Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010987.1 Corchorus capsularis cultivar CVL-1 contig11008, 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: 29625
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:5494 original size:24 final size:24
Alignment explanation
Indices: 5467--5538 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
5457 TTGACTATTT
5467 AGCCGGAATATTAGGAAATACTAA
1 AGCCGGAATATTAGGAAATACTAA
* * **
5491 AGCC-GAA-ATT-TG-ACTA-TTT
1 AGCCGGAATATTAGGAAATACTAA
5510 AGCCGGAATATTAGGAAATACTAA
1 AGCCGGAATATTAGGAAATACTAA
5534 AGCCG
1 AGCCG
5539 AAATTCCACA
Statistics
Matches: 35, Mismatches: 8, Indels: 10
0.66 0.15 0.19
Matches are distributed among these distances:
19 5 0.14
20 6 0.17
21 4 0.11
22 4 0.11
23 6 0.17
24 10 0.29
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (24 bp):
AGCCGGAATATTAGGAAATACTAA
Found at i:5518 original size:43 final size:43
Alignment explanation
Indices: 5457--5543 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
5447 CAAGAAAAAG
5457 TTGACTATTTAGCCGGAATATTAGGAAATACTAAAGCCGAAAT
1 TTGACTATTTAGCCGGAATATTAGGAAATACTAAAGCCGAAAT
5500 TTGACTATTTAGCCGGAATATTAGGAAATACTAAAGCCGAAAT
1 TTGACTATTTAGCCGGAATATTAGGAAATACTAAAGCCGAAAT
5543 T
1 T
5544 CCACATGGCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (43 bp):
TTGACTATTTAGCCGGAATATTAGGAAATACTAAAGCCGAAAT
Found at i:10567 original size:32 final size:32
Alignment explanation
Indices: 10531--10595 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
10521 GGTAATCAAG
10531 TAAAAAGTAATCAAGTGAGCAATTAAATGGAT
1 TAAAAAGTAATCAAGTGAGCAATTAAATGGAT
10563 TAAAAAGTAATCAAGTGAGCAATTAAATGGAT
1 TAAAAAGTAATCAAGTGAGCAATTAAATGGAT
10595 T
1 T
10596 GAGTGAGCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.26
Consensus pattern (32 bp):
TAAAAAGTAATCAAGTGAGCAATTAAATGGAT
Found at i:27176 original size:11 final size:12
Alignment explanation
Indices: 27162--27190 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
27152 TGATATTTTA
27162 TTATTAAAATG-
1 TTATTAAAATGT
27173 TTATTAAAATGT
1 TTATTAAAATGT
27185 TTATTA
1 TTATTA
27191 TTATTGAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TTATTAAAATGT
Found at i:28255 original size:31 final size:31
Alignment explanation
Indices: 28217--28281 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
28207 AACTGAACTA
* *
28217 ACTCAAACATCCAAGATTTAAAGATCTGGAG
1 ACTCAAACATCAAAGATCTAAAGATCTGGAG
28248 ACTCAAACATCAAAGATCTAAAGATCTGGAG
1 ACTCAAACATCAAAGATCTAAAGATCTGGAG
28279 ACT
1 ACT
28282 GAAAACCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (31 bp):
ACTCAAACATCAAAGATCTAAAGATCTGGAG
Found at i:29550 original size:55 final size:55
Alignment explanation
Indices: 29484--29593 Score: 193
Period size: 55 Copynumber: 2.0 Consensus size: 55
29474 CAACCAACAC
*
29484 TAAATGCCCGATGGCTTTAATCCAAGATTCAATGTTCCATTTCTATACTTTTTTT
1 TAAATGCCCGATGGCTTTAATCCAAGATTCAATGTTCCATTTCTACACTTTTTTT
* *
29539 TAAATGCCCGATGGCTTTAATCGAAGATTCAATGTTCCATTTCTACGCTTTTTTT
1 TAAATGCCCGATGGCTTTAATCCAAGATTCAATGTTCCATTTCTACACTTTTTTT
29594 CATCCAAAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.43
Consensus pattern (55 bp):
TAAATGCCCGATGGCTTTAATCCAAGATTCAATGTTCCATTTCTACACTTTTTTT
Done.