Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1055

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, 620

Length: 1034
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41


Found at i:720 original size:15 final size:16

Alignment explanation


    Indices: 680--720  Score: 50
    Period size: 15  Copynumber: 2.6  Consensus size: 16

        670 AATAATATTT

                             
        680 TAATTTTTATATTATAA
          1 TAATTTTTA-ATTATAA

                        *   
        697 TAA-TTTTAATTTTAA
          1 TAATTTTTAATTATAA

                      
        712 -AATTTTTAA
          1 TAATTTTTAA

        721 AATATTAAAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 4
        0.81            0.04        0.15

Matches are distributed among these distances:
  14    2  0.09
  15   12  0.55
  16    5  0.23
  17    3  0.14

ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59


Consensus pattern (16 bp):   
TAATTTTTAATTATAA

Found at i:762 original size:21 final size:21

Alignment explanation


    Indices: 710--762  Score: 65
    Period size: 21  Copynumber: 2.6  Consensus size: 21

        700 TTTTAATTTT

                                 
        710 AAAATT-TTTAAAATATTAAA
          1 AAAATTATTTAAAATATTAAA

                *  *              
        730 AAAAATAATTAATAATATT-AA
          1 AAAATTATTTAA-AATATTAAA

                        
        751 AAAATTATTTAA
          1 AAAATTATTTAA

        763 CTATTAATAA


Statistics
Matches: 27,  Mismatches: 4, Indels: 3
        0.79            0.12        0.09

Matches are distributed among these distances:
  20    5  0.19
  21   16  0.59
  22    6  0.22

ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38


Consensus pattern (21 bp):   
AAAATTATTTAAAATATTAAA

Found at i:882 original size:22 final size:23

Alignment explanation


    Indices: 834--880  Score: 71
    Period size: 21  Copynumber: 2.1  Consensus size: 23

        824 TTAAGTTGGG

                  *                
        834 TTTAAATTATTTTTTATATAAAA
          1 TTTAAAATATTTTTTATATAAAA

                                   
        857 TTTAAAAT-TTTTTTAT-TAAAA
          1 TTTAAAATATTTTTTATATAAAA

               
        878 TTT
          1 TTT

        881 TATCGATTCT


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  21    8  0.35
  22    8  0.35
  23    7  0.30

ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60


Consensus pattern (23 bp):   
TTTAAAATATTTTTTATATAAAA

Found at i:958 original size:15 final size:14

Alignment explanation


    Indices: 940--990  Score: 50
    Period size: 15  Copynumber: 3.5  Consensus size: 14

        930 TATTATAATT

                           
        940 TTAAAATTATAAAAA
          1 TTAAAA-TATAAAAA

                      *   
        955 TTAAAATAT-TAAA
          1 TTAAAATATAAAAA

                            
        968 TATAATAATATAAAAA
          1 T-TAA-AATATAAAAA

             *     
        984 TCAAAAT
          1 TTAAAAT

        991 GATACTTTTA


Statistics
Matches: 30,  Mismatches: 3, Indels: 7
        0.75            0.08        0.17

Matches are distributed among these distances:
  13    4  0.13
  14    9  0.30
  15   13  0.43
  16    4  0.13

ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33


Consensus pattern (14 bp):   
TTAAAATATAAAAA
Done.