Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011922.1 Corchorus olitorius cultivar O-4 contig11955, 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, 750
Length: 1250
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Found at i:304 original size:154 final size:154
Alignment explanation
Indices: 1--1250 Score: 1877
Period size: 154 Copynumber: 8.1 Consensus size: 154
* * *
1 TTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACCAAATTGATTATAGTTAGGCCAT-A
1 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAA
* * ** *
65 A-AATGGAAAG-AAAGAATTGAGGTTTGCCAAATCGAAAACGATTCAAAACGTCACTAATTGGCC
66 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCC
*
128 CCGATAGGTCCAAAATAACAAGTG
131 CCGATAGGCCCAAAATAACAAGTG
* *
152 TTCCAAATGAGTTAAAAACTTCACAGTGTACTAATCTCACCAAAATGATTATAGTTAGTCCATAA
1 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAA
*
217 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCC
66 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCC
* *
282 CCGATAGGCACAAATTAACAAGTG
131 CCGATAGGCCCAAAATAACAAGTG
* *
306 TTCCAAATGAGCTAAAACCTTCACAGTGGACGAATCTCACCAAAATGATTATAGTTAGTCCATAA
1 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAA
* * *
371 AAAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACAAATGGGCC
66 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCC
* *
436 CTGATAGGCCCAAAATAACAAGTA
131 CCGATAGGCCCAAAATAACAAGTG
* * * *
460 TTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCATCAAAATGATTATTGTTAGGCCATAA
1 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAA
* * * **
525 ACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAACACGATCCAAGAA-GTCACTAATGGGC
66 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA-AACGGAACTAATGGGC
*
589 CCCGATAGGTCCAAAATAACAAGTG
130 CCCGATAGGCCCAAAATAACAAGTG
* *
614 TTCCAAATGAGCTAAAAA-TTTACAATGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAA
1 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAA
* * *
678 AAAATGGAAAGAAATGC-TCTGAGGTTTGCCAAATCGAAGACGATTGAAAACGGAACTAATGGGC
66 ACAATGGAAAGAAAAGCAT-TGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGC
*
742 CCCGATAGGCCCAAAAAAACAAGTG
130 CCCGATAGGCCCAAAATAACAAGTG
* * * *
767 TTCCAAATGAGCTAAAAACTTCGCAGTGGACTAATCTCACCAAAATGACTATAGTTAGTTCACAA
1 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAA
* * *
832 AAAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCC
66 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCC
*
897 CCGATAGGCCCAAAATAACAAGTT
131 CCGATAGGCCCAAAATAACAAGTG
* * *
921 TTCCAAATAAGCTAAGAACTTCACAGTGGACTAATCTCACCAAATTGATTATAGTTAGGT-CATA
1 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA-GTCCATA
* ** *
985 AACAATGGAAAGAAAAGCATTGATGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATTGGC
65 AACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGC
1050 CCCGATA-GCTCCAAAATAACAAGTG
130 CCCGATAGGC-CCAAAATAACAAGTG
*
1075 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATATCACCAAAATGATTATAGTTAGTCCATAA
1 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAA
*
1140 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAATGGAACTAATGGGG
66 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTC-AAAACGGAACTAAT-GGG
1205 CCCCCGATAGGCCCAAAAATAACAAGTG
129 -CCCCGATAGGCCC-AAAATAACAAGTG
1233 TTCCAAAATGAGCTAAAA
1 TTCC-AAATGAGCTAAAA
Statistics
Matches: 992, Mismatches: 90, Indels: 26
0.90 0.08 0.02
Matches are distributed among these distances:
151 58 0.06
152 5 0.01
153 147 0.15
154 722 0.73
155 16 0.02
156 2 0.00
157 10 0.01
158 19 0.02
159 13 0.01
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (154 bp):
TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAA
ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCC
CCGATAGGCCCAAAATAACAAGTG
Found at i:861 original size:461 final size:462
Alignment explanation
Indices: 1--1250 Score: 2071
Period size: 461 Copynumber: 2.7 Consensus size: 462
1 TTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACCAAATTGATTATAGTTAGGCCAT-A
1 TTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACCAAATTGATTATAGTTAGGCCATAA
*
65 A-AATGGAAAG-AAAGAATTGAGGTTTGCCAAATCGAAAACGATTCAAAACGTCACTAATTGGCC
66 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAAACGATTCAAAACGTCACTAATTGGCC
* *
128 CCGATAGGTCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGTACTAATCTCACC
131 CCGATAGGTCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
193 AAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
196 AAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
* * **
258 GATTCAAAATGGAACTAATGGGCCCCGATAGGCACAAATTAACAAGTGTTCCAAATGAGCTAAAA
261 GATTAAAAATGGAACTAATGGGCCCCGATAGGCCCAAAAAAACAAGTGTTCCAAATGAGCTAAAA
* * *
323 CCTTCACAGTGGACGAATCTCACCAAAATGATTATAGTTAGTCCATAAAAAATGGAAAGAAAAGC
326 ACTTCACAGTGGACGAATCTCACCAAAATGACTATAGTTAGTCCACAAAAAATGGAAAGAAAAGC
*
388 TTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACAAATGGGCCCTGATAGGCCCAAAATA
391 TTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACAAATGGGCCCCGATAGGCCCAAAATA
453 ACAAGTA
456 ACAAGTA
* * *
460 TTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCATCAAAATGATTATTGTTAGGCCATAA
1 TTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACCAAATTGATTATAGTTAGGCCATAA
* * * *
525 ACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAACACGATCCAAGAA-GTCACTAATGGGC
66 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAAACGATTCAA-AACGTCACTAATTGGC
* *
589 CCCGATAGGTCCAAAATAACAAGTGTTCCAAATGAGCTAAAAA-TTTACAATGGACTAATCTCAC
130 CCCGATAGGTCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAC
* *
653 CAAAATGATTATAGTTAGTCCATAAAAAATGGAAAGAAATGC-TCTGAGGTTTGCCAAATCGAAG
195 CAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCAT-TGAGGTTTGCCAAATCGAAG
* *
717 ACGATTGAAAACGGAACTAATGGGCCCCGATAGGCCCAAAAAAACAAGTGTTCCAAATGAGCTAA
259 ACGATTAAAAATGGAACTAATGGGCCCCGATAGGCCCAAAAAAACAAGTGTTCCAAATGAGCTAA
* * *
782 AAACTTCGCAGTGGACTAATCTCACCAAAATGACTATAGTTAGTTCACAAAAAATGGAAAGAAAA
324 AAACTTCACAGTGGACGAATCTCACCAAAATGACTATAGTTAGTCCACAAAAAATGGAAAGAAAA
* *
847 GCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAA
389 GCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACAAATGGGCCCCGATAGGCCCAAAA
*
912 TAACAAGTT
454 TAACAAGTA
* *
921 TTCCAAATAAGCTAAGAACTTCACAGTGGACTAATCTCACCAAATTGATTATAGTTAGGTCATAA
1 TTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACCAAATTGATTATAGTTAGGCCATAA
* *
986 ACAATGGAAAGAAAAGCATTGATGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATTGGCC
66 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAAACGATTCAAAACGTCACTAATTGGCC
* *
1051 CCGATAGCTCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATATCACC
131 CCGATAGGTCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
1116 AAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
196 AAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
1181 GATTCAAAAATGGAACTAATGGGGCCCCCGATAGGCCCAAAAATAACAAGTGTTCCAAAATGAGC
261 GATT-AAAAATGGAACTAAT-GGG-CCCCGATAGGCCCAAAAA-AACAAGTGTTCC-AAATGAGC
1246 TAAAA
321 TAAAA
Statistics
Matches: 731, Mismatches: 47, Indels: 18
0.92 0.06 0.02
Matches are distributed among these distances:
459 60 0.08
460 5 0.01
461 434 0.59
462 170 0.23
463 16 0.02
464 3 0.00
465 18 0.02
466 12 0.02
467 13 0.02
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (462 bp):
TTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACCAAATTGATTATAGTTAGGCCATAA
ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAAACGATTCAAAACGTCACTAATTGGCC
CCGATAGGTCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
AAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
GATTAAAAATGGAACTAATGGGCCCCGATAGGCCCAAAAAAACAAGTGTTCCAAATGAGCTAAAA
ACTTCACAGTGGACGAATCTCACCAAAATGACTATAGTTAGTCCACAAAAAATGGAAAGAAAAGC
TTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACAAATGGGCCCCGATAGGCCCAAAATA
ACAAGTA
Done.