Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010599.1 Corchorus capsularis cultivar CVL-1 contig10620, 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: 44800
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:449 original size:6 final size:6
Alignment explanation
Indices: 426--525 Score: 55
Period size: 6 Copynumber: 16.2 Consensus size: 6
416 GGCAATTGGG
*
426 CGGGTT CGGG-- CGGTTT CGGGTT CGGGTACTT CGGGTT CGGGTATTTT
1 CGGGTT CGGGTT CGGGTT CGGGTT CGGG---TT CGGGTT CGGG----TT
* * * **
473 CGGGTT TGGGCT C-GGAT CGGGTT CGGGTT CGGGCC CGGG-T CGGGTT
1 CGGGTT CGGGTT CGGGTT CGGGTT CGGGTT CGGGTT CGGGTT CGGGTT
519 CGGGTT C
1 CGGGTT C
526 ATTTTTGATA
Statistics
Matches: 73, Mismatches: 10, Indels: 22
0.70 0.10 0.21
Matches are distributed among these distances:
4 3 0.04
5 8 0.11
6 50 0.68
9 6 0.08
10 6 0.08
ACGTcount: A:0.03, C:0.20, G:0.46, T:0.31
Consensus pattern (6 bp):
CGGGTT
Found at i:460 original size:15 final size:16
Alignment explanation
Indices: 440--478 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
430 TTCGGGCGGT
440 TTCGGGTTCGGGTA-C
1 TTCGGGTTCGGGTATC
*
455 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATC
471 TTCGGGTT
1 TTCGGGTT
479 TGGGCTCGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.05, C:0.15, G:0.38, T:0.41
Consensus pattern (16 bp):
TTCGGGTTCGGGTATC
Found at i:500 original size:23 final size:23
Alignment explanation
Indices: 471--525 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
461 TTCGGGTATT
* *
471 TTCGGGTTTGGGCTCGGATCGGG
1 TTCGGGTTCGGGCCCGGATCGGG
*
494 TTCGGGTTCGGGCCCGGGTCGGG
1 TTCGGGTTCGGGCCCGGATCGGG
517 TTCGGGTTC
1 TTCGGGTTC
526 ATTTTTGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.02, C:0.22, G:0.47, T:0.29
Consensus pattern (23 bp):
TTCGGGTTCGGGCCCGGATCGGG
Found at i:1279 original size:16 final size:17
Alignment explanation
Indices: 1258--1319 Score: 76
Period size: 16 Copynumber: 3.8 Consensus size: 17
1248 ATTATTTTGA
1258 TCTCGGGTTCGGGT-TT
1 TCTCGGGTTCGGGTATT
*
1274 TCTCGGGTTTGGGTATT
1 TCTCGGGTTCGGGTATT
*
1291 T-TCGGGTTCGGGTAAT
1 TCTCGGGTTCGGGTATT
*
1307 T-TCGGATTCGGGT
1 TCTCGGGTTCGGGT
1320 TCGGACAGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
16 38 0.93
17 3 0.07
ACGTcount: A:0.06, C:0.15, G:0.37, T:0.42
Consensus pattern (17 bp):
TCTCGGGTTCGGGTATT
Found at i:4734 original size:92 final size:92
Alignment explanation
Indices: 4594--4874 Score: 562
Period size: 92 Copynumber: 3.1 Consensus size: 92
4584 TTCCTTTGGA
4594 AGAATGATTGCTTGGGTCTGTCCCAGCCCATCCCCAAACACAATCTAAATGTCTAATAAGTTTTG
1 AGAATGATTGCTTGGGTCTGTCCCAGCCCATCCCCAAACACAATCTAAATGTCTAATAAGTTTTG
4659 ATATTGGTCAATGATCATAATATACTT
66 ATATTGGTCAATGATCATAATATACTT
4686 AGAATGATTGCTTGGGTCTGTCCCAGCCCATCCCCAAACACAATCTAAATGTCTAATAAGTTTTG
1 AGAATGATTGCTTGGGTCTGTCCCAGCCCATCCCCAAACACAATCTAAATGTCTAATAAGTTTTG
4751 ATATTGGTCAATGATCATAATATACTT
66 ATATTGGTCAATGATCATAATATACTT
4778 AGAATGATTGCTTGGGTCTGTCCCAGCCCATCCCCAAACACAATCTAAATGTCTAATAAGTTTTG
1 AGAATGATTGCTTGGGTCTGTCCCAGCCCATCCCCAAACACAATCTAAATGTCTAATAAGTTTTG
4843 ATATTGGTCAATGATCATAATATACTT
66 ATATTGGTCAATGATCATAATATACTT
4870 AGAAT
1 AGAAT
4875 ATTTAAAGGT
Statistics
Matches: 189, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 189 1.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (92 bp):
