Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1779

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: 16451
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30


Found at i:8965 original size:18 final size:17

Alignment explanation


    Indices: 8915--8975  Score: 59
    Period size: 19  Copynumber: 3.4  Consensus size: 17

       8905 ATTATTGCAA

                        *   *
       8915 TTAAAATTTTTTAAAAA
          1 TTAAAATTTTTTTAAAT

                       *       
       8932 TTAAATTATTTGTTTAAAT
          1 TTAAA--ATTTTTTTAAAT

                               
       8951 TTAAAATTTTATTTAATAT
          1 TTAAAATTTT-TTTAA-AT

                  
       8970 TTAAAA
          1 TTAAAA

       8976 AGTTAAATTT


Statistics
Matches: 36,  Mismatches: 4, Indels: 6
        0.78            0.09        0.13

Matches are distributed among these distances:
  17    9  0.25
  18    5  0.14
  19   22  0.61

ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52


Consensus pattern (17 bp):   
TTAAAATTTTTTTAAAT

Found at i:14190 original size:2 final size:2

Alignment explanation


    Indices: 14183--14220  Score: 58
    Period size: 2  Copynumber: 19.0  Consensus size: 2

      14173 TAAACACTAT

                        *      *                                    
      14183 TA TA TA TA GA TA TC TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      14221 GAAGAGAGAG


Statistics
Matches: 32,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47


Consensus pattern (2 bp):   
TA

Done.