Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014321.1 Corchorus capsularis cultivar CVL-1 contig14342, 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: 33780
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1033 original size:33 final size:32
Alignment explanation
Indices: 989--1155 Score: 172
Period size: 33 Copynumber: 5.1 Consensus size: 32
979 GGCGCGGTGC
989 CCAACCGTGGTGTGCCGTCCTCGTAGGATGGCA
1 CCAACCGTGGTGTGCCGTCCTCG-AGGATGGCA
* *
1022 CCAACCATGGTGTGCCGTCCTCCTAGGATGGCA
1 CCAACCGTGGTGTGCCGTCCT-CGAGGATGGCA
* * * *
1055 TCAACCGTGGTGTGCCGTCCTAGGAGGACGGTA
1 CCAACCGTGGTGTGCCGTCCT-CGAGGATGGCA
* * * * *
1088 TCAACCGTGTTGTGCCGACCTTCGGGGACGGCA
1 CCAACCGTGGTGTGCCGTCC-TCGAGGATGGCA
* *
1121 CCAACCGTGGTGCGCCGTCCTCCGGGGATGGCA
1 CCAACCGTGGTGTGCCGTCCT-CGAGGATGGCA
1154 CC
1 CC
1156 GTATCTAAAT
Statistics
Matches: 112, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
32 1 0.01
33 109 0.97
34 2 0.02
ACGTcount: A:0.16, C:0.32, G:0.33, T:0.20
Consensus pattern (32 bp):
CCAACCGTGGTGTGCCGTCCTCGAGGATGGCA
Found at i:1198 original size:17 final size:16
Alignment explanation
Indices: 1176--1208 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
1166 CAATCTTTTA
1176 AAAAAAATATTTAAAAT
1 AAAAAAAT-TTTAAAAT
1193 AAAAAAATTTTAAAAT
1 AAAAAAATTTTAAAAT
1209 TATTTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAAAAATTTTAAAAT
Found at i:5362 original size:48 final size:46
Alignment explanation
Indices: 5266--5388 Score: 126
Period size: 48 Copynumber: 2.6 Consensus size: 46
5256 TAATTTGAAC
**
5266 TTTCTAACAACTTCTTCAAACTCTCAACCTTTCAAACCCTAAACTTCA
1 TTTCTAACAACTTCTTCAAACT-TC-ATTTTTCAAACCCTAAACTTCA
* *
5314 TTTCTAACAACTTCTTCAAACTTCATTTTTAACAAATCTTCAAA-TTCA
1 TTTCTAACAACTTCTTCAAACTTCATTTTT--CAAACCCT-AAACTTCA
* *
5362 TTTTTAACAA-ATCTTCAAA-TTCATTTT
1 TTTCTAACAACTTCTTCAAACTTCATTTT
5389 CCTTCATTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
46 12 0.18
47 10 0.15
48 41 0.62
49 3 0.05
ACGTcount: A:0.34, C:0.25, G:0.00, T:0.41
Consensus pattern (46 bp):
TTTCTAACAACTTCTTCAAACTTCATTTTTCAAACCCTAAACTTCA
Found at i:5366 original size:24 final size:23
Alignment explanation
Indices: 5310--5388 Score: 122
Period size: 23 Copynumber: 3.3 Consensus size: 23
5300 AACCCTAAAC
* *
5310 TTCATTTCTAACAACTTCTTCAAA
1 TTCATTTTTAACAA-ATCTTCAAA
5334 CTTCATTTTTAACAAATCTTCAAA
1 -TTCATTTTTAACAAATCTTCAAA
5358 TTCATTTTTAACAAATCTTCAAA
1 TTCATTTTTAACAAATCTTCAAA
5381 TTCATTTT
1 TTCATTTT
5389 CCTTCATTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
23 31 0.60
24 8 0.15
25 13 0.25
ACGTcount: A:0.34, C:0.20, G:0.00, T:0.46
Consensus pattern (23 bp):
TTCATTTTTAACAAATCTTCAAA
Found at i:5426 original size:26 final size:26
Alignment explanation
Indices: 5397--5464 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
5387 TTCCTTCATT
5397 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
5423 TTAATAATAAACTAATTATATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
5449 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
5465 AAACTAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.35
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:5464 original size:15 final size:14
Alignment explanation
Indices: 5403--5464 Score: 55
Period size: 11 Copynumber: 4.7 Consensus size: 14
5393 CATTTTAATC
5403 ATAAACTAATT-AA
1 ATAAACTAATTAAA
5416 AT--ACTAATTAATA
