Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1738

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, 808

Length: 1348
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.23

Warning! 196 characters in sequence are not A, C, G, or T


Found at i:1084 original size:18 final size:17

Alignment explanation


    Indices: 1063--1107  Score: 54
    Period size: 18  Copynumber: 2.5  Consensus size: 17

       1053 GAGTGACGAG

                              
       1063 AGAAAAAGAAACTGAAAA
          1 AGAAAAA-AAACTGAAAA

                       *      
       1081 AGAAACAAAAATTGAAAA
          1 AGAAA-AAAAACTGAAAA

                     
       1099 AGAGAAAAA
          1 AGA-AAAAA

       1108 GATTGGAGAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 4
        0.83            0.03        0.14

Matches are distributed among these distances:
  18   20  0.83
  19    4  0.17

ACGTcount: A:0.73, C:0.04, G:0.16, T:0.07


Consensus pattern (17 bp):   
AGAAAAAAAACTGAAAA

Found at i:1112 original size:18 final size:18

Alignment explanation


    Indices: 1061--1112  Score: 52
    Period size: 18  Copynumber: 2.8  Consensus size: 18

       1051 AAGAGTGACG

                         *      
       1061 AGAGAAAAAGAAACTGAAAA
          1 AGAGAAAAAG--ATTGAAAA

                      *        
       1081 AGA-AACAAAAATTGAAAA
          1 AGAGAA-AAAGATTGAAAA

                          
       1099 AGAGAAAAAGATTG
          1 AGAGAAAAAGATTG

       1113 GAGAAAGAAA


Statistics
Matches: 27,  Mismatches: 3, Indels: 6
        0.75            0.08        0.17

Matches are distributed among these distances:
  18   17  0.63
  19    4  0.15
  20    6  0.22

ACGTcount: A:0.67, C:0.04, G:0.19, T:0.10


Consensus pattern (18 bp):   
AGAGAAAAAGATTGAAAA
Done.