Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022042.1 Corchorus olitorius cultivar O-4 contig22075, 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: 3422
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31


Found at i:803 original size:35 final size:35

Alignment explanation


    Indices: 764--902  Score: 192
    Period size: 34  Copynumber: 4.0  Consensus size: 35

        754 AATTTCGTCA

                                               
        764 GGTTTAAGTTTTCAAATTGGGAAAGTTCCCATCAG
          1 GGTTTAAGTTTTCAAATTGGGAAAGTTCCCATCAG

                    *                           
        799 GGTTT-AGCTTTCAAATTGGGAAAGTTCCCATCGAG
          1 GGTTTAAGTTTTCAAATTGGGAAAGTTCCCATC-AG

            **                               * 
        834 TTTTTAAGTTTTCAAATTGGGAAAGTTCCCA-CCG
          1 GGTTTAAGTTTTCAAATTGGGAAAGTTCCCATCAG

                 *         *                   
        868 GGTTTTAGTTTTCAATTTAGGGAAAGTTCCCATCA
          1 GGTTTAAGTTTTCAAATT-GGGAAAGTTCCCATCA

        903 TTTTCAGCTT


Statistics
Matches: 90,  Mismatches: 10, Indels: 7
        0.84            0.09        0.07

Matches are distributed among these distances:
  34   41  0.46
  35   24  0.27
  36   25  0.28

ACGTcount: A:0.27, C:0.16, G:0.22, T:0.36


Consensus pattern (35 bp):   
GGTTTAAGTTTTCAAATTGGGAAAGTTCCCATCAG

Found at i:854 original size:70 final size:71

Alignment explanation


    Indices: 766--901  Score: 222
    Period size: 70  Copynumber: 1.9  Consensus size: 71

        756 TTTCGTCAGG

                                                                             
        766 TTTAAGTTTTCAAATTGGGAAAGTTCCCATCAGGG-TTTAGCTTTCAAATT-GGGAAAGTTCCCA
          1 TTTAAGTTTTCAAATTGGGAAAGTTCCCA-CAGGGTTTTAGCTTTCAAATTAGGGAAAGTTCCCA

                   
        829 TCGAGTT
         65 TCGAGTT

                                          *         *      *                 
        836 TTTAAGTTTTCAAATTGGGAAAGTTCCCACCGGGTTTTAGTTTTCAATTTAGGGAAAGTTCCCAT
          1 TTTAAGTTTTCAAATTGGGAAAGTTCCCACAGGGTTTTAGCTTTCAAATTAGGGAAAGTTCCCAT

             
        901 C
         66 C

        902 ATTTTCAGCT


Statistics
Matches: 61,  Mismatches: 3, Indels: 3
        0.91            0.04        0.04

Matches are distributed among these distances:
  69    4  0.07
  70   42  0.69
  71   15  0.25

ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37


Consensus pattern (71 bp):   
TTTAAGTTTTCAAATTGGGAAAGTTCCCACAGGGTTTTAGCTTTCAAATTAGGGAAAGTTCCCAT
CGAGTT
Done.