Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012209.1 Corchorus olitorius cultivar O-4 contig12242, 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, 967
Length: 1613
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Found at i:283 original size:154 final size:153
Alignment explanation
Indices: 3--810 Score: 1160
Period size: 154 Copynumber: 5.2 Consensus size: 153
1 GG
3 GGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGTGCCCCGAAAGGCCCAAAATAACAAG
1 GGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGT-CCCCGAAAGGCCCAAAATAACAAG
* * *
68 TGTTCCAATTGAGCTAAAAACTTCACAGTGGACAAATCTCACCAAAATAATTATAGTTAGGCCAT
65 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
*
133 AAACAATGGTAAGAAAAGCATTGA
130 AAACAATGGAAAGAAAAGCATTGA
* *** *
157 GGTTTGCCAAATCGAAGACGATTCTAAACTTCACTAATAGTCCCCGACAGGCCCAAAATAACAAG
1 GGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAAT-GTCCCCGAAAGGCCCAAAATAACAAG
*
222 TGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
65 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
287 AAACAATGGAAAGAAAAGCATTGA
130 AAACAATGGAAAGAAAAGCATTGA
*
311 GGTTTGCCAAATCG-AGACAATTCAAAACAGAACTAATG-CGCCTC-AATAGGCCCAAAAAAATA
1 GGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGTC-CC-CGAA-AGGCCC---AAAATA
* * *
373 ACAAGTTTTCCAAATGACCTAAAAACTTCACAGTGGACTAATCTCACCAAAAGGATTATAGTTAG
60 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
438 GCCATAAACAATGGAAAGAAAAGCATTCG-
125 GCCATAAACAATGGAAAGAAAAGCATT-GA
** * * * * *
467 GAATTGACAAATCTAAGACGATTCAAAACGGAACTTATGGGCCCCGAAAGGCCCAAAATAACAAG
1 GGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAAT-GTCCCCGAAAGGCCCAAAATAACAAG
* *
532 TGTTCCAATTGAGCTAAAAACTTCACAGTGGACTAATCTCACGAAAATGATTATAGTTAGGCCAT
65 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
* *
597 AAACAATGGAAAGAAAGGCATCGAA
130 AAACAATGGAAAGAAAAGCATTG-A
* * * *
622 GG-TTGCTAAATCGAAGACGATTCAAAAC-GTCACTAATGGTCCCCGATAGGCCCAAAATAAAAA
1 GGTTTGCCAAATCGAAGACGATTCAAAACAG-AACTAAT-GTCCCCGAAAGGCCCAAAATAACAA
* * *
685 GCGTTCCAAATGATCTAAAAACTTCATAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
64 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
750 TAAACAATGGAAAGAAAAGCATTGA
129 TAAACAATGGAAAGAAAAGCATTGA
*
775 GGTTTGCCAAATCGAAGACAATTCAAAACAGAACTA
1 GGTTTGCCAAATCGAAGACGATTCAAAACAGAACTA
811 TAATGATCAT
Statistics
Matches: 584, Mismatches: 53, Indels: 34
0.87 0.08 0.05
Matches are distributed among these distances:
151 1 0.00
152 4 0.01
153 30 0.05
154 407 0.70
155 4 0.01
156 104 0.18
157 28 0.05
158 5 0.01
159 1 0.00
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.21
Consensus pattern (153 bp):
GGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGTCCCCGAAAGGCCCAAAATAACAAGT
GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATA
AACAATGGAAAGAAAAGCATTGA
Found at i:635 original size:310 final size:307
Alignment explanation
Indices: 3--810 Score: 1176
Period size: 310 Copynumber: 2.6 Consensus size: 307
1 GG
3 GGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGTGCCCCGAA-AGGCCCAAAATAACAA
1 GGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATG-GCCCC-AATAGGCCCAAAATAACAA
* * * *
67 GTGTTCCAATTGAGCTAAAAACTTCACAGTGGACAAATCTCACCAAAATAATTATAGTTAGGCCA
64 GTGTTCCAAATGACCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
* * ***
132 TAAACAATGGTAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCTAAACTTCACTAATAG
129 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATAG
* *
197 TCCCCGACAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTC
194 GCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTC
*
262 ACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA
259 ACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGA
* *
311 GGTTTGCCAAATCG-AGACAATTCAAAACAGAACTAATGCGCCTCAATAGGCCCAAAAAAATAAC
1 GGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATG-GCCCCAATAGGCCC---AAAATAAC
* *
375 AAGTTTTCCAAATGACCTAAAAACTTCACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGC
62 AAGTGTTCCAAATGACCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
** * * * *
440 CATAAACAATGGAAAGAAAAGCATTCG-GAATTGACAAATCTAAGACGATTCAAAACGGAACTTA
127 CATAAACAATGGAAAGAAAAGCATT-GAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAA
* * *
504 TGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAATTGAGCTAAAAACTTCACAGTGGACTAAT
191 TAGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAAT
* *
569 CTCACGAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGGCATCGAA
256 CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCG-A
* * * *
622 GG-TTGCTAAATCGAAGACGATTCAAAAC-GTCACTAATGGTCCCCGATAGGCCCAAAATAAAAA
1 GGTTTGCCAAATCGAAGACGATTCAAAACAG-AACTAATGG-CCCCAATAGGCCCAAAATAACAA
* * *
685 GCGTTCCAAATGATCTAAAAACTTCATAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
64 GTGTTCCAAATGACCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
*
750 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCAAAACAGAACTA
129 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTA
811 TAATGATCAT
Statistics
Matches: 445, Mismatches: 45, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
306 2 0.00
307 34 0.08
308 135 0.30
310 239 0.54
311 35 0.08
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.21
Consensus pattern (307 bp):
GGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGCCCCAATAGGCCCAAAATAACAAGT
GTTCCAAATGACCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATA
AACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATAGGC
CCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCAC
CAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGA
Done.