Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022011.1 Corchorus olitorius cultivar O-4 contig22044, 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: 22989
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:1591 original size:30 final size:28
Alignment explanation
Indices: 1557--1612 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
1547 TCGGTAATGG
*
1557 AGGATTCAAAATGTACACAAAATAAAAATT
1 AGGATGCAAAATG-A-ACAAAATAAAAATT
* *
1587 AGGATGCAATATGATCAAAATAAAAA
1 AGGATGCAAAATGAACAAAATAAAAA
1613 AAATTAGGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 11 0.48
29 1 0.04
30 11 0.48
ACGTcount: A:0.57, C:0.09, G:0.12, T:0.21
Consensus pattern (28 bp):
AGGATGCAAAATGAACAAAATAAAAATT
Found at i:4622 original size:13 final size:13
Alignment explanation
Indices: 4604--4631 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4594 TCAAAGGGTG
4604 TTTAACACACCTC
1 TTTAACACACCTC
4617 TTTAACACACCTC
1 TTTAACACACCTC
4630 TT
1 TT
4632 GAGATCTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.36, G:0.00, T:0.36
Consensus pattern (13 bp):
TTTAACACACCTC
Found at i:11297 original size:21 final size:20
Alignment explanation
Indices: 11246--11300 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
11236 AAGTTATCCC
* *
11246 TATTTGGTGTAATGATCTCT
1 TATTAGGTGTAATGATATCT
* *
11266 T-TTAAGTGTAATGGTATCAT
1 TATTAGGTGTAATGATATC-T
11286 TATTAGGTGTAATGA
1 TATTAGGTGTAATGA
11301 AAAATTAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 13 0.48
20 3 0.11
21 11 0.41
ACGTcount: A:0.27, C:0.05, G:0.22, T:0.45
Consensus pattern (20 bp):
TATTAGGTGTAATGATATCT
Found at i:14948 original size:302 final size:302
Alignment explanation
Indices: 14402--14989 Score: 1167
Period size: 302 Copynumber: 1.9 Consensus size: 302
14392 TCTATGACTG
14402 AAAGGGCATTGTTTTTCAATGGCGTGGAGCTCTACACGCATATATAATTTCTCCTTCAGGGAGAC
1 AAAGGGCATTGTTTTTCAATGGCGTGGAGCTCTACACGCATATATAATTTCTCCTTCAGGGAGAC
14467 CAAATAAATATCAACCAAATGTTGATTCGTACGACTAGTACGAGCCCTGTGTTCAGTCATTCCAT
66 CAAATAAATATCAACCAAATGTTGATTCGTACGACTAGTACGAGCCCTGTGTTCAGTCATTCCAT
*
14532 AGGCTTCTGGCCATTTAAGATTCATAGAGCATCTTTCATTCTCATGAGAATAATATGTATATGCT
131 AGGCTTCTGGCCATTTAAGATTCATAGAGAATCTTTCATTCTCATGAGAATAATATGTATATGCT
14597 TAAAGCCTCAACAGGGGCATAATAAGTATTGGTTATGGCCTCTATAATGGCCCATAGTAATTATT
196 TAAAGCCTCAACAGGGGCATAATAAGTATTGGTTATGGCCTCTATAATGGCCCATAGTAATTATT
14662 TCCAATATGTTCATGGCCTTTCTTATTATTTCCATAGTAAAC
261 TCCAATATGTTCATGGCCTTTCTTATTATTTCCATAGTAAAC
14704 AAAGGGCATTGTTTTTCAATGGCGTGGAGCTCTACACGCATATATAATTTCTCCTTCAGGGAGAC
1 AAAGGGCATTGTTTTTCAATGGCGTGGAGCTCTACACGCATATATAATTTCTCCTTCAGGGAGAC
14769 CAAATAAATATCAACCAAATGTTGATTCGTACGACTAGTACGAGCCCTGTGTTCAGTCATTCCAT
66 CAAATAAATATCAACCAAATGTTGATTCGTACGACTAGTACGAGCCCTGTGTTCAGTCATTCCAT
14834 AGGCTTCTGGCCATTTAAGATTCATAGAGAATCTTTCATTCTCATGAGAATAATATGTATATGCT
131 AGGCTTCTGGCCATTTAAGATTCATAGAGAATCTTTCATTCTCATGAGAATAATATGTATATGCT
14899 TAAAGCCTCAACAGGGGCATAATAAGTATTGGTTATGGCCTCTATAATGGCCCATAGTAATTATT
196 TAAAGCCTCAACAGGGGCATAATAAGTATTGGTTATGGCCTCTATAATGGCCCATAGTAATTATT
14964 TCCAATATGTTCATGGCCTTTCTTAT
261 TCCAATATGTTCATGGCCTTTCTTAT
14990 AGCTCATGAT
Statistics
Matches: 285, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
302 285 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Consensus pattern (302 bp):
AAAGGGCATTGTTTTTCAATGGCGTGGAGCTCTACACGCATATATAATTTCTCCTTCAGGGAGAC
CAAATAAATATCAACCAAATGTTGATTCGTACGACTAGTACGAGCCCTGTGTTCAGTCATTCCAT
AGGCTTCTGGCCATTTAAGATTCATAGAGAATCTTTCATTCTCATGAGAATAATATGTATATGCT
TAAAGCCTCAACAGGGGCATAATAAGTATTGGTTATGGCCTCTATAATGGCCCATAGTAATTATT
TCCAATATGTTCATGGCCTTTCTTATTATTTCCATAGTAAAC
Found at i:16245 original size:30 final size:30
Alignment explanation
Indices: 16160--16552 Score: 561
Period size: 30 Copynumber: 13.0 Consensus size: 30
16150 TTGGAAATTT
* *
16160 ATCATGACAACTTCTGGTGTCAATTGAATAAA
1 ATCATGACAACTTCTGGTGTCAATTG--CAAG
* * ** * *
16192 ATTATGACATCTTCAAGTATCAATTGCAAC
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* *
16222 ATCATGACAACTTATGGTGTCAATTGCAAC
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
16252 ATCATGACAACTTCTGGTGTCAATTGCAAC
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
16282 ATCATGACAACTTCTGGTGTCAATTGCAAA
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
16312 ATCATGACAACTTCTGGTGTCAATTGCAAA
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
16342 ATCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
16372 ATTATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
16402 ATCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
16432 AGCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* * *
16462 ATTATGACAACTTCTGGTGTCATTTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* *
16492 ACCATGACAACTTCTGGTGTCAATTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* * *
16522 ACCATGACAACTTCTGGTGTCATTTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
16552 A
1 A
16553 AAAAAAATTG
Statistics
Matches: 334, Mismatches: 27, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
30 313 0.94
32 21 0.06
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (30 bp):
ATCATGACAACTTCTGGTGTCAATTGCAAG
Found at i:18633 original size:13 final size:13
Alignment explanation
Indices: 18617--18647 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
18607 ATCCATTTTT
18617 ATTATCTATACTA
1 ATTATCTATACTA
18630 ATTATCTATACTA
1 ATTATCTATACTA
18643 ATTAT
1 ATTAT
18648 AAAGCCAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTATCTATACTA
Found at i:20131 original size:22 final size:20
Alignment explanation
Indices: 20087--20133 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
20077 AAAACTAAAT
* *
20087 TTCAATTCATCTCACAAATA
1 TTCAATTCATCTAACAAACA
20107 TTCAATTCATCTAAAACAAACA
1 TTCAATTCATCT--AACAAACA
20129 TTCAA
1 TTCAA
20134 CAATTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 12 0.52
22 11 0.48
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (20 bp):
TTCAATTCATCTAACAAACA
Done.