Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015851.1 Corchorus capsularis cultivar CVL-1 contig15872, 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: 16678
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3939 original size:22 final size:22
Alignment explanation
Indices: 3914--3998 Score: 109
Period size: 22 Copynumber: 3.9 Consensus size: 22
3904 ACTAAGACTA
*
3914 TGGCTGTGAGATTCGGCCATAG
1 TGGCCGTGAGATTCGGCCATAG
* *
3936 TGGCCGTGAGATTCGGCCTTGG
1 TGGCCGTGAGATTCGGCCATAG
3958 TGGCCGTGAGA-TCTGGCCATAG
1 TGGCCGTGAGATTC-GGCCATAG
* *
3980 TGGTCATGAGATTCGGCCA
1 TGGCCGTGAGATTCGGCCA
3999 CATAATGGTA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
21 2 0.04
22 50 0.93
23 2 0.04
ACGTcount: A:0.16, C:0.21, G:0.36, T:0.26
Consensus pattern (22 bp):
TGGCCGTGAGATTCGGCCATAG
Found at i:3969 original size:44 final size:44
Alignment explanation
Indices: 3914--3997 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
3904 ACTAAGACTA
* *
3914 TGGCTGTGAGAT-TCGGCCATAGTGGCCGTGAGATTCGGCCTTGG
1 TGGCCGTGAGATCT-GGCCATAGTGGCCATGAGATTCGGCCTTGG
*
3958 TGGCCGTGAGATCTGGCCATAGTGGTCATGAGATTCGGCC
1 TGGCCGTGAGATCTGGCCATAGTGGCCATGAGATTCGGCC
3998 ACATAATGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 35 0.97
45 1 0.03
ACGTcount: A:0.15, C:0.21, G:0.37, T:0.26
Consensus pattern (44 bp):
TGGCCGTGAGATCTGGCCATAGTGGCCATGAGATTCGGCCTTGG
Found at i:4613 original size:17 final size:17
Alignment explanation
Indices: 4591--4639 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 17
4581 TTTTCTTTTG
4591 GACTCTTGTCTACTTGA
1 GACTCTTGTCTACTTGA
4608 GACTCTTGTCTACATACTTGA
1 GACTCTTG--T-C-TACTTGA
4629 GACTCTTGTCT
1 GACTCTTGTCT
4640 CCATCATTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
17 9 0.32
18 1 0.04
19 2 0.07
20 1 0.04
21 15 0.54
ACGTcount: A:0.18, C:0.24, G:0.16, T:0.41
Consensus pattern (17 bp):
GACTCTTGTCTACTTGA
Found at i:6078 original size:27 final size:27
Alignment explanation
Indices: 6048--6105 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
6038 GACAACCCAA
* * *
6048 TTTCTGTTCACGCCAAAAAATATTTGT
1 TTTCAGTTCACGACAAAAAATATCTGT
6075 TTTCAGTTCACGACAAAAAATATCTGT
1 TTTCAGTTCACGACAAAAAATATCTGT
6102 TTTC
1 TTTC
6106 GGTCAATGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (27 bp):
TTTCAGTTCACGACAAAAAATATCTGT
Found at i:6444 original size:2 final size:2
Alignment explanation
Indices: 6439--6472 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
6429 TCGTTTTTTT
6439 AG AG AG AG AG AG AG AG -G AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
6473 TTAGTCCCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6460 original size:15 final size:15
Alignment explanation
Indices: 6440--6469 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6430 CGTTTTTTTA
6440 GAGAGAGAGAGAGAG
1 GAGAGAGAGAGAGAG
6455 GAGAGAGAGAGAGAG
1 GAGAGAGAGAGAGAG
6470 AGATTAGTCC
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:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (15 bp):
GAGAGAGAGAGAGAG
Found at i:6461 original size:17 final size:17
Alignment explanation
Indices: 6439--6471 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
6429 TCGTTTTTTT
6439 AGAGAGAGAGAGAGAGG
1 AGAGAGAGAGAGAGAGG
6456 AGAGAGAGAGAGAGAG
1 AGAGAGAGAGAGAGAG
6472 ATTAGTCCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (17 bp):
AGAGAGAGAGAGAGAGG
Found at i:8510 original size:43 final size:44
Alignment explanation
Indices: 8463--8545 Score: 125
Period size: 43 Copynumber: 1.9 Consensus size: 44
8453 AGCGTGCCAA
8463 TCAATTTTGCA-TAAAAATTGATAAAAAGATGCGAG-GAAAATAT
1 TCAATTTTGCAGTAAAAA-TGATAAAAAGATGCGAGTGAAAATAT
* *
8506 TCAATTTTGTAGTAAAAATGATAAAAAGGTGCGAGTGAAA
1 TCAATTTTGCAGTAAAAATGATAAAAAGATGCGAGTGAAA
8546 TGTAAAGATT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
43 26 0.72
44 10 0.28
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (44 bp):
TCAATTTTGCAGTAAAAATGATAAAAAGATGCGAGTGAAAATAT
Found at i:8852 original size:22 final size:22
Alignment explanation
Indices: 8818--8869 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
8808 GATTTACAAA
8818 TGAGAG-TGAAAGCCAAGG-GCT
1 TGAGAGTTGAAAG-CAAGGAGCT
*
8839 TGAGAGTTGAAAGCACGGAGCT
1 TGAGAGTTGAAAGCAAGGAGCT
8861 TGAGAGTTG
1 TGAGAGTTG
8870 TAATCACGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 10 0.36
22 18 0.64
ACGTcount: A:0.31, C:0.12, G:0.38, T:0.19
Consensus pattern (22 bp):
TGAGAGTTGAAAGCAAGGAGCT
Found at i:8877 original size:22 final size:22
Alignment explanation
Indices: 8836--8884 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
8826 AAAGCCAAGG
*
8836 GCTTGAGAGTTGAAAGCACGGA
1 GCTTGAGAGTTGAAAGCACGAA
* *
8858 GCTTGAGAGTTGTAATCACGAA
1 GCTTGAGAGTTGAAAGCACGAA
8880 GCTTG
1 GCTTG
8885 TTTTGATTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.24
Consensus pattern (22 bp):
GCTTGAGAGTTGAAAGCACGAA
Found at i:12179 original size:21 final size:21
Alignment explanation
Indices: 12153--12195 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12143 TTTCCCGCAA
12153 CAAGTCCCGGGCAGGAATTGT
1 CAAGTCCCGGGCAGGAATTGT
* * *
12174 CAAGTCCTGGGTAGGACTTGT
1 CAAGTCCCGGGCAGGAATTGT
12195 C
1 C
12196 CTACAATTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.23, G:0.33, T:0.23
Consensus pattern (21 bp):
CAAGTCCCGGGCAGGAATTGT
Found at i:14155 original size:10 final size:10
Alignment explanation
Indices: 14140--14165 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
14130 AGTTGCTGCC
14140 AAATTCCAGA
1 AAATTCCAGA
14150 AAATTCCAGA
1 AAATTCCAGA
14160 AAATTC
1 AAATTC
14166 TAAAGTCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (10 bp):
AAATTCCAGA
Found at i:15390 original size:20 final size:21
Alignment explanation
Indices: 15351--15390 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
15341 GCTTGGTCCC
* *
15351 TTTGCTTCCAAATTTCAATTT
1 TTTGCTACCAAATCTCAATTT
15372 TTTGCTACCAAA-CTCAATT
1 TTTGCTACCAAATCTCAATT
15391 CCAACTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.45
Consensus pattern (21 bp):
TTTGCTACCAAATCTCAATTT
Done.