Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019849.1 Corchorus olitorius cultivar O-4 contig19882, 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: 19804
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Found at i:8524 original size:17 final size:17
Alignment explanation
Indices: 8499--8533 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
8489 TATCCCTCGA
*
8499 CTCTTCTCTTCTTCTTC
1 CTCTCCTCTTCTTCTTC
8516 CTCTCCTCTTCTTCTTC
1 CTCTCCTCTTCTTCTTC
8533 C
1 C
8534 CTCGACGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (17 bp):
CTCTCCTCTTCTTCTTC
Found at i:11329 original size:30 final size:30
Alignment explanation
Indices: 11295--12318 Score: 1362
Period size: 30 Copynumber: 34.2 Consensus size: 30
11285 AATGATAAAT
* * *
11295 CAGGATAAAAATATAGCGATGATCCTCAAC
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
*
11325 CAGGATTAAAATAAAGCAATG-GCCTTCAAC
1 CAGGATTAAAATAAAGCAATGATCC-TCAAC
* * **
11355 TATGATTAAAATAAAGCAACAATCCTCAAC
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
* *
11385 CAGGATTAAAATGATGCAAAT-ATCCTCAAC
1 CAGGATTAAAATAAAGC-AATGATCCTCAAC
* ** *
11415 CATGATTAAAATGGAGCGAAT-ATCCTCAAT
1 CAGGATTAAAATAAAGC-AATGATCCTCAAC
* *
11445 CAGGATTAAAATGAAGCAATGATCCTTAAC
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
11475 CAGGATTAAAATAAAGCAATGATCCTCAAC
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
* **
11505 CAGGATTAATATAAAGCAATGATCCGAAAC
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
11535 CAGGATTAAAATAAAGCAATGATCCTCAAC
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
* * **
11565 CAAGATTAAAATGAAGTGATGATCCTCAAC
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
* *
11595 CAGGATTAGAATAAAGCAATGATCCTCAAA
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
* * *
11625 CATGATTAACATAAAGCAATGATCCTCAAA
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
* *
11655 CAGGATTACAATAAAGCAATGATCCTCAAA
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
* *
11685 CAGGATTAACATAAAGCAATGATCCTCAAA
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
* * *
11715 CAAGATTAAAATAGAGCAATGATCCTCAAA
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
* *
11745 CAGGATTAACATAAAGCAATGATCCTCAAA
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
* *
11775 CAGGATTAAAATGAAGCAATGATCTTCAAC
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
*
11805 CAGGATTAAAATAAAGCAAATGATCCTCAAA
1 CAGGATTAAAATAAAGC-AATGATCCTCAAC
* *
11836 CAGGATTAAAATATAGCAATGATCCTCAAA
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
* * *
11866 CAGGATCAACATAAAGCAATGATCCTCAAA
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
*
11896 CAGGATTAAAATAAAGCAACGATCCTCAAC
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
*
11926 CAGGATTAAAATAAAGCAACGATCCTCAAC
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
* * *
11956 CAGGATTAAAATGATGTAATGATCCTCAAC
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
11986 CAGGATTAAAAT-AA-C---GATCCTCAAC
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
*
12011 CAGGATTAAAATAAAGCAACGATCCTCAAC
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
*
12041 CAGGATTAAAATAAAGCAACGATCCTCAAC
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
12071 CAGGATTAAAATAAAGCAATGATCCTCAAC
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
* *
12101 CAGGATTAAAATAAAGCAAATGACCCTCAAA
1 CAGGATTAAAATAAAGC-AATGATCCTCAAC
* *
12132 CAAGATTAAAATAAAGCAAATGATCCTCAAA
1 CAGGATTAAAATAAAGC-AATGATCCTCAAC
* *
12163 CAGGATTAAAATATAGCAATGATCCTCAAA
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
* * *
12193 CAGGATCAACATAAAGCAATGATCCTCAAA
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
*
12223 CAGGATTAAAATAAAGCAACGATCCTCAAC
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
*
12253 CAGGATTAAAATAAAGCAACGATCCTCAAC
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
*
12283 CAGGATCAAAATAAAGCAATGATCCTCAAC
1 CAGGATTAAAATAAAGCAATGATCCTCAAC
12313 CAGGAT
1 CAGGAT
12319 GGAAATTAAC
Statistics
Matches: 891, Mismatches: 92, Indels: 22
0.89 0.09 0.02
Matches are distributed among these distances:
25 22 0.02
26 2 0.00
27 1 0.00
29 6 0.01
30 774 0.87
31 86 0.10
ACGTcount: A:0.46, C:0.20, G:0.14, T:0.20
Consensus pattern (30 bp):
CAGGATTAAAATAAAGCAATGATCCTCAAC
Found at i:12661 original size:168 final size:168
Alignment explanation
Indices: 12383--12822 Score: 695
Period size: 168 Copynumber: 2.6 Consensus size: 168
12373 GGTTTTTTAT
*
12383 CAATGCAAACTCTGAAAAGAGACCTTA-AACAAGGATTTTAACTTAAACATGAACTTTTGATGAA
1 CAATGCAAACTCTGAATAGAGACC-TAGAACAAGGATTTTAACTTAAACATGAACTTTTGATGAA
12447 AAACTTGATGAAATCAAATGGCACCCGGAGGTTTTATCAATTGCCCGGAAGACTTATCAGAATTA
65 AAACTTGATGAAATCAAATGGCACCCGGAGGTTTTATCAATTGCCCGGAAGACTTATCAGAATTA
* *
12512 ATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTAC
130 ATACCCGGAGGTTTCTGAATTCGTGCCCAGAGGACTTAC
* *
12551 CAATGCAAACTGTGAATTGAGACCTAGAACAAGGATTTTAACTTAAACATGAACTTTTGATGAAA
1 CAATGCAAACTCTGAATAGAGACCTAGAACAAGGATTTTAACTTAAACATGAACTTTTGATGAAA
* *
12616 AAATTGATGAAATCAAATGGCACCCGGAGGTTTTATCAATTGCCCGGAGGACTTATCAGAATTAA
66 AACTTGATGAAATCAAATGGCACCCGGAGGTTTTATCAATTGCCCGGAAGACTTATCAGAATTAA
12681 TACCCGGAGGTTTCTGAATTCGTGCCCAGAGGACTTAC
131 TACCCGGAGGTTTCTGAATTCGTGCCCAGAGGACTTAC
* * * * *
12719 CAACGCAAACTCTGAATAGAGACCTTGACCAAGGATTTTAGCTTAAACATGAA-TCTTTGGTGAA
1 CAATGCAAACTCTGAATAGAGACCTAGAACAAGGATTTTAACTTAAACATGAACT-TTTGATGAA
* * ** *
12783 AAACTTGATAAAATGAAATGATAGCCGGAGGTTTTATCAA
65 AAACTTGATGAAATCAAATGGCACCCGGAGGTTTTATCAA
12823 ATGGAAATAA
Statistics
Matches: 250, Mismatches: 20, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
167 3 0.01
168 247 0.99
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (168 bp):
CAATGCAAACTCTGAATAGAGACCTAGAACAAGGATTTTAACTTAAACATGAACTTTTGATGAAA
AACTTGATGAAATCAAATGGCACCCGGAGGTTTTATCAATTGCCCGGAAGACTTATCAGAATTAA
TACCCGGAGGTTTCTGAATTCGTGCCCAGAGGACTTAC
Found at i:14580 original size:6 final size:6
Alignment explanation
Indices: 14548--14577 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
14538 TCAATTCCAT
*
14548 TTTTGA TTTTGA TTTTGA TTTTGA ATTTGA
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA
14578 ATTATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.20, C:0.00, G:0.17, T:0.63
Consensus pattern (6 bp):
TTTTGA
Found at i:18973 original size:16 final size:15
Alignment explanation
Indices: 18948--18980 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
18938 TTCTTTTCCA
18948 TTTTTTTTTTCATTT
1 TTTTTTTTTTCATTT
18963 TTTTCTTTTTTCATTT
1 TTTT-TTTTTTCATTT
18979 TT
1 TT
18981 CATTTATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTTTTTTCATTT
Done.