Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold809

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: 2582
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39


Found at i:597 original size:13 final size:12

Alignment explanation


    Indices: 564--611  Score: 53
    Period size: 12  Copynumber: 3.9  Consensus size: 12

        554 TTTAAAAATA

                        
        564 AAAATTATTTTT
          1 AAAATTATTTTT

                *         
        576 AATAGTTATTTTTT
          1 AA-AATTA-TTTTT

                    *   
        590 AAAATTATCTTT
          1 AAAATTATTTTT

                       
        602 AAAA-TATTTT
          1 AAAATTATTTT

        612 AAAGATGATA


Statistics
Matches: 30,  Mismatches: 4, Indels: 5
        0.77            0.10        0.13

Matches are distributed among these distances:
  11    5  0.17
  12   10  0.33
  13    8  0.27
  14    7  0.23

ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56


Consensus pattern (12 bp):   
AAAATTATTTTT

Found at i:1477 original size:3 final size:3

Alignment explanation


    Indices: 1464--1503  Score: 66
    Period size: 3  Copynumber: 14.0  Consensus size: 3

       1454 GGCTAAAGGA

                                                                   
       1464 TAT TAT T-T TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

       1504 GTGGAGAATA


Statistics
Matches: 35,  Mismatches: 0, Indels: 4
        0.90            0.00        0.10

Matches are distributed among these distances:
   2    4  0.11
   3   31  0.89

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68


Consensus pattern (3 bp):   
TAT

Found at i:1480 original size:11 final size:11

Alignment explanation


    Indices: 1464--1503  Score: 62
    Period size: 11  Copynumber: 3.5  Consensus size: 11

       1454 GGCTAAAGGA

                       
       1464 TATTATTTTAT
          1 TATTATTTTAT

                  *    
       1475 TATTATATTAT
          1 TATTATTTTAT

                        
       1486 TATTATTATTAT
          1 TATTATT-TTAT

                  
       1498 TATTAT
          1 TATTAT

       1504 GTGGAGAATA


Statistics
Matches: 26,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  11   16  0.62
  12   10  0.38

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68


Consensus pattern (11 bp):   
TATTATTTTAT

Done.