Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold266

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: 653600
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.32

Warning! 22668 characters in sequence are not A, C, G, or T


File 3 of 3

Found at i:645614 original size:20 final size:19

Alignment explanation


    Indices: 645589--645633  Score: 54
    Period size: 19  Copynumber: 2.3  Consensus size: 19

     645579 CGGGACTAAA

                   *        *   
     645589 TCAAAAATTTAGAGAATTTT
          1 TCAAAAAATTAGA-AAATTT

                       *       
     645609 TCAAAAAATTATAAAATTT
          1 TCAAAAAATTAGAAAATTT

                  
     645628 TCAAAA
          1 TCAAAA

     645634 CTGCAAGGGT


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  19   11  0.50
  20   11  0.50

ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36


Consensus pattern (19 bp):   
TCAAAAAATTAGAAAATTT

Found at i:647154 original size:25 final size:25

Alignment explanation


    Indices: 647103--647192  Score: 110
    Period size: 25  Copynumber: 3.6  Consensus size: 25

     647093 GTACATGTAT

                          *    *     
     647103 GCTCATACGAGCTGTA-AATGGTAA
          1 GCTCATACGAGCTGAATAACGGTAA

                * *                  
     647127 GCTCCTCCGAGCTGAATAACGGTAA
          1 GCTCATACGAGCTGAATAACGGTAA

                           *  *      
     647152 GCTCATACGAGCTGAGTATCGGTAA
          1 GCTCATACGAGCTGAATAACGGTAA

                   *        
     647177 GCTCATAAGAGCTGAA
          1 GCTCATACGAGCTGAA

     647193 ATCGATAACC


Statistics
Matches: 55,  Mismatches: 10, Indels: 1
        0.83            0.15        0.02

Matches are distributed among these distances:
  24   13  0.24
  25   42  0.76

ACGTcount: A:0.31, C:0.21, G:0.26, T:0.22


Consensus pattern (25 bp):   
GCTCATACGAGCTGAATAACGGTAA

Done.