Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006029.1 Corchorus olitorius cultivar O-4 contig06054, 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, 940

Length: 1567
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34


Found at i:401 original size:27 final size:28

Alignment explanation


    Indices: 363--467  Score: 88
    Period size: 27  Copynumber: 3.8  Consensus size: 28

        353 TGAGCAATGG

                *           *           
        363 AGTAGAAATGACCAAACTGCCCCCT-GA
          1 AGTAAAAATGACCAAAATGCCCCCTAGA

                *       *     *        *
        390 AGTATAAATGACTAAAATACCCCCTAGG
          1 AGTAAAAATGACCAAAATGCCCCCTAGA

            *                        *  
        418 TGTAAAAATGACCAAAATG-CCCCTGGA
          1 AGTAAAAATGACCAAAATGCCCCCTAGA

            *  **       *          
        445 CGTGCAAATGACGAAAATGCCCC
          1 AGTAAAAATGACCAAAATGCCCC

        468 TGAACGTGCA


Statistics
Matches: 61,  Mismatches: 15, Indels: 3
        0.77            0.19        0.04

Matches are distributed among these distances:
  27   42  0.69
  28   19  0.31

ACGTcount: A:0.39, C:0.26, G:0.18, T:0.17


Consensus pattern (28 bp):   
AGTAAAAATGACCAAAATGCCCCCTAGA

Found at i:468 original size:27 final size:27

Alignment explanation


    Indices: 423--498  Score: 116
    Period size: 27  Copynumber: 2.8  Consensus size: 27

        413 CTAGGTGTAA

                                *      
        423 AAATGACCAAAATGCCCCTGGACGTGC
          1 AAATGACCAAAATGCCCCTGAACGTGC

                   *                   
        450 AAATGACGAAAATGCCCCTGAACGTGC
          1 AAATGACCAAAATGCCCCTGAACGTGC

                   *     *        
        477 AAATGACTAAAATCCCCCTGAA
          1 AAATGACCAAAATGCCCCTGAA

        499 TGACCTCAAA


Statistics
Matches: 45,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  27   45  1.00

ACGTcount: A:0.38, C:0.28, G:0.18, T:0.16


Consensus pattern (27 bp):   
AAATGACCAAAATGCCCCTGAACGTGC
Done.