Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013992.1 Corchorus capsularis cultivar CVL-1 contig14013, 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: 13645
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:435 original size:55 final size:54
Alignment explanation
Indices: 344--455 Score: 179
Period size: 55 Copynumber: 2.1 Consensus size: 54
334 AAAAAAAAGG
*
344 AAATATTAAAATCATACAAATACTAAAACAAAAAAAATGAAGATTAACAATGAT
1 AAATATTAAAATCATAAAAATACTAAAACAAAAAAAATGAAGATTAACAATGAT
* * *
398 AAATATTCAAATCATAAAATATACTAAAACAACAAAAATGAAGATTGACAATGAT
1 AAATATTAAAATCATAAAA-ATACTAAAACAAAAAAAATGAAGATTAACAATGAT
453 AAA
1 AAA
456 GATCACGTAC
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
54 17 0.32
55 36 0.68
ACGTcount: A:0.62, C:0.10, G:0.06, T:0.22
Consensus pattern (54 bp):
AAATATTAAAATCATAAAAATACTAAAACAAAAAAAATGAAGATTAACAATGAT
Found at i:8318 original size:16 final size:16
Alignment explanation
Indices: 8282--8342 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 16
8272 AACCCGCCCG
*
8282 AACCCGAACCCGAAAT
1 AACCCGAACCCGAAAC
* *
8298 TACCCGAACCCGAGAC
1 AACCCGAACCCGAAAC
* * *
8314 AACCCAAATCCGAACC
1 AACCCGAACCCGAAAC
**
8330 CGCCCGAACCCGA
1 AACCCGAACCCGA
8343 CCCGAGCCTG
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.36, C:0.44, G:0.15, T:0.05
Consensus pattern (16 bp):
AACCCGAACCCGAAAC
Found at i:10139 original size:34 final size:34
Alignment explanation
Indices: 10101--10173 Score: 130
Period size: 34 Copynumber: 2.1 Consensus size: 34
10091 AATATAAGTA
10101 ATTTTAATGG-TATTTTAGTAATTGACTAATTAAG
1 ATTTTAA-GGATATTTTAGTAATTGACTAATTAAG
10135 ATTTTAAGGATATTTTAGTAATTGACTAATTAAG
1 ATTTTAAGGATATTTTAGTAATTGACTAATTAAG
10169 ATTTT
1 ATTTT
10174 TGAGTTCGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 2 0.05
34 36 0.95
ACGTcount: A:0.36, C:0.03, G:0.14, T:0.48
Consensus pattern (34 bp):
ATTTTAAGGATATTTTAGTAATTGACTAATTAAG
Found at i:11389 original size:401 final size:392
Alignment explanation
Indices: 10660--11412 Score: 1078
Period size: 401 Copynumber: 1.9 Consensus size: 392
10650 TTCTAAGCAA
*
10660 TTTTGCTTTATTTTGGTAGTCGTATGTGTCATTTTACCCCTATATTTCTCATATTTGCTATTGAA
1 TTTTGCTTTATTTTGGTAGTCGTATGTGTCATTTTACCCCTATATTTCTCATATTTCCTATTGAA
* *
10725 GCCTCATTTGGAACTATGTTTTAGAAAGATGAAGATTTAGAGCCATTTTGGATCAATTAGGGGAA
66 GCCTAATTTGGAACTATGTTTTAGAAAGATGAAGATTTAGAGCCATTTTGGATCAATTAGGAGAA
* * *
10790 ACTATTGATTTTATCTCATTTCGACCCATTAGGCTGGTTTGAGTCCATGAAGCCCAAATTGACAA
131 ACTATTGATTTTATCTCATTTCGAACCAGTAGGCTGGTTTGAGTCCATGAAGCACAAATTGACAA
* * * * * *
10855 GTCATATGTCTTGAAACCTAAATTTGATATTTTTAGGCGTAATTCGTTAATATGGAAGCCCAAAA
196 GCCAGATATATTGAAACCTAAATTTGATATTCTTAGGCGCAATTCGTTAATATGGAAGCCCAAAA
* *
10920 AAGGAGTTCAATTCCAATCAGTAACTATGATGCGATAATAATCCAGCCCTAATGCAGCATTGTTA
261 AAGGAGTTCAAGTCCAATCAGTAACTATGATGCGATAATAATCCAACCCTAATGCAGCATTGTTA
10985 AATCCTATTCAAAGGAGGACTTCACAAGAAAATTCATATCTTTTGATCCAGAGCTCAAAAAAATG
326 AATCCTATTCAAAGGAGGACTTCACAAGAAAATTCATATCTTTTGATCCAGAGCTCAAAAAAATG
11050 AG
391 AG
* * * **
11052 TTTTGTTTTATTTTGGTAGTCGTATGTGTCGTTTTACCCCTATATTTCTCATTTTTCCTATTTTA
1 TTTTGCTTTATTTTGGTAGTCGTATGTGTCATTTTACCCCTATATTTCTCATATTTCCTATTGAA
* * * *
11117 GACC-AATTTGGAGCTATGTTTTAGAAATATGAAGATTTAGAGGCATTTTGGATCAATTTGGAGA
66 G-CCTAATTTGGAACTATGTTTTAGAAAGATGAAGATTTAGAGCCATTTTGGATCAATTAGGAGA
*
11181 AACTATTGATTTTGTCTCATTTCGAACCAGTAGGTCCATTAGACCCGTTTGAGTCCATGAAGCAC
130 AACTATTGATTTTATCTCATTTCGAACCAGTAGG--C--T-G----GTTTGAGTCCATGAAGCAC
* ** *
11246 AAATTGTCAAGCCAGATATATTGAAGGCTAAATTTGATATTCTTAGGTGCAATTCGTTAATATGG
186 AAATTGACAAGCCAGATATATTGAAACCTAAATTTGATATTCTTAGGCGCAATTCGTTAATATGG
* * * * * *
11311 AAGCCCGAAAATGGAGTTCAAGTCCAATCAGTAATTATGATGC-AGTAATGATTCAACCCTGATG
251 AAGCCCAAAAAAGGAGTTCAAGTCCAATCAGTAACTATGATGCGA-TAATAATCCAACCCTAATG
*
11375 CAGCATTGTTAAATCCTATTGAAAGGAGGACTTCACAA
315 CAGCATTGTTAAATCCTATTCAAAGGAGGACTTCACAA
11413 TAGCAGTTTT
Statistics
Matches: 315, Mismatches: 35, Indels: 13
0.87 0.10 0.04
Matches are distributed among these distances:
392 145 0.46
393 2 0.01
394 1 0.00
396 1 0.00
397 1 0.00
400 1 0.00
401 164 0.52
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (392 bp):
TTTTGCTTTATTTTGGTAGTCGTATGTGTCATTTTACCCCTATATTTCTCATATTTCCTATTGAA
GCCTAATTTGGAACTATGTTTTAGAAAGATGAAGATTTAGAGCCATTTTGGATCAATTAGGAGAA
ACTATTGATTTTATCTCATTTCGAACCAGTAGGCTGGTTTGAGTCCATGAAGCACAAATTGACAA
GCCAGATATATTGAAACCTAAATTTGATATTCTTAGGCGCAATTCGTTAATATGGAAGCCCAAAA
AAGGAGTTCAAGTCCAATCAGTAACTATGATGCGATAATAATCCAACCCTAATGCAGCATTGTTA
AATCCTATTCAAAGGAGGACTTCACAAGAAAATTCATATCTTTTGATCCAGAGCTCAAAAAAATG
AG
Found at i:13633 original size:15 final size:14
Alignment explanation
Indices: 13593--13635 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
13583 CACGTCACTT
13593 TTTTTATAAAAAATA
1 TTTTTA-AAAAAATA
**
13608 TTTTTTCAAAAATCA
1 TTTTTAAAAAAAT-A
13623 TTTTTAAAAAAAT
1 TTTTTAAAAAAAT
13636 TGAAAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (14 bp):
TTTTTAAAAAAATA
Done.