Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2168

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, 639

Length: 1065
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.34

Warning! 2 characters in sequence are not A, C, G, or T


Found at i:234 original size:16 final size:16

Alignment explanation


    Indices: 215--250  Score: 54
    Period size: 16  Copynumber: 2.2  Consensus size: 16

        205 GTAGAAACAT

                *     *     
        215 GAAATTCAAGCATCAA
          1 GAAAATCAAGAATCAA

                            
        231 GAAAATCAAGAATCAA
          1 GAAAATCAAGAATCAA

                
        247 GAAA
          1 GAAA

        251 CATGAAATTA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  16   18  1.00

ACGTcount: A:0.58, C:0.14, G:0.14, T:0.14


Consensus pattern (16 bp):   
GAAAATCAAGAATCAA

Found at i:1061 original size:18 final size:17

Alignment explanation


    Indices: 993--1061  Score: 68
    Period size: 18  Copynumber: 3.8  Consensus size: 17

        983 TTTATTTTTA

                             
        993 TTTTT-ATTTTTTTCTT
          1 TTTTTAATTTTTTTCTT

                    *    *    
       1009 TTTATTAACTTTTGTCTT
          1 TTT-TTAATTTTTTTCTT

                                
       1027 TCTCTTTAAATTTTTTTCTT
          1 T-T-TTT-AATTTTTTTCTT

                           
       1047 TTTTTAAGTTTTTTT
          1 TTTTTAA-TTTTTTT

       1062 TTAT


Statistics
Matches: 43,  Mismatches: 4, Indels: 10
        0.75            0.07        0.18

Matches are distributed among these distances:
  16    3  0.07
  17    4  0.09
  18   20  0.47
  19    4  0.09
  20   12  0.28

ACGTcount: A:0.13, C:0.09, G:0.03, T:0.75


Consensus pattern (17 bp):   
TTTTTAATTTTTTTCTT
Done.