Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012219.1 Corchorus olitorius cultivar O-4 contig12252, 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: 15805
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Found at i:8408 original size:33 final size:33
Alignment explanation
Indices: 8344--8501 Score: 100
Period size: 33 Copynumber: 4.8 Consensus size: 33
8334 GCTTGCCAAA
* * * * *
8344 ATTGAAGAAGAACGAAGATAGTATCTTGCTTGC
1 ATTGAAGAAGAAAGAAGACAGGAGCTGGCTTGC
*
8377 ATTGAAGAAGAAAGACGACAGGAGCTGGCTTGC
1 ATTGAAGAAGAAAGAAGACAGGAGCTGGCTTGC
* * * * ** *
8410 CTTGAAAAAGAGAGAAGACATGATTTGGCTCGC
1 ATTGAAGAAGAAAGAAGACAGGAGCTGGCTTGC
* * * * * **
8443 TTTCAACAAGAGAGAAGACAAGAGCTGGCTCAC
1 ATTGAAGAAGAAAGAAGACAGGAGCTGGCTTGC
* * * *
8476 CTTAAAGAAGACAGAAGACATGAGCT
1 ATTGAAGAAGAAAGAAGACAGGAGCT
8502 TGATCGTTTA
Statistics
Matches: 99, Mismatches: 26, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 99 1.00
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.19
Consensus pattern (33 bp):
ATTGAAGAAGAAAGAAGACAGGAGCTGGCTTGC
Found at i:10535 original size:11 final size:11
Alignment explanation
Indices: 10519--10544 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
10509 GTTTTAGATC
10519 TTTTCTTCTAG
1 TTTTCTTCTAG
10530 TTTTCTTCTAG
1 TTTTCTTCTAG
10541 TTTT
1 TTTT
10545 TAGGCCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:13488 original size:64 final size:64
Alignment explanation
Indices: 13394--13539 Score: 152
Period size: 64 Copynumber: 2.3 Consensus size: 64
13384 GGCCCCTAAA
* * * * * *
13394 GAAGGAAACGCCTCTAAATAGTAGCACATAAAGAA-CAAAACGTCCC-CAAATAGTGGTGCTTAA
1 GAAGAAAACGCCACAAAATAGTAGCACATAAA-AACCAAAAC-ACCCTCAAATAGAGGCGCTTAA
13457 T
64 T
* * * * *
13458 GAAGAAAACGCCCCAAAATAGTGGCGCATAAAAACCAAAACACCCTGAAATAGAGGCGCTTGAT
1 GAAGAAAACGCCACAAAATAGTAGCACATAAAAACCAAAACACCCTCAAATAGAGGCGCTTAAT
*
13522 AAAGAAAACGCCACAAAA
1 GAAGAAAACGCCACAAAA
13540 CACAATATAC
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
63 5 0.07
64 63 0.93
ACGTcount: A:0.46, C:0.22, G:0.18, T:0.14
Consensus pattern (64 bp):
GAAGAAAACGCCACAAAATAGTAGCACATAAAAACCAAAACACCCTCAAATAGAGGCGCTTAAT
Found at i:13498 original size:32 final size:30
Alignment explanation
Indices: 13399--13516 Score: 83
Period size: 32 Copynumber: 3.7 Consensus size: 30
13389 CTAAAGAAGG
* * *
13399 AAACGCCTCTAAATAGTAGCACATAAAGAACA
1 AAACGCC-CCAAATAGTGGCGCATAAA-AACA
* * * *
13431 AAACGTCCCCAAATAGTGGTGCTTAATGAAGA
1 AAACG-CCCCAAATAGTGGCGCATAA-AAACA
13463 AAACGCCCCAAAATAGTGGCGCATAAAAACCA
1 AAACGCCCC-AAATAGTGGCGCATAAAAA-CA
* * *
13495 AAACACCCTGAAATAGAGGCGC
1 AAACGCCC-CAAATAGTGGCGC
13517 TTGATAAAGA
Statistics
Matches: 67, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
31 6 0.09
32 59 0.88
33 2 0.03
ACGTcount: A:0.44, C:0.24, G:0.18, T:0.14
Consensus pattern (30 bp):
AAACGCCCCAAATAGTGGCGCATAAAAACA
Found at i:15481 original size:21 final size:21
Alignment explanation
Indices: 15455--15525 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
15445 CTTAGGCAAT
15455 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
15476 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
15497 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
15518 TCCAATGA
1 TCCAATGA
15526 ACTTCTAGCA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 3 0.06
21 44 0.94
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:15629 original size:62 final size:62
Alignment explanation
Indices: 15556--15691 Score: 263
Period size: 62 Copynumber: 2.2 Consensus size: 62
15546 TCTTCAAGCC
*
15556 TCCTTGCCGCATATGCACATTCCCTCCAAGATCTCCATTGTGCTCTTCTAGACCATGATGAG
1 TCCTTGGCGCATATGCACATTCCCTCCAAGATCTCCATTGTGCTCTTCTAGACCATGATGAG
15618 TCCTTGGCGCATATGCACATTCCCTCCAAGATCTCCATTGTGCTCTTCTAGACCATGATGAG
1 TCCTTGGCGCATATGCACATTCCCTCCAAGATCTCCATTGTGCTCTTCTAGACCATGATGAG
15680 TCCTTGGCGCAT
1 TCCTTGGCGCAT
15692 CATCCCCTCT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 73 1.00
ACGTcount: A:0.20, C:0.32, G:0.18, T:0.31
Consensus pattern (62 bp):
TCCTTGGCGCATATGCACATTCCCTCCAAGATCTCCATTGTGCTCTTCTAGACCATGATGAG
Done.