Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015271.1 Corchorus capsularis cultivar CVL-1 contig15292, 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: 8855
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:2889 original size:14 final size:14
Alignment explanation
Indices: 2870--2898 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2860 GATACGAATC
2870 TAGTTGTATATCGG
1 TAGTTGTATATCGG
2884 TAGTTGTATATCGG
1 TAGTTGTATATCGG
2898 T
1 T
2899 CCAAATCCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.28, T:0.45
Consensus pattern (14 bp):
TAGTTGTATATCGG
Found at i:4031 original size:32 final size:32
Alignment explanation
Indices: 3945--4136 Score: 197
Period size: 32 Copynumber: 6.0 Consensus size: 32
3935 GGCGCATCAT
* * **
3945 AAGTTATCAGTAGAATGAAGTAGTAGTAAAAG
1 AAGTAATCAGCAGAATGAAGTAAAAGTAAAAG
* ** * *
3977 GAGTAATCAGTGGAA-AAGAGTAATAGTAAAAG
1 AAGTAATCAGCAGAATGA-AGTAAAAGTAAAAG
* *
4009 AAGGAATCAGCAGAGTGAAGTAAAAGTAAAAG
1 AAGTAATCAGCAGAATGAAGTAAAAGTAAAAG
* *
4041 AAGTAATCAACAGAATGGAGTAAAAGTAAAAG
1 AAGTAATCAGCAGAATGAAGTAAAAGTAAAAG
* *
4073 AAGTAAACAGCAAAATGAAGTAAAAGTAAAAG
1 AAGTAATCAGCAGAATGAAGTAAAAGTAAAAG
* * * *
4105 AAGAAATTAGCAGAATGAAGTAGAATTAAAAG
1 AAGTAATCAGCAGAATGAAGTAAAAGTAAAAG
4137 GAGTCAAAGG
Statistics
Matches: 132, Mismatches: 26, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
31 1 0.01
32 130 0.98
33 1 0.01
ACGTcount: A:0.54, C:0.05, G:0.24, T:0.17
Consensus pattern (32 bp):
AAGTAATCAGCAGAATGAAGTAAAAGTAAAAG
Found at i:4147 original size:9 final size:9
Alignment explanation
Indices: 4131--4238 Score: 107
Period size: 9 Copynumber: 12.4 Consensus size: 9
4121 GAAGTAGAAT
4131 TAAAAGGAG
1 TAAAAGGAG
*
4140 TCAAAGGAG
1 TAAAAGGAG
4149 TAAAAGGAG
1 TAAAAGGAG
*
4158 TAAAAGAAG
1 TAAAAGGAG
*
4167 TAAAAAGAG
1 TAAAAGGAG
*
4176 TAAAAAGAG
1 TAAAAGGAG
*
4185 TAAAA-AAG
1 TAAAAGGAG
4193 TAAAAGGAG
1 TAAAAGGAG
*
4202 TAAAAGAAG
1 TAAAAGGAG
*
4211 T--AA-TAG
1 TAAAAGGAG
*
4217 TAAAGGGAG
1 TAAAAGGAG
*
4226 TAAAATGAG
1 TAAAAGGAG
4235 TAAA
1 TAAA
4239 CAGTAGTAAT
Statistics
Matches: 82, Mismatches: 13, Indels: 8
0.80 0.13 0.08
Matches are distributed among these distances:
6 3 0.04
7 2 0.02
8 8 0.10
9 69 0.84
ACGTcount: A:0.59, C:0.01, G:0.26, T:0.14
Consensus pattern (9 bp):
TAAAAGGAG
Found at i:4236 original size:24 final size:23
Alignment explanation
Indices: 4142--4243 Score: 87
Period size: 24 Copynumber: 4.0 Consensus size: 23
4132 AAAAGGAGTC
4142 AAAGGAGTAAAAGGAGTAAAAGAAGTA
1 AAAGGAGTAAAA-GAGT--AA-AAGTA
*
4169 AAAAGAGTAAAAAGAGTAAAAAAGTA
1 AAAGGAGT-AAAAGAGT--AAAAGTA
*
4195 AAAGGAGTAAAAGAAGTAATAGTA
1 AAAGGAGTAAAAG-AGTAAAAGTA
*
4219 AAGGGAGTAAAATGAGTAAACAGTA
1 AAAGGAGTAAAA-GAGTAAA-AGTA
4244 GTAATTAGCT
Statistics
Matches: 66, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
