Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold676

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: 53497
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.10

Warning! 35749 characters in sequence are not A, C, G, or T


Found at i:8175 original size:20 final size:20

Alignment explanation


    Indices: 8150--8196  Score: 60
    Period size: 20  Copynumber: 2.4  Consensus size: 20

       8140 AGCTCGTTTC

                          *      
       8150 CAGCTCACTT-GAGCTCAAGT
          1 CAGCTCA-TTCGAGATCAAGT

                              * 
       8170 CAGCTCATTCGAGATCAATT
          1 CAGCTCATTCGAGATCAAGT

                   
       8190 CAGCTCA
          1 CAGCTCA

       8197 ATTTTAACCC


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  19    2  0.08
  20   22  0.92

ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26


Consensus pattern (20 bp):   
CAGCTCATTCGAGATCAAGT

Found at i:44979 original size:23 final size:23

Alignment explanation


    Indices: 44953--44997  Score: 72
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      44943 TTTCTTACTG

                       *           
      44953 TAGTAATTTTCGGGATATTACAA
          1 TAGTAATTTTCAGGATATTACAA

                 *                
      44976 TAGTACTTTTCAGGATATTACA
          1 TAGTAATTTTCAGGATATTACA

      44998 GTGAGGGGGT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  23   20  1.00

ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40


Consensus pattern (23 bp):   
TAGTAATTTTCAGGATATTACAA

Found at i:49800 original size:18 final size:18

Alignment explanation


    Indices: 49779--49820  Score: 57
    Period size: 18  Copynumber: 2.3  Consensus size: 18

      49769 TCAGAAACCT

                              
      49779 CTTCTTCTTCAGCAACAA
          1 CTTCTTCTTCAGCAACAA

                *     *       
      49797 CTTCCTCTTCTGCAACAA
          1 CTTCTTCTTCAGCAACAA

             *    
      49815 CCTCTT
          1 CTTCTT

      49821 TCTCAATAAC


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.21, C:0.38, G:0.05, T:0.36


Consensus pattern (18 bp):   
CTTCTTCTTCAGCAACAA

Found at i:53299 original size:14 final size:15

Alignment explanation


    Indices: 53259--53296  Score: 58
    Period size: 15  Copynumber: 2.5  Consensus size: 15

      53249 AAAAAAACAA

                       *    
      53259 AAAAAAAATTCAAAAG
          1 AAAAAAAATT-GAAAG

                           
      53275 AAAAAAAATTGAAAG
          1 AAAAAAAATTGAAAG

                   
      53290 AAAAAAA
          1 AAAAAAA

      53297 TTGTATACGG


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  15   11  0.52
  16   10  0.48

ACGTcount: A:0.79, C:0.03, G:0.08, T:0.11


Consensus pattern (15 bp):   
AAAAAAAATTGAAAG
Done.