Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011619.1 Corchorus olitorius cultivar O-4 contig11652, 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: 2109
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Found at i:285 original size:156 final size:156
Alignment explanation
Indices: 1--1010 Score: 1632
Period size: 156 Copynumber: 6.5 Consensus size: 156
* * * *
1 AATGGCCCAAATTAACAAGTGTTCAAAATGAGTTAAGAACTTTACAATGGACTAAACTTACCAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAA
* * *
66 GTGATAATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGAT
131 TTTTAAAACCGAACTAATGGGCCCCG
131 TTTTAAAACCGAACTAATGGGCCCCG
* * *
157 AATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACACTGGACTAGTCTTACCAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAA
* *
222 ATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAACCGAAGACGAT
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGAT
*
287 TTTTAAAACCTAACTAATGGGCCCCG
131 TTTTAAAACCGAACTAATGGGCCCCG
*
313 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTTACAATGGACTAATCTTACCAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAA
* * * *
378 GTGATCATAGTTAGGCCATAAAAAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGAT
443 TTTTAAAACCGAACTAATGGGCCCCG
131 TTTTAAAACCGAACTAATGGGCCCCG
* * * * * *
469 AATGGTCCAAAATAACAAGTGTTCAAAATGAGTTAAAAACTTCACAATGGACTAGTCTAACAAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAA
*
534 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGTCAAATCGAAGACGA-
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGAT
* * *
598 -TTCAAAACCGAACTAATAGACCCCG
131 TTTTAAAACCGAACTAATGGGCCCCG
623 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAA
* * * * *
688 GTGGTCATACTTAGGCCATAAACAATGGAAAGAAAAGCATTGTTGTTTGCCAAATCGAAGACGAT
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGAT
753 TTTTAAAACCGAACTAATGGGCCCCG
131 TTTTAAAACCGAACTAATGGGCCCCG
* * *
779 AATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAA
*
844 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGTCAAATCGAAGACGA-
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGAT
* * *
908 -TTCAAAACCGAACTAATAGACCCCG
131 TTTTAAAACCGAACTAATGGGCCCCG
933 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAA
998 ATGATTATAGTTA
66 ATGATTATAGTTA
1011 TGATACGAAT
Statistics
Matches: 783, Mismatches: 69, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
154 236 0.30
156 547 0.70
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (156 bp):
AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAA
ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGAT
TTTTAAAACCGAACTAATGGGCCCCG
Found at i:804 original size:310 final size:310
Alignment explanation
Indices: 1--1010 Score: 1777
Period size: 310 Copynumber: 3.3 Consensus size: 310
* * * *
1 AATGGCCCAAATTAACAAGTGTTCAAAATGAGTTAAGAACTTTACAATGGACTAAACTTACCAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAA
*
66 GTGATAATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
66 GTGATCATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
*
131 TTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAGAA
131 TTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAAAA
* *
196 CTTCACACTGGACTAGTCTTACCAAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGCA
196 CTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
* * * * * *
261 TTGTGGTTTGCCAAACCGAAGACGATTTTTAAAACCTAACTAATGGGCCCCG
261 TTGTGGTTTGTCAAATCGAAGACGA--TTCAAAACCGAACTAATAGACCCCG
*
313 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTTACAATGGACTAATCTTACCAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAA
*
378 GTGATCATAGTTAGGCCATAAAAAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
66 GTGATCATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
*
443 TTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAAGTGTTCAAAATGAGTTAAAAA
131 TTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAAAA
* *
508 CTTCACAATGGACTAGTCTAACAAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
196 CTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
573 TTGTGGTTTGTCAAATCGAAGACGATTCAAAACCGAACTAATAGACCCCG
261 TTGTGGTTTGTCAAATCGAAGACGATTCAAAACCGAACTAATAGACCCCG
623 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAA
* * * *
688 GTGGTCATACTTAGGCCATAAACAATGGAAAGAAAAGCATTGTTGTTTGCCAAATCGAAGACGAT
66 GTGATCATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
753 TTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAAAA
131 TTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAAAA
818 CTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
196 CTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
883 TTGTGGTTTGTCAAATCGAAGACGATTCAAAACCGAACTAATAGACCCCG
261 TTGTGGTTTGTCAAATCGAAGACGATTCAAAACCGAACTAATAGACCCCG
933 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAA
* *
998 ATGATTATAGTTA
66 GTGATCATAGTTA
1011 TGATACGAAT
Statistics
Matches: 668, Mismatches: 30, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
310 396 0.59
312 272 0.41
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (310 bp):
AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAA
GTGATCATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
TTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAAAA
CTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
TTGTGGTTTGTCAAATCGAAGACGATTCAAAACCGAACTAATAGACCCCG
Found at i:892 original size:466 final size:465
Alignment explanation
Indices: 1--1010 Score: 1635
Period size: 466 Copynumber: 2.2 Consensus size: 465
* * *
1 AATGGCCCAAATTAACAAGTGTTCAAAATGAGTTAAGAACTTTACAATGGACTAAACTTACCAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGTTAAGAACTTCACAATGGACTAATCTTACCAAA
* *
66 GTGATAATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGA-
* * * *
131 TTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAGAA
130 TTTCAAAACCGAACTAATAGACCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAA
* * * **
196 CTTCACACTGGACTAGTCTTACCAAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGCA
195 CTTCACAATGGACTAATCTTACCAAAATGATCATACTTAGGCCATAAACAATGGAAAGAAAAGCA
*
261 TTGTGGTTTGCCAAACCGAAGACGATTTTTAAAACCTAACTAATGGGCCCCGAATGGCCCAAAAT
260 TTGTGGTTTGCCAAACCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAAT
* * *
326 AACAAGTGTTCAAAATGAGCTAAGAACTTTACAATGGACTAATCTTACCAAAGTGATCATAGTTA
325 AACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAATCTTACCAAAATGATCATAGTTA
*
391 GGCCATAAAAAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAA
390 GGCCATAAAAAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGA--TTCAAAACCGAA
* *
456 CTAATGGGCCCCG
453 CTAATAGACCCCG
* * * * *
469 AATGGTCCAAAATAACAAGTGTTCAAAATGAGTTAAAAACTTCACAATGGACTAGTCTAACAAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGTTAAGAACTTCACAATGGACTAATCTTACCAAA
* *
534 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGTCAAATCGAAGACGA-
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
598 TTCAAAACCGAACTAATAGACCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAAC
131 TTCAAAACCGAACTAATAGACCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAAC
* *
663 TTCACAATGGACTAATCTTACCAAAGTGGTCATACTTAGGCCATAAACAATGGAAAGAAAAGCAT
196 TTCACAATGGACTAATCTTACCAAAATGATCATACTTAGGCCATAAACAATGGAAAGAAAAGCAT
* * *
728 TGTTGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATA
261 TGTGGTTTGCCAAACCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATA
* *
793 ACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAG
326 ACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAATCTTACCAAAATGATCATAGTTAG
* * *
858 GCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGTCAAATCGAAGACGATTCAAAACCGAACTA
391 GCCATAAAAAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGATTCAAAACCGAACTA
923 ATAGACCCCG
456 ATAGACCCCG
*
933 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGTTAAGAACTTCACAATGGACTAATCTTACCAAA
998 ATGATTATAGTTA
66 ATGATTATAGTTA
1011 TGATACGAAT
Statistics
Matches: 498, Mismatches: 44, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
464 94 0.19
466 287 0.58
468 117 0.23
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (465 bp):
AATGGCCCAAAATAACAAGTGTTCAAAATGAGTTAAGAACTTCACAATGGACTAATCTTACCAAA
ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
TTCAAAACCGAACTAATAGACCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAAC
TTCACAATGGACTAATCTTACCAAAATGATCATACTTAGGCCATAAACAATGGAAAGAAAAGCAT
TGTGGTTTGCCAAACCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATA
ACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAATCTTACCAAAATGATCATAGTTAG
GCCATAAAAAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGATTCAAAACCGAACTA
ATAGACCCCG
Done.