24 22 0.33
25 10 0.15
26 15 0.23
27 15 0.23
28 4 0.06
ACGTcount: A:0.60, C:0.01, G:0.25, T:0.14
Consensus pattern (23 bp):
AAAGGAGTAAAAGAGTAAAAGTA
Found at i:4303 original size:67 final size:67
Alignment explanation
Indices: 4215--4353 Score: 208
Period size: 67 Copynumber: 2.1 Consensus size: 67
4205 AAGAAGTAAT
* ** *
4215 AGTAAAGGGAGTAAAATGAGTAAACAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAAACAG
1 AGTAAAAGGAGTAAAATGAGTAAACAGTAGTAATTAGCTTAATTCAGAACAATTAAGTTAAACAA
4280 GA
66 GA
* *
4282 AGTAAAAGGAGT-AAATGGAGTAACCAGTAGTAATTAGCTTAATTCAGAACAATTAAGTTAATCA
1 AGTAAAAGGAGTAAAAT-GAGTAAACAGTAGTAATTAGCTTAATTCAGAACAATTAAGTTAAACA
4346 AGA
65 AGA
4349 AGTAA
1 AGTAA
4354 GTAGTAAACA
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 4 0.06
67 61 0.94
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.25
Consensus pattern (67 bp):
AGTAAAAGGAGTAAAATGAGTAAACAGTAGTAATTAGCTTAATTCAGAACAATTAAGTTAAACAA
GA
Found at i:5810 original size:68 final size:71
Alignment explanation
Indices: 5678--5883 Score: 222
Period size: 68 Copynumber: 2.9 Consensus size: 71
5668 CTCTTTTTAG
* * * * * * *
5678 ATTAAATTGTTTATTGACTCCACTTAATTATCTTGAATTAAGCTAT-TTTATTGACTCCACTTAA
1 ATTAAGTTCTTTATT-ACTCTACTAAATTACCCTGAATTAAG-T-TCTTTATTGACTCTACTTAA
5742 TTACCCTGA
63 TTACCCTGA
*
5751 ATTAAGTTCTTTATT-CT-T-CTAAATTACCCTGAATTAAGTTCTTTATTGGCTCTACTTAATTA
1 ATTAAGTTCTTTATTACTCTACTAAATTACCCTGAATTAAGTTCTTTATTGACTCTACTTAATTA
5813 CCCTGA
66 CCCTGA
* * ** * *
5819 ATTAAGTTCTTTATTGACTCTACTTAATTACCCTAAATTAAGCCCTTTATTAACTTTACTTAATT
1 ATTAAGTTCTTTATT-ACTCTACTAAATTACCCTGAATTAAGTTCTTTATTGACTCTACTTAATT
5884 TACTTCCCTG
Statistics
Matches: 113, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
67 1 0.01
68 41 0.36
69 17 0.15
70 2 0.02
71 3 0.03
72 36 0.32
73 13 0.12
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.45
Consensus pattern (71 bp):
ATTAAGTTCTTTATTACTCTACTAAATTACCCTGAATTAAGTTCTTTATTGACTCTACTTAATTA
CCCTGA
Found at i:5819 original size:36 final size:36
Alignment explanation
Indices: 5678--5883 Score: 242
Period size: 36 Copynumber: 5.8 Consensus size: 36
5668 CTCTTTTTAG
* * * * *
5678 ATTAAATTGTTTATTGACTCCACTTAATTATCTTGA
1 ATTAAGTTCTTTATTGACTCTACTTAATTACCCTGA
*
5714 ATTAAGCTAT-TTTATTGACTCCACTTAATTACCCTGA
1 ATTAAG-T-TCTTTATTGACTCTACTTAATTACCCTGA
*
5751 ATTAAGTTCTTTATT--CT-T-CTAAATTACCCTGA
1 ATTAAGTTCTTTATTGACTCTACTTAATTACCCTGA
*
5783 ATTAAGTTCTTTATTGGCTCTACTTAATTACCCTGA
1 ATTAAGTTCTTTATTGACTCTACTTAATTACCCTGA
*
5819 ATTAAGTTCTTTATTGACTCTACTTAATTACCCTAA
1 ATTAAGTTCTTTATTGACTCTACTTAATTACCCTGA
** * *
5855 ATTAAGCCCTTTATTAACTTTACTTAATT
1 ATTAAGTTCTTTATTGACTCTACTTAATT
5884 TACTTCCCTG
Statistics
Matches: 151, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
32 28 0.19
34 4 0.03
35 2 0.01
36 84 0.56
37 32 0.21
