Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold899

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: 15056
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30


Found at i:85 original size:2 final size:2

Alignment explanation


    Indices: 78--104  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

         68 TGCTAACCAA

                                                    
         78 AG AG AG AG AG AG AG AG AG AG AG AG AG A
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG A

        105 AGAAACTATT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00


Consensus pattern (2 bp):   
AG

Found at i:3816 original size:16 final size:17

Alignment explanation


    Indices: 3779--3843  Score: 60
    Period size: 17  Copynumber: 3.6  Consensus size: 17

       3769 ACTATAGATT

                    *        
       3779 ATATAAAAGTAAATATA
          1 ATATAAAAATAAATATA

                        *    
       3796 ATATAAAAATAATTA-A
          1 ATATAAAAATAAATATA

                                 
       3812 ATATAATATATATAAAATATA
          1 ATATAA-A-A-AT-AAATATA

                       
       3833 ATTATAAAAAT
          1 A-TATAAAAAT

       3844 CTTTTAAAAT


Statistics
Matches: 39,  Mismatches: 3, Indels: 10
        0.75            0.06        0.19

Matches are distributed among these distances:
  16    7  0.18
  17   14  0.36
  18    1  0.03
  19    4  0.10
  20    5  0.13
  21    3  0.08
  22    5  0.13

ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34


Consensus pattern (17 bp):   
ATATAAAAATAAATATA

Found at i:13906 original size:21 final size:21

Alignment explanation


    Indices: 13882--13942  Score: 52
    Period size: 21  Copynumber: 2.9  Consensus size: 21

      13872 CAGTCTACAG

                                  
      13882 AGTCACATTCCCAACCTA-ACC
          1 AGTCACATTCCCAACCTATA-C

                *  *  *  *       
      13903 AGTCTCAGTCACAGCCTATAC
          1 AGTCACATTCCCAACCTATAC

             **                
      13924 AACCACATTCCCAACCTAT
          1 AGTCACATTCCCAACCTAT

      13943 TTTTGACATT


Statistics
Matches: 29,  Mismatches: 10, Indels: 2
        0.71            0.24        0.05

Matches are distributed among these distances:
  21   28  0.97
  22    1  0.03

ACGTcount: A:0.33, C:0.39, G:0.07, T:0.21


Consensus pattern (21 bp):   
AGTCACATTCCCAACCTATAC
Done.