Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g00785.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: 3451
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37


Found at i:101 original size:35 final size:35

Alignment explanation


    Indices: 32--111  Score: 101
    Period size: 35  Copynumber: 2.3  Consensus size: 35

         22 CAGTTTTCCG

                                 *      **     
         32 AAATCCCTTATTTTTTTCCTCTAAAAATTTTCCCC
          1 AAATCCCTTATTTTTTTCCTCCAAAAATAATCCCC

                                                 
         67 AAATCCCTTATTTTTTTCC-CCAAATCAA-AATCCCC
          1 AAATCCCTTATTTTTTTCCTCCAAA--AATAATCCCC

                      
        102 AAATCCCTTA
          1 AAATCCCTTA

        112 GATTTTCCCT


Statistics
Matches: 40,  Mismatches: 3, Indels: 4
        0.85            0.06        0.09

Matches are distributed among these distances:
  34    4  0.10
  35   34  0.85
  36    2  0.05

ACGTcount: A:0.30, C:0.31, G:0.00, T:0.39


Consensus pattern (35 bp):   
AAATCCCTTATTTTTTTCCTCCAAAAATAATCCCC

Found at i:2970 original size:24 final size:24

Alignment explanation


    Indices: 2943--2994  Score: 86
    Period size: 24  Copynumber: 2.2  Consensus size: 24

       2933 GAGATTCATG

                  *                 
       2943 AAGTAGTTGCAGATATTCTAAAAA
          1 AAGTAGATGCAGATATTCTAAAAA

                *                   
       2967 AAGTGGATGCAGATATTCTAAAAA
          1 AAGTAGATGCAGATATTCTAAAAA

                
       2991 AAGT
          1 AAGT

       2995 GGACTTCTAC


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  24   26  1.00

ACGTcount: A:0.46, C:0.08, G:0.19, T:0.27


Consensus pattern (24 bp):   
AAGTAGATGCAGATATTCTAAAAA

Found at i:2995 original size:24 final size:24

Alignment explanation


    Indices: 2950--2997  Score: 96
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       2940 ATGAAGTAGT

                                    
       2950 TGCAGATATTCTAAAAAAAGTGGA
          1 TGCAGATATTCTAAAAAAAGTGGA

                                    
       2974 TGCAGATATTCTAAAAAAAGTGGA
          1 TGCAGATATTCTAAAAAAAGTGGA

       2998 CTTCTACACT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.46, C:0.08, G:0.21, T:0.25


Consensus pattern (24 bp):   
TGCAGATATTCTAAAAAAAGTGGA
Done.