Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013300.1 Corchorus capsularis cultivar CVL-1 contig13321, 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: 11711
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30
Found at i:1096 original size:23 final size:23
Alignment explanation
Indices: 1049--1102 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1039 CAAAGAAAAA
**
1049 TCAAAATGAAGAAATTGAAGCTT
1 TCAAAATGAAGAAATAAAAGCTT
* *
1072 TCAAAATTAAGAAATAAAAGGTT
1 TCAAAATGAAGAAATAAAAGCTT
1095 TCCAAAAT
1 T-CAAAAT
1103 CAAAAGTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.52, C:0.09, G:0.13, T:0.26
Consensus pattern (23 bp):
TCAAAATGAAGAAATAAAAGCTT
Found at i:5512 original size:23 final size:22
Alignment explanation
Indices: 5469--5513 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
5459 ACGTTGGCAT
*
5469 TAAATAATAAGAAGAATAAGAA
1 TAAATAATAAGAAGAAAAAGAA
5491 TAAAGTAATAA-AATGAAAAAGAA
1 TAAA-TAATAAGAA-GAAAAAGAA
5514 ATGTTTCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.69, C:0.00, G:0.13, T:0.18
Consensus pattern (22 bp):
TAAATAATAAGAAGAAAAAGAA
Found at i:6192 original size:20 final size:23
Alignment explanation
Indices: 6167--6214 Score: 75
Period size: 20 Copynumber: 2.2 Consensus size: 23
6157 ATTCCCATAT
6167 AAAAGAAAAAA-AA-AGAG-GAA
1 AAAAGAAAAAATAAGAGAGAGAA
6187 AAAAGAAAAAATAAGAGAGAGAA
1 AAAAGAAAAAATAAGAGAGAGAA
6210 AAAAG
1 AAAAG
6215 GCACTTGGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.44
21 2 0.08
22 4 0.16
23 8 0.32
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (23 bp):
AAAAGAAAAAATAAGAGAGAGAA
Found at i:7360 original size:34 final size:35
Alignment explanation
Indices: 7306--7371 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 35
7296 TTCCATTTGT
7306 GAGTCCAAGATCAAAATTCGC-TTTCAAAATAAGA
1 GAGTCCAAGATCAAAATTCGCTTTTCAAAATAAGA
* * *
7340 GAGTCCATGATCGAAGTTCGCTTTTCAAAATA
1 GAGTCCAAGATCAAAATTCGCTTTTCAAAATA
7372 GGATTGCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 18 0.64
35 10 0.36
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (35 bp):
GAGTCCAAGATCAAAATTCGCTTTTCAAAATAAGA
Found at i:7397 original size:50 final size:50
Alignment explanation
Indices: 7340--7468 Score: 186
Period size: 50 Copynumber: 2.6 Consensus size: 50
7330 CAAAATAAGA
* * * * *
7340 GAGTCCATGATCGAAGTTCGCTTTTCAAAATAGGATTGCATTCCATTTGT
1 GAGTCCATGATCAAAATTTGCTTTTCAAAATAAGATTACATTCCATTTGT
*
7390 GAGTCCATGATCAAAATTTGCTTTTCAAAATAAGTTTACATTCCATTTGT
1 GAGTCCATGATCAAAATTTGCTTTTCAAAATAAGATTACATTCCATTTGT
* *
7440 GAGTACAAGATCAAAATTTGCTTTTCAAA
1 GAGTCCATGATCAAAATTTGCTTTTCAAA
7469 GGGCATTTTA
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 71 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (50 bp):
GAGTCCATGATCAAAATTTGCTTTTCAAAATAAGATTACATTCCATTTGT
Found at i:8159 original size:139 final size:138
Alignment explanation
Indices: 8016--8405 Score: 535
Period size: 139 Copynumber: 2.9 Consensus size: 138
8006 TTCCATAAGT
8016 CAAACTCGTTTCCATACGAGTCAATTCAAGCCTTGGTTCCATCCAAGTATTCAGGGGCTTTTCCA
1 CAAACTCGTTTCCATACGAGTCAATTCAAGCCTTGGTTCCATCCAAG-ATTCAGGGGCTTTTCCA
**
8081 CAAGCCAAACTCGTTTCCATAAGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAGCGGCTTT
65 CAAGCCAAACTCGTTTCCATAAGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAAAGGCTTT
8146 TCCACAAAC
130 TCCACAAAC
* *
8155 CAAACTCGTTCCCATACGAGTCAGTTCAA-CCTTTGGTTCCATCCAAGCATTCAGGGGCTTTTCC
1 CAAACTCGTTTCCATACGAGTCAATTCAAGCC-TTGGTTCCATCCAAG-ATTCAGGGGCTTTTCC
* *
8219 ACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCGGCAAAGGCTT
64 ACAAGCCAAACTCGTTTCCATAAGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAAAGGCTT
*
8284 TTCCACAAGC
129 TTCCACAAAC
* ** * * * *
8294 CAAACTCATTTCCACCCGAGTCAATT-TAGCCTTGGTTACAT-C-AG---CAAGGGCTTTTCTAC
1 CAAACTCGTTTCCATACGAGTCAATTCAAGCCTTGGTTCCATCCAAGATTCAGGGGCTTTTCCAC
* * * *
8353 TAGCCAAACTCGTTTCCATATGAGTTAGTT-TAGCCTTGGTTCCATCCAAGCAG
66 AAGCCAAACTCGTTTCCATAAGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
8406 GGGCTTTTGC
Statistics
Matches: 227, Mismatches: 22, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
131 21 0.09
132 40 0.18
136 2 0.01
137 1 0.00
138 12 0.05
139 151 0.67
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (138 bp):
CAAACTCGTTTCCATACGAGTCAATTCAAGCCTTGGTTCCATCCAAGATTCAGGGGCTTTTCCAC
AAGCCAAACTCGTTTCCATAAGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAAAGGCTTTT
CCACAAAC
Found at i:8176 original size:69 final size:69
Alignment explanation
Indices: 8003--8405 Score: 507
Period size: 70 Copynumber: 5.9 Consensus size: 69
7993 AATGCTTCGA
* * * * *
8003 CTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCAATTCAAGCCTTGGTTCCATCCAAGTATTC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA-GC
8068 AGGGG
65 AGGGG
*
8073 CTTTTCCACAAGCCAAACTCGTTTCCATAAGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
*
8138 GCGG
66 GGGG
* * *
8142 CTTTTCCACAAACCAAACTCGTTCCCATACGAGTCAGTTCAA-CCTTTGGTTCCATCCAAGCATT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCC-TTGGTTCCATCCAAGCA-G
8206 CAGGGG
64 CAGGGG
*
8212 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCGGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
**
8277 AAGG
66 GGGG
* ** * * *
8281 CTTTTCCACAAGCCAAACTCATTTCCACCCGAGTCAATT-TAGCCTTGGTTACAT-C-AGCA--A
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
8341 -GGG
66 GGGG
* * * * *
8344 CTTTTCTACTAGCCAAACTCGTTTCCATATGAGTTAGTT-TAGCCTTGGTTCCATCCAAGCAG
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
8406 GGGCTTTTGC
Statistics
Matches: 292, Mismatches: 35, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
63 47 0.16
64 2 0.01
65 4 0.01
66 3 0.01
67 1 0.00
68 15 0.05
69 100 0.34
70 118 0.40
71 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (69 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
GGGG
Found at i:11166 original size:2 final size:2
Alignment explanation
Indices: 11159--11183 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11149 TTTGGAATTA
11159 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
11184 AGGAAAATTA
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
Done.