Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold243

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: 726772
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


File 5 of 5

Found at i:725202 original size:30 final size:29

Alignment explanation


    Indices: 725168--725227  Score: 77
    Period size: 30  Copynumber: 2.0  Consensus size: 29

     725158 GATAAAAAAA

                             *             
     725168 TAATAAA-TATGATATGTATATATAAATTTT
          1 TAATAAATTATGATA--AATATATAAATTTT

                                          
     725198 TAATAAATTTATGATAAATATATAAATTTT
          1 TAATAAA-TTATGATAAATATATAAATTTT

     725228 AGATCAAAAA


Statistics
Matches: 27,  Mismatches: 1, Indels: 4
        0.84            0.03        0.12

Matches are distributed among these distances:
  30   20  0.74
  32    7  0.26

ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47


Consensus pattern (29 bp):   
TAATAAATTATGATAAATATATAAATTTT

Found at i:725318 original size:16 final size:17

Alignment explanation


    Indices: 725288--725320  Score: 50
    Period size: 16  Copynumber: 2.0  Consensus size: 17

     725278 AATTATTTTA

                      *      
     725288 ATTTATTTATTATTAAT
          1 ATTTATTTATAATTAAT

                             
     725305 ATTTA-TTATAATTAAT
          1 ATTTATTTATAATTAAT

     725321 TAAATAATAT


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  16   10  0.67
  17    5  0.33

ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61


Consensus pattern (17 bp):   
ATTTATTTATAATTAAT

Done.