Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1797

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: 10759
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30


Found at i:481 original size:6 final size:6

Alignment explanation


    Indices: 459--501  Score: 70
    Period size: 6  Copynumber: 7.3  Consensus size: 6

        449 TTGGCAACAA

                     *                                         
        459 AAAAAT AATAA- AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AA
          1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AA

        502 TATTATATAA


Statistics
Matches: 34,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
   5    4  0.12
   6   30  0.88

ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16


Consensus pattern (6 bp):   
AAAAAT

Found at i:2575 original size:27 final size:28

Alignment explanation


    Indices: 2437--2562  Score: 209
    Period size: 28  Copynumber: 4.5  Consensus size: 28

       2427 TAAATTGTAC

                                      * 
       2437 AGCACTAAGTGTGCGAGCTTGATTATGT
          1 AGCACTAAGTGTGCGAGCTTGATTATAT

                                      * 
       2465 AGCACTAAGTGTGCGAGCTTGATTATGT
          1 AGCACTAAGTGTGCGAGCTTGATTATAT

                             *          
       2493 AGCACTAAGTGTGCGAGTTTGATTATAT
          1 AGCACTAAGTGTGCGAGCTTGATTATAT

                                        
       2521 AGCACTAAGTGTGCGAG-TTGATTATAT
          1 AGCACTAAGTGTGCGAGCTTGATTATAT

                  *        
       2548 AGCACTGAGTGTGCG
          1 AGCACTAAGTGTGCG

       2563 GACTTAATAT


Statistics
Matches: 95,  Mismatches: 3, Indels: 1
        0.96            0.03        0.01

Matches are distributed among these distances:
  27   24  0.25
  28   71  0.75

ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32


Consensus pattern (28 bp):   
AGCACTAAGTGTGCGAGCTTGATTATAT

Found at i:10579 original size:28 final size:28

Alignment explanation


    Indices: 10548--10700  Score: 256
    Period size: 28  Copynumber: 5.5  Consensus size: 28

      10538 TAAATTGTAC

                                        
      10548 AGCACTAAGTGTGCGAGCTTGATTATGT
          1 AGCACTAAGTGTGCGAGCTTGATTATGT

                                        
      10576 AGCACTAAGT-TGCGAGCTTGATTATGT
          1 AGCACTAAGTGTGCGAGCTTGATTATGT

                                        
      10603 AGCACTAAGTGTGCGAGCTTGATTATGT
          1 AGCACTAAGTGTGCGAGCTTGATTATGT

                             *        * 
      10631 AGCACTAAGTGTGCGAGTTTGATTATAT
          1 AGCACTAAGTGTGCGAGCTTGATTATGT

                                      * 
      10659 AGCACTAAGTGTGCGAG-TTGATTATAT
          1 AGCACTAAGTGTGCGAGCTTGATTATGT

                  *        
      10686 AGCACTGAGTGTGCG
          1 AGCACTAAGTGTGCG

      10701 GACTTAATAT


Statistics
Matches: 121,  Mismatches: 3, Indels: 3
        0.95            0.02        0.02

Matches are distributed among these distances:
  27   51  0.42
  28   70  0.58

ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32


Consensus pattern (28 bp):   
AGCACTAAGTGTGCGAGCTTGATTATGT

Found at i:10613 original size:55 final size:56

Alignment explanation


    Indices: 10548--10700  Score: 256
    Period size: 55  Copynumber: 2.8  Consensus size: 56

      10538 TAAATTGTAC

                                                                  * 
      10548 AGCACTAAGTGTGCGAGCTTGATTATGTAGCACTAAGT-TGCGAGCTTGATTATGT
          1 AGCACTAAGTGTGCGAGCTTGATTATGTAGCACTAAGTGTGCGAGCTTGATTATAT

                                                         *          
      10603 AGCACTAAGTGTGCGAGCTTGATTATGTAGCACTAAGTGTGCGAGTTTGATTATAT
          1 AGCACTAAGTGTGCGAGCTTGATTATGTAGCACTAAGTGTGCGAGCTTGATTATAT

                                      *       *        
      10659 AGCACTAAGTGTGCGAG-TTGATTATATAGCACTGAGTGTGCG
          1 AGCACTAAGTGTGCGAGCTTGATTATGTAGCACTAAGTGTGCG

      10701 GACTTAATAT


Statistics
Matches: 93,  Mismatches: 4, Indels: 2
        0.94            0.04        0.02

Matches are distributed among these distances:
  55   61  0.66
  56   32  0.34

ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32


Consensus pattern (56 bp):   
AGCACTAAGTGTGCGAGCTTGATTATGTAGCACTAAGTGTGCGAGCTTGATTATAT

Found at i:10663 original size:83 final size:83

Alignment explanation


    Indices: 10548--10700  Score: 254
    Period size: 83  Copynumber: 1.8  Consensus size: 83

      10538 TAAATTGTAC

                                      *                           *          
      10548 AGCACTAAGTGTGCGAGCTTGATTATGTAGCACTAAGT-TGCGAGCTTGATTATGTAGCACTAAG
          1 AGCACTAAGTGTGCGAGCTTGATTATATAGCACTAAGTGTGCGAG-TTGATTATATAGCACTAAG

                               
      10612 TGTGCGAGCTTGATTATGT
         65 TGTGCGAGCTTGATTATGT

                             *                                           *   
      10631 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGT
          1 AGCACTAAGTGTGCGAGCTTGATTATATAGCACTAAGTGTGCGAGTTGATTATATAGCACTAAGT

                 
      10696 GTGCG
         66 GTGCG

      10701 GACTTAATAT


Statistics
Matches: 65,  Mismatches: 4, Indels: 2
        0.92            0.06        0.03

Matches are distributed among these distances:
  83   59  0.91
  84    6  0.09

ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32


Consensus pattern (83 bp):   
AGCACTAAGTGTGCGAGCTTGATTATATAGCACTAAGTGTGCGAGTTGATTATATAGCACTAAGT
GTGCGAGCTTGATTATGT

Done.