Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006523.1 Corchorus capsularis cultivar CVL-1 contig06544, 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: 34089
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1439 original size:131 final size:131
Alignment explanation
Indices: 1183--1428 Score: 386
Period size: 131 Copynumber: 1.9 Consensus size: 131
1173 TTGTTTAAAT
*
1183 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAACATCCATCTAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAACATCCATATAACTA
*
1248 TTTCATTTTTACCATTTTACTATTTTAATTAAAAAAAATTGATATATTAGAAAGTTTTAAACATA
66 TTTCATTTTTACCATTTTACTACTTTAATTAAAAAAAATTGATATATTAGAAAGTTTTAAACATA
1313 C
131 C
* * *
1314 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATTCTTATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAACATCCATATAACTA
* * * *
1379 TTTTATTTTTGATCATTTTACTCCTTTAATT-AAAAAACTTAGATATATTA
66 TTTCATTTTT-ACCATTTTACTACTTTAATTAAAAAAAATT-GATATATTA
1429 TAATTTTTAA
Statistics
Matches: 104, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
131 78 0.75
132 26 0.25
ACGTcount: A:0.37, C:0.12, G:0.03, T:0.48
Consensus pattern (131 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAACATCCATATAACTA
TTTCATTTTTACCATTTTACTACTTTAATTAAAAAAAATTGATATATTAGAAAGTTTTAAACATA
C
Found at i:3152 original size:18 final size:18
Alignment explanation
Indices: 3129--3183 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
3119 CTGCCATGTC
3129 ATATTTTTTATTAAAAAA
1 ATATTTTTTATTAAAAAA
3147 ATATTTTTTA--AAAAAA
1 ATATTTTTTATTAAAAAA
3163 TATATATTTTT-TTAAAAAA
1 -ATAT-TTTTTATTAAAAAA
3182 AT
1 AT
3184 TGGGTGAGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 6 0.18
17 4 0.12
18 17 0.52
19 6 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATTTTTTATTAAAAAA
Found at i:3159 original size:15 final size:16
Alignment explanation
Indices: 3134--3165 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3124 ATGTCATATT
3134 TTTTATTAAAAAAATA
1 TTTTATTAAAAAAATA
3150 TTTT-TTAAAAAAATA
1 TTTTATTAAAAAAATA
3165 T
1 T
3166 ATATTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTTATTAAAAAAATA
Found at i:6194 original size:41 final size:41
Alignment explanation
Indices: 6135--6212 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
6125 TTTTTAACTA
*
6135 GGGGCCAAACCTGGATTTAATTTCTTACCTTAATTATCAGG
1 GGGGCCAAACCTGAATTTAATTTCTTACCTTAATTATCAGG
* * *
6176 GGGGCTAAACCTGAATTTAATTTGTTTCCTTAATTAT
1 GGGGCCAAACCTGAATTTAATTTCTTACCTTAATTAT
6213 TAGGAGGGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (41 bp):
GGGGCCAAACCTGAATTTAATTTCTTACCTTAATTATCAGG
Found at i:8692 original size:21 final size:20
Alignment explanation
Indices: 8668--8724 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
8658 CATTCATGGG
8668 AAAATAATAATAATTATTCCA
1 AAAATAATAATAATTATT-CA
* * *
8689 AAAATAATTATTATTATTTA
1 AAAATAATAATAATTATTCA
*
8709 ATAATAATTAATAATT
1 AAAATAA-TAATAATT
8725 TCGGTCCTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
20 7 0.24
21 22 0.76
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAATAATAATAATTATTCA
Found at i:13789 original size:30 final size:30
Alignment explanation
Indices: 13750--13856 Score: 187
Period size: 30 Copynumber: 3.5 Consensus size: 30
13740 GAGTATGAAG
13750 AGGAGGAAGATTCTGATCTCTTTGTTTGTGA
1 AGGA-GAAGATTCTGATCTCTTTGTTTGTGA
13781 AGGAGAAGATTCTGATCTCTTTGTTTGTGA
1 AGGAGAAGATTCTGATCTCTTTGTTTGTGA
13811 AGGAGAAGATTCTGATCTCTTTGTTTGTGA
1 AGGAGAAGATTCTGATCTCTTTGTTTGTGA
* *
13841 AGGAGAACAATCTGAT
1 AGGAGAAGATTCTGAT
13857 TTTGTTCTTG
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
30 70 0.95
31 4 0.05
ACGTcount: A:0.26, C:0.10, G:0.27, T:0.36
Consensus pattern (30 bp):
AGGAGAAGATTCTGATCTCTTTGTTTGTGA
Found at i:13946 original size:45 final size:45
Alignment explanation
Indices: 13830--13936 Score: 196
Period size: 45 Copynumber: 2.4 Consensus size: 45
13820 TTCTGATCTC
**
13830 TTTGTTTGTGAAGGAGAACAATCTGATTTTGTTCTTGATGAAGGA
1 TTTGTTTGTGAAGGAGAACAATCTGATTTCCTTCTTGATGAAGGA
13875 TTTGTTTGTGAAGGAGAACAATCTGATTTCCTTCTTGATGAAGGA
1 TTTGTTTGTGAAGGAGAACAATCTGATTTCCTTCTTGATGAAGGA
13920 TTTGTTTGTGAAGGAGA
1 TTTGTTTGTGAAGGAGA
13937 GGATTCTGAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 60 1.00
ACGTcount: A:0.26, C:0.07, G:0.27, T:0.39
Consensus pattern (45 bp):
TTTGTTTGTGAAGGAGAACAATCTGATTTCCTTCTTGATGAAGGA
Found at i:13958 original size:45 final size:45
Alignment explanation
Indices: 13830--13959 Score: 176
Period size: 45 Copynumber: 2.9 Consensus size: 45
13820 TTCTGATCTC
13830 TTTGTTTGTGAAGGAGAACAATCTGATTTTGT-TCTTGATGAAGGA
1 TTTGTTTGTGAAGGAGAACAATCTGA-TTTGTCTCTTGATGAAGGA
*
13875 TTTGTTTGTGAAGGAGAACAATCTGATTT-CCTTCTTGATGAAGGA
1 TTTGTTTGTGAAGGAGAACAATCTGATTTGTC-TCTTGATGAAGGA
** *
13920 TTTGTTTGTGAAGGAGAGGATTCTGATCTTGTCT-TTGATG
1 TTTGTTTGTGAAGGAGAACAATCTGAT-TTGTCTCTTGATG
13960 GAAAAAGACT
Statistics
Matches: 76, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
44 3 0.04
45 69 0.91
46 3 0.04
47 1 0.01
ACGTcount: A:0.24, C:0.08, G:0.27, T:0.41
Consensus pattern (45 bp):
TTTGTTTGTGAAGGAGAACAATCTGATTTGTCTCTTGATGAAGGA
Found at i:15637 original size:16 final size:16
Alignment explanation
Indices: 15588--15637 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
15578 GATAATTCAT
15588 CAAATACTTTATCAAA
1 CAAATACTTTATCAAA
* *
15604 C--ATA-TTCAACAAA
1 CAAATACTTTATCAAA
*
15617 AAAATACTTTATCAAA
1 CAAATACTTTATCAAA
15633 CAAAT
1 CAAAT
15638 TTAGAAACAA
Statistics
Matches: 25, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
13 7 0.28
14 3 0.12
15 3 0.12
16 12 0.48
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.28
Consensus pattern (16 bp):
CAAATACTTTATCAAA
Found at i:16363 original size:105 final size:106
Alignment explanation
Indices: 16189--16451 Score: 325
Period size: 107 Copynumber: 2.5 Consensus size: 106
16179 AATTTTTCTA
* ** * * *
16189 ACCCTTAAAATAAAATTTTACTTTTGATTT-GGGCTAAATTTAGTG-AATTAATTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
**
16252 TTTCTAAAACCCTATAACAAT-ATTATTAATTATGGAACTT
66 TTTCTAAAACCCTATAACAATAATTATTAATTATAAAACTT
* * * * * *
16292 ATCCTTAAAATGAAAATAAAATTTTAATTTGGGGCTAAACTCAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
* *
16357 TTTCTAAAACCCTATAACAATAAATTATTAATTTTAAAATTT
66 TTTCTAAAACCCTATAACAAT-AATTATTAATTATAAAACTT
** *
16399 ACCCTTAAAATAAAAATAAAATTTTAATTTGGAACTAAACTTAATGAAATTAA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAA
16452 GGTTAAACTT
Statistics
Matches: 133, Mismatches: 23, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
103 23 0.17
104 13 0.10
105 36 0.27
107 61 0.46
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (106 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
TTTCTAAAACCCTATAACAATAATTATTAATTATAAAACTT
Found at i:22857 original size:15 final size:15
Alignment explanation
Indices: 22837--22888 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
22827 CTCGAACCTG
*
22837 GAAAAACCCGAATCC
1 GAAAAACCAGAATCC
**
22852 GAAAAAGCTTGAATCC
1 GAAAAA-CCAGAATCC
* *
22868 GAAAAATCAGAACCC
1 GAAAAACCAGAATCC
22883 GAAAAA
1 GAAAAA
22889 ACCTGAACCC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
15 17 0.57
16 13 0.43
ACGTcount: A:0.52, C:0.23, G:0.15, T:0.10
Consensus pattern (15 bp):
GAAAAACCAGAATCC
Found at i:22857 original size:16 final size:16
Alignment explanation
Indices: 22838--22901 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 16
22828 TCGAACCTGG
* *
22838 AAAAACCCGAATCCGA
1 AAAAACCTGAACCCGA
* * *
22854 AAAAGCTTGAATCCG-
1 AAAAACCTGAACCCGA
* *
22869 AAAAATCAGAACCCGA
1 AAAAACCTGAACCCGA
22885 AAAAACCTGAACCCGA
1 AAAAACCTGAACCCGA
22901 A
1 A
22902 TCCGAAGATG
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
15 10 0.27
16 27 0.73
ACGTcount: A:0.50, C:0.27, G:0.14, T:0.09
Consensus pattern (16 bp):
AAAAACCTGAACCCGA
Found at i:24592 original size:25 final size:25
Alignment explanation
Indices: 24543--24593 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
24533 TTAGTAGAAT
*
24543 AATTGTAAAAGTTTATTTCTAAAAA
1 AATTGTAAAAGTATATTTCTAAAAA
24568 AATTGTAAAAGAATATATTT-TAAAAA
1 AATTGTAAAAG--TATATTTCTAAAAA
24594 TTCTAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 6 0.26
27 6 0.26
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (25 bp):
AATTGTAAAAGTATATTTCTAAAAA
Found at i:25675 original size:31 final size:31
Alignment explanation
Indices: 25637--25702 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
25627 AATTTTATGT
* *
25637 TTTCCGATTGTACCCCTTTTTT-AAAAATATA
1 TTTCCGATTATA-CCATTTTTTAAAAAATATA
25668 TTTCCGATTATACCATTTTTTAAAAAATATA
1 TTTCCGATTATACCATTTTTTAAAAAATATA
25699 TTTC
1 TTTC
25703 TAAATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 8 0.25
31 24 0.75
ACGTcount: A:0.32, C:0.17, G:0.05, T:0.47
Consensus pattern (31 bp):
TTTCCGATTATACCATTTTTTAAAAAATATA
Found at i:30956 original size:29 final size:29
Alignment explanation
Indices: 30914--30972 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
30904 GCTAGTAGTA
30914 ACTATAGTACATCTAAATAAAAAAAACAC
1 ACTATAGTACATCTAAATAAAAAAAACAC
30943 ACTATAGTACATCTAAATAAAAAAAACAC
1 ACTATAGTACATCTAAATAAAAAAAACAC
30972 A
1 A
30973 TTTAACGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.59, C:0.17, G:0.03, T:0.20
Consensus pattern (29 bp):
ACTATAGTACATCTAAATAAAAAAAACAC
Done.