Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011299.1 Corchorus capsularis cultivar CVL-1 contig11320, 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: 12632
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:142 original size:21 final size:21
Alignment explanation
Indices: 86--142 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 21
76 AACCAAGTCC
86 ATATATAGGTTTGAATAG-AT
1 ATATATAGGTTTGAATAGAAT
* * *
106 -T-T-TATGATT-AAGAGAAT
1 ATATATAGGTTTGAATAGAAT
123 ATATATAGGTTTGAATAGAA
1 ATATATAGGTTTGAATAGAA
143 ATTTATATGA
Statistics
Matches: 26, Mismatches: 6, Indels: 9
0.63 0.15 0.22
Matches are distributed among these distances:
16 4 0.15
17 7 0.27
18 2 0.08
19 2 0.08
20 5 0.19
21 6 0.23
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (21 bp):
ATATATAGGTTTGAATAGAAT
Found at i:1973 original size:13 final size:13
Alignment explanation
Indices: 1944--1990 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
1934 AATCTAAATC
*
1944 TAAAGCATATT-A
1 TAAAGCAAATTAA
1956 TAAAGCAAATTAA
1 TAAAGCAAATTAA
*
1969 TAAAGCAGATTAA
1 TAAAGCAAATTAA
1982 TAAAGCAAA
1 TAAAGCAAA
1991 CAATAATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
12 10 0.32
13 21 0.68
ACGTcount: A:0.57, C:0.09, G:0.11, T:0.23
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:1995 original size:25 final size:25
Alignment explanation
Indices: 1944--1996 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
1934 AATCTAAATC
* *
1944 TAAAGCATATTATAAAGCAAATTAA
1 TAAAGCAGATTATAAAGCAAATCAA
1969 TAAAGCAGATTAATAAAGCAAA-CAA
1 TAAAGCAGATT-ATAAAGCAAATCAA
1994 TAA
1 TAA
1997 TTATAAAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.58, C:0.09, G:0.09, T:0.23
Consensus pattern (25 bp):
TAAAGCAGATTATAAAGCAAATCAA
Found at i:9022 original size:6 final size:6
Alignment explanation
Indices: 9011--9036 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
9001 AAAGCAAAAC
9011 AAATCT AAATCT AAATCT AAATCT AA
1 AAATCT AAATCT AAATCT AAATCT AA
9037 TGCAGATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATCT
Found at i:11033 original size:94 final size:94
Alignment explanation
Indices: 10926--11103 Score: 293
Period size: 94 Copynumber: 1.9 Consensus size: 94
10916 CCTTATCTAG
* *
10926 TTTTTATTTGTCTTACTATATTGTGTATGGCAAGCCATGGTTTTACATGTCGAAACTTGGGAAAT
1 TTTTTATTTGTCTTACTATATTGTGTATGGCAAGCCATGGTTTTACATGTCCAAACATGGGAAAT
* *
10991 TTCGTGAATGTTGTCCTTACAGATAAGTT
66 TCCATGAATGTTGTCCTTACAGATAAGTT
* *
11020 TTTTTTTTTGTCTTACTATATTGTGTATGGCAAGCCATGGTTTTAGATGTCCAAACATGGGAAAT
1 TTTTTATTTGTCTTACTATATTGTGTATGGCAAGCCATGGTTTTACATGTCCAAACATGGGAAAT
*
11085 TCCATGATTGTTGTCCTTA
66 TCCATGAATGTTGTCCTTA
11104 TTTTTAACTG
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
94 77 1.00
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (94 bp):
TTTTTATTTGTCTTACTATATTGTGTATGGCAAGCCATGGTTTTACATGTCCAAACATGGGAAAT
TCCATGAATGTTGTCCTTACAGATAAGTT
Found at i:11176 original size:21 final size:21
Alignment explanation
Indices: 11150--11193 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
11140 CTCAGGTTTT
11150 TATTTTTCTTACTATAATGTG
1 TATTTTTCTTACTATAATGTG
*
11171 TATTTTTCTTACTATAGTGTG
1 TATTTTTCTTACTATAATGTG
11192 TA
1 TA
11194 CGGTGTCCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.09, G:0.11, T:0.57
Consensus pattern (21 bp):
TATTTTTCTTACTATAATGTG
Found at i:11336 original size:33 final size:33
Alignment explanation
Indices: 11270--11337 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
11260 CTATTGTGCC
**
11270 ATGGTTTTAAATGTAGAAACTTGGGAACTAAAT
1 ATGGTTTTAAATGTAGAAACTTGGGAAAGAAAT
*
11303 ATGGTTTTACATGTAGAAACTTGGGAAAGAAAT
1 ATGGTTTTAAATGTAGAAACTTGGGAAAGAAAT
11336 AT
1 AT
11338 ATTAATACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (33 bp):
ATGGTTTTAAATGTAGAAACTTGGGAAAGAAAT
Found at i:11347 original size:33 final size:33
Alignment explanation
Indices: 11280--11347 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
11270 ATGGTTTTAA
** * *
11280 ATGTAGAAACTTGGGAACTAAATATGGTTTTAC
1 ATGTAGAAACTTGGGAAAGAAATATGATTATAC
11313 ATGTAGAAACTTGGGAAAGAAATAT-ATTAATAC
1 ATGTAGAAACTTGGGAAAGAAATATGATT-ATAC
11346 AT
1 AT
11348 TATTGGCCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 2 0.07
33 28 0.93
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.31
Consensus pattern (33 bp):
ATGTAGAAACTTGGGAAAGAAATATGATTATAC
Done.