Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015057.1 Corchorus olitorius cultivar O-4 contig15090, 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: 2174
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39


Found at i:1063 original size:46 final size:43

Alignment explanation


    Indices: 985--1069  Score: 143
    Period size: 45  Copynumber: 1.9  Consensus size: 43

        975 AATTCCTATG

                                                       
        985 TAATATATATAATAACTGAAATACTTACATTAATTAAATGTAA
          1 TAATATATATAATAACTGAAATACTTACATTAATTAAATGTAA

                                                      
       1028 TAATAATACTATAATAACTGAAATACTATACATTAATTAAAT
          1 TAAT-ATA-TATAATAACTGAAATACT-TACATTAATTAAAT

       1070 TCTTAGGTAT


Statistics
Matches: 39,  Mismatches: 0, Indels: 3
        0.93            0.00        0.07

Matches are distributed among these distances:
  43    4  0.10
  44    3  0.08
  45   18  0.46
  46   14  0.36

ACGTcount: A:0.52, C:0.08, G:0.04, T:0.36


Consensus pattern (43 bp):   
TAATATATATAATAACTGAAATACTTACATTAATTAAATGTAA

Found at i:1105 original size:25 final size:24

Alignment explanation


    Indices: 1060--1106  Score: 67
    Period size: 25  Copynumber: 1.9  Consensus size: 24

       1050 ATACTATACA

                           **       
       1060 TTAATTAAATTCTTAGGTATTTTT
          1 TTAATTAAATTCTTAACTATTTTT

                                   
       1084 TTAATTCAAATTCTTAACTATTT
          1 TTAATT-AAATTCTTAACTATTT

       1107 GTGCAAAAGT


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  24    6  0.30
  25   14  0.70

ACGTcount: A:0.32, C:0.09, G:0.04, T:0.55


Consensus pattern (24 bp):   
TTAATTAAATTCTTAACTATTTTT

Found at i:1915 original size:36 final size:36

Alignment explanation


    Indices: 1858--1927  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       1848 GAGATTTTGG

                         *                      
       1858 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
          1 AGAAATATGATAACCAAAATTACAAAAAATGTAATA

                *           *                 
       1894 AGAATTATGATAACCATAATTACAAAAAATGTAA
          1 AGAAATATGATAACCAAAATTACAAAAAATGTAA

       1928 CGTTATTGAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.59, C:0.07, G:0.09, T:0.26


Consensus pattern (36 bp):   
AGAAATATGATAACCAAAATTACAAAAAATGTAATA
Done.