Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g01735.P1

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: 2220
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.36


Found at i:905 original size:53 final size:53

Alignment explanation


    Indices: 825--926  Score: 143
    Period size: 53  Copynumber: 1.9  Consensus size: 53

        815 CCATGGCAAC

                         *                       *               
        825 ATGTGATATGTGATTTCCGTATAAGACCACAACTAGGCTATGGCATCGGAGAG
          1 ATGTGATATGTGACTTCCGTATAAGACCACAACTAGGATATGGCATCGGAGAG

                                          * *  *              
        878 ATGTGATTATGTG-CTTCCGTATAAGACCATATCTGGGATATGGCATCGG
          1 ATGTGA-TATGTGACTTCCGTATAAGACCACAACTAGGATATGGCATCGG

        927 TGTGATATGT


Statistics
Matches: 43,  Mismatches: 5, Indels: 2
        0.86            0.10        0.04

Matches are distributed among these distances:
  53   37  0.86
  54    6  0.14

ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29


Consensus pattern (53 bp):   
ATGTGATATGTGACTTCCGTATAAGACCACAACTAGGATATGGCATCGGAGAG

Found at i:954 original size:47 final size:47

Alignment explanation


    Indices: 879--984  Score: 151
    Period size: 47  Copynumber: 2.2  Consensus size: 47

        869 ATCGGAGAGA

                          *  *     *                         
        879 TGTGATTATGTGCTTCCGTATAAGACCATATCTGGGATATGGCATCG-G
          1 TGTGA-TATGTGCTACCATATAAAACCATATCTGGGATATGGCAT-GAG

                           *                               
        927 TGTGATATGTGCTACTATATAAAACCATATCTGGGATATGGCATGAG
          1 TGTGATATGTGCTACCATATAAAACCATATCTGGGATATGGCATGAG

                       
        974 TGTGATATGTG
          1 TGTGATATGTG

        985 ATTCGTGTAA


Statistics
Matches: 53,  Mismatches: 4, Indels: 3
        0.88            0.07        0.05

Matches are distributed among these distances:
  46    1  0.02
  47   47  0.89
  48    5  0.09

ACGTcount: A:0.26, C:0.13, G:0.26, T:0.34


Consensus pattern (47 bp):   
TGTGATATGTGCTACCATATAAAACCATATCTGGGATATGGCATGAG
Done.