Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009969.1 Corchorus capsularis cultivar CVL-1 contig09990, 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: 43750
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:445 original size:23 final size:23
Alignment explanation
Indices: 415--461 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
405 TGCTCTGTAC
415 ACTCTTGTAAGTAGAGGGACTAA
1 ACTCTTGTAAGTAGAGGGACTAA
438 ACTCTTGTAAGTAGAGGGACTAA
1 ACTCTTGTAAGTAGAGGGACTAA
461 A
1 A
462 ATGGAGCGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.26
Consensus pattern (23 bp):
ACTCTTGTAAGTAGAGGGACTAA
Found at i:3674 original size:28 final size:28
Alignment explanation
Indices: 3634--3689 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
3624 AATTTAAAGT
3634 TAATTTGTTCCATTAGTTATGCATGAAA
1 TAATTTGTTCCATTAGTTATGCATGAAA
3662 TAATTTGTTCCATTAGTTATGCATGAAA
1 TAATTTGTTCCATTAGTTATGCATGAAA
3690 ATAGAACTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (28 bp):
TAATTTGTTCCATTAGTTATGCATGAAA
Found at i:7163 original size:47 final size:47
Alignment explanation
Indices: 7109--7202 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
7099 GCAATAGTAG
7109 ATCCATGCCGGAGATCCCATTACTGTGTAACGCATGCCGAAGAATAC
1 ATCCATGCCGGAGATCCCATTACTGTGTAACGCATGCCGAAGAATAC
7156 ATCCATGCCGGAGATCCCATTACTGTGTAACGCATGCCGAAGAATAC
1 ATCCATGCCGGAGATCCCATTACTGTGTAACGCATGCCGAAGAATAC
7203 GTAGATAGTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (47 bp):
ATCCATGCCGGAGATCCCATTACTGTGTAACGCATGCCGAAGAATAC
Found at i:12527 original size:29 final size:29
Alignment explanation
Indices: 12485--12558 Score: 114
Period size: 29 Copynumber: 2.6 Consensus size: 29
12475 TCCAAAAATT
*
12485 ATAAACTCAGGAGTTTTTTTTTTT-TGGCA
1 ATAAACTCAGGAGTTTTTTTTTTTAT-GAA
12514 ATAAACTCAGGAGTTTTTTTTTTTATGAA
1 ATAAACTCAGGAGTTTTTTTTTTTATGAA
*
12543 ATAAACTCAGAAGTTT
1 ATAAACTCAGGAGTTT
12559 AATAGAATGT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
29 41 0.98
30 1 0.02
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (29 bp):
ATAAACTCAGGAGTTTTTTTTTTTATGAA
Found at i:21717 original size:2 final size:2
Alignment explanation
Indices: 21710--21739 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21700 GTCAAATGTG
21710 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21740 TCTTTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24932 original size:29 final size:30
Alignment explanation
Indices: 24878--24939 Score: 81
Period size: 33 Copynumber: 2.0 Consensus size: 30
24868 TTATTTATTT
24878 ATGGGACTATATATATGGCCTTTCAAAAAAAAA
1 ATGGGACTATATATATGG-C--TCAAAAAAAAA
*
24911 ATGGGACTATATATATGG-TCAAGAAAAAA
1 ATGGGACTATATATATGGCTCAAAAAAAAA
24940 TTGCTGCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 10 0.36
33 18 0.64
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.26
Consensus pattern (30 bp):
ATGGGACTATATATATGGCTCAAAAAAAAA
Found at i:30573 original size:30 final size:28
Alignment explanation
Indices: 30499--30582 Score: 91
Period size: 30 Copynumber: 2.9 Consensus size: 28
30489 TATAACGCCA
*
30499 AGGACAATTTGCCCTGAGC-TTCAAATC
1 AGGACAATTTGCCCTGAACTTTCAAATC
* *
30526 -GCGACAACTTGCTCCTGAATTTTCAAATTC
1 AG-GACAATTTGC-CCTGAACTTTCAAA-TC
30556 AGGACAATTTGTCCCTGAACTTTCAAA
1 AGGACAATTTG-CCCTGAACTTTCAAA
30583 ATTAAAACAA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
26 1 0.02
27 9 0.20
28 5 0.11
29 6 0.13
30 23 0.50
31 2 0.04
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (28 bp):
AGGACAATTTGCCCTGAACTTTCAAATC
Found at i:40176 original size:19 final size:19
Alignment explanation
Indices: 40117--40181 Score: 60
Period size: 21 Copynumber: 3.2 Consensus size: 19
40107 AAGAGAGGGA
40117 AAGAAGAAAGAGAGAAAAGAG
1 AAGAA-AAAGAGA-AAAAGAG
* *
40138 AAGAAAAAAACGAAGTAAGAG
1 AAGAAAAAGA-GAA-AAAGAG
40159 AA-AAAAAGAGATAAAAGAG
1 AAGAAAAAGAGA-AAAAGAG
40178 AAGA
1 AAGA
40182 GCGCAATAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
19 9 0.25
20 13 0.36
21 14 0.39
ACGTcount: A:0.69, C:0.02, G:0.26, T:0.03
Consensus pattern (19 bp):
AAGAAAAAGAGAAAAAGAG
Done.