Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012056.1 Corchorus olitorius cultivar O-4 contig12089, 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: 2056
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Found at i:1589 original size:154 final size:154
Alignment explanation
Indices: 1329--2053 Score: 1175
Period size: 154 Copynumber: 4.7 Consensus size: 154
1319 GATTCGTATC
* * *
1329 AGTTAGGCCATAAACAATGGAAAGGAAAGCATTGAGGTTTGCCAAATCGAAAACGATTCAATAC-
1 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACA
* * **
1393 GTCACTAATGGGCCCCGATAAGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAGGTCACAGT
66 G-AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
1458 GGACTAATCTCACCAAAATGATTAT
130 GGACTAATCTCACCAAAATGATTAT
* * *
1483 AGTTAGGCCATAAACGATGGAAAGAAAAGCATTGAGGTCTGCCAAATCGAAGACGATTTAAAACA
1 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACA
* * * *
1548 GAACTAAAGGGCCCCGATAGGCCCAAAATAAGAAGTATTCCAAATGAGCTAAACACTTCACAGTG
66 GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
1613 GACTAATCTCACCAAAATGATTAT
131 GACTAATCTCACCAAAATGATTAT
* *
1637 AGTTAGGACATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG
1 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACA
1702 GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
66 GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
*
1767 GACTAATCTCACCAAAATAATTAT
131 GACTAATCTCACCAAAATGATTAT
* * * * ** *
1791 AGTTAGGCCTTAAACAATTGAAAGAAAAGTATTGAGGTTTGCCAAATCGTAGACGATTCAGTA-T
1 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACA
* *
1855 GTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAGTTCACAGT
66 G-AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
1920 GGACTAATCTCACCAAAATGATTAT
130 GGACTAATCTCACCAAAATGATTAT
*
1945 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTCTGCCAAATCGAAGACGATTCAAAACA
1 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACA
2010 GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
66 GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
2054 ATG
Statistics
Matches: 524, Mismatches: 44, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
153 1 0.00
154 521 0.99
155 2 0.00
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.21
Consensus pattern (154 bp):
AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACA
GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
GACTAATCTCACCAAAATGATTAT
Done.