Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1649

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, 866

Length: 1444
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24


Found at i:169 original size:28 final size:28

Alignment explanation


    Indices: 136--211  Score: 118
    Period size: 28  Copynumber: 2.7  Consensus size: 28

        126 TTGTAGATTC

                                        
        136 GAAAAAAAATAGAAAAAAAAATTGAAAA
          1 GAAAAAAAATAGAAAAAAAAATTGAAAA

                       *                 
        164 GAAAAAAAAATCG-AAAAAAAATTGAAAA
          1 G-AAAAAAAATAGAAAAAAAAATTGAAAA

                      *         
        192 GAAAAAAAATTGAAAAAAAA
          1 GAAAAAAAATAGAAAAAAAA

        212 TTGCATACGG


Statistics
Matches: 44,  Mismatches: 2, Indels: 4
        0.88            0.04        0.08

Matches are distributed among these distances:
  27   10  0.23
  28   24  0.55
  29   10  0.23

ACGTcount: A:0.78, C:0.01, G:0.11, T:0.11


Consensus pattern (28 bp):   
GAAAAAAAATAGAAAAAAAAATTGAAAA

Found at i:180 original size:27 final size:27

Alignment explanation


    Indices: 136--214  Score: 122
    Period size: 27  Copynumber: 2.9  Consensus size: 27

        126 TTGTAGATTC

                      *                 
        136 GAAAAAAAATAGAAAAAAAAATTGAAAA
          1 GAAAAAAAATCG-AAAAAAAATTGAAAA

                                        
        164 GAAAAAAAAATCGAAAAAAAATTGAAAA
          1 G-AAAAAAAATCGAAAAAAAATTGAAAA

                      *            
        192 GAAAAAAAATTGAAAAAAAATTG
          1 GAAAAAAAATCGAAAAAAAATTG

        215 CATACGGTCT


Statistics
Matches: 48,  Mismatches: 2, Indels: 3
        0.91            0.04        0.06

Matches are distributed among these distances:
  27   21  0.44
  28   17  0.35
  29   10  0.21

ACGTcount: A:0.75, C:0.01, G:0.11, T:0.13


Consensus pattern (27 bp):   
GAAAAAAAATCGAAAAAAAATTGAAAA

Found at i:195 original size:16 final size:16

Alignment explanation


    Indices: 149--211  Score: 73
    Period size: 16  Copynumber: 4.2  Consensus size: 16

        139 AAAAAATAGA

                            
        149 AAAAAAAATTGAAAAG
          1 AAAAAAAATTGAAAAG

                         ** 
        165 -AAAAAAA---AATCG
          1 AAAAAAAATTGAAAAG

                            
        177 AAAAAAAATTGAAAAG
          1 AAAAAAAATTGAAAAG

                            
        193 AAAAAAAATTGAAAA-
          1 AAAAAAAATTGAAAAG

                
        208 AAAA
          1 AAAA

        212 TTGCATACGG


Statistics
Matches: 39,  Mismatches: 4, Indels: 9
        0.75            0.08        0.17

Matches are distributed among these distances:
  12    3  0.08
  13    7  0.18
  15   11  0.28
  16   18  0.46

ACGTcount: A:0.78, C:0.02, G:0.10, T:0.11


Consensus pattern (16 bp):   
AAAAAAAATTGAAAAG
Done.