Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1609

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: 38408
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34


Found at i:1372 original size:21 final size:20

Alignment explanation


    Indices: 1334--1372  Score: 51
    Period size: 21  Copynumber: 1.9  Consensus size: 20

       1324 AAATTAAATT

                      *  *      
       1334 TTTATAATTTTAATTTTATC
          1 TTTATAATTTAAAATTTATC

                               
       1354 TTTACTAATTTAAAATTTA
          1 TTTA-TAATTTAAAATTTA

       1373 AAAAAAATTA


Statistics
Matches: 16,  Mismatches: 2, Indels: 1
        0.84            0.11        0.05

Matches are distributed among these distances:
  20    4  0.25
  21   12  0.75

ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59


Consensus pattern (20 bp):   
TTTATAATTTAAAATTTATC

Found at i:9028 original size:21 final size:20

Alignment explanation


    Indices: 8990--9028  Score: 51
    Period size: 21  Copynumber: 1.9  Consensus size: 20

       8980 AAATTAAATT

                      *  *      
       8990 TTTATAATTTTAATTTTATC
          1 TTTATAATTTAAAATTTATC

                               
       9010 TTTACTAATTTAAAATTTA
          1 TTTA-TAATTTAAAATTTA

       9029 AAAAAAATTA


Statistics
Matches: 16,  Mismatches: 2, Indels: 1
        0.84            0.11        0.05

Matches are distributed among these distances:
  20    4  0.25
  21   12  0.75

ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59


Consensus pattern (20 bp):   
TTTATAATTTAAAATTTATC

Found at i:16704 original size:21 final size:20

Alignment explanation


    Indices: 16666--16704  Score: 51
    Period size: 21  Copynumber: 1.9  Consensus size: 20

      16656 AAATTAAATT

                      *  *      
      16666 TTTATAATTTTAATTTTATC
          1 TTTATAATTTAAAATTTATC

                               
      16686 TTTACTAATTTAAAATTTA
          1 TTTA-TAATTTAAAATTTA

      16705 AAAAAAATTA


Statistics
Matches: 16,  Mismatches: 2, Indels: 1
        0.84            0.11        0.05

Matches are distributed among these distances:
  20    4  0.25
  21   12  0.75

ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59


Consensus pattern (20 bp):   
TTTATAATTTAAAATTTATC

Found at i:24381 original size:21 final size:20

Alignment explanation


    Indices: 24343--24381  Score: 51
    Period size: 21  Copynumber: 1.9  Consensus size: 20

      24333 AAATTAAATT

                      *  *      
      24343 TTTATAATTTTAATTTTATC
          1 TTTATAATTTAAAATTTATC

                               
      24363 TTTACTAATTTAAAATTTA
          1 TTTA-TAATTTAAAATTTA

      24382 AAAAAAATTA


Statistics
Matches: 16,  Mismatches: 2, Indels: 1
        0.84            0.11        0.05

Matches are distributed among these distances:
  20    4  0.25
  21   12  0.75

ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59


Consensus pattern (20 bp):   
TTTATAATTTAAAATTTATC

Found at i:32054 original size:21 final size:20

Alignment explanation


    Indices: 32016--32054  Score: 51
    Period size: 21  Copynumber: 1.9  Consensus size: 20

      32006 AAATTAAATT

                      *  *      
      32016 TTTATAATTTTAATTTTATC
          1 TTTATAATTTAAAATTTATC

                               
      32036 TTTACTAATTTAAAATTTA
          1 TTTA-TAATTTAAAATTTA

      32055 AAAAAAATTA


Statistics
Matches: 16,  Mismatches: 2, Indels: 1
        0.84            0.11        0.05

Matches are distributed among these distances:
  20    4  0.25
  21   12  0.75

ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59


Consensus pattern (20 bp):   
TTTATAATTTAAAATTTATC
Done.