Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2036

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: 22273
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:8111 original size:51 final size:51

Alignment explanation


    Indices: 8054--8159  Score: 169
    Period size: 51  Copynumber: 2.1  Consensus size: 51

       8044 GCCTTCAAAG

                   *                                 *          
       8054 TTTACATGTTCTATCAATTTGGTATTGATTTAATAAATTTATC-CAACAATA
          1 TTTACATATTCTATCAATTTGGTATTGATTTAATAAATTTAGCTC-ACAATA

                                   *                           
       8105 TTTACATATTCTATCAATTTGGTCTTGATTTAATAAATTTAGCTCACAATA
          1 TTTACATATTCTATCAATTTGGTATTGATTTAATAAATTTAGCTCACAATA

                
       8156 TTTA
          1 TTTA

       8160 TACTTTTTGT


Statistics
Matches: 51,  Mismatches: 3, Indels: 2
        0.91            0.05        0.04

Matches are distributed among these distances:
  51   50  0.98
  52    1  0.02

ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46


Consensus pattern (51 bp):   
TTTACATATTCTATCAATTTGGTATTGATTTAATAAATTTAGCTCACAATA

Found at i:11141 original size:3 final size:3

Alignment explanation


    Indices: 11133--11158  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

      11123 TCTCCTTAGG

                                              
      11133 TTA TTA TTA TTA TTA TTA TTA TTA TT
          1 TTA TTA TTA TTA TTA TTA TTA TTA TT

      11159 TATCAATCAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69


Consensus pattern (3 bp):   
TTA

Found at i:14357 original size:6 final size:6

Alignment explanation


    Indices: 14348--14376  Score: 58
    Period size: 6  Copynumber: 4.8  Consensus size: 6

      14338 TATAAATTTA

                                             
      14348 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
          1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA

      14377 ACCTTCATGA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   23  1.00

ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14


Consensus pattern (6 bp):   
AAAAAT

Found at i:21852 original size:15 final size:15

Alignment explanation


    Indices: 21832--21865  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

      21822 CCCCCCCAAA

                           
      21832 AAAAAAAAAAAAAAG
          1 AAAAAAAAAAAAAAG

                  *     *  
      21847 AAAAAAGAAAAAGAG
          1 AAAAAAAAAAAAAAG

                
      21862 AAAA
          1 AAAA

      21866 CGGAAGAAAC


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00


Consensus pattern (15 bp):   
AAAAAAAAAAAAAAG

Found at i:21863 original size:8 final size:7

Alignment explanation


    Indices: 21829--21865  Score: 51
    Period size: 7  Copynumber: 5.4  Consensus size: 7

      21819 CCCCCCCCCC

                   
      21829 AAAAA-A
          1 AAAAAGA

                   
      21835 AAAAA-A
          1 AAAAAGA

                   
      21841 AAAAAGA
          1 AAAAAGA

                   
      21848 AAAAAGA
          1 AAAAAGA

                    
      21855 AAAAGAGA
          1 AAAA-AGA

               
      21863 AAA
          1 AAA

      21866 CGGAAGAAAC


Statistics
Matches: 29,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   6   11  0.38
   7   12  0.41
   8    6  0.21

ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00


Consensus pattern (7 bp):   
AAAAAGA
Done.