Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006743.1 Corchorus olitorius cultivar O-4 contig06768, 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, 613

Length: 1022
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39


Found at i:823 original size:39 final size:40

Alignment explanation


    Indices: 767--846  Score: 126
    Period size: 39  Copynumber: 2.0  Consensus size: 40

        757 TTTAATTCCT

                                                    
        767 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

                     *          *         *         
        807 ATGTAATA-CTATAATAACTGAAATACTTATATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

             
        846 A
          1 A

        847 GTCTTAGGTA


Statistics
Matches: 37,  Mismatches: 3, Indels: 1
        0.90            0.07        0.02

Matches are distributed among these distances:
  39   29  0.78
  40    8  0.22

ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38


Consensus pattern (40 bp):   
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

Found at i:837 original size:18 final size:18

Alignment explanation


    Indices: 777--837  Score: 52
    Period size: 17  Copynumber: 3.2  Consensus size: 18

        767 ATGTAATATA

                      *       
        777 TATAATAACTAAAATACT
          1 TATAATAACTGAAATACT

                        *  *      
        795 TACATTAATTAAATGTAATAC-
          1 T--A-TAA-TAACTGAAATACT

                              
        816 TATAATAACTGAAATACT
          1 TATAATAACTGAAATACT

                
        834 TATA
          1 TATA

        838 TTAATTAAAG


Statistics
Matches: 33,  Mismatches: 5, Indels: 10
        0.69            0.10        0.21

Matches are distributed among these distances:
  17   10  0.30
  18    8  0.24
  19    1  0.03
  20    1  0.03
  21    4  0.12
  22    9  0.27

ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36


Consensus pattern (18 bp):   
TATAATAACTGAAATACT

Found at i:877 original size:24 final size:23

Alignment explanation


    Indices: 838--883  Score: 74
    Period size: 24  Copynumber: 2.0  Consensus size: 23

        828 AATACTTATA

                                   
        838 TTAATTAAAGTCTTAGGTATTTT
          1 TTAATTAAAGTCTTAGGTATTTT

                      *            
        861 TTAATTCAAATTCTTAGGTATTT
          1 TTAATT-AAAGTCTTAGGTATTT

        884 GTGCAAACGT


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  23    6  0.29
  24   15  0.71

ACGTcount: A:0.30, C:0.07, G:0.11, T:0.52


Consensus pattern (23 bp):   
TTAATTAAAGTCTTAGGTATTTT
Done.