Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013962.1 Corchorus olitorius cultivar O-4 contig13995, 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: 5948
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31


Found at i:845 original size:28 final size:27

Alignment explanation


    Indices: 805--858  Score: 90
    Period size: 28  Copynumber: 2.0  Consensus size: 27

        795 AATAATATTC

                                *       
        805 AAATTATAAAATTTTACAAGTAACAAAA
          1 AAATTATAAAATTTTAC-AGGAACAAAA

                                      
        833 AAATTATAAAATTTTACAGGAACAAA
          1 AAATTATAAAATTTTACAGGAACAAA

        859 TTTCCTAAAT


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  27    8  0.32
  28   17  0.68

ACGTcount: A:0.59, C:0.07, G:0.06, T:0.28


Consensus pattern (27 bp):   
AAATTATAAAATTTTACAGGAACAAAA

Found at i:4079 original size:49 final size:48

Alignment explanation


    Indices: 3984--4120  Score: 172
    Period size: 49  Copynumber: 2.9  Consensus size: 48

       3974 GAGCGTGCCA

                         *         *                  *      
       3984 ATCAATTTTGTCAAAAAAATTGATAAAAAGTGCAA-TGAAAATTAAAAC
          1 ATCAATTTTGTCATAAAAATTGAGAAAAAGTGCAAGT-AAAAATAAAAC

                        *                                   *
       4032 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAG
          1 ATCAATTTTGTCATAAAAATTGAGAAAAAG-TGCAAGTAAAAATAAAAC

            *                                         
       4081 TTCAATTTTGT-AGTAAAAATTGAGAAAAAGTGC-AGTAAAA
          1 ATCAATTTTGTCA-TAAAAATTGAGAAAAAGTGCAAGTAAAA

       4121 TGTAAAGGAT


Statistics
Matches: 79,  Mismatches: 7, Indels: 7
        0.85            0.08        0.08

Matches are distributed among these distances:
  47    7  0.09
  48   30  0.38
  49   41  0.52
  50    1  0.01

ACGTcount: A:0.52, C:0.07, G:0.14, T:0.28


Consensus pattern (48 bp):   
ATCAATTTTGTCATAAAAATTGAGAAAAAGTGCAAGTAAAAATAAAAC
Done.