Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3054

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: 27910
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:113 original size:15 final size:15

Alignment explanation


    Indices: 93--127  Score: 70
    Period size: 15  Copynumber: 2.3  Consensus size: 15

         83 AAATGAAAGA

                           
         93 TATGTGTTACATTAC
          1 TATGTGTTACATTAC

                           
        108 TATGTGTTACATTAC
          1 TATGTGTTACATTAC

                 
        123 TATGT
          1 TATGT

        128 TTGTACTGGG


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   20  1.00

ACGTcount: A:0.26, C:0.11, G:0.14, T:0.49


Consensus pattern (15 bp):   
TATGTGTTACATTAC

Found at i:11649 original size:29 final size:29

Alignment explanation


    Indices: 11616--11675  Score: 120
    Period size: 29  Copynumber: 2.1  Consensus size: 29

      11606 TTAAATAGAT

                                         
      11616 ATTTTTATGGAAACTTAAAGAATCATCTC
          1 ATTTTTATGGAAACTTAAAGAATCATCTC

                                         
      11645 ATTTTTATGGAAACTTAAAGAATCATCTC
          1 ATTTTTATGGAAACTTAAAGAATCATCTC

              
      11674 AT
          1 AT

      11676 CTTTCTCTCT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  29   31  1.00

ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38


Consensus pattern (29 bp):   
ATTTTTATGGAAACTTAAAGAATCATCTC

Found at i:21655 original size:19 final size:20

Alignment explanation


    Indices: 21615--21655  Score: 57
    Period size: 20  Copynumber: 2.1  Consensus size: 20

      21605 CTAAACTGAT

                             *  
      21615 AACTCAGAAAATTTTTTGAA
          1 AACTCAGAAAATTTTTTCAA

                *               
      21635 AACTTAGAAAA-TTTTTCAA
          1 AACTCAGAAAATTTTTTCAA

              
      21654 AA
          1 AA

      21656 TACCAGGGAC


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  19    9  0.47
  20   10  0.53

ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34


Consensus pattern (20 bp):   
AACTCAGAAAATTTTTTCAA
Done.