Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013333.1 Corchorus capsularis cultivar CVL-1 contig13354, 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: 21790
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:2619 original size:19 final size:18
Alignment explanation
Indices: 2586--2621 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2576 TTGAAATAAT
2586 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
2604 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
2622 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:4172 original size:24 final size:24
Alignment explanation
Indices: 4107--4176 Score: 78
Period size: 24 Copynumber: 3.0 Consensus size: 24
4097 GCTAGTATTT
*
4107 TGACAAAAAATTTCAATAG-G-CTCA
1 TGAC-AAAAATTTCAA-AGAGCCTAA
4131 TGAC--AAATTT-AAAGAGCCTAA
1 TGACAAAAATTTCAAAGAGCCTAA
4152 TGACAAAAATTTCAAAGAGCCTAA
1 TGACAAAAATTTCAAAGAGCCTAA
4176 T
1 T
4177 ATTTTTAAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
19 2 0.05
20 3 0.08
21 13 0.32
23 6 0.15
24 16 0.40
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (24 bp):
TGACAAAAATTTCAAAGAGCCTAA
Found at i:14313 original size:24 final size:24
Alignment explanation
Indices: 14253--14311 Score: 86
Period size: 25 Copynumber: 2.5 Consensus size: 24
14243 TTCAAACCCT
14253 AAACTTCATTTCTAACAATTTCTTC
1 AAACTTCATTTCTAACAA-TTCTTC
14278 AAACTTCATTTCTAACGAA-TCTTC
1 AAACTTCATTTCTAAC-AATTCTTC
14302 AAA-TTCATTT
1 AAACTTCATTT
14312 TCCTTCATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
23 7 0.21
24 8 0.24
25 16 0.48
26 2 0.06
ACGTcount: A:0.34, C:0.22, G:0.02, T:0.42
Consensus pattern (24 bp):
AAACTTCATTTCTAACAATTCTTC
Found at i:14350 original size:26 final size:26
Alignment explanation
Indices: 14321--14388 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
14311 TTCCTTCATT
*
14321 TTAATCATAAACTAATTAAATACTAA
1 TTAAACATAAACTAATTAAATACTAA
* *
14347 TTAACCATAAACTAATTAAATATTAA
1 TTAAACATAAACTAATTAAATACTAA
14373 TTAAACATAAACTAAT
1 TTAAACATAAACTAAT
14389 AAACTAAGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (26 bp):
TTAAACATAAACTAATTAAATACTAA
Found at i:14362 original size:15 final size:14
Alignment explanation
Indices: 14321--14388 Score: 58
Period size: 15 Copynumber: 5.1 Consensus size: 14
14311 TTCCTTCATT
14321 TTAATCATAAACTAA
1 TTAA-CATAAACTAA
14336 TTAA-AT--ACTAA
1 TTAACATAAACTAA
14347 TTAACCATAAACTAA
1 TTAA-CATAAACTAA
*
14362 TTAA-AT--ATTAA
1 TTAACATAAACTAA
14373 TTAAACATAAACTAA
1 TT-AACATAAACTAA
14388 T
1 T
14389 AAACTAAGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
11 15 0.35
12 2 0.05
13 8 0.19
15 18 0.42
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (14 bp):
TTAACATAAACTAA
Found at i:14726 original size:21 final size:22
Alignment explanation
Indices: 14702--14746 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
14692 CAAAAATTAT
*
14702 AAAAAGGGGG-CGGTATTTAGC
1 AAAAAGGGGGACAGTATTTAGC
*
14723 -AAAAGGGGGACAGTGTTTAGC
1 AAAAAGGGGGACAGTATTTAGC
14744 AAA
1 AAA
14747 CCCCTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
20 9 0.45
21 9 0.45
22 2 0.10
ACGTcount: A:0.38, C:0.09, G:0.36, T:0.18
Consensus pattern (22 bp):
AAAAAGGGGGACAGTATTTAGC
Found at i:14728 original size:20 final size:21
Alignment explanation
Indices: 14703--14746 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
14693 AAAAATTATA
*
14703 AAAAGGGGG-CGGTATTTAGC
1 AAAAGGGGGACAGTATTTAGC
*
14723 AAAAGGGGGACAGTGTTTAGC
1 AAAAGGGGGACAGTATTTAGC
14744 AAA
1 AAA
14747 CCCCTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.36, C:0.09, G:0.36, T:0.18
Consensus pattern (21 bp):
AAAAGGGGGACAGTATTTAGC
Found at i:15692 original size:2 final size:2
Alignment explanation
Indices: 15685--15709 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15675 AAAATCTTGA
15685 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
15710 CTCTATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17465 original size:16 final size:16
Alignment explanation
Indices: 17442--17503 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
17432 ATTTGTAAAG
*
17442 AGAAAAAGAAGAGAAA
1 AGAAAAAGAAAAGAAA
* *
17458 ATAAAAAGAAAATAAA
1 AGAAAAAGAAAAGAAA
*
17474 AGAAAAAGGAAAGGAAA
1 AGAAAAA-GAAAAGAAA
*
17491 AGGAAAAGGAAAA
1 A-GAAAAAGAAAA
17504 ATAATTATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
16 19 0.53
17 12 0.33
18 5 0.14
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (16 bp):
AGAAAAAGAAAAGAAA
Found at i:17498 original size:12 final size:12
Alignment explanation
Indices: 17471--17503 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
17461 AAAAGAAAAT
*
17471 AAAAGAAAAAGG
1 AAAAGGAAAAGG
17483 -AAAGGAAAAGG
1 AAAAGGAAAAGG
17494 AAAAGGAAAA
1 AAAAGGAAAA
17504 ATAATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
AAAAGGAAAAGG
Found at i:20962 original size:145 final size:145
Alignment explanation
Indices: 20699--20989 Score: 582
Period size: 145 Copynumber: 2.0 Consensus size: 145
20689 ATTGACTCAA
20699 AGTTATACAATCGTATATTAAGGATCAACCGGGTGACTTGAAGGCGGTAGCTTTTTAAGAATGAG
1 AGTTATACAATCGTATATTAAGGATCAACCGGGTGACTTGAAGGCGGTAGCTTTTTAAGAATGAG
20764 TCATATATTGTGAATCATTAGTCGAGTTGACTGGTTGAGCTAAGGTCTCTTACTGGTTTTGAACA
66 TCATATATTGTGAATCATTAGTCGAGTTGACTGGTTGAGCTAAGGTCTCTTACTGGTTTTGAACA
20829 AGATTATTGCCGTTG
131 AGATTATTGCCGTTG
20844 AGTTATACAATCGTATATTAAGGATCAACCGGGTGACTTGAAGGCGGTAGCTTTTTAAGAATGAG
1 AGTTATACAATCGTATATTAAGGATCAACCGGGTGACTTGAAGGCGGTAGCTTTTTAAGAATGAG
20909 TCATATATTGTGAATCATTAGTCGAGTTGACTGGTTGAGCTAAGGTCTCTTACTGGTTTTGAACA
66 TCATATATTGTGAATCATTAGTCGAGTTGACTGGTTGAGCTAAGGTCTCTTACTGGTTTTGAACA
20974 AGATTATTGCCGTTG
131 AGATTATTGCCGTTG
20989 A
1 A
20990 CATTTTTGTT
Statistics
Matches: 146, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
145 146 1.00
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (145 bp):
AGTTATACAATCGTATATTAAGGATCAACCGGGTGACTTGAAGGCGGTAGCTTTTTAAGAATGAG
TCATATATTGTGAATCATTAGTCGAGTTGACTGGTTGAGCTAAGGTCTCTTACTGGTTTTGAACA
AGATTATTGCCGTTG
Done.