Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: evm.model.Scaffold401.22

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, 392

Length: 654
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24


Found at i:487 original size:69 final size:66

Alignment explanation


    Indices: 363--556  Score: 172
    Period size: 66  Copynumber: 2.9  Consensus size: 66

        353 CCGGTGGTTT

                  *   *  *             *        *  *    ****  *          **  
        363 CAGAATGCCTGAATATGGGGATCCTGCCGGATTTAGGATACCTGGCTTTGGAGATCCCATAGGGC
          1 CAGAATACCTAAACATGGGGATCCTGCAGGATTTAGAATGCCTGAAAATGAAGATCCCATAAAGC

             
        428 A
         66 A

                                                        *                    
        429 CAGAATACCTGAAGAACATGGGGATCCTGCAGGATTTAGAATGCTTGAAAATGAAGATCCCATAA
          1 CAGAATACCT--A-AACATGGGGATCCTGCAGGATTTAGAATGCCTGAAAATGAAGATCCCATAA

              **
        494 AGTT
         63 AGCA

                  *                           *         **     *       
        498 CAGAATGCCTAAACATGGGGATCCTGCAGGATTTCGAATGCCTGGGAATGATGATCCCA
          1 CAGAATACCTAAACATGGGGATCCTGCAGGATTTAGAATGCCTGAAAATGAAGATCCCA

        557 CTGGATTCAC


Statistics
Matches: 103,  Mismatches: 22, Indels: 6
        0.79            0.17        0.05

Matches are distributed among these distances:
  66   52  0.50
  67    1  0.01
  69   50  0.49

ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23


Consensus pattern (66 bp):   
CAGAATACCTAAACATGGGGATCCTGCAGGATTTAGAATGCCTGAAAATGAAGATCCCATAAAGC
A

Found at i:537 original size:33 final size:34

Alignment explanation


    Indices: 443--541  Score: 89
    Period size: 33  Copynumber: 3.0  Consensus size: 34

        433 ATACCTGAAG

                                   *      *   
        443 AACATGGGGATCCTGCAGGATTTAGAATGCTTGA
          1 AACATGGGGATCCTGCAGGATTTCGAATGCCTGA

                  **          ** *              
        477 AA-ATGAAGATCC--CATAAAGTTCAGAATGCCT-A
          1 AACATGGGGATCCTGCA-GGATTTC-GAATGCCTGA

                                             
        509 AACATGGGGATCCTGCAGGATTTCGAATGCCTG
          1 AACATGGGGATCCTGCAGGATTTCGAATGCCTG

        542 GGAATGATGA


Statistics
Matches: 47,  Mismatches: 12, Indels: 12
        0.66            0.17        0.17

Matches are distributed among these distances:
  31    2  0.04
  32    6  0.13
  33   31  0.66
  34    6  0.13
  35    2  0.04

ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24


Consensus pattern (34 bp):   
AACATGGGGATCCTGCAGGATTTCGAATGCCTGA
Done.