106--3134 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3096 ATAATCCTAT
3106 TTTTTGAATTGGG
1 TTTTTGAATTGGG
3119 TTTTTG-ATTGGG
1 TTTTTGAATTGGG
3131 TTTT
1 TTTT
3135 AATTCTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.10, C:0.00, G:0.28, T:0.62
Consensus pattern (13 bp):
TTTTTGAATTGGG
Found at i:3799 original size:17 final size:17
Alignment explanation
Indices: 3777--3810 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3767 AAAAAGATTT
*
3777 TCAAAAATCCAAAATAA
1 TCAAAAATCAAAAATAA
*
3794 TCAAAATTCAAAAATAA
1 TCAAAAATCAAAAATAA
3811 AAAAAAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.15, G:0.00, T:0.21
Consensus pattern (17 bp):
TCAAAAATCAAAAATAA
Found at i:4558 original size:22 final size:22
Alignment explanation
Indices: 4533--4576 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
4523 ATGTTAAAAG
4533 TTAA-AACTAAAACTAAAAATCC
1 TTAATAACTAAAAC-AAAAATCC
**
4555 TTAATTCCTAAAACAAAAATCC
1 TTAATAACTAAAACAAAAATCC
4577 CTAACACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.55, C:0.20, G:0.00, T:0.25
Consensus pattern (22 bp):
TTAATAACTAAAACAAAAATCC
Found at i:4845 original size:122 final size:122
Alignment explanation
Indices: 4623--4867 Score: 427
Period size: 122 Copynumber: 2.0 Consensus size: 122
4613 AGCTGTCAAG
4623 CTCCACATCCAGCCGCCTCAGCACGTCGTTGTATCGTCGCCGTCAGATCGTCTCCGTCAACCTAC
1 CTCCACATCCAGCCGCCTCAGCACGTCGTTGTATCGTCGCCGTCAGATCGTCTCCGTCAACCTAC
4688 CTTATACTGCTACTATTACTTATTTCTCTTCTTCTACTTCTTCATCACTGGTTAAAA
66 CTTATACTGCTACTATTACTTATTTCTCTTCTTCTACTTCTTCATCACTGGTTAAAA
* * *
4745 CTCCACATCCAGCTGCCTCAGCACGTCGTTGTATCGTTGCCTTCAGATCGTCTCCGTCAACCTAC
1 CTCCACATCCAGCCGCCTCAGCACGTCGTTGTATCGTCGCCGTCAGATCGTCTCCGTCAACCTAC
* * * *
4810 CTTCTGCTGCTACTATTACTTATTTCTCTTTTTCTACTTCTTCTTCACTGGTTAAAA
66 CTTATACTGCTACTATTACTTATTTCTCTTCTTCTACTTCTTCATCACTGGTTAAAA
4867 C
1 C
4868 GGATAGAAAC
Statistics
Matches: 116, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
122 116 1.00
ACGTcount: A:0.18, C:0.33, G:0.12, T:0.36
Consensus pattern (122 bp):
CTCCACATCCAGCCGCCTCAGCACGTCGTTGTATCGTCGCCGTCAGATCGTCTCCGTCAACCTAC
CTTATACTGCTACTATTACTTATTTCTCTTCTTCTACTTCTTCATCACTGGTTAAAA
Found at i:9228 original size:13 final size:13
Alignment explanation
Indices: 9210--9234 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9200 GTTGCTGATA
9210 TGATAATGCCACG
1 TGATAATGCCACG
9223 TGATAATGCCAC
1 TGATAATGCCAC
9235 ATTTCTGGTT
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:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
TGATAATGCCACG
Found at i:9280 original size:32 final size:32
Alignment explanation
Indices: 9244--9374 Score: 172
Period size: 32 Copynumber: 4.1 Consensus size: 32
9234 CATTTCTGGT
* *
9244 TTGGTCCGACGTGGCAATGCGACGTCATTGGC
1 TTGGTCCGACGTAGCAATGCGACGTCATCGGC
* *
9276 TTGGTCCGACGTAGTAATGTGACGTCATCGGC
1 TTGGTCCGACGTAGCAATGCGACGTCATCGGC
* * * *
9308 TTGGTCTGATGTAGCAATGTGACGTTATCGGC
1 TTGGTCCGACGTAGCAATGCGACGTCATCGGC
* *
9340 TTGGTCCGACGTGGCAATGCGATGTCATCGGC
1 TTGGTCCGACGTAGCAATGCGACGTCATCGGC
9372 TTG
1 TTG
9375 ATCTGATGAT
Statistics
Matches: 85, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 85 1.00
ACGTcount: A:0.17, C:0.21, G:0.33, T:0.29
Consensus pattern (32 bp):
TTGGTCCGACGTAGCAATGCGACGTCATCGGC
Found at i:9600 original size:23 final size:23
Alignment explanation
Indices: 9570--9614 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
9560 ACAACTTGGA
9570 GTGGGCAATGATGAATTTCTCAG
1 GTGGGCAATGATGAATTTCTCAG
*
9593 GTGGGCAATGATGACTTTCTCA
1 GTGGGCAATGATGAATTTCTCA
9615 AGAAGGAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (23 bp):
GTGGGCAATGATGAATTTCTCAG
Done.