AGAATGATTGCTTGGGTCTGTCCCAGCCCATCCCCAAACACAATCTAAATGTCTAATAAGTTTTG
ATATTGGTCAATGATCATAATATACTT
Found at i:24808 original size:15 final size:15
Alignment explanation
Indices: 24764--24814 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
24754 AAATAATATT
24764 TTAATTATTCCATTA
1 TTAATTATTCCATTA
** *
24779 TT--TT-TTTAATCA
1 TTAATTATTCCATTA
24791 TTAATTATTCCATTA
1 TTAATTATTCCATTA
24806 TTAATTATT
1 TTAATTATT
24815 AGATTATATA
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
12 7 0.26
13 2 0.07
14 2 0.07
15 16 0.59
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.59
Consensus pattern (15 bp):
TTAATTATTCCATTA
Found at i:24820 original size:15 final size:15
Alignment explanation
Indices: 24764--24826 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
24754 AAATAATATT
*
24764 TTAATTATTCCATTA
1 TTAATTATTACATTA
* *
24779 TT--TTTTTA-ATCA
1 TTAATTATTACATTA
*
24791 TTAATTATTCCATTA
1 TTAATTATTACATTA
*
24806 TTAATTATTAGATTA
1 TTAATTATTACATTA
24821 TATAAT
1 T-TAAT
24827 ACGTATATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
12 5 0.14
13 4 0.11
14 4 0.11
15 19 0.53
16 4 0.11
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.56
Consensus pattern (15 bp):
TTAATTATTACATTA
Found at i:27157 original size:19 final size:19
Alignment explanation
Indices: 27125--27168 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
27115 TTTTGATTTT
* *
27125 TTATATAAATTATTATTAA
1 TTATATAAAGTATTAGTAA
*
27144 TTATATAGAGTATTAGTAA
1 TTATATAAAGTATTAGTAA
27163 TCTATA
1 T-TATA
27169 GATTAAGGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (19 bp):
TTATATAAAGTATTAGTAA
Found at i:27634 original size:16 final size:17
Alignment explanation
Indices: 27613--27650 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
27603 TTACTATTAA
**
27613 AAAAAATA-ATTTCAAT
1 AAAAAATATATTAAAAT
27629 AAAAAATATATTAAAAT
1 AAAAAATATATTAAAAT
27646 AAAAA
1 AAAAA
27651 TATTTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAAAATATATTAAAAT
Found at i:38848 original size:31 final size:29
Alignment explanation
Indices: 38806--38891 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 29
38796 AATGCCCTTT
* *
38806 TACCCCCTAAACTTGTATTGTTTGGACAATC
1 TACCCCATAAACTT-TAAT-TTTGGACAATC
* * *
38837 TACCCTATAAACTTTAATTTTGGACATTT
1 TACCCCATAAACTTTAATTTTGGACAATC
*
38866 TACCCCATAAACTCTCAATTTTGGAC
1 TACCCCATAAACT-TTAATTTTGGAC
38892 TTTTCCCCGT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
29 21 0.45
30 14 0.30
31 12 0.26
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.37
Consensus pattern (29 bp):
TACCCCATAAACTTTAATTTTGGACAATC
Found at i:38895 original size:29 final size:29
Alignment explanation
Indices: 38803--38899 Score: 90
Period size: 29 Copynumber: 3.3 Consensus size: 29
38793 CTTAATGCCC
* * *
38803 TTTTACCCCCTAAACTTGTATTGTTTGGACA
1 TTTTACCCCATAAACTT-CAAT-TTTGGACA
* * * *
38834 ATCTACCCTATAAACTTTAATTTTGGACA
1 TTTTACCCCATAAACTTCAATTTTGGACA
38863 TTTTACCCCATAAACTCTCAATTTTGGAC-
1 TTTTACCCCATAAACT-TCAATTTTGGACA
38892 TTTT-CCCC
1 TTTTACCCC
38900 GTCTCGCCCG
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
28 4 0.07
29 25 0.45
30 14 0.25
31 13 0.23
ACGTcount: A:0.26, C:0.26, G:0.08, T:0.40
Consensus pattern (29 bp):
TTTTACCCCATAAACTTCAATTTTGGACA
Done.