Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006937.1 Corchorus capsularis cultivar CVL-1 contig06958, 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: 67015
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:2120 original size:24 final size:24
Alignment explanation
Indices: 2086--2133 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
2076 TCAACTTATT
* *
2086 GGTCTTTTCTTCCTCTATGGAAAA
1 GGTCTTCTCTTCCCCTATGGAAAA
2110 GGTCTTCTCTTCCCCTATGGAAAA
1 GGTCTTCTCTTCCCCTATGGAAAA
2134 TGCTCGATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.38
Consensus pattern (24 bp):
GGTCTTCTCTTCCCCTATGGAAAA
Found at i:3712 original size:21 final size:20
Alignment explanation
Indices: 3688--3726 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
3678 ATACTCAACA
3688 ATGGAGTATATATATATAAAC
1 ATGGAGTATATAT-TATAAAC
3709 ATGGAGTATATATTATAA
1 ATGGAGTATATATTATAA
3727 CTATTACAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.46, C:0.03, G:0.15, T:0.36
Consensus pattern (20 bp):
ATGGAGTATATATTATAAAC
Found at i:7083 original size:65 final size:65
Alignment explanation
Indices: 6931--7084 Score: 157
Period size: 65 Copynumber: 2.3 Consensus size: 65
6921 TTAATAACTG
** * * * *
6931 GATAACCACCTATATTTTAATTTTGATAACCTCGATTGGAATTTTGACAACTGCCCTATATAATT
1 GATAACCA-CTAT-TTAAAATTTTAATAACCTCAATTGAAATTTTGACAACTGCCCTATAAAATT
6996 AT
64 AT
* * ** *
6998 GATAACCATTCTTTGTAATTTTAATAACTTCAATTGAAATTTTGACAACTGCCCTATAAAA-TAT
1 GATAACCACTATTTAAAATTTTAATAACCTCAATTGAAATTTTGACAACTGCCCTATAAAATTA-
7062 T
65 T
**
7063 GATAATTACTATTTAAAATTTT
1 GATAACCACTATTTAAAATTTT
7085 GAAAACCACC
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
64 2 0.03
65 60 0.83
66 2 0.03
67 8 0.11
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (65 bp):
GATAACCACTATTTAAAATTTTAATAACCTCAATTGAAATTTTGACAACTGCCCTATAAAATTAT
Found at i:7163 original size:22 final size:21
Alignment explanation
Indices: 7138--7212 Score: 55
Period size: 22 Copynumber: 3.5 Consensus size: 21
7128 TTTGATTCAA
7138 TTGATAACCACCAAATGAAATT
1 TTGATAACCACC-AATGAAATT
* * *
7160 TTGATGACGACC-CTGTATAATT
1 TTGATAACCACCAATG-A-AATT
*
7182 TTGATAACC-TCATATGAAATT
1 TTGATAACCACCA-ATGAAATT
*
7203 TTGGTAACCA
1 TTGATAACCA
7213 TCTTTTGTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
20 2 0.05
21 14 0.35
22 22 0.55
23 2 0.05
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.33
Consensus pattern (21 bp):
TTGATAACCACCAATGAAATT
Found at i:7226 original size:22 final size:21
Alignment explanation
Indices: 7177--7235 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 21
7167 CGACCCTGTA
7177 TAATTTTGATAACCTCATATG
1 TAATTTTGATAACCTCATATG
* * * *
7198 AAATTTTGGTAACCATCTTTTG
1 TAATTTTGATAACC-TCATATG
7220 TAATTTTGATAACCTC
1 TAATTTTGATAACCTC
7236 CATAAAATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 14 0.45
22 17 0.55
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (21 bp):
TAATTTTGATAACCTCATATG
Found at i:7294 original size:22 final size:22
Alignment explanation
Indices: 7269--7320 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
7259 CTTACGAGAC
* *
7269 TTTGATGACAATCTTTTGAAAT
1 TTTGATAACAATCCTTTGAAAT
* *
7291 TTTGATAACTATCCTTTGTAAT
1 TTTGATAACAATCCTTTGAAAT
*
7313 TTTTATAA
1 TTTGATAA
7321 ACACTTTATG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.50
Consensus pattern (22 bp):
TTTGATAACAATCCTTTGAAAT
Found at i:11242 original size:39 final size:39
Alignment explanation
Indices: 11199--11278 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
11189 GCTGAAACTT
11199 GAGACTAAACCTAGAGCTAAATCAGTGTC-TGAATTTTAG
1 GAGACTAAACCTAGAGCTAAATCAGTG-CATGAATTTTAG
*
11238 GAGACTAAACCTAGTGCTAAATCAGTGCATGAATTTTAG
1 GAGACTAAACCTAGAGCTAAATCAGTGCATGAATTTTAG
11277 GA
1 GA
11279 AGAAATTTGA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
38 1 0.03
39 38 0.97
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (39 bp):
GAGACTAAACCTAGAGCTAAATCAGTGCATGAATTTTAG
Found at i:24620 original size:2 final size:2
Alignment explanation
Indices: 24613--24637 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24603 AAAAAGAATA
24613 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
24638 CTCCCTCTGT
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:30740 original size:17 final size:18
Alignment explanation
Indices: 30713--30751 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
30703 GCCAAAGTTT
30713 TAAAAAGTATAATAA-AAA
1 TAAAAAGTATAA-AATAAA
30731 TAAAAA-TATAAAATAAA
1 TAAAAAGTATAAAATAAA
30748 TAAA
1 TAAA
30752 TCCTACGGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 2 0.10
17 12 0.60
18 6 0.30
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (18 bp):
TAAAAAGTATAAAATAAA
Found at i:38332 original size:23 final size:23
Alignment explanation
Indices: 38306--38373 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 23
38296 GCAAATTGAA
38306 TTAGTTAAAGATCACTTGACTTG
1 TTAGTTAAAGATCACTTGACTTG
* * *
38329 TTAG-TAAACA--AATTGA---A
1 TTAGTTAAAGATCACTTGACTTG
*
38346 ATAGTTAAAGATCACTTGACTTG
1 TTAGTTAAAGATCACTTGACTTG
38369 TTAGT
1 TTAGT
38374 AAAATAAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 12
0.61 0.16 0.24
Matches are distributed among these distances:
17 3 0.10
18 5 0.16
20 10 0.32
22 5 0.16
23 8 0.26
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (23 bp):
TTAGTTAAAGATCACTTGACTTG
Found at i:38352 original size:40 final size:40
Alignment explanation
Indices: 38297--38376 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
38287 ATAAATGTTG
*
38297 CAAATTGAATTAGTTAAAGATCACTTGACTTGTTAGTAAA
1 CAAATTGAAATAGTTAAAGATCACTTGACTTGTTAGTAAA
38337 CAAATTGAAATAGTTAAAGATCACTTGACTTGTTAGTAAA
1 CAAATTGAAATAGTTAAAGATCACTTGACTTGTTAGTAAA
38377 ATAAAAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (40 bp):
CAAATTGAAATAGTTAAAGATCACTTGACTTGTTAGTAAA
Found at i:43557 original size:74 final size:74
Alignment explanation
Indices: 43475--43623 Score: 253
Period size: 74 Copynumber: 2.0 Consensus size: 74
43465 GGGAAATGTA
* * * *
43475 TAATTACGAAAAAGGGTAGAAGGAAAAGGAATGGGGGAAACTCATAGATGGGCCTTTTAGTCATC
1 TAATTACGAAAAAGGATAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCCTTTTAGTCACC
43540 CGAAAAGTG
66 CGAAAAGTG
*
43549 TAATTACGAAAAAGGATAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTTTAGTCACC
1 TAATTACGAAAAAGGATAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCCTTTTAGTCACC
43614 CGAAAAGTG
66 CGAAAAGTG
43623 T
1 T
43624 GAAAAGACCA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.40, C:0.11, G:0.29, T:0.20
Consensus pattern (74 bp):
TAATTACGAAAAAGGATAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCCTTTTAGTCACC
CGAAAAGTG
Found at i:43945 original size:20 final size:20
Alignment explanation
Indices: 43917--43957 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
43907 ACACAACTAA
43917 TTAAACATGTTAAG-TGTGTT
1 TTAAACATGTT-AGTTGTGTT
*
43937 TTAATCATGTTAGTTGTGTT
1 TTAAACATGTTAGTTGTGTT
43957 T
1 T
43958 AACACGGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.24, C:0.05, G:0.20, T:0.51
Consensus pattern (20 bp):
TTAAACATGTTAGTTGTGTT
Found at i:48349 original size:20 final size:21
Alignment explanation
Indices: 48312--48353 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
48302 TTACAAAGAA
*
48312 AACTCACAATTTCGTGAGAGT
1 AACTCACAATTCCGTGAGAGT
48333 AACTCAC-ATTCCGTGAGAGT
1 AACTCACAATTCCGTGAGAGT
48353 A
1 A
48354 GAACCCAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (21 bp):
AACTCACAATTCCGTGAGAGT
Found at i:54279 original size:2 final size:2
Alignment explanation
Indices: 54232--54263 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
54222 AGTATGTTAT
54232 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54264 GTAGTAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54290 original size:20 final size:20
Alignment explanation
Indices: 54253--54295 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
54243 ATATATATAT
* *
54253 ATATATATATAGTAGTAAAA
1 ATATATAAATACTAGTAAAA
* *
54273 ATATATAAATACTCGTAATA
1 ATATATAAATACTAGTAAAA
54293 ATA
1 ATA
54296 GTGATTGGAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (20 bp):
ATATATAAATACTAGTAAAA
Found at i:59938 original size:15 final size:15
Alignment explanation
Indices: 59914--59972 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
59904 TGCTAGGGTG
*
59914 AATGGCGCAAACAAC
1 AATGGTGCAAACAAC
*
59929 AATGGTGCAAACCAC
1 AATGGTGCAAACAAC
**
59944 AATGGTGTGAACAAC
1 AATGGTGCAAACAAC
* *
59959 TATGGTGCGAACAA
1 AATGGTGCAAACAA
59973 TCATGTTGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.15
Consensus pattern (15 bp):
AATGGTGCAAACAAC
Done.