Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g03150.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: 6151
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31


Found at i:650 original size:23 final size:23

Alignment explanation


    Indices: 626--718  Score: 109
    Period size: 23  Copynumber: 4.0  Consensus size: 23

        616 AATTGTGATG

                    *  *           *
        626 TTAAAGTGCTGCAAATTGAAGTGT
          1 TTAAAGTGTTGTAAATTGAAGT-A

                        *          
        650 TTAAA-TGTTGTGAATTGAAGTA
          1 TTAAAGTGTTGTAAATTGAAGTA

                                   
        672 TTAAAGTGTTGTAAATTGAAGTA
          1 TTAAAGTGTTGTAAATTGAAGTA

                    *               
        695 TTTAAA-TTTTGTAAATTGAAGTA
          1 -TTAAAGTGTTGTAAATTGAAGTA

             
        718 T
          1 T

        719 CTAAGTACTG


Statistics
Matches: 61,  Mismatches: 6, Indels: 6
        0.84            0.08        0.08

Matches are distributed among these distances:
  22    6  0.10
  23   45  0.74
  24   10  0.16

ACGTcount: A:0.37, C:0.02, G:0.20, T:0.41


Consensus pattern (23 bp):   
TTAAAGTGTTGTAAATTGAAGTA

Found at i:655 original size:46 final size:46

Alignment explanation


    Indices: 626--736  Score: 152
    Period size: 46  Copynumber: 2.4  Consensus size: 46

        616 AATTGTGATG

                                  *            *          
        626 TTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTGTGAATTGAAGTA
          1 TTAAAGTGCTGCAAATTGAAGTATTTAAATGTTGTAAATTGAAGTA

                    *  *                  *               
        672 TTAAAGTGTTGTAAATTGAAGTATTTAAATTTTGTAAATTGAAGTA
          1 TTAAAGTGCTGCAAATTGAAGTATTTAAATGTTGTAAATTGAAGTA

                    *           
        718 TCT-AAGTACTGCAAATTGA
          1 T-TAAAGTGCTGCAAATTGA

        737 GATGTTTTAT


Statistics
Matches: 56,  Mismatches: 8, Indels: 2
        0.85            0.12        0.03

Matches are distributed among these distances:
  46   55  0.98
  47    1  0.02

ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39


Consensus pattern (46 bp):   
TTAAAGTGCTGCAAATTGAAGTATTTAAATGTTGTAAATTGAAGTA

Found at i:733 original size:23 final size:22

Alignment explanation


    Indices: 638--736  Score: 81
    Period size: 23  Copynumber: 4.3  Consensus size: 22

        628 AAAGTGCTGC

                       *    * *    
        638 AAATTGAAGTGTTTAAATGTTGT
          1 AAATTGAAGT-ATTAAGTATTGT

            *                 *    
        661 GAATTGAAGTATTAAAGTGTTGT
          1 AAATTGAAGTATT-AAGTATTGT

                            * *    
        684 AAATTGAAGTATTTAAATTTTGT
          1 AAATTGAAGTA-TTAAGTATTGT

                               *  *
        707 AAATTGAAGTATCTAAGTACTGC
          1 AAATTGAAGTAT-TAAGTATTGT

                   
        730 AAATTGA
          1 AAATTGA

        737 GATGTTTTAT


Statistics
Matches: 63,  Mismatches: 10, Indels: 6
        0.80            0.13        0.08

Matches are distributed among these distances:
  22    3  0.05
  23   58  0.92
  24    2  0.03

ACGTcount: A:0.38, C:0.03, G:0.19, T:0.39


Consensus pattern (22 bp):   
AAATTGAAGTATTAAGTATTGT
Done.