Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g01571.F16

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: 4366
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27


Found at i:3140 original size:57 final size:54

Alignment explanation


    Indices: 3079--3215  Score: 139
    Period size: 57  Copynumber: 2.4  Consensus size: 54

       3069 AGCAGCTTTT

                              *                          *      *    
       3079 ACAGCAACAGTATCAGCAACAGCCACAGCTGCTACAAGTGCAACAGCAATATCTTCA
          1 ACAGCAACAGTATCAGCAGCAGCCACAGCTGCTAC-A--GCAACAACAATATATTCA

                      *   *   *                 *             *      
       3136 ACAGCAACAATTACCCTATCAGCAGCCACAGCTGCTGCAGCAACAACAATTTATTCA
          1 ACAGCAAC-AGTA-TC-AGCAGCAGCCACAGCTGCTACAGCAACAACAATATATTCA

                          *        
       3193 ACAGCAACAGTATCTGCAGCAGC
          1 ACAGCAACAGTATCAGCAGCAGC

       3216 AGCAGCAACA


Statistics
Matches: 65,  Mismatches: 12, Indels: 9
        0.76            0.14        0.10

Matches are distributed among these distances:
  54    7  0.11
  55    1  0.02
  56    3  0.05
  57   31  0.48
  58    3  0.05
  59    2  0.03
  60   18  0.28

ACGTcount: A:0.37, C:0.31, G:0.15, T:0.17


Consensus pattern (54 bp):   
ACAGCAACAGTATCAGCAGCAGCCACAGCTGCTACAGCAACAACAATATATTCA

Found at i:3919 original size:70 final size:70

Alignment explanation


    Indices: 3832--3973  Score: 275
    Period size: 70  Copynumber: 2.0  Consensus size: 70

       3822 TTAATAATGA

                                                                             
       3832 AAGCTTAAAGTTTAAACTTGATCAACTTTGTCTGATAATGAGAAGAAAATGTCAATTGAAGAGCT
          1 AAGCTTAAAGTTTAAACTTGATCAACTTTGTCTGATAATGAGAAGAAAATGTCAATTGAAGAGCT

                 
       3897 CCTGG
         66 CCTGG

                                                       *                     
       3902 AAGCTTAAAGTTTAAACTTGATCAACTTTGTCTGATAATGAGAGGAAAATGTCAATTGAAGAGCT
          1 AAGCTTAAAGTTTAAACTTGATCAACTTTGTCTGATAATGAGAAGAAAATGTCAATTGAAGAGCT

                 
       3967 CCTGG
         66 CCTGG

              
       3972 AA
          1 AA

       3974 CATACTGCAT


Statistics
Matches: 71,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  70   71  1.00

ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30


Consensus pattern (70 bp):   
AAGCTTAAAGTTTAAACTTGATCAACTTTGTCTGATAATGAGAAGAAAATGTCAATTGAAGAGCT
CCTGG
Done.