Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold947

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: 3944
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30


Found at i:2615 original size:22 final size:22

Alignment explanation


    Indices: 2590--2661  Score: 71
    Period size: 19  Copynumber: 3.5  Consensus size: 22

       2580 AGAATAAAAT

                                  
       2590 AATGAAATAACAAGAACATAAA
          1 AATGAAATAACAAGAACATAAA

                    *    *  *    *
       2612 AATG--ATGA-AATAAAATAAT
          1 AATGAAATAACAAGAACATAAA

                                  
       2631 AA-GAAATAACAAGAACATAAA
          1 AATGAAATAACAAGAACATAAA

               *      
       2652 AATAAAATAA
          1 AATGAAATAA

       2662 TAAAAGACAA


Statistics
Matches: 37,  Mismatches: 9, Indels: 8
        0.69            0.17        0.15

Matches are distributed among these distances:
  18    1  0.03
  19   10  0.27
  20    6  0.16
  21   10  0.27
  22   10  0.27

ACGTcount: A:0.69, C:0.06, G:0.08, T:0.17


Consensus pattern (22 bp):   
AATGAAATAACAAGAACATAAA

Found at i:2643 original size:40 final size:39

Alignment explanation


    Indices: 2577--2654  Score: 131
    Period size: 40  Copynumber: 2.0  Consensus size: 39

       2567 CAAACATGAC

                                                   
       2577 ATGAGAATAAAATAATGAAATAACAAGAACATAAAAATG
          1 ATGAGAATAAAATAATGAAATAACAAGAACATAAAAATG

                                                    
       2616 ATGA-AATAAAATAATAAGAAATAACAAGAACATAAAAAT
          1 ATGAGAATAAAATAAT--GAAATAACAAGAACATAAAAAT

       2655 AAAATAATAA


Statistics
Matches: 37,  Mismatches: 0, Indels: 3
        0.93            0.00        0.08

Matches are distributed among these distances:
  38   11  0.30
  39    4  0.11
  40   22  0.59

ACGTcount: A:0.67, C:0.05, G:0.10, T:0.18


Consensus pattern (39 bp):   
ATGAGAATAAAATAATGAAATAACAAGAACATAAAAATG

Found at i:2664 original size:40 final size:38

Alignment explanation


    Indices: 2582--2666  Score: 118
    Period size: 40  Copynumber: 2.2  Consensus size: 38

       2572 ATGACATGAG

                                               ** 
       2582 AATAAAATAATGAAATAACAAGAACATAAAAATGATGA
          1 AATAAAATAATGAAATAACAAGAACATAAAAATGAAAA

                                                    
       2620 AATAAAATAATAAGAAATAACAAGAACATAAAAAT-AAAA
          1 AATAAAATAAT--GAAATAACAAGAACATAAAAATGAAAA

                    
       2659 TAATAAAA
          1 -AATAAAA

       2667 GACAATAATA


Statistics
Matches: 42,  Mismatches: 2, Indels: 4
        0.88            0.04        0.08

Matches are distributed among these distances:
  38   11  0.26
  39    2  0.05
  40   29  0.69

ACGTcount: A:0.71, C:0.05, G:0.07, T:0.18


Consensus pattern (38 bp):   
AATAAAATAATGAAATAACAAGAACATAAAAATGAAAA
Done.