Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g00931.F1

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: 4499
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37


Found at i:4020 original size:43 final size:42

Alignment explanation


    Indices: 3972--4052  Score: 117
    Period size: 43  Copynumber: 1.9  Consensus size: 42

       3962 AATTTTATGA

                           *                           
       3972 CCTTTAGAGGCATTTTTGGGAGAAGCGCCGCTAAAGGTCGTGG
          1 CCTTTAGAGGCATTTGTGGGAGAA-CGCCGCTAAAGGTCGTGG

                   *  **                          
       4015 CCTTTAGCGGTGTTTGTGGGAGAACGCCGCTAAAGGTC
          1 CCTTTAGAGGCATTTGTGGGAGAACGCCGCTAAAGGTC

       4053 ATGACTTTTA


Statistics
Matches: 34,  Mismatches: 4, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  42   14  0.41
  43   20  0.59

ACGTcount: A:0.20, C:0.20, G:0.35, T:0.26


Consensus pattern (42 bp):   
CCTTTAGAGGCATTTGTGGGAGAACGCCGCTAAAGGTCGTGG

Found at i:4063 original size:42 final size:43

Alignment explanation


    Indices: 3968--4071  Score: 138
    Period size: 42  Copynumber: 2.4  Consensus size: 43

       3958 TTTAAATTTT

                       *   *   *                       
       3968 ATGACCTTTAGAGGCATTTTTGGGAGAAGCGCCGCTAAAGGTC
          1 ATGACCTTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTC

            *  *          *                            
       4011 GTGGCCTTTAGCGGTGTTTGTGGGAGAA-CGCCGCTAAAGGTC
          1 ATGACCTTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTC

                 *             
       4053 ATGACTTTTAGCGGCGTTT
          1 ATGACCTTTAGCGGCGTTT

       4072 CCTATAGCCG


Statistics
Matches: 51,  Mismatches: 10, Indels: 1
        0.82            0.16        0.02

Matches are distributed among these distances:
  42   29  0.57
  43   22  0.43

ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29


Consensus pattern (43 bp):   
ATGACCTTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTC
Done.