Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold579

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: 31470
ACGTcount: A:0.05, C:0.02, G:0.02, T:0.05

Warning! 26791 characters in sequence are not A, C, G, or T


Found at i:1346 original size:49 final size:49

Alignment explanation


    Indices: 1274--1377  Score: 181
    Period size: 49  Copynumber: 2.1  Consensus size: 49

       1264 AAAAAAAAAC

                            *                  * *           
       1274 AAATTAAAATTAAGTTTAATATCATGAATCAAAAGGTGAACACTTTATA
          1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA

                                                             
       1323 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
          1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA

                  
       1372 AAATTA
          1 AAATTA

       1378 TAACACGTGA


Statistics
Matches: 52,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  49   52  1.00

ACGTcount: A:0.50, C:0.11, G:0.08, T:0.32


Consensus pattern (49 bp):   
AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA

Found at i:31051 original size:13 final size:13

Alignment explanation


    Indices: 31033--31067  Score: 61
    Period size: 13  Copynumber: 2.7  Consensus size: 13

      31023 TGATTTTATG

                         
      31033 AAAATTTCGTTAA
          1 AAAATTTCGTTAA

                       * 
      31046 AAAATTTCGTTCA
          1 AAAATTTCGTTAA

                     
      31059 AAAATTTCG
          1 AAAATTTCG

      31068 ACGTTTGGGC


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  13   21  1.00

ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37


Consensus pattern (13 bp):   
AAAATTTCGTTAA

Found at i:31425 original size:19 final size:20

Alignment explanation


    Indices: 31396--31441  Score: 69
    Period size: 20  Copynumber: 2.4  Consensus size: 20

      31386 TTCTAAGCCC

                                
      31396 CGTTTTT-AATG-TTCTTTA
          1 CGTTTTTGAATGTTTCTTTA

                           *    
      31414 CGTTTTTGAATGTTTTTTTA
          1 CGTTTTTGAATGTTTCTTTA

                    
      31434 CGTTTTTG
          1 CGTTTTTG

      31442 GAGTCCCGAT


Statistics
Matches: 25,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  18    7  0.28
  19    4  0.16
  20   14  0.56

ACGTcount: A:0.13, C:0.09, G:0.15, T:0.63


Consensus pattern (20 bp):   
CGTTTTTGAATGTTTCTTTA

Done.