Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold499

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: 21717
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:11464 original size:15 final size:15

Alignment explanation


    Indices: 11444--11472  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

      11434 TATGGCTCTC

                           
      11444 TCTTTTTTCTTTTTT
          1 TCTTTTTTCTTTTTT

                          
      11459 TCTTTTTTCTTTTT
          1 TCTTTTTTCTTTTT

      11473 GTACGCATTT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86


Consensus pattern (15 bp):   
TCTTTTTTCTTTTTT

Found at i:17495 original size:29 final size:30

Alignment explanation


    Indices: 17441--17510  Score: 81
    Period size: 30  Copynumber: 2.4  Consensus size: 30

      17431 AAATATTATT

                 *                *       
      17441 TTTTAGAAAATAAATTTTAT-ACTTTTTAA
          1 TTTTAAAAAATAAATTTTATAATTTTTTAA

                                         * 
      17470 TTTTAAAAAATAAA-TTTATAAATTTTTTTA
          1 TTTTAAAAAATAAATTTTAT-AATTTTTTAA

                *      
      17500 TTTTTAAAAAT
          1 TTTTAAAAAAT

      17511 CTTAAAAGTT


Statistics
Matches: 35,  Mismatches: 4, Indels: 3
        0.83            0.10        0.07

Matches are distributed among these distances:
  28    5  0.14
  29   13  0.37
  30   17  0.49

ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53


Consensus pattern (30 bp):   
TTTTAAAAAATAAATTTTATAATTTTTTAA

Found at i:17503 original size:30 final size:30

Alignment explanation


    Indices: 17422--17510  Score: 92
    Period size: 29  Copynumber: 3.0  Consensus size: 30

      17412 ATTGATTTTT

                    *    *  *        *    
      17422 TAAATTTAAAAATATTATT-TTTTAGAAAA
          1 TAAATTTATAAATTTTTTTATTTTAAAAAA

                      * *     *           
      17451 TAAATTT-TATACTTTTTAATTTTAAAAAA
          1 TAAATTTATAAATTTTTTTATTTTAAAAAA

                                    *     
      17480 TAAATTTATAAATTTTTTTATTTTTAAAAA
          1 TAAATTTATAAATTTTTTTATTTTAAAAAA

             
      17510 T
          1 T

      17511 CTTAAAAGTT


Statistics
Matches: 47,  Mismatches: 11, Indels: 3
        0.77            0.18        0.05

Matches are distributed among these distances:
  28    5  0.11
  29   23  0.49
  30   19  0.40

ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52


Consensus pattern (30 bp):   
TAAATTTATAAATTTTTTTATTTTAAAAAA
Done.