Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold214

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: 304316
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35


File 4 of 4

Found at i:303934 original size:9 final size:9

Alignment explanation


    Indices: 303909--303983  Score: 50
    Period size: 9  Copynumber: 8.3  Consensus size: 9

     303899 TAGATAAAAA

                     
     303909 ATTATATTT
          1 ATTATATTT

                      
     303918 A-TATTATTT
          1 ATTA-TATTT

                     *
     303927 ATTATATTAG
          1 ATTATATT-T

                      
     303937 ATTATATTTT
          1 ATTATA-TTT

                      
     303947 AATTAT-TTT
          1 -ATTATATTT

                *    
     303956 A-TAAATTT
          1 ATTATATTT

                 *   
     303964 ATTATTTTT
          1 ATTATATTT

            *        
     303973 TTTAT-TTT
          1 ATTATATTT

               
     303981 ATT
          1 ATT

     303984 TTATATAATT


Statistics
Matches: 52,  Mismatches: 7, Indels: 15
        0.70            0.09        0.20

Matches are distributed among these distances:
   7    2  0.04
   8   12  0.23
   9   23  0.44
  10    8  0.15
  11    7  0.13

ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67


Consensus pattern (9 bp):   
ATTATATTT

Found at i:304139 original size:22 final size:23

Alignment explanation


    Indices: 304113--304175  Score: 76
    Period size: 22  Copynumber: 2.7  Consensus size: 23

     304103 CATAGGTCAA

                                   
     304113 ATATAAATTATTTATTTTTAAAT
          1 ATATAAATTATTTATTTTTAAAT

                       *           
     304136 -TATAAATTATGT-TTTTTAAAT
          1 ATATAAATTATTTATTTTTAAAT

              *                
     304157 ATTTGAAATGTATTTATTT
          1 ATAT-AAAT-TATTTATTT

     304176 AAAAATTTTA


Statistics
Matches: 33,  Mismatches: 3, Indels: 6
        0.79            0.07        0.14

Matches are distributed among these distances:
  21    9  0.27
  22   13  0.39
  23    4  0.12
  24    4  0.12
  25    3  0.09

ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57


Consensus pattern (23 bp):   
ATATAAATTATTTATTTTTAAAT

Done.