Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g01366.F2

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: 3772
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24


Found at i:2181 original size:21 final size:22

Alignment explanation


    Indices: 2157--2198  Score: 61
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       2147 TTAGTCAAGG

                                   
       2157 AGCTTG-TGTCTCT-ACAAGAAA
          1 AGCTTGAT-TCTCTAACAAGAAA

                                 
       2178 AGCTTGATTCTCTAACAAGAA
          1 AGCTTGATTCTCTAACAAGAA

       2199 GGTGGACTGA


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  21   11  0.58
  22    8  0.42

ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29


Consensus pattern (22 bp):   
AGCTTGATTCTCTAACAAGAAA

Found at i:3024 original size:90 final size:90

Alignment explanation


    Indices: 2869--3105  Score: 404
    Period size: 90  Copynumber: 2.6  Consensus size: 90

       2859 CCATTTCCAA

                                              *  *                      *    
       2869 AATTGATGAGCATTTACTTGAAGCAGAACCAAACTACAGTGTAGAGGATGAGAAAGAGATTGACT
          1 AATTGATGAGCATTTACTTGAAGCAGAACCAAACAACGGTGTAGAGGATGAGAAAGAGATCGACT

                                     
       2934 TGTTCAAAGAGTTGCCAGCTGGAGT
         66 TGTTCAAAGAGTTGCCAGCTGGAGT

                                                                             
       2959 AATTGATGAGCATTTACTTGAAGCAGAACCAAACAACGGTGTAGAGGATGAGAAAGAGATCGACT
          1 AATTGATGAGCATTTACTTGAAGCAGAACCAAACAACGGTGTAGAGGATGAGAAAGAGATCGACT

                                     
       3024 TGTTCAAAGAGTTGCCAGCTGGAGT
         66 TGTTCAAAGAGTTGCCAGCTGGAGT

                                     *  *            *                
       3049 AATTGATGAGCATTTACTTGAAGCAAAATCAAACAACGGTGCACG-GGATGAGAAAGA
          1 AATTGATGAGCATTTACTTGAAGCAGAACCAAACAACGGTGTA-GAGGATGAGAAAGA

       3106 AGTAGAGATC


Statistics
Matches: 140,  Mismatches: 6, Indels: 2
        0.95            0.04        0.01

Matches are distributed among these distances:
  90  139  0.99
  91    1  0.01

ACGTcount: A:0.37, C:0.14, G:0.27, T:0.22


Consensus pattern (90 bp):   
AATTGATGAGCATTTACTTGAAGCAGAACCAAACAACGGTGTAGAGGATGAGAAAGAGATCGACT
TGTTCAAAGAGTTGCCAGCTGGAGT

Done.