Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011868.1 Corchorus olitorius cultivar O-4 contig11901, 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: 9815
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:1582 original size:2 final size:2
Alignment explanation
Indices: 1575--1607 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1565 TAATATTTAG
*
1575 TA TA TA TA TA TA TA TA TA TA TT TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1608 ATTTTCGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:3698 original size:5 final size:5
Alignment explanation
Indices: 3688--3712 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3678 TCAAATGAGA
3688 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
3713 CACAAGAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:5105 original size:439 final size:439
Alignment explanation
Indices: 4307--5121 Score: 1027
Period size: 439 Copynumber: 1.9 Consensus size: 439
4297 CGATATTACA
* * * * * * *
4307 TTTATGCTATTTAATTCTTTACAAATTCTGGGTTGGACGTCTTAACATTTCAGTTTTGTTTTTTT
1 TTTATGCTATTGAATCCTTTACAAATTATAGGTTGGACGTCTTAACATTTCACTTTTATTTTTGT
* *
4372 ATTTTTTGTTCTATATCTCCGATCAAGATGATTCAAGTGTCTATTAAAAGATAATTTAATGATCT
66 ATTTTTTATTCTATATCTCCAATCAAGATGATTCAAGTGTCTATTAAAAGATAATTTAATGATCT
* * * * *
4437 ACAACTTTCATTAAGAACTCAAAAGCCAATTTTTAGGTTTTGATTCTAAAAAATGCTTCCGAAAT
131 AAAACTTTCATTAAGAACTCAAAAGCCAATTTTGAGCTTTAGATTCTAAAAAATGCTTCCAAAAT
* * *
4502 TTGGATGTCTCGATTTCAGGTCTATCTAATATCGTATAATTCTCGATCCATGTGTCCGATTGAAG
196 TTGGATGTCTCGATTACAGGTCTATCTAATATCATATAATTCTCGATCCATGTGTCCGATTCAAG
* * * * ** * * * * *
4567 TTATTGAAATATGGGTTGAAAGGTTATTGTGTGATCTATGACTTTCATTATGGGCCCGCAAGCTG
261 TTATTCAAATATCGGTTAAAACGTTATTACGTGATCTACGACTTTCATGAAGGACCCGAAAGCTG
* * * * *
4632 AATTTGATTAATGAGTTTCATGGAGGGTTCAAGAAGGAATTTCTATGTTTCTTCTCTATAAACTA
326 AATTTGATTAATGAATTTCATGAAGGGCTCAAGAAGAAATTTCTATATTTCTTCTCTATAAACTA
4697 ATCAATTTTTTGCTGGATTATTTATCTAATGACCCTCATACCTTTATGC
391 ATCAATTTTTTGCTGGATTATTTATCTAATGACCCTCATACCTTTATGC
*
4746 TTTATGCTATTGAATCCTTTAC-AATTATAGGTTGGACGAT-TTAACGCTTTGC-CTTTTATTTT
1 TTTATGCTATTGAATCCTTTACAAATTATAGGTTGGACG-TCTTAAC-ATTT-CACTTTTATTTT
* * * * *
4808 TGTATTTTTTATTCTATTTGTCCAATTAAGGTGATTCAAGTGTCTATTAAAAGATAATTTCATGA
63 TGTATTTTTTATTCTATATCTCCAATCAAGATGATTCAAGTGTCTATTAAAAGATAATTTAATGA
* *
4873 TCTAAAACTTTCATTAAGGACTCAAAAGCCAATTTTGAGCTTTCAG-TTCTAAAACAA-GTTTCC
128 TCTAAAACTTTCATTAAGAACTCAAAAGCCAATTTTGAGCTTT-AGATTCTAAAA-AATGCTTCC
**
4936 AAAATTTGG-TGGTCTCGATTGAC-GGTCTATCTAATATCATATAAATT-TTTATCCATGTG-CC
191 AAAATTTGGAT-GTCTCGATT-ACAGGTCTATCTAATATCATAT-AATTCTCGATCCATGTGTCC
* * *
4997 TGATTCAAGTTGTTCAAATGTCGGTTAAAACGTTGTTACGTGATCTACGACTTTCATGAAGGACC
253 -GATTCAAGTTATTCAAATATCGGTTAAAACGTTATTACGTGATCTACGACTTTCATGAAGGACC
* * * * *
5062 TGAAAGCTGAATTTGTTTGATGAATTTCATTAAGGGCTCAAGAAGAAATTTTTATATTTC
317 CGAAAGCTGAATTTGATTAATGAATTTCATGAAGGGCTCAAGAAGAAATTTCTATATTTC
5122 GAGAATTCTA
Statistics
Matches: 316, Mismatches: 51, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
438 22 0.07
439 285 0.90
440 9 0.03
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (439 bp):
TTTATGCTATTGAATCCTTTACAAATTATAGGTTGGACGTCTTAACATTTCACTTTTATTTTTGT
ATTTTTTATTCTATATCTCCAATCAAGATGATTCAAGTGTCTATTAAAAGATAATTTAATGATCT
AAAACTTTCATTAAGAACTCAAAAGCCAATTTTGAGCTTTAGATTCTAAAAAATGCTTCCAAAAT
TTGGATGTCTCGATTACAGGTCTATCTAATATCATATAATTCTCGATCCATGTGTCCGATTCAAG
TTATTCAAATATCGGTTAAAACGTTATTACGTGATCTACGACTTTCATGAAGGACCCGAAAGCTG
AATTTGATTAATGAATTTCATGAAGGGCTCAAGAAGAAATTTCTATATTTCTTCTCTATAAACTA
ATCAATTTTTTGCTGGATTATTTATCTAATGACCCTCATACCTTTATGC
Found at i:9052 original size:139 final size:140
Alignment explanation
Indices: 8802--9066 Score: 331
Period size: 139 Copynumber: 1.9 Consensus size: 140
8792 TTACCCCAAA
* * * *
8802 TATTTGTAACTGTCGAAATATGATGTTGTGCATGTAACTTTGAAATCGCTGAATACCTTGAAAAG
1 TATTTGTAACTGCCCAAATATGATGTTATGCATGTAACTTTGAAATCGATGAATACCTTGAAAAG
* * * ***
8867 AGGTTACAAGCATTTGTAACTGCCCAAATATGATGTTGTGCATGTAACCTCC-AATTACTATATA
66 AGGTTACAAGCACTTGTAACCGCCCAAATATAATGCCATGCATGTAACCTCCAAATTACTATATA
8931 TCTTGAAAAG
131 TCTTGAAAAG
* * *
8941 TATTTGTAACTGCCCAAATATGATGTTATGCATGTAACTTCT-AAA-CTATTAGATACCTTGAAT
1 TATTTGTAACTGCCCAAATATGATGTTATGCATGTAACTT-TGAAATCGATGA-ATACCTTGAAA
* * *
9004 AGATGTTACAA-CTACTTGTAACCGTCCAAATATAATGCCATTCATGTAACCTCCAAATTACTA
64 AGAGGTTACAAGC-ACTTGTAACCGCCCAAATATAATGCCATGCATGTAACCTCCAAATTACTA
9067 AACATTTGTA
Statistics
Matches: 106, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
138 4 0.04
139 93 0.88
140 9 0.08
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (140 bp):
TATTTGTAACTGCCCAAATATGATGTTATGCATGTAACTTTGAAATCGATGAATACCTTGAAAAG
AGGTTACAAGCACTTGTAACCGCCCAAATATAATGCCATGCATGTAACCTCCAAATTACTATATA
TCTTGAAAAG
Done.