Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013778.1 Corchorus capsularis cultivar CVL-1 contig13799, 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: 20700
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:38 original size:17 final size:17
Alignment explanation
Indices: 12--48 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
2 TAGTTTATGG
12 TAGTTTTTTTTAAATAGA
1 TAGTTTTTTTTAAAT-GA
30 TAGTTTTTTTTAAATGA
1 TAGTTTTTTTTAAATGA
47 TA
1 TA
49 AATAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (17 bp):
TAGTTTTTTTTAAATGA
Found at i:2761 original size:26 final size:26
Alignment explanation
Indices: 2712--2761 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
2702 ATACTCCCAC
*
2712 TGTCCCTTTTTATCTATCGGTTTTCT
1 TGTCCCTTTTTATCTATCAGTTTTCT
*
2738 TGTCCCTTTTTATCTATCATTTTT
1 TGTCCCTTTTTATCTATCAGTTTT
2762 GGACATAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.10, C:0.22, G:0.08, T:0.60
Consensus pattern (26 bp):
TGTCCCTTTTTATCTATCAGTTTTCT
Found at i:3691 original size:17 final size:17
Alignment explanation
Indices: 3669--3701 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3659 GTGAGTATAA
*
3669 AATTTCATCTATATTAG
1 AATTTCATCCATATTAG
3686 AATTTCATCCATATTA
1 AATTTCATCCATATTA
3702 ATGTATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.45
Consensus pattern (17 bp):
AATTTCATCCATATTAG
Found at i:4499 original size:8 final size:8
Alignment explanation
Indices: 4492--4537 Score: 60
Period size: 8 Copynumber: 5.9 Consensus size: 8
4482 CAAAAAAAAA
4492 AAAGAAAAG
1 AAAG-AAAG
4501 AAA--AAG
1 AAAGAAAG
*
4507 AAAGATAG
1 AAAGAAAG
4515 AAAGAAAG
1 AAAGAAAG
4523 AAAGAAAG
1 AAAGAAAG
4531 AAAGAAA
1 AAAGAAA
4538 TGGAAGTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
6 6 0.18
8 24 0.73
9 3 0.09
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (8 bp):
AAAGAAAG
Found at i:4504 original size:12 final size:11
Alignment explanation
Indices: 4489--4537 Score: 55
Period size: 12 Copynumber: 4.3 Consensus size: 11
4479 TTGCAAAAAA
4489 AAAAAAGAAA-
1 AAAAAAGAAAG
4499 AGAAAAAGAAAG
1 A-AAAAAGAAAG
*
4511 ATAGAAAGAAAG
1 A-AAAAAGAAAG
4523 AAAGAAAGAAAG
1 AAA-AAAGAAAG
4535 AAA
1 AAA
4538 TGGAAGTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 1 0.03
11 10 0.30
12 22 0.67
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:4510 original size:4 final size:4
Alignment explanation
Indices: 4503--4537 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
4493 AAGAAAAGAA
*
4503 AAAG AAAG ATAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
4538 TGGAAGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:4794 original size:31 final size:31
Alignment explanation
Indices: 4736--4794 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
4726 GTTATATAAG
*
4736 TAAGGATATAATAGGTATTTTAAAAGTTAAA
1 TAAGGATATAATAGGTATTTCAAAAGTTAAA
*
4767 TAAGGATATAATAGGTATTTCAGAAGTT
1 TAAGGATATAATAGGTATTTCAAAAGTT
4795 TCTCAAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.02, G:0.19, T:0.36
Consensus pattern (31 bp):
TAAGGATATAATAGGTATTTCAAAAGTTAAA
Found at i:6382 original size:31 final size:32
Alignment explanation
Indices: 6347--6419 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
6337 CCAAATTGAT
* *
6347 AGAAAAATTAACCCTCGAACTTTGACAAAA-A
1 AGAAAAATTAACCATCAAACTTTGACAAAATA
* *
6378 AGAAAAAAGTAGCCATCAAACTTTGACAAAATA
1 AG-AAAAATTAACCATCAAACTTTGACAAAATA
6411 AGACAAAAT
1 AGA-AAAAT
6420 GGTACCTGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
31 2 0.06
32 25 0.74
33 7 0.21
ACGTcount: A:0.55, C:0.16, G:0.11, T:0.18
Consensus pattern (32 bp):
AGAAAAATTAACCATCAAACTTTGACAAAATA
Found at i:8090 original size:19 final size:19
Alignment explanation
Indices: 8075--8114 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
8065 TGGAATATAT
8075 ATTTGGTTTTGCAATATTG
1 ATTTGGTTTTGCAATATTG
8094 ATTTGGTTTTGCAATATTG
1 ATTTGGTTTTGCAATATTG
8113 AT
1 AT
8115 GCTGAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.05, G:0.20, T:0.53
Consensus pattern (19 bp):
ATTTGGTTTTGCAATATTG
Found at i:8253 original size:19 final size:20
Alignment explanation
Indices: 8213--8250 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
8203 ATTAGTTTCC
*
8213 TTTCATTACTTAGCAAAAAT
1 TTTCAATACTTAGCAAAAAT
8233 TTTCAATACTTAGCAAAA
1 TTTCAATACTTAGCAAAA
8251 TTTCCATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.37
Consensus pattern (20 bp):
TTTCAATACTTAGCAAAAAT
Found at i:8979 original size:2 final size:2
Alignment explanation
Indices: 8924--8961 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
8914 CACTTACTAG
8924 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8962 AAAGATAAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17689 original size:17 final size:18
Alignment explanation
Indices: 17654--17690 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
17644 TAAACCCCAT
*
17654 TACAGACTTATGCAAGCA
1 TACAAACTTATGCAAGCA
17672 TACAAACTTATG-AAGCA
1 TACAAACTTATGCAAGCA
17689 TA
1 TA
17691 GGGGTCGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (18 bp):
TACAAACTTATGCAAGCA
Found at i:20643 original size:20 final size:20
Alignment explanation
Indices: 20618--20657 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
20608 GAGGAATGGA
*
20618 TGTAAAAAATTAGATCTAGG
1 TGTAAAAAAATAGATCTAGG
20638 TGTAAAAAAATAGATCTAGG
1 TGTAAAAAAATAGATCTAGG
20658 GGCTGAGCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.28
Consensus pattern (20 bp):
TGTAAAAAAATAGATCTAGG
Done.