1 ATAAACTAATTAA-A
5429 ATAAACTAATT---
1 ATAAACTAATTAAA
*
5440 ATATACTAATTAAA
1 ATAAACTAATTAAA
5454 CATAAACTAAT
1 -ATAAACTAAT
5465 AAACTAAGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
11 17 0.44
12 1 0.03
13 5 0.13
15 16 0.41
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAAACTAATTAAA
Found at i:5534 original size:4 final size:4
Alignment explanation
Indices: 5525--5551 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5515 GCTTGGCCAT
5525 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
5552 TTTTTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:5565 original size:12 final size:12
Alignment explanation
Indices: 5550--5583 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5540 CTTTCTTTCT
5550 TTTTTTTTTAAA
1 TTTTTTTTTAAA
5562 TTTTTTTTTAAA
1 TTTTTTTTTAAA
* *
5574 ATATTTTTTA
1 TTTTTTTTTA
5584 CATCAACCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTTTTTAAA
Found at i:5567 original size:13 final size:13
Alignment explanation
Indices: 5549--5582 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
5539 TCTTTCTTTC
*
5549 TTTTTTTTTTAAA
1 TTTTTTTTTAAAA
5562 TTTTTTTTTAAAA
1 TTTTTTTTTAAAA
5575 TATTTTTT
1 T-TTTTTT
5583 ACATCAACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTAAAA
Found at i:5756 original size:21 final size:22
Alignment explanation
Indices: 5726--5766 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5716 AAAAAGAGAG
**
5726 GGGGGCCGGTATTTAGCAAAAA
1 GGGGGCCGGTAAATAGCAAAAA
5748 GGGGG-CGGTAAATAGCAAA
1 GGGGGCCGGTAAATAGCAAA
5767 CCCCCATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.34, C:0.12, G:0.39, T:0.15
Consensus pattern (22 bp):
GGGGGCCGGTAAATAGCAAAAA
Found at i:8623 original size:35 final size:35
Alignment explanation
Indices: 8575--8665 Score: 155
Period size: 35 Copynumber: 2.6 Consensus size: 35
8565 GTTCTTGAAC
*
8575 ATTTATCTAAGACAATCTTCTAATATGTAATGTGA
1 ATTTATCTAAGACAAACTTCTAATATGTAATGTGA
*
8610 ATTTATCTGAGACAAACTTCTAATATGTAATGTGA
1 ATTTATCTAAGACAAACTTCTAATATGTAATGTGA
*
8645 ATTTATCTAAGACAGACTTCT
1 ATTTATCTAAGACAAACTTCT
8666 TGTTTGTCTT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 52 1.00
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.38
Consensus pattern (35 bp):
ATTTATCTAAGACAAACTTCTAATATGTAATGTGA
Found at i:15682 original size:15 final size:15
Alignment explanation
Indices: 15662--15691 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
15652 TAAGTGATGA
15662 ATGTAATCAAGAGTT
1 ATGTAATCAAGAGTT
15677 ATGTAATCAAGAGTT
1 ATGTAATCAAGAGTT
15692 GAAGTTTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (15 bp):
ATGTAATCAAGAGTT
Found at i:15882 original size:2 final size:2
Alignment explanation
Indices: 15875--15906 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
15865 CGTATGAATC
15875 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15907 ACTATGAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20444 original size:32 final size:32
Alignment explanation
Indices: 20406--20466 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
20396 CTTGATTTGC
*
20406 TGCATCTGATGGATGGATATCATCCCAAAGCA
1 TGCATCTGATGGATGGATACCATCCCAAAGCA
20438 TGCATCTGATGGATGGATACCATCCCAAA
1 TGCATCTGATGGATGGATACCATCCCAAA
20467 ACACATAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (32 bp):
TGCATCTGATGGATGGATACCATCCCAAAGCA
Found at i:25017 original size:20 final size:21
Alignment explanation
Indices: 24992--25052 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 21
24982 ATGACATGAC
24992 ATGAAAGGC-AAACCCTAACT
1 ATGAAAGGCTAAACCCTAACT
* *
25012 ATGAAATGCTAAACCCTAAGT
1 ATGAAAGGCTAAACCCTAACT
25033 GAGATGAAA-GCTAAACCCTA
1 ---ATGAAAGGCTAAACCCTA
25053 GCCATGACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 8 0.23
21 10 0.29
23 11 0.31
24 6 0.17
ACGTcount: A:0.44, C:0.21, G:0.16, T:0.18
Consensus pattern (21 bp):
ATGAAAGGCTAAACCCTAACT
Found at i:25049 original size:23 final size:24
Alignment explanation
Indices: 24988--25078 Score: 79
Period size: 25 Copynumber: 3.9 Consensus size: 24
24978 AAAAATGACA
24988 TGACATGAAAGGC-AAACCCTAA-C
1 TGACATGAAA-GCTAAACCCTAAGC
25011 T---ATGAAATGCTAAACCCTAAG-
1 TGACATGAAA-GCTAAACCCTAAGC
*
25032 TGAGATGAAAGCTAAACCCT-AGCC
1 TGACATGAAAGCTAAACCCTAAG-C
*
25056 ATGACATGAAAGCCAAACCCTAA
1 -TGACATGAAAGCTAAACCCTAA
25079 CATGTCATCT
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
20 8 0.14
21 10 0.18
22 2 0.04
23 11 0.20
24 6 0.11
25 18 0.32
26 1 0.02
ACGTcount: A:0.43, C:0.24, G:0.16, T:0.16
Consensus pattern (24 bp):
TGACATGAAAGCTAAACCCTAAGC
Found at i:26364 original size:6 final size:6
Alignment explanation
Indices: 26353--26387 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
26343 CTTAAAATAA
26353 AATTTT AATTTT AATTTT AATTTT AATTTT AATTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTT
26388 GGGCTAAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
AATTTT
Found at i:26569 original size:100 final size:103
Alignment explanation
Indices: 26377--26635 Score: 411
Period size: 100 Copynumber: 2.5 Consensus size: 103
26367 TTTTAATTTT
* *
26377 AATTTTAATTT-GGGCTAAACTTAGTG-AATTAGTTATATATTTTATTTCTAAAACCCTATAACA
1 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAA-CCAATAACA
*
26440 ATATTATTAATTATGGAATTTACCCTTAAAATAAAAATAA
65 ATA-TATTAATTATGAAATTTACCCTTAAAATAAAAATAA
*
26480 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTTCTAAAACCAAT-AC-A
1 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCAATAACAA
* *
26543 TA-ATTAATTTTGAAATTTACCCTTAAAATAAAAATAT
66 TATATTAATTATGAAATTTACCCTTAAAATAAAAATAA
26580 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAAC
1 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAAC
26636 TATATGATAA
Statistics
Matches: 147, Mismatches: 7, Indels: 7
0.91 0.04 0.04
Matches are distributed among these distances:
100 87 0.59
102 3 0.02
103 13 0.09
104 19 0.13
105 25 0.17
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.42
Consensus pattern (103 bp):
AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCAATAACAA
TATATTAATTATGAAATTTACCCTTAAAATAAAAATAA
Found at i:28945 original size:2 final size:2
Alignment explanation
Indices: 28938--28968 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28928 TATTTTCGGG
28938 AT AT AT 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 AT AT AT A
28969 GTCGTAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30520 original size:14 final size:14
Alignment explanation
Indices: 30501--30528 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
30491 CTCGCTATAC
30501 CACTGGACACATAT
1 CACTGGACACATAT
30515 CACTGGACACATAT
1 CACTGGACACATAT
30529 GACATAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (14 bp):
CACTGGACACATAT
Done.