Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009701.1 Corchorus capsularis cultivar CVL-1 contig09722, 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: 41633
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:648 original size:75 final size:74
Alignment explanation
Indices: 494--633 Score: 228
Period size: 75 Copynumber: 1.9 Consensus size: 74
484 ATCTTCAATA
* *
494 TTTA-TTTGTTTCTTAAAATATCTCCTAAATCTTCCACAATTTGGCAAGATTTAGAAAATATTCT
1 TTTATTTTATTTCTTAAAATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCT
**
558 CAACTTTAT
66 CAACTAAAT
567 TATTATTTTATTTCTTAAAATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTC
1 T-TTATTTTATTTCTTAAAATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTC
632 TC
65 TC
634 TTTACAAATT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
73 1 0.02
74 3 0.05
75 59 0.94
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (74 bp):
TTTATTTTATTTCTTAAAATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCT
CAACTAAAT
Found at i:3523 original size:45 final size:44
Alignment explanation
Indices: 3472--3604 Score: 212
Period size: 45 Copynumber: 3.0 Consensus size: 44
3462 TAATAGAGTA
3472 GTGGAATTACTAAAAGATCACTACCCCGAATTAATGATAAGCTGG
1 GTGGAATTACTAAAAGATC-CTACCCCGAATTAATGATAAGCTGG
3517 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
1 GTGGAATTACTAAAAGAT-CCTACCCCGAATTAATGATAAGCTGG
* * *
3562 GTGGAATTACTAAAAGATCCATACCCCGGATTAGTGATGAGCT
1 GTGGAATTACTAAAAGATCC-TACCCCGAATTAATGATAAGCT
3605 AGAGAAGTAA
Statistics
Matches: 83, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
44 2 0.02
45 80 0.96
46 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (44 bp):
GTGGAATTACTAAAAGATCCTACCCCGAATTAATGATAAGCTGG
Found at i:9545 original size:20 final size:18
Alignment explanation
Indices: 9520--9564 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
9510 ACATATGTTT
9520 TACTAATAAATAATAATATA
1 TACTAATAAAT-A-AATATA
* *
9540 TACTAACAAATAAATATT
1 TACTAATAAATAAATATA
9558 TACTAAT
1 TACTAAT
9565 TTTGCTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 11 0.50
19 1 0.05
20 10 0.45
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.36
Consensus pattern (18 bp):
TACTAATAAATAAATATA
Found at i:9953 original size:32 final size:31
Alignment explanation
Indices: 9865--9959 Score: 109
Period size: 31 Copynumber: 3.0 Consensus size: 31
9855 AAATCGTGCT
* * * * *
9865 ACATGTATCAAAAAGTGACACATGTCACGCC
1 ACATGTTTCAAAAAATGACACGTGGCATGCC
* *
9896 ACGTGTTTCAAAAAGTGACACGTGGCATGCC
1 ACATGTTTCAAAAAATGACACGTGGCATGCC
*
9927 ACATGTTTCAAAAAATGGCACTGTGGCATGCC
1 ACATGTTTCAAAAAATGACAC-GTGGCATGCC
9959 A
1 A
9960 TGTGCACAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 44 0.80
32 11 0.20
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (31 bp):
ACATGTTTCAAAAAATGACACGTGGCATGCC
Found at i:14539 original size:16 final size:16
Alignment explanation
Indices: 14520--14565 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
14510 TTTTTCTGTT
14520 TTTTGTTTTTGTTTCG
1 TTTTGTTTTTGTTTCG
14536 TTTTGTTTTTGTTTCG
1 TTTTGTTTTTGTTTCG
14552 TTTTCG-TTTTGTTT
1 TTTT-GTTTTTGTTT
14566 TTGTTGCGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
16 28 0.97
17 1 0.03
ACGTcount: A:0.00, C:0.07, G:0.17, T:0.76
Consensus pattern (16 bp):
TTTTGTTTTTGTTTCG
Found at i:14547 original size:22 final size:23
Alignment explanation
Indices: 14519--14570 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
14509 GTTTTTCTGT
*
14519 TTTTTGTTTTTG-TTTCGTTTTG
1 TTTTTGTTTTCGTTTTCGTTTTG
14541 TTTTTG-TTTCGTTTTCGTTTTG
1 TTTTTGTTTTCGTTTTCGTTTTG
14563 TTTTTGTT
1 TTTTTGTT
14571 GCGCTTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 4 0.15
22 22 0.81
23 1 0.04
ACGTcount: A:0.00, C:0.06, G:0.17, T:0.77
Consensus pattern (23 bp):
TTTTTGTTTTCGTTTTCGTTTTG
Found at i:14604 original size:15 final size:15
Alignment explanation
Indices: 14584--14614 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
14574 CTTTTCAATT
14584 TTTTGAAAACAAAAA
1 TTTTGAAAACAAAAA
*
14599 TTTTGAAAACAGAAA
1 TTTTGAAAACAAAAA
14614 T
1 T
14615 AGCCTACCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.06, G:0.10, T:0.29
Consensus pattern (15 bp):
TTTTGAAAACAAAAA
Found at i:14760 original size:111 final size:111
Alignment explanation
Indices: 14566--14788 Score: 419
Period size: 111 Copynumber: 2.0 Consensus size: 111
14556 CGTTTTGTTT
*
14566 TTGTTGCGCTTTTCAATTTTTTGAAAACAAAAATTTTGAAAACAGAAATAGCCTACCAAACATGT
1 TTGTTGCGCTTTTCAATTTTTTGAAAACAAAAATTTTGAAAACAGAAACAGCCTACCAAACATGT
*
14631 TTTCAAAAACAGAAAATTGGCAACAGAAAAACAGAAACAAAAACAA
66 TTTCAAAAACAAAAAATTGGCAACAGAAAAACAGAAACAAAAACAA
*
14677 TTGTTGCGCTTTTCAATTTTTTGAAAACAAAAGTTTTGAAAACAGAAACAGCCTACCAAACATGT
1 TTGTTGCGCTTTTCAATTTTTTGAAAACAAAAATTTTGAAAACAGAAACAGCCTACCAAACATGT
14742 TTTCAAAAACAAAAAATTGGCAACAGAAAAACAGAAACAAAAACAA
66 TTTCAAAAACAAAAAATTGGCAACAGAAAAACAGAAACAAAAACAA
14788 T
1 T
14789 GTCAAACAGG
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 109 1.00
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (111 bp):
TTGTTGCGCTTTTCAATTTTTTGAAAACAAAAATTTTGAAAACAGAAACAGCCTACCAAACATGT
TTTCAAAAACAAAAAATTGGCAACAGAAAAACAGAAACAAAAACAA
Found at i:15761 original size:1 final size:1
Alignment explanation
Indices: 15755--15783 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
15745 TTGCACCTGC
15755 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
15784 CAGTTTCAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:19246 original size:17 final size:18
Alignment explanation
Indices: 19224--19257 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
19214 AAAGCCTGGT
*
19224 TGGTGGTGGTGG-GATGA
1 TGGTGGCGGTGGTGATGA
19241 TGGTGGCGGTGGTGATG
1 TGGTGGCGGTGGTGATG
19258 GTCCACCGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.09, C:0.03, G:0.59, T:0.29
Consensus pattern (18 bp):
TGGTGGCGGTGGTGATGA
Found at i:19308 original size:30 final size:30
Alignment explanation
Indices: 19272--19337 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
19262 ACCGTAGTTA
*
19272 TGGTGGAGGTGTTGGGGTGGTGGTGGCTCG
1 TGGTGGAGGTGTGGGGGTGGTGGTGGCTCG
*
19302 TGGTGGAGGTGTGGGGGTGGTGGTGGTTCG
1 TGGTGGAGGTGTGGGGGTGGTGGTGGCTCG
19332 TGGTGG
1 TGGTGG
19338 TGGCGTGGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.03, C:0.05, G:0.62, T:0.30
Consensus pattern (30 bp):
TGGTGGAGGTGTGGGGGTGGTGGTGGCTCG
Found at i:19336 original size:13 final size:11
Alignment explanation
Indices: 19288--19353 Score: 50
Period size: 11 Copynumber: 6.1 Consensus size: 11
19278 AGGTGTTGGG
19288 GTGGTGGTGGC
1 GTGGTGGTGGC
* *
19299 -TCGTGGTGGA
1 GTGGTGGTGGC
19309 G-GTGTGG-GG-
1 GTG-GTGGTGGC
19318 GTGGTGGTGGTTC
1 GTGGTGGTGG--C
19331 GTGGTGGTGGC
1 GTGGTGGTGGC
*
19342 GTGGTGGCGGC
1 GTGGTGGTGGC
19353 G
1 G
19354 GCGGCGATTC
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
9 5 0.11
10 13 0.30
11 16 0.36
13 10 0.23
ACGTcount: A:0.02, C:0.09, G:0.62, T:0.27
Consensus pattern (11 bp):
GTGGTGGTGGC
Found at i:19348 original size:3 final size:3
Alignment explanation
Indices: 19272--19340 Score: 52
Period size: 3 Copynumber: 23.0 Consensus size: 3
19262 ACCGTAGTTA
* * * *
19272 TGG TGG AGG TGT TGG -GG TGG TGG TGG CTCG TGG TGG AGG T-G TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG -TGG TGG TGG TGG TGG TGG
* *
19316 GGG TGG TGG TGG TTCG TGG TGG TGG
1 TGG TGG TGG TGG -TGG TGG TGG TGG
19341 CGTGGTGGCG
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
2 4 0.08
3 42 0.84
4 4 0.08
ACGTcount: A:0.03, C:0.04, G:0.62, T:0.30
Consensus pattern (3 bp):
TGG
Found at i:22814 original size:12 final size:12
Alignment explanation
Indices: 22797--22839 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
22787 TTTATTTGTA
22797 ATTTGTTTGTTT
1 ATTTGTTTGTTT
22809 ATTTGTTTGTTT
1 ATTTGTTTGTTT
*
22821 ATTTATTTGTTT
1 ATTTGTTTGTTT
*
22833 ATCTGTT
1 ATTTGTT
22840 AGGTAGATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.12, C:0.02, G:0.14, T:0.72
Consensus pattern (12 bp):
ATTTGTTTGTTT
Found at i:22819 original size:16 final size:16
Alignment explanation
Indices: 22798--22832 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
22788 TTATTTGTAA
*
22798 TTTGTTTGTTTATTTG
1 TTTGTTTATTTATTTG
22814 TTTGTTTATTTATTTG
1 TTTGTTTATTTATTTG
22830 TTT
1 TTT
22833 ATCTGTTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.09, C:0.00, G:0.14, T:0.77
Consensus pattern (16 bp):
TTTGTTTATTTATTTG
Found at i:26550 original size:11 final size:11
Alignment explanation
Indices: 26534--26559 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
26524 ACACATCCAA
26534 AAAAATAAAAT
1 AAAAATAAAAT
26545 AAAAATAAAAT
1 AAAAATAAAAT
26556 AAAA
1 AAAA
26560 GGATGGGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:40472 original size:21 final size:20
Alignment explanation
Indices: 40448--40487 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40438 CATTCATAGC
*
40448 AATCGAAATTTCAGTTCTAAA
1 AATC-AAATTTCACTTCTAAA
*
40469 AATCTAATTTCACTTCTAA
1 AATCAAATTTCACTTCTAA
40488 GAGATTAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (20 bp):
AATCAAATTTCACTTCTAAA
Done.