Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011033.1 Corchorus olitorius cultivar O-4 contig11066, 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, 627
Length: 1045
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Found at i:299 original size:154 final size:154
Alignment explanation
Indices: 1--1045 Score: 1491
Period size: 154 Copynumber: 6.8 Consensus size: 154
* * * ** *
1 AATGGAAA-AAAAGCATCGAGGTTTGCCAAATCAAAGACGATTCAAAATGGAACTAATGGGCCCC
1 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCT
* * *
65 GAAAGGCACAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTCACTAA
66 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAA
*
130 AATGATTATAGTTAGGCCATAAAT
131 AATGATTATAGTTAGGCCATAAAC
* * *
154 AATGGAAAGAAAACCATTAAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCTT
1 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCT
* * *
219 GATAGGCCCATAATAACAGGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTGATCTCACTAA
66 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAA
* *
284 AATGGTTATGGTTAGGCCATCATAAAC
131 AATGATTATAGTTAGG-C--CATAAAC
* * * * ** * *
311 AATGAAAAGAAAAGCATCGAGGGTTGCCAAATTGAAGACGATTCAAAACGGAACTAATAGACCC-
1 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCT
* * * * * *
375 CAAAGGCACAAAATAACAAGTGTTCCAAATTAGCTAAAACCTCCACAGTGGACTAATCTCACTAA
66 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAA
440 AATGATTATAGTTAGGCCATAAAC
131 AATGATTATAGTTAGGCCATAAAC
* * * *
464 AATGGAAAGAAAAGCATTGAAGTTTGCGAAATCGAAGACGGTTCAAAACGTCACTAACGGGCCCT
1 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCT
* * *
529 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTTACAGTGGACTAATCTTACCAA
66 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAA
*
594 AATGATTGTAGTTAGGCCATAAAC
131 AATGATTATAGTTAGGCCATAAAC
* *
618 AATGGAAAGAAACGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGTGCCCT
1 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCT
* * *
683 GATAGGCCCAAAATAACAGGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTGATCTCACTTA
66 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAA
* *
748 AATGATTAAACTTAGGCCATAAAC
131 AATGATTATAGTTAGGCCATAAAC
* *
772 AATGGAAAGAAACGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAGTAATGGGCCCT
1 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCT
* *
837 GATAGGCCCAAAATAACAAGTGTTCCAAATAGAGCTAAAAACTTTAACAGTGGACTAATCTCACC
66 GATAGGCCCAAAATAACAAGTGTTCCAAAT-GAGCTAAAAAC-TTCACAGTGGACTAATCTCACT
902 AAAATGATTATAGTTAGGCCATAAAC
129 AAAATGATTATAGTTAGGCCATAAAC
* * ** *
928 AATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
1 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCT
* * * *
993 GAAAGGCACAAAATAACAAGTGTTCCAAATTAACTAAAAACTTCACAGTGGAC
66 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
Statistics
Matches: 787, Mismatches: 98, Indels: 13
0.88 0.11 0.01
Matches are distributed among these distances:
153 67 0.09
154 441 0.56
155 22 0.03
156 198 0.25
157 59 0.07
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (154 bp):
AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCT
GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAA
AATGATTATAGTTAGGCCATAAAC
Found at i:579 original size:310 final size:308
Alignment explanation
Indices: 1--1045 Score: 1610
Period size: 310 Copynumber: 3.4 Consensus size: 308
* * *
1 AATGGAAA-AAAAGCATCGAGGTTTGCCAAATCAAAGACGATTCAAAATGGAACTAATGGGCCCC
1 AATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
*
65 GAAAGGCACAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTCACTAA
66 GAAAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAA
* *
130 AATGATTATAGTTAGGCCATAAATAATGGAAAGAAAACCATT-AAGGTTTGCCAAATCGAAGACG
131 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAA-GTTTGCCAAATCGAAGACG
* * *
194 ATTCAAAACGTCACTAATGGGCCTTGATAGGCCCATAATAACAGGTGTTCCAAATGAGCTAAAAA
195 ATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAA
* * * * *
259 CTTCACAGTGGACTGATCTCACTAAAATGGTTATGGTTAGGCCATCATAAAC
260 CTTTACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG-C--CATAAAC
* * * *
311 AATGAAAAGAAAAGCATCGAGGGTTGCCAAATTGAAGACGATTCAAAACGGAACTAATAGACCCC
1 AATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
* * *
376 -AAAGGCACAAAATAACAAGTGTTCCAAATTAGCTAAAACCTCCACAGTGGACTAATCTCACTAA
66 GAAAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAA
* *
440 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGTTTGCGAAATCGAAGACGG
131 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGTTTGCCAAATCGAAGACGA
*
505 TTCAAAACGTCACTAACGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAC
196 TTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAC
* *
570 TTTACAGTGGACTAATCTTACCAAAATGATTGTAGTTAGGCCATAAAC
261 TTTACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
* * * ** * *
618 AATGGAAAGAAACGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGTGCCCT
1 AATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
* * * * *
683 GATAGGCCCAAAATAACAGGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTGATCTCACTTA
66 GAAAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAA
* * * *
748 AATGATTAAACTTAGGCCATAAACAATGGAAAGAAACGCATTGAGGTTTGCCAAATCGAAGACGA
131 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGTTTGCCAAATCGAAGACGA
*
813 TTCAAAACGTCAGTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATAGAGCTAAAAA
196 TTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAAT-GAGCTAAAAA
878 CTTTAACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
260 CTTT-ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
928 AATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
1 AATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
* *
993 GAAAGGCACAAAATAACAAGTGTTCCAAATTAACTAAAAACTTCACAGTGGAC
66 GAAAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
Statistics
Matches: 663, Mismatches: 67, Indels: 10
0.90 0.09 0.01
Matches are distributed among these distances:
307 61 0.09
308 167 0.25
309 15 0.02
310 368 0.56
311 52 0.08
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (308 bp):
AATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
GAAAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAA
AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGTTTGCCAAATCGAAGACGA
TTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAC
TTTACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
Found at i:889 original size:464 final size:463
Alignment explanation
Indices: 1--1045 Score: 1585
Period size: 464 Copynumber: 2.3 Consensus size: 463
* *
1 AATGGAAA-AAAAGCATCGAGGTTTGCCAAATCAAAGACGATTCAAAATGGAACTAATGGGCCCC
1 AATGGAAAGAAAAGCATCGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
* *
65 GAAAGGCACAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTCACTAA
66 GAAAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
*
130 AATGATTATAGTTAGGCCATAAATAATGGAAAGAAAACCATTAAGGTTTGCCAAATCGAAGACGA
131 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAACCATTAAGGTTTGCCAAATCGAAGACGA
* *
195 TTCAAAACGTCACTAATGGGCCTTGATAGGCCCATAATAACAGGTGTTCCAAATGAGCTAAAAAC
196 TTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAGGTGTTCCAAATGAGCTAAAAAC
* ***
260 TTCACAGTGGACTGATCTCACTAAAATGGTTATGGTTAGGCCATCATAAACAATGAAAAGAAAAG
261 TTCACAGTGGACTGATCTCACTAAAATGATTAAACTTAGGCCA-CATAAACAATGAAAAGAAAAG
*
325 CATCGAGGGTTGCCAAATTGAAGACGATTCAAAACGGAACTAATAGACCCCAAAGGCACAAAATA
325 CATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATAGACCCCAAAGGCACAAAATA
* * *
390 ACAAGTGTTCCAAATTAGCTAAAACCTCCACAGTGGACTAATCTCACTAAAATGATTATAGTTAG
390 ACAAGTGTTCCAAATGAGCTAAAACCTCAACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
455 GCCATAAAC
455 GCCATAAAC
* * * * ** * *
464 AATGGAAAGAAAAGCATTGAAGTTTGCGAAATCGAAGACGGTTCAAAACGTCACTAACGGGCCCT
1 AATGGAAAGAAAAGCATCGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
* * * *
529 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTTACAGTGGACTAATCTTACCAA
66 GAAAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
* *
594 AATGATTGTAGTTAGGCCATAAACAATGGAAAG-AAACGCATTGAGGTTTGCCAAATCGAAGACG
131 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAC-CATTAAGGTTTGCCAAATCGAAGACG
*
658 ATTCAAAACGTCACTAATGTGCCCTGATAGGCCCAAAATAACAGGTGTTCCAAATGAGCTAAAAA
195 ATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAGGTGTTCCAAATGAGCTAAAAA
* * *
723 CTTCACAGTGGACTGATCTCACTTAAATGATTAAACTTAGG-C-CATAAACAATGGAAAGAAACG
260 CTTCACAGTGGACTGATCTCACTAAAATGATTAAACTTAGGCCACATAAACAATGAAAAGAAAAG
* * ** * * * * * *
786 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAGTAATGGGCCCTGATAGGCCCAAAAT
325 CATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATAGACCC-CAAAGGCACAAAAT
* *
851 AACAAGTGTTCCAAATAGAGCTAAAAACTTTAACAGTGGACTAATCTCACCAAAATGATTATAGT
389 AACAAGTGTTCCAAAT-GAGCT-AAAACCTCAACAGTGGACTAATCTCACCAAAATGATTATAGT
916 TAGGCCATAAAC
452 TAGGCCATAAAC
*
928 AATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
1 AATGGAAAGAAAAGCATCGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
* *
993 GAAAGGCACAAAATAACAAGTGTTCCAAATTAACTAAAAACTTCACAGTGGAC
66 GAAAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
Statistics
Matches: 518, Mismatches: 59, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
461 61 0.12
462 27 0.05
463 17 0.03
464 413 0.80
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (463 bp):
AATGGAAAGAAAAGCATCGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
GAAAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAACCATTAAGGTTTGCCAAATCGAAGACGA
TTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAGGTGTTCCAAATGAGCTAAAAAC
TTCACAGTGGACTGATCTCACTAAAATGATTAAACTTAGGCCACATAAACAATGAAAAGAAAAGC
ATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATAGACCCCAAAGGCACAAAATAA
CAAGTGTTCCAAATGAGCTAAAACCTCAACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
CCATAAAC
Done.