Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1060

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: 3070
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37


Found at i:27 original size:16 final size:16

Alignment explanation


    Indices: 6--38  Score: 57
    Period size: 16  Copynumber: 2.1  Consensus size: 16

          1 AAGTA

                  *         
          6 AAAGAATAAAAGAAAC
          1 AAAGAAGAAAAGAAAC

                            
         22 AAAGAAGAAAAGAAAC
          1 AAAGAAGAAAAGAAAC

             
         38 A
          1 A

         39 GAGTCCATTC


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.76, C:0.06, G:0.15, T:0.03


Consensus pattern (16 bp):   
AAAGAAGAAAAGAAAC

Found at i:2923 original size:40 final size:40

Alignment explanation


    Indices: 2847--2923  Score: 102
    Period size: 40  Copynumber: 1.9  Consensus size: 40

       2837 TAAAAAAATT

                      *    *               *        
       2847 AATAATTTACCATTTTTAATAATTTTTTATATTTTTTTAC
          1 AATAATTTACAATTTCTAATAATTTTTTATACTTTTTTAC

                    *                             
       2887 AATAATTTGCAATTTCTAATAA-TTTTTATAACTTTTT
          1 AATAATTTACAATTTCTAATAATTTTTTAT-ACTTTTT

       2924 CATAGTTTTT


Statistics
Matches: 32,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  39    7  0.22
  40   25  0.78

ACGTcount: A:0.34, C:0.08, G:0.01, T:0.57


Consensus pattern (40 bp):   
AATAATTTACAATTTCTAATAATTTTTTATACTTTTTTAC
Done.