Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1612

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: 20954
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34


Found at i:8804 original size:33 final size:32

Alignment explanation


    Indices: 8743--8804  Score: 88
    Period size: 33  Copynumber: 1.9  Consensus size: 32

       8733 TTCGACCTCA

                             **             
       8743 CTCTTTTTTTTTATTTCTTTTTCTTTTTCAAT
          1 CTCTTTTTTTTTATTTCGATTTCTTTTTCAAT

                         *                
       8775 CTCTTTTTCTTTTCTTTCGATTTCTTTTTC
          1 CTCTTTTT-TTTTATTTCGATTTCTTTTTC

       8805 TCGCTCGTAC


Statistics
Matches: 26,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  32    8  0.31
  33   18  0.69

ACGTcount: A:0.06, C:0.19, G:0.02, T:0.73


Consensus pattern (32 bp):   
CTCTTTTTTTTTATTTCGATTTCTTTTTCAAT

Found at i:9747 original size:13 final size:13

Alignment explanation


    Indices: 9731--9755  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       9721 TTTATACTTC

                         
       9731 AATTTTTTTTTTG
          1 AATTTTTTTTTTG

                        
       9744 AATTTTTTTTTT
          1 AATTTTTTTTTT

       9756 TTTTTTTCAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80


Consensus pattern (13 bp):   
AATTTTTTTTTTG

Found at i:15634 original size:20 final size:20

Alignment explanation


    Indices: 15611--15657  Score: 67
    Period size: 20  Copynumber: 2.4  Consensus size: 20

      15601 GGGTTAAGAT

                            *   
      15611 TGAGCTGACTTGAGCTTGAA
          1 TGAGCTGACTTGAGCTCGAA

                *              *
      15631 TGAGTTGACTTGAGCTCGAG
          1 TGAGCTGACTTGAGCTCGAA

                   
      15651 TGAGCTG
          1 TGAGCTG

      15658 GAAACAAGCT


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  20   23  1.00

ACGTcount: A:0.21, C:0.15, G:0.34, T:0.30


Consensus pattern (20 bp):   
TGAGCTGACTTGAGCTCGAA
Done.