Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006915.1 Corchorus capsularis cultivar CVL-1 contig06936, 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: 39625
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:1428 original size:81 final size:82
Alignment explanation
Indices: 1334--1489 Score: 278
Period size: 82 Copynumber: 1.9 Consensus size: 82
1324 TTTTTATATG
*
1334 TTACTCAACT-AAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTTATTTT
1 TTACTCAACTAAAAAAATCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTTATTTT
*
1398 ACCGTTTTACTACTATT
66 ACCATTTTACTACTATT
1415 TTACTCAACTAAAAAAATCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTTATTTT
1 TTACTCAACTAAAAAAATCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTTATTTT
*
1480 ATCATTTTAC
66 ACCATTTTAC
1490 AATTTTAATT
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
81 10 0.14
82 61 0.86
ACGTcount: A:0.35, C:0.13, G:0.01, T:0.51
Consensus pattern (82 bp):
TTACTCAACTAAAAAAATCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTTATTTT
ACCATTTTACTACTATT
Found at i:1654 original size:2 final size:2
Alignment explanation
Indices: 1638--1680 Score: 52
Period size: 2 Copynumber: 21.5 Consensus size: 2
1628 AAGTAATATC
* *
1638 AG AG AG A- AG ATG AG AG AG AG AG TG AG AG GG AG AG AG AG AG AG
1 AG AG AG AG AG A-G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1680 A
1 A
1681 AGGAACAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.49, T:0.05
Consensus pattern (2 bp):
AG
Found at i:5478 original size:15 final size:16
Alignment explanation
Indices: 5433--5478 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
5423 GGTAATTTTC
5433 TCGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
*
5449 TCGGCTCA-TCTGGGTT
1 TCGGGTCATTC-GGGTT
5465 T-GGGTCATTCGGGT
1 TCGGGTCATTCGGGT
5479 CTACTGGGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.07, C:0.20, G:0.37, T:0.37
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:6180 original size:22 final size:22
Alignment explanation
Indices: 6149--6206 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
6139 GTTTATAATA
**
6149 TTCTCGGGTCATTTGGGTTAAC
1 TTCTCGGGTCATTCAGGTTAAC
*
6171 TTCTCAGGTCATTCAGGTTAAC
1 TTCTCGGGTCATTCAGGTTAAC
6193 TTCTCGGGTCATTC
1 TTCTCGGGTCATTC
6207 GGCTTATGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (22 bp):
TTCTCGGGTCATTCAGGTTAAC
Found at i:11810 original size:7 final size:8
Alignment explanation
Indices: 11793--11822 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
11783 GATTAATTAA
11793 TTTTTATT
1 TTTTTATT
11801 TTTTTATTT
1 TTTTTA-TT
11810 TTTTTATT
1 TTTTTATT
11818 TTTTT
1 TTTTT
11823 TAAGCAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTATT
Found at i:11814 original size:10 final size:9
Alignment explanation
Indices: 11793--11824 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
11783 GATTAATTAA
11793 TTTTTA-TT
1 TTTTTATTT
11801 TTTTTATTT
1 TTTTTATTT
11810 TTTTTATTT
1 TTTTTATTT
11819 TTTTTA
1 TTTTTA
11825 AGCAGAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 6 0.26
9 17 0.74
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTATTT
Found at i:12582 original size:6 final size:6
Alignment explanation
Indices: 12571--12624 Score: 108
Period size: 6 Copynumber: 9.0 Consensus size: 6
12561 TCCAAATAGA
12571 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
12619 ACAAAT
1 ACAAAT
12625 GCATGCAATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
ACAAAT
Found at i:20843 original size:33 final size:33
Alignment explanation
Indices: 20779--20844 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
20769 ATCTTAATTT
* *
20779 ACGAACATAAACGAGGTATAAACGAGCTATTAA
1 ACGAACATAAACGAGATATAAACCAGCTATTAA
20812 ACGAACAATAAACGA-ATACTAAACCAG-TATTAA
1 ACGAAC-ATAAACGAGATA-TAAACCAGCTATTAA
20845 TCGAGCATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 14 0.48
34 15 0.52
ACGTcount: A:0.52, C:0.17, G:0.14, T:0.18
Consensus pattern (33 bp):
ACGAACATAAACGAGATATAAACCAGCTATTAA
Found at i:21282 original size:27 final size:26
Alignment explanation
Indices: 21209--21287 Score: 90
Period size: 26 Copynumber: 3.0 Consensus size: 26
21199 GGTATTAGGG
* *
21209 TCAC-CTAGGGGCATTTCGGTCATTT
1 TCACACTAAGGGCATTTTGGTCATTT
*
21234 TCGCACTAAGGGCATTTTGGTCATTT
1 TCACACTAAGGGCATTTTGGTCATTT
*
21260 AT-ACACTCAGTGGCATTTTGGTCATTT
1 -TCACACTAAG-GGCATTTTGGTCATTT
21287 T
1 T
21288 TAAGTCCACT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
25 3 0.07
26 26 0.57
27 17 0.37
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (26 bp):
TCACACTAAGGGCATTTTGGTCATTT
Found at i:23823 original size:19 final size:19
Alignment explanation
Indices: 23799--23835 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
23789 ATTATCCTAT
23799 ATAAAATATCCAAAAATCG
1 ATAAAATATCCAAAAATCG
23818 ATAAAATATCCAAAAATC
1 ATAAAATATCCAAAAATC
23836 CTTAACTTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.59, C:0.16, G:0.03, T:0.22
Consensus pattern (19 bp):
ATAAAATATCCAAAAATCG
Found at i:23952 original size:19 final size:18
Alignment explanation
Indices: 23919--23955 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
23909 TTGAAATAAT
23919 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
23937 TCTTCAAATTATCTTCAAG
1 TCTTC-AATGATCTTCAAG
23956 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:34285 original size:19 final size:18
Alignment explanation
Indices: 34252--34288 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
34242 TTGAAATAAT
34252 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
34270 TCTTCAAATTATCTTCAAG
1 TCTTC-AATGATCTTCAAG
34289 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:39588 original size:2 final size:2
Alignment explanation
Indices: 39583--39623 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
39573 ATATATATAT
39583 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
39624 TG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.