Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011727.1 Corchorus olitorius cultivar O-4 contig11760, 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, 852
Length: 1421
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Found at i:787 original size:154 final size:154
Alignment explanation
Indices: 5--1416 Score: 2140
Period size: 154 Copynumber: 9.2 Consensus size: 154
1 AGTA
* *
5 GTTCCAAATGAAGTCT-AAAAC-TCA-AGTGGACTAATCTTACTAAAATGATTATAGTTAGGCCA
1 GTTCCAAATG-AG-CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
* * *
67 TAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAGCGGAAATAATGG
64 TAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGG
*
132 GCCCCGAAAGGCCCAAAATAACAAGT
129 GCCCCGATAGGCCCAAAATAACAAGT
* *
158 GTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCCCACCAAAATGATTATAGTTAGGCCATA
1 GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATA
**
223 AACAATGGAAAGAAAAGCATTGAGGGTT-CCAAATCGAAGACGATTCAAAACGTCACTAATGGGC
66 AACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGC
*
287 CCCGATAGGCCCAAAATAAAAAGT
131 CCCGATAGGCCCAAAATAACAAGT
* *
311 GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCAATA
1 GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATA
*
376 AACAATGGAAAGAAAAGCATTAAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGC
66 AACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGC
* *
441 CTCGATACGCCCCAAAATAACAAGT
131 CCCGATA-GGCCCAAAATAACAAGT
466 GTTCCAAATGAGCTAGAAAACTTCACAGTGGACTAATCTCAACCAAAATGATTATAGTTAGG-CA
1 GTTCCAAATGAGCTA-AAAACTTCACAGTGGACTAATCTC-ACCAAAATGATTATAGTTAGGCCA
* * ** *
530 AAAACAATGGAAAGAAAAGCATTGAGGGTT-CCAAATCGAAAACGATTCAAAACGTCACTAAAGG
64 TAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGG
*
594 GCCCCCGATAGGCCCAAAATTAAGAAGT
129 G-CCCCGATAGGCCCAAAA-TAACAAGT
* *
622 GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAACGATAAT-GTTAGGCCATA
1 GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATA
* * * **
686 AACAATGGAAAAAAAAGTATTGAGGGTTGCCAAATCGAAGATGATTCAAAACGTCACTAATGGGC
66 AACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGC
751 CCCGATAGGCCCAAAATAACAAGT
131 CCCGATAGGCCCAAAATAACAAGT
775 GAATT-CAAATGAGCTAAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
1 G--TTCCAAATGAGCT-AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
* * **
839 ATAAACAATGGAAGGAAAAGCATTGAGGGTTG-CAAATCAAAGACGATTCAAAACGTCACTAATG
63 ATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG
* * * *
903 GGACCCGATAGGCCCATAATAAAAACT
128 GGCCCCGATAGGCCCAAAATAACAAGT
* * *
930 TTTCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAATTAGGCCATA
1 GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATA
* * * **
995 AACAATGGAAAAAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAGAACGGAACTGATGGTT
66 AACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGC
*
1060 CTCGATAGGCCCAAAATAACAAGT
131 CCCGATAGGCCCAAAATAACAAGT
* * *
1084 GTTCCAAATGAGCTAAAAACTTCACTGTGGATTAATCTCACCAAAATGATTATAGTAAGGCCATA
1 GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATA
* * *
1149 AACATTGTAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGTC
66 AACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGC
* * *
1214 CTCGATATGCCCGAAATAACAAGT
131 CCCGATAGGCCCAAAATAACAAGT
1238 GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATA
1 GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATA
* *
1303 AACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATTGAAGACAATTCAAAACGGAACTAATGGGC
66 AACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGC
*
1368 CCCGAAAGGCCCAAAATAACAAGT
131 CCCGATAGGCCCAAAATAACAAGT
1392 GTTCCAAATGAGCTAAAAAACTTCA
1 GTTCCAAATGAGCT-AAAAACTTCA
1417 AAGTT
Statistics
Matches: 1148, Mismatches: 93, Indels: 34
0.90 0.07 0.03
Matches are distributed among these distances:
151 2 0.00
152 7 0.01
153 247 0.22
154 526 0.46
155 227 0.20
156 119 0.10
157 20 0.02
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Consensus pattern (154 bp):
GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATA
AACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGC
CCCGATAGGCCCAAAATAACAAGT
Done.