Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold437

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: 325478
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34


File 3 of 3

Found at i:325048 original size:2 final size:2

Alignment explanation


    Indices: 325041--325102  Score: 73
    Period size: 2  Copynumber: 34.0  Consensus size: 2

     325031 TAGAAATTAA

                                                                          
     325041 CT CT CT CT CT CT CT CT CT CT -T CT C- CT C- CT -T CT CT CT CT
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT

             *                                    
     325079 CG CT C- CT CT CT -T CT CT CT CT CT CT
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT

     325103 GGTCCACAGC


Statistics
Matches: 52,  Mismatches: 2, Indels: 12
        0.79            0.03        0.18

Matches are distributed among these distances:
   1    6  0.12
   2   46  0.88

ACGTcount: A:0.00, C:0.50, G:0.02, T:0.48


Consensus pattern (2 bp):   
CT

Found at i:325075 original size:20 final size:21

Alignment explanation


    Indices: 325043--325100  Score: 84
    Period size: 20  Copynumber: 2.8  Consensus size: 21

     325033 GAAATTAACT

                              *   
     325043 CTCTCTCTCTCTCTCTCTTCTC
          1 CTCTCT-TCTCTCTCTCTGCTC

                                 
     325065 CTC-CTTCTCTCTCTC-GCTC
          1 CTCTCTTCTCTCTCTCTGCTC

                             
     325084 CTCTCTTCTCTCTCTCT
          1 