38 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.45
Consensus pattern (36 bp):
ATTAAGTTCTTTATTGACTCTACTTAATTACCCTGA
Found at i:5917 original size:41 final size:41
Alignment explanation
Indices: 5872--6051 Score: 256
Period size: 41 Copynumber: 4.4 Consensus size: 41
5862 CCTTTATTAA
* * *
5872 CTTTACTTAATTTACTTCCCTGAAATTAAGTCTGTGCT-TGT
1 CTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTAT-T
*
5913 CTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTATA
1 CTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTATT
* *
5954 CTTTACTTAATTTCCTTCCTTGAAATTAAGTATGTGCTATT
1 CTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTATT
* *
5995 CTTGACCTAATTTCCTTCCTTCAAATTAAGTCTGTGCT-TGT
1 CTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTAT-T
6036 CTTTACCTAATTTCCT
1 CTTTACCTAATTTCCT
6052 GTGATATCAT
Statistics
Matches: 125, Mismatches: 12, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
40 1 0.01
41 123 0.98
42 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (41 bp):
CTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTATT
Found at i:5939 original size:82 final size:82
Alignment explanation
Indices: 5853--6029 Score: 232
Period size: 82 Copynumber: 2.2 Consensus size: 82
5843 TAATTACCCT
* * *
5853 AAATTAAGCCCTTTATTA-ACTTTACTTAATTTACTTCCCTGAAATTAAGTCTGTGCT-TGTCTT
1 AAATTAAG-CCTGTACTATACTTTACTTAATTTACTTCCCTGAAATTAAGTATGTGCTAT-TCTT
* *
5916 TACCTAATTTCCTTCCTTG
64 GACCTAATTTCCTTCCTTC
* * * *
5935 AAATTAAGTCTGTGCTATACTTTACTTAATTTCCTTCCTTGAAATTAAGTATGTGCTATTCTTGA
1 AAATTAAGCCTGTACTATACTTTACTTAATTTACTTCCCTGAAATTAAGTATGTGCTATTCTTGA
6000 CCTAATTTCCTTCCTTC
66 CCTAATTTCCTTCCTTC
*
6017 AAATTAAGTCTGT
1 AAATTAAGCCTGT
6030 GCTTGTCTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
81 5 0.06
82 78 0.93
83 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (82 bp):
AAATTAAGCCTGTACTATACTTTACTTAATTTACTTCCCTGAAATTAAGTATGTGCTATTCTTGA
CCTAATTTCCTTCCTTC
Found at i:7725 original size:21 final size:20
Alignment explanation
Indices: 7701--7748 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
7691 TAGATTTAGA
* *
7701 TTTAATTTACTTTGCTTAGTT
1 TTTAATTTA-ATTGCTTACTT
* *
7722 TTTAGTTTAATTGCTTTCTT
1 TTTAATTTAATTGCTTACTT
7742 TTTAATT
1 TTTAATT
7749 GATAATTTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.19, C:0.08, G:0.08, T:0.65
Consensus pattern (20 bp):
TTTAATTTAATTGCTTACTT
Found at i:8031 original size:20 final size:20
Alignment explanation
Indices: 8006--8049 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
7996 TTTTTTCTAA
8006 GAAAAAAAAAAATTCGCGTC
1 GAAAAAAAAAAATTCGCGTC
* *
8026 GAAAAAAAAAAATTTGTGTC
1 GAAAAAAAAAAATTCGCGTC
8046 GAAA
1 GAAA
8050 TAAATTTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.57, C:0.09, G:0.16, T:0.18
Consensus pattern (20 bp):
GAAAAAAAAAAATTCGCGTC
Done.