Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold769

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: 30605
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:4943 original size:16 final size:19

Alignment explanation


    Indices: 4917--4956  Score: 59
    Period size: 16  Copynumber: 2.3  Consensus size: 19

       4907 TTTCAGTTCT

                               
       4917 AAAACAGAAATAAC-T-CA
          1 AAAACAGAAATAACATACA

                               
       4934 AAAACA-AAATAACATACA
          1 AAAACAGAAATAACATACA

                 
       4952 AAAAC
          1 AAAAC

       4957 CTACTCGTAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  16    7  0.33
  17    7  0.33
  18    7  0.33

ACGTcount: A:0.70, C:0.17, G:0.03, T:0.10


Consensus pattern (19 bp):   
AAAACAGAAATAACATACA

Found at i:10855 original size:30 final size:32

Alignment explanation


    Indices: 10789--10855  Score: 75
    Period size: 30  Copynumber: 2.2  Consensus size: 32

      10779 TAATAAAAGT

                   *                  * *   
      10789 AAAATTTTATTTTAATCCCTTTAAAATTGATA
          1 AAAATTTGATTTTAATCCCTTTAAAAATCATA

                             *             *
      10821 AAAATTTGA-TTTAAT-TCTTTAAAAATCATG
          1 AAAATTTGATTTTAATCCCTTTAAAAATCATA

                 
      10851 AAAAT
          1 AAAAT

      10856 ATAGGCTATT


Statistics
Matches: 30,  Mismatches: 5, Indels: 2
        0.81            0.14        0.05

Matches are distributed among these distances:
  30   16  0.53
  31    6  0.20
  32    8  0.27

ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43


Consensus pattern (32 bp):   
AAAATTTGATTTTAATCCCTTTAAAAATCATA

Found at i:11626 original size:19 final size:21

Alignment explanation


    Indices: 11602--11640  Score: 55
    Period size: 19  Copynumber: 2.0  Consensus size: 21

      11592 GCTTACTGTT

                  *              
      11602 TTTTTTTCTT-TTT-CGATTA
          1 TTTTTTACTTATTTACGATTA

                                
      11621 TTTTTTACTTATTTACGATT
          1 TTTTTTACTTATTTACGATT

      11641 TTAAAAAAAG


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19    9  0.53
  20    3  0.18
  21    5  0.29

ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69


Consensus pattern (21 bp):   
TTTTTTACTTATTTACGATTA

Found at i:25466 original size:22 final size:22

Alignment explanation


    Indices: 25440--25490  Score: 102
    Period size: 22  Copynumber: 2.3  Consensus size: 22

      25430 AAAAATGTTA

                                  
      25440 ATTTTATCCTGAATCCTTTTAC
          1 ATTTTATCCTGAATCCTTTTAC

                                  
      25462 ATTTTATCCTGAATCCTTTTAC
          1 ATTTTATCCTGAATCCTTTTAC

                   
      25484 ATTTTAT
          1 ATTTTAT

      25491 TCAAAACAAA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   29  1.00

ACGTcount: A:0.24, C:0.20, G:0.04, T:0.53


Consensus pattern (22 bp):   
ATTTTATCCTGAATCCTTTTAC
Done.