Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011512.1 Corchorus olitorius cultivar O-4 contig11545, 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: 2011
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Found at i:321 original size:156 final size:156
Alignment explanation
Indices: 1--1309 Score: 2049
Period size: 156 Copynumber: 8.4 Consensus size: 156
* * *
1 GAATGG-CCTAAATAACAAGTGTTC-AAATGAGC-AAGAACTTTACAATGGACTAATCTTA-CAA
1 GAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAA
* * *
62 AATGATCATAGTTAGGCTATAAACAATGAAAAGAAAAGCATTGTGGTTTGCCAAAATCGAAGACG
66 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCC-AAATCGAAGACG
127 ATTTTTAAAACCGAACTAATGGGCCCC
130 ATTTTTAAAACCGAACTAATGGGCCCC
* * *
154 GAATGGTCCAAAATAACATGTGTTCAAAATGAGCTAAGAACTTTACAATGGACTAGTCTTACCAA
1 GAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAA
* * *
219 AATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGTTGTTTGCCAAACCGAAGACGA
66 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA
*
284 TTTTTAAAACCTAACTAATGGGCCCC
131 TTTTTAAAACCGAACTAATGGGCCCC
* * *
310 AAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTTACAATGGACTAATCTTACCAA
1 GAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAA
* *
375 AATGATCATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGA
66 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA
440 TTTTTAAAACCGAACTAATGGGCCCC
131 TTTTTAAAACCGAACTAATGGGCCCC
* * * *
466 GAATGGTCCAAAATAACAAGTGTTC-AAATGAGCTAAAAACTTCACAATGGACTAGTCTAACAAA
1 GAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAA
* * *
530 AATGACTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTTGTTTGCCAAACCGAAGACGA
66 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA
** *
595 --TTTAAAACTTAACTAATTGGCCCC
131 TTTTTAAAACCGAACTAATGGGCCCC
* *
619 GAATGGCCCAAAATAACAAGTATTCAAAATGAGTTAAGAACTTCACAATGGACTAGTCTTACCAA
1 GAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAA
*
684 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACAA
66 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA
*
749 TTTTTCAAACCGAACTAATGGGCCCC
131 TTTTTAAAACCGAACTAATGGGCCCC
* * *
775 GAATGGCCCAAAATAACAAGTGTTCAAACTGAGCTAAAAACTTCACAATGGACTAATCTTACCAA
1 GAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAA
* * *
840 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTTCCAAATCGAAGACTA
66 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA
905 TTTTTAAAACCGAACTAATGGG-CCC
131 TTTTTAAAACCGAACTAATGGGCCCC
*
930 GAATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAA
1 GAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAA
* * *
995 AATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGTTGTTTGCCAAACCGAAGACGA
66 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA
* *
1060 TTTTTAAAACCTAACTAACGGGCCCC
131 TTTTTAAAACCGAACTAATGGGCCCC
* * * *
1086 GAATGGCCCAAAATAACAAGTGTTCAAAATAAGTTAAGAACTTTACAATGGACTAATCTTACCAA
1 GAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAA
* * * * *
1151 AGTGATCATAGATAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAATTCGAAGACGA
66 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA
1216 TTTTTAAAACCGAACTAATGGGCCCC
131 TTTTTAAAACCGAACTAATGGGCCCC
* * *
1242 GAATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACATTGGACTAGTCTTACCAA
1 GAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAA
1307 AAT
66 AAT
1310 TGATACGAAT
Statistics
Matches: 1055, Mismatches: 93, Indels: 13
0.91 0.08 0.01
Matches are distributed among these distances:
153 50 0.05
154 112 0.11
155 245 0.23
156 598 0.57
157 50 0.05
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (156 bp):
GAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAA
AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA
TTTTTAAAACCGAACTAATGGGCCCC
Found at i:588 original size:311 final size:312
Alignment explanation
Indices: 1--1309 Score: 2049
Period size: 311 Copynumber: 4.2 Consensus size: 312
* * *
1 GAATGG-CCTAAATAACAAGTGTTC-AAATGAGC-AAGAACTTTACAATGGACTAATCTTA-CAA
1 GAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAA
* *
62 AATGATCATAGTTAGGCTATAAACAATGAAAAGAAAAGCATTGTGGTTTGCCAAAATCGAAGACG
66 AATGATCATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCC-AAATCGAAGACG
* * *
127 ATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACATGTGTTCAAAATGAGCTAAG
130 ATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAA
* * *
192 AACTTTACAATGGACTAGTCTTACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAG
195 AACTTCACAATGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * *
257 CATTGTTGTTTGCCAAACCGAAGACGATTTTTAAAACCTAACTAATGGGCCCC
260 CATTATGGTTTGCCAAACCGAAGACGATTTTTAAAACCGAACTAATGGGCCCC
* * *
310 AAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTTACAATGGACTAATCTTACCAA
1 GAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAA
*
375 AATGATCATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGA
66 AATGATCATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA
*
440 TTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAAGTGTTC-AAATGAGCTAAAA
131 TTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAA
* * * *
504 ACTTCACAATGGACTAGTCTAACAAAAATGACTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
196 ACTTCACAATGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
* * ** *
569 ATTGTTGTTTGCCAAACCGAAGACGA--TTTAAAACTTAACTAATTGGCCCC
261 ATTATGGTTTGCCAAACCGAAGACGATTTTTAAAACCGAACTAATGGGCCCC
* *
619 GAATGGCCCAAAATAACAAGTATTCAAAATGAGTTAAGAACTTCACAATGGACTAGTCTTACCAA
1 GAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAA
* *
684 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACAA
66 AATGATCATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA
* *
749 TTTTTCAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAACTGAGCTAAAA
131 TTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAA
814 ACTTCACAATGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
196 ACTTCACAATGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
* * *
879 ATTATGGTTTTCCAAATCGAAGACTATTTTTAAAACCGAACTAATGGG-CCC
261 ATTATGGTTTGCCAAACCGAAGACGATTTTTAAAACCGAACTAATGGGCCCC
*
930 GAATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAA
1 GAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAA
* * * *
995 AATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGTTGTTTGCCAAACCGAAGACGA
66 AATGATCATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA
* * * * *
1060 TTTTTAAAACCTAACTAACGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAATAAGTTAAGA
131 TTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAA
* * * *
1125 ACTTTACAATGGACTAATCTTACCAAAGTGATCATAGATAGGCCATAAACAATGGAAAGAAAAGC
196 ACTTCACAATGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
**
1190 ATTATGGTTTGCCAATTCGAAGACGATTTTTAAAACCGAACTAATGGGCCCC
261 ATTATGGTTTGCCAAACCGAAGACGATTTTTAAAACCGAACTAATGGGCCCC
* * *
1242 GAATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACATTGGACTAGTCTTACCAA
1 GAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAA
1307 AAT
66 AAT
1310 TGATACGAAT
Statistics
Matches: 932, Mismatches: 60, Indels: 13
0.93 0.06 0.01
Matches are distributed among these distances:
309 198 0.21
310 111 0.12
311 396 0.42
312 175 0.19
313 52 0.06
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (312 bp):
GAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAA
AATGATCATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA
TTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAA
ACTTCACAATGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
ATTATGGTTTGCCAAACCGAAGACGATTTTTAAAACCGAACTAATGGGCCCC
Found at i:1007 original size:465 final size:466
Alignment explanation
Indices: 1--1309 Score: 2142
Period size: 465 Copynumber: 2.8 Consensus size: 466
* * *
1 GAATGG-CCTAAATAACAAGTGTTCAAATGAGC-AAGAACTTTACAATGGACTAATCTTA-CAAA
1 GAATGGTCCAAAATAACAAGTGTTCAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAAA
* * * * *
63 ATGATCATAGTTAGGCTATAAACAATGAAAAGAAAAGCATTGTGGTTTGCCAAAATCGAAGACGA
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTTGTTTGCC-AAACCGAAGACGA
* * * *
128 TTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACATGTGTTCAAAATGAGCTAAGA
130 -TTTTAAAACCTAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGTTAAGA
*
193 ACTTTACAATGGACTAGTCTTACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGC
194 ACTTTACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
* * * *
258 ATTGTTGTTTGCCAAACCGAAGACGATTTTTAAAACCTAACTAATGGGCCCCAAATGGCCCAAAA
259 ATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAA
* *
323 TAACAAGTGTTCAAAATGAGCTAAGAACTTTACAATGGACTAATCTTACCAAAATGATCATAGTT
324 TAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAATCTTACCAAAATGATCATAGTT
388 AGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGATTTTTAAAACCGA
389 AGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGATTTTTAAAACCGA
453 ACTAATGGGCCCC
454 ACTAATGGGCCCC
* * *
466 GAATGGTCCAAAATAACAAGTGTTCAAATGAGCTAAAAACTTCACAATGGACTAGTCTAACAAAA
1 GAATGGTCCAAAATAACAAGTGTTCAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAAA
*
531 ATGACTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTTGTTTGCCAAACCGAAGACGA-
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTTGTTTGCCAAACCGAAGACGAT
* * *
595 TTTAAAACTTAACTAATTGGCCCCGAATGGCCCAAAATAACAAGTATTCAAAATGAGTTAAGAAC
131 TTTAAAACCTAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGTTAAGAAC
*
660 TTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
196 TTTACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
* *
725 TGTGGTTTGCCAAATCGAAGACAATTTTTCAAACCGAACTAATGGGCCCCGAATGGCCCAAAATA
261 TGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATA
* *
790 ACAAGTGTTCAAACTGAGCTAAAAACTTCACAATGGACTAATCTTACCAAAATGATTATAGTTAG
326 ACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAATCTTACCAAAATGATCATAGTTAG
* *
855 GCCATAAACAATGGAAAGAAAAGCATTATGGTTTTCCAAATCGAAGACTATTTTTAAAACCGAAC
391 GCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAAC
920 TAATGGG-CCC
456 TAATGGGCCCC
930 GAATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAA
1 GAATGGTCCAAAATAACAAGTGTTC-AAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAA
*
995 AATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGTTGTTTGCCAAACCGAAGACGA
65 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTTGTTTGCCAAACCGAAGACGA
* *
1060 TTTTTAAAACCTAACTAACGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAATAAGTTAAGA
130 -TTTTAAAACCTAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGTTAAGA
* * * *
1125 ACTTTACAATGGACTAATCTTACCAAAGTGATCATAGATAGGCCATAAACAATGGAAAGAAAAGC
194 ACTTTACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
* * *
1190 ATTATGGTTTGCCAATTCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAA
259 ATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAA
* *
1255 TAACAAGTGTTCAAAATGAGCTAAAAACTTCACATTGGACTAGTCTTACCAAAAT
324 TAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAATCTTACCAAAAT
1310 TGATACGAAT
Statistics
Matches: 782, Mismatches: 56, Indels: 10
0.92 0.07 0.01
Matches are distributed among these distances:
464 28 0.04
465 416 0.53
466 25 0.03
467 264 0.34
468 49 0.06
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (466 bp):
GAATGGTCCAAAATAACAAGTGTTCAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAAA
ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTTGTTTGCCAAACCGAAGACGAT
TTTAAAACCTAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGTTAAGAAC
TTTACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
TGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATA
ACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAATCTTACCAAAATGATCATAGTTAG
GCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAAC
TAATGGGCCCC
Done.