Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016169.1 Corchorus capsularis cultivar CVL-1 contig16190, 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: 27166
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1505 original size:52 final size:52
Alignment explanation
Indices: 1424--1531 Score: 191
Period size: 52 Copynumber: 2.1 Consensus size: 52
1414 ATTTGATAAA
* *
1424 GAGATCATAAAGGGCAAAATAGACGGCCAAATAAGGTCAAACATATCTCACC
1 GAGATCATAAAGGACAAAATAGACAGCCAAATAAGGTCAAACATATCTCACC
1476 GAGATCATAAAGGACAAAATAGACAGCCAAATAAGGTCAAACATATCTCACC
1 GAGATCATAAAGGACAAAATAGACAGCCAAATAAGGTCAAACATATCTCACC
1528 -AGAT
1 GAGAT
1532 GACTCCCACT
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
51 4 0.07
52 50 0.93
ACGTcount: A:0.46, C:0.20, G:0.18, T:0.16
Consensus pattern (52 bp):
GAGATCATAAAGGACAAAATAGACAGCCAAATAAGGTCAAACATATCTCACC
Found at i:4199 original size:6 final size:6
Alignment explanation
Indices: 4184--4234 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
4174 GAGCTCTTAG
* * * * *
4184 TATTCT TATTCC TATTCT TATTCC TATTCC CATTTC TATTCC TATTTC
1 TATTCC TATTCC TATTCC TATTCC TATTCC TATTCC TATTCC TATTCC
4232 TAT
1 TAT
4235 CCAAATTATA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.18, C:0.25, G:0.00, T:0.57
Consensus pattern (6 bp):
TATTCC
Found at i:4507 original size:2 final size:2
Alignment explanation
Indices: 4490--4599 Score: 55
Period size: 2 Copynumber: 60.5 Consensus size: 2
4480 TATAAATTAT
* * *
4490 TA TA AA TA TA TA -A TA TA TA TA -A TA -A TA TA AA GA -A T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
4527 AA TA AA TA T- TA TA TA TA T- TA -A TA TA TA TGA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
* * *
4566 TA CA AA T- TA TA TT TA -A T- TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4600 TAATAAAAGG
Statistics
Matches: 82, Mismatches: 13, Indels: 26
0.68 0.11 0.21
Matches are distributed among these distances:
1 12 0.15
2 68 0.83
3 2 0.02
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:10838 original size:31 final size:31
Alignment explanation
Indices: 10793--10873 Score: 76
Period size: 31 Copynumber: 2.5 Consensus size: 31
10783 TTTTTTATCT
* *
10793 TGTTTGTAGGCTCAAATTGATC-ACTTTTTGCAA
1 TGTTT-TA-GCTCAAATTGAGCAAC-TTTTGAAA
*
10826 -GTTTTAGACTCAATTTGAGCAACTTTTGAAA
1 TGTTTTAG-CTCAAATTGAGCAACTTTTGAAA
*
10857 TGTTTAAGCTCAAATTG
1 TGTTTTAGCTCAAATTG
10874 GTGCCTCTCG
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
30 1 0.03
31 27 0.68
32 12 0.30
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (31 bp):
TGTTTTAGCTCAAATTGAGCAACTTTTGAAA
Found at i:13301 original size:14 final size:14
Alignment explanation
Indices: 13269--13300 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
13259 AAGAATGGAG
13269 GAAAAGAAGAAAAA
1 GAAAAGAAGAAAAA
13283 GAAAAG-AGAAAAA
1 GAAAAGAAGAAAAA
13296 GAAAA
1 GAAAA
13301 ATGGCGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
GAAAAGAAGAAAAA
Found at i:13684 original size:20 final size:20
Alignment explanation
Indices: 13659--13700 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
13649 TCCCAAAGAA
13659 CCTAGGCCTATATGAAGGCT
1 CCTAGGCCTATATGAAGGCT
13679 CCTAGGCCTATATGAAGGCT
1 CCTAGGCCTATATGAAGGCT
13699 CC
1 CC
13701 CTCTTCCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (20 bp):
CCTAGGCCTATATGAAGGCT
Found at i:20399 original size:30 final size:31
Alignment explanation
Indices: 20311--20406 Score: 115
Period size: 30 Copynumber: 3.1 Consensus size: 31
20301 AAAGGGTCAA
* *
20311 ATGGCCGGTTGTGCCCGGATGGC-CCATGCG
1 ATGGCCGGTTGTGGCCGGATTGCTCCATGCG
* * *
20341 TTGGCCAGTTGTGGCCGGTTGATGCTCCATGCG
1 ATGGCCGGTTGTGGCCGGAT--TGCTCCATGCG
20374 ATGGCCGGTTGTGGCCGG-TTGCTCCATGCG
1 ATGGCCGGTTGTGGCCGGATTGCTCCATGCG
20404 ATG
1 ATG
20407 TCGCATGCGA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
30 30 0.54
32 3 0.05
33 23 0.41
ACGTcount: A:0.09, C:0.26, G:0.39, T:0.26
Consensus pattern (31 bp):
ATGGCCGGTTGTGGCCGGATTGCTCCATGCG
Done.