Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002370.1 Corchorus olitorius cultivar O-4 contig02370, 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, 634
Length: 1057
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Found at i:533 original size:289 final size:291
Alignment explanation
Indices: 4--1057 Score: 1258
Period size: 289 Copynumber: 3.5 Consensus size: 291
1 CCC
*
4 GAAAGGCCCAAAATAACAAGTGTCCCGAATGAGCTAAAAACTTCACAGTGGACTAAGCTCACCAA
1 GAAAGGCCCAAAATAACAAGTGTCCCAAATGAGCTAAAAACTTCACAGTGGACTAAGCTCACCAA
* * * * *
69 ATTGATTACAGTTAGTCCATAAATAATGGAAAGAAAAGCATTGAGGTTTGCTAAATCGAAGACGA
66 ATAGATTACAGTTAGGCCATAAACAATGGAAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
* *
134 TTCAAAATGGAACTAATGGGCCCCGAAATGCCCAAAATAACAAGTTTTCCAAATGAGCTAAAAAC
131 TTCAAAATGGAACTAATTGGCCCCGAAAAGCCCAAAATAACAAGTTTTCCAAATGAGCTAAAAAC
* *
199 TTCACAGTAGATTAATCTCTCCAAAATCATTATTGTTAGGCCAAAAAGAATGGAAAGAAAAGC-A
196 TTCACAGTGGA-TAATCTCTCCAAAATCATTATAGTTAGGCCAAAAAGAATGGAAAGAAAAGCAA
*
263 TT-GA-GATTCAAAACGTCACTAATGGGCCTT
260 TTAGACGATTCAAAACGTCACTAATGGGCCCT
* * ** * *
293 GAAATGCCCGAAATAACAAGTGTTACAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACGAT
1 GAAAGGCCCAAAATAACAAGTGTCCCAAATGAGCTAAAAACTTCACAGTGGACTAAGCTCACCA-
* * *
358 AA-AGATTATAGTTAGGCCATAAACAATGGAAAAAAAAGCATTGAGTTTTGCCAATTCGAAGACG
65 AATAGATTACAGTTAGGCCATAAACAATGGAAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACG
*
422 ATTCAAAATGGAACTAATTGGCCCCGAAAAGACCAAAATAACAAGTTTTCCAAATGAGCTAAAAA
130 ATTCAAAATGGAACTAATTGGCCCCGAAAAGCCCAAAATAACAAGTTTTCCAAATGAGCTAAAAA
487 CTTCACAGTGGATAAATCTCTCCAAAATCATTATAGTTAGGCCAAAAAGAATGGAAAGAAAAGCA
195 CTTCACAGTGGAT-AATCTCTCCAAAATCATTATAGTTAGGCCAAAAAGAATGGAAAGAAAAGCA
552 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCT
259 ---A----T------T---AGACGATTCAAAACGTCACTAATGGGCCCT
* * * * *
601 GAAATGCCCAAAATAACAAGTGTTCCAAATCAGCTAAAAACTTTACAGTGGACTAATCTCACCAA
1 GAAAGGCCCAAAATAACAAGTGTCCCAAATGAGCTAAAAACTTCACAGTGGACTAAGCTCACCAA
*
666 A-ATGATTATAGTTAGGCCATAAACAATGGAAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACG
66 ATA-GATTACAGTTAGGCCATAAACAATGGAAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACG
* ** * * *
730 ATTCAAAACGTCACTAA-TGGTCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAA
130 ATTCAAAATGGAACTAATTGGCCCCGAAAAGCCCAAAATAACAAGTTTTCCAAATGAGCTAAAAA
* * *** *
794 CTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATTGAAAAAAAAAAA
195 CTTCACAGTGGA-TAATCTCTCCAAAATCATTATAGTTAGGCC--AAA-AA--GAATGGAAAGAA
* * *
859 GCACTAGGGTTTGGCAAATTGAAGATGATTCAAAACAG-AACTAATGGGCCCC
254 --A--A-------GC-AATT--AGACGATTCAAAAC-GTCACTAATGGGCCCT
*
911 GAAAGGCCCAAAATAACAAGTGTCCCGAATGAGCTAAAAACTTCACAGTGGACTAAGCTCACCAA
1 GAAAGGCCCAAAATAACAAGTGTCCCAAATGAGCTAAAAACTTCACAGTGGACTAAGCTCACCAA
* * * * *
976 ATTGATTACAGTTAGTCCATAAATAATGGAAAGAAAAGCATTGAGGTTTGCTAAATCGAAGACGA
66 ATAGATTACAGTTAGGCCATAAACAATGGAAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
1041 TTCAAAATGGAACTAAT
131 TTCAAAATGGAACTAAT
Statistics
Matches: 663, Mismatches: 59, Indels: 64
0.84 0.08 0.08
Matches are distributed among these distances:
288 1 0.00
289 233 0.35
290 2 0.00
293 1 0.00
297 1 0.00
303 1 0.00
307 87 0.13
308 158 0.24
309 3 0.00
310 159 0.24
311 2 0.00
312 8 0.01
314 1 0.00
316 1 0.00
317 1 0.00
321 1 0.00
323 2 0.00
324 1 0.00
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (291 bp):
GAAAGGCCCAAAATAACAAGTGTCCCAAATGAGCTAAAAACTTCACAGTGGACTAAGCTCACCAA
ATAGATTACAGTTAGGCCATAAACAATGGAAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
TTCAAAATGGAACTAATTGGCCCCGAAAAGCCCAAAATAACAAGTTTTCCAAATGAGCTAAAAAC
TTCACAGTGGATAATCTCTCCAAAATCATTATAGTTAGGCCAAAAAGAATGGAAAGAAAAGCAAT
TAGACGATTCAAAACGTCACTAATGGGCCCT
Found at i:549 original size:154 final size:154
Alignment explanation
Indices: 267--1057 Score: 1095
Period size: 154 Copynumber: 5.1 Consensus size: 154
257 AAAGCATTGA
** ** * * *
267 GATTCAAAACGTCACTAATGGGCCTTGAAATGCCCGAAATAACAAGTGTTACAAATGAGCTAAAA
1 GATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
*
332 ACTTCACAGTGGACTAATCTCACGATAAA-GATTATAGTTAGGCCATAAACAATGGAAAAAAAAG
66 ACTTCACAGTGGACTAATCTCACCA-AAATGATTATAGTTAGGCCATAAACAATGGAAAAAAAAG
* *
396 CATTGAGTTTTGCCAATTCGAAGAC
130 CATTGAGGTTTGCCAAATCGAAGAC
* * * * *
421 GATTCAAAATGGAACTAATTGGCCCCGAAAAGACCAAAATAACAAGTTTTCCAAATGAGCTAAAA
1 GATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
* * * * *
486 ACTTCACAGTGGA-TAAATCTCTCCAAAATCATTATAGTTAGGCCAAAAAGAATGGAAAGAAAAG
66 ACTTCACAGTGGACT-AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAAAAAAG
550 CATTGAGGTTTGCCAAATCGAAGAC
130 CATTGAGGTTTGCCAAATCGAAGAC
** * * *
575 GATTCAAAACGTCACTAATGGGCCCTGAAATGCCCAAAATAACAAGTGTTCCAAATCAGCTAAAA
1 GATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
*
640 ACTTTACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAAAAAAGC
66 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAAAAAAGC
705 ATTGAGGTTTGCCAAATCGAAGAC
131 ATTGAGGTTTGCCAAATCGAAGAC
** *
729 GATTCAAAACGTCACTAAT-GGTCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
1 GATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
*
793 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATTGAAAAAAAAAA
66 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA-TG--GAAAAAAA
* * * *
858 AGCACT-AGGGTTTGGCAAATTGAAGAT
128 AGCATTGA-GGTTTGCCAAATCGAAGAC
* * *
885 GATTCAAAACAGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTCCCGAATGAGCTAAAA
1 GATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
* * * * * *
950 ACTTCACAGTGGACTAAGCTCACCAAATTGATTACAGTTAGTCCATAAATAATGGAAAGAAAAGC
66 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAAAAAAGC
*
1015 ATTGAGGTTTGCTAAATCGAAGAC
131 ATTGAGGTTTGCCAAATCGAAGAC
*
1039 GATTCAAAATGGAACTAAT
1 GATTCAAAACGGAACTAAT
Statistics
Matches: 564, Mismatches: 64, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
153 96 0.17
154 330 0.59
155 3 0.01
156 46 0.08
157 89 0.16
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (154 bp):
GATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAAAAAAGC
ATTGAGGTTTGCCAAATCGAAGAC
Found at i:976 original size:310 final size:308
Alignment explanation
Indices: 267--1057 Score: 1142
Period size: 310 Copynumber: 2.6 Consensus size: 308
257 AAAGCATTGA
* * *
267 GATTCAAAACGTCACTAATGGGCCTTGAAATGCCCGAAATAACAAGTGTTACAAATGAGCTAAAA
1 GATTCAAAACGTCACTAATGGGCCCTGAAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
*
332 ACTTCACAGTGGACTAATCTCACGATAAA-GATTATAGTTAGGCCATAAACAATGGAAAAAAAAG
66 ACTTCACAGTGGACTAATCTCACCA-AAATGATTATAGTTAGGCCATAAACAATGGAAAAAAAAG
* * *
396 CATTGAGTTTTGCCAATTCGAAGACGATTCAAAATGGAACTAATTGGCCCCGAAAAGACCAAAAT
130 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATTGGCCCCGAAAAGACCAAAAT
* *
461 AACAAGTTTTCCAAATGAGCTAAAAACTTCACAGTGGATAAATCTCTCCAAAATCATTATAGTTA
195 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGATAAATCTCACCAAAATCATTATAGTTA
* * * *
526 GGCCAAAAAGAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
260 GGCCAAAAACAATGAAAAAAAAAGCATAGAGGTTTGCCAAATCGAAGAC
*
575 GATTCAAAACGTCACTAATGGGCCCTGAAATGCCCAAAATAACAAGTGTTCCAAATCAGCTAAAA
1 GATTCAAAACGTCACTAATGGGCCCTGAAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
*
640 ACTTTACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAAAAAAGC
66 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAAAAAAGC
** * * *
705 ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAA-TGGTCCCGAAAGGCCCAAAATA
131 ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATTGGCCCCGAAAAGACCAAAATA
*
769 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT-AATCTCACCAAAATGATTATAGTTA
196 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA-TAAATCTCACCAAAATCATTATAGTTA
* * * *
833 GGCCATAAACAATTGAAAAAAAAAAAGCACTAG-GGTTTGGCAAATTGAAGAT
260 GGCCAAAAACAA-TG--AAAAAAAAAGCA-TAGAGGTTTGCCAAATCGAAGAC
* * * * *
885 GATTCAAAACAG-AACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTCCCGAATGAGCTAAA
1 GATTCAAAAC-GTCACTAATGGGCCCTGAAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA
* * * * * *
949 AACTTCACAGTGGACTAAGCTCACCAAATTGATTACAGTTAGTCCATAAATAATGGAAAGAAAAG
65 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAAAAAAG
* *
1014 CATTGAGGTTTGCTAAATCGAAGACGATTCAAAATGGAACTAAT
130 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
Statistics
Matches: 433, Mismatches: 42, Indels: 13
0.89 0.09 0.03
Matches are distributed among these distances:
307 91 0.21
308 160 0.37
310 179 0.41
311 3 0.01
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (308 bp):
GATTCAAAACGTCACTAATGGGCCCTGAAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAAAAAAGC
ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATTGGCCCCGAAAAGACCAAAATA
ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGATAAATCTCACCAAAATCATTATAGTTAG
GCCAAAAACAATGAAAAAAAAAGCATAGAGGTTTGCCAAATCGAAGAC
Done.