Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: evm.model.Scaffold2329.8

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: 10383
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.29


Found at i:147 original size:22 final size:22

Alignment explanation


    Indices: 104--152  Score: 55
    Period size: 22  Copynumber: 2.2  Consensus size: 22

         94 CTCCATAAGG

                         *  *     
        104 AAAAGTTGAAGAATTTTGAGAA
          1 AAAAGTTGAAGAACTTGGAGAA

            *                      
        126 GAAAGTTGAA-AACTTGGCAGAA
          1 AAAAGTTGAAGAACTTGG-AGAA

                 
        148 AAAAG
          1 AAAAG

        153 AGACAGAGTG


Statistics
Matches: 22,  Mismatches: 4, Indels: 2
        0.79            0.14        0.07

Matches are distributed among these distances:
  21    5  0.23
  22   17  0.77

ACGTcount: A:0.51, C:0.04, G:0.24, T:0.20


Consensus pattern (22 bp):   
AAAAGTTGAAGAACTTGGAGAA

Found at i:804 original size:39 final size:39

Alignment explanation


    Indices: 746--834  Score: 160
    Period size: 39  Copynumber: 2.3  Consensus size: 39

        736 GATCGGTTGC

                                                   
        746 GTGCAAGGTTGTGTCCAGGGTTGAATAAAGAAGAGAAGA
          1 GTGCAAGGTTGTGTCCAGGGTTGAATAAAGAAGAGAAGA

                          *           *            
        785 GTGCAAGGTTGTGTGCAGGGTTGAATGAAGAAGAGAAGA
          1 GTGCAAGGTTGTGTCCAGGGTTGAATAAAGAAGAGAAGA

                       
        824 GTGCAAGGTTG
          1 GTGCAAGGTTG

        835 AATGAAGGAA


Statistics
Matches: 48,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  39   48  1.00

ACGTcount: A:0.33, C:0.07, G:0.39, T:0.21


Consensus pattern (39 bp):   
GTGCAAGGTTGTGTCCAGGGTTGAATAAAGAAGAGAAGA

Found at i:835 original size:27 final size:27

Alignment explanation


    Indices: 797--850  Score: 83
    Period size: 27  Copynumber: 2.0  Consensus size: 27

        787 GCAAGGTTGT

                 *                      
        797 GTGCAGGGTTGAATGAA-GAAGAGAAGA
          1 GTGCAAGGTTGAATGAAGGAA-AGAAGA

                                       
        824 GTGCAAGGTTGAATGAAGGAAAGAAGA
          1 GTGCAAGGTTGAATGAAGGAAAGAAGA

        851 TTCTTCTTGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  27   22  0.88
  28    3  0.12

ACGTcount: A:0.43, C:0.04, G:0.39, T:0.15


Consensus pattern (27 bp):   
GTGCAAGGTTGAATGAAGGAAAGAAGA
Done.