Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3474

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, 444

Length: 740
ACGTcount: A:0.16, C:0.11, G:0.09, T:0.27

Warning! 274 characters in sequence are not A, C, G, or T


Found at i:35 original size:9 final size:9

Alignment explanation


    Indices: 23--98  Score: 75
    Period size: 9  Copynumber: 8.3  Consensus size: 9

         13 CTATTTTGAC

                     
         23 TTTGATTTT
          1 TTTGATTTT

                      
         32 TTTGATTTTT
          1 TTTGA-TTTT

                *     
         42 ATTTTATTTT
          1 -TTTGATTTT

               *     
         52 TTTCA-TTT
          1 TTTGATTTT

               *     
         60 TTTAATTTT
          1 TTTGATTTT

                      
         69 TTTGATTTTT
          1 TTTGA-TTTT

               *     
         79 TTTTATTTT
          1 TTTGATTTT

                     
         88 TTT-ATTTT
          1 TTTGATTTT

               
         96 TTT
          1 TTT

         99 TCTAGTCTGA


Statistics
Matches: 58,  Mismatches: 5, Indels: 9
        0.81            0.07        0.12

Matches are distributed among these distances:
   8   15  0.26
   9   23  0.40
  10   16  0.28
  11    4  0.07

ACGTcount: A:0.13, C:0.01, G:0.04, T:0.82


Consensus pattern (9 bp):   
TTTGATTTT

Found at i:39 original size:21 final size:20

Alignment explanation


    Indices: 6--60  Score: 65
    Period size: 20  Copynumber: 2.6  Consensus size: 20

          1 TTTTC

                                  
          6 TTTTTTTCTATTTTGACTTTGA
          1 TTTTTTTC-ATTTTGA-TTTGA

                   *     *    * 
         28 TTTTTTTGATTTTTATTTTA
          1 TTTTTTTCATTTTGATTTGA

                         
         48 TTTTTTTCATTTT
          1 TTTTTTTCATTTT

         61 TTAATTTTTT


Statistics
Matches: 29,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
  20   16  0.55
  21    6  0.21
  22    7  0.24

ACGTcount: A:0.13, C:0.05, G:0.05, T:0.76


Consensus pattern (20 bp):   
TTTTTTTCATTTTGATTTGA

Found at i:54 original size:8 final size:8

Alignment explanation


    Indices: 43--98  Score: 67
    Period size: 8  Copynumber: 6.5  Consensus size: 8

         33 TTGATTTTTA

                    
         43 TTTTATTT
          1 TTTTATTT

                     
         51 TTTTCATTT
          1 TTTT-ATTT

               *    
         60 TTTAATTT
          1 TTTTATTT

                       
         68 TTTTGATTTTT
          1 TTTT-A--TTT

                    
         79 TTTTATTT
          1 TTTTATTT

                    
         87 TTTTATTT
          1 TTTTATTT

                
         95 TTTT
          1 TTTT

         99 TCTAGTCTGA


Statistics
Matches: 42,  Mismatches: 2, Indels: 8
        0.81            0.04        0.15

Matches are distributed among these distances:
   8   26  0.62
   9    8  0.19
  10    1  0.02
  11    7  0.17

ACGTcount: A:0.12, C:0.02, G:0.02, T:0.84


Consensus pattern (8 bp):   
TTTTATTT

Found at i:99 original size:37 final size:37

Alignment explanation


    Indices: 27--97  Score: 128
    Period size: 37  Copynumber: 2.0  Consensus size: 37

         17 TTTGACTTTG

                                                 
         27 ATTTTTTTGATTTTTATTTTATTTTTTTCATTTTTTA
          1 ATTTTTTTGATTTTTATTTTATTTTTTTCATTTTTTA

                                                
         64 ATTTTTTTGATTTTT-TTTTATTTTTTT-ATTTTTT
          1 ATTTTTTTGATTTTTATTTTATTTTTTTCATTTTTT

         98 TTCTAGTCTG


Statistics
Matches: 34,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
  35    7  0.21
  36   12  0.35
  37   15  0.44

ACGTcount: A:0.14, C:0.01, G:0.03, T:0.82


Consensus pattern (37 bp):   
ATTTTTTTGATTTTTATTTTATTTTTTTCATTTTTTA
Done.