Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014497.1 Corchorus olitorius cultivar O-4 contig14530, 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: 24012
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Found at i:6 original size:1 final size:1
Alignment explanation
Indices: 1--44 Score: 88
Period size: 1 Copynumber: 44.0 Consensus size: 1
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
45 CCAAGAAGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:4125 original size:48 final size:49
Alignment explanation
Indices: 4069--4164 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 49
4059 TGGTGGCAGT
*
4069 GTGGAGTTGGATGACTCGGCAATATC-ATCGAGGTGGAGCAAAATTGGC
1 GTGGAGTTGGATGACTCGGCAATATCGATCGAGATGGAGCAAAATTGGC
* *
4117 GTGGAGTTGGATGACTCTGCAATATCGATTGAGATGGAGCAAAATTGG
1 GTGGAGTTGGATGACTCGGCAATATCGATCGAGATGGAGCAAAATTGG
4165 TAATCTTTGG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 25 0.57
49 19 0.43
ACGTcount: A:0.28, C:0.12, G:0.34, T:0.25
Consensus pattern (49 bp):
GTGGAGTTGGATGACTCGGCAATATCGATCGAGATGGAGCAAAATTGGC
Found at i:4487 original size:13 final size:13
Alignment explanation
Indices: 4471--4496 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4461 GGCCGTGAAA
4471 TATTTGATTTACT
1 TATTTGATTTACT
4484 TATTTGATTTACT
1 TATTTGATTTACT
4497 GATAAAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (13 bp):
TATTTGATTTACT
Found at i:4540 original size:28 final size:28
Alignment explanation
Indices: 4509--4572 Score: 103
Period size: 27 Copynumber: 2.3 Consensus size: 28
4499 TAAAATGAAG
*
4509 TTTAAATGGGTTTAGTAGAAATAGCTCT
1 TTTAAATGGGGTTAGTAGAAATAGCTCT
4537 TTT-AATGGGGTTAGTAGAAATAGCTCT
1 TTTAAATGGGGTTAGTAGAAATAGCTCT
*
4564 TTTATATGG
1 TTTAAATGG
4573 CCACAAACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 26 0.79
28 7 0.21
ACGTcount: A:0.30, C:0.06, G:0.23, T:0.41
Consensus pattern (28 bp):
TTTAAATGGGGTTAGTAGAAATAGCTCT
Found at i:10563 original size:21 final size:22
Alignment explanation
Indices: 10537--10589 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
10527 AATATAGTAG
10537 TAGCATTTAAAACTTA-TTTGA
1 TAGCATTTAAAACTTATTTTGA
*
10558 TAGCA-TT-AAAGTTATTTTGA
1 TAGCATTTAAAACTTATTTTGA
*
10578 TAACATCTTAAA
1 TAGCAT-TTAAA
10590 CAGTTTTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 6 0.23
20 11 0.42
21 5 0.19
22 2 0.08
23 2 0.08
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (22 bp):
TAGCATTTAAAACTTATTTTGA
Found at i:12607 original size:24 final size:24
Alignment explanation
Indices: 12575--12623 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
12565 ACATTTTGCT
12575 TATTCCAGCAAATATAAGACTTGG
1 TATTCCAGCAAATATAAGACTTGG
12599 TATTCCAGCAAATATAAGACTTGG
1 TATTCCAGCAAATATAAGACTTGG
12623 T
1 T
12624 CAACAATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (24 bp):
TATTCCAGCAAATATAAGACTTGG
Found at i:16752 original size:33 final size:33
Alignment explanation
Indices: 16710--16776 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
16700 TTAATTTGTT
16710 GTTATTTGCCTCACAGGCAGTGCAGGTTCAAAG
1 GTTATTTGCCTCACAGGCAGTGCAGGTTCAAAG
* *
16743 GTTATTTGCCTCATAGGCAGTGCATGTTCAAAG
1 GTTATTTGCCTCACAGGCAGTGCAGGTTCAAAG
16776 G
1 G
16777 GAAGCTGATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (33 bp):
GTTATTTGCCTCACAGGCAGTGCAGGTTCAAAG
Found at i:19416 original size:27 final size:27
Alignment explanation
Indices: 19378--19433 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
19368 GGCTCCTTTT
19378 GGTAGGTAGGAAAGAATGTGATAATAA
1 GGTAGGTAGGAAAGAATGTGATAATAA
19405 GGTAGGTAGGAAAGAATGTGATAATAA
1 GGTAGGTAGGAAAGAATGTGATAATAA
19432 GG
1 GG
19434 AAAGAATAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.36, T:0.21
Consensus pattern (27 bp):
GGTAGGTAGGAAAGAATGTGATAATAA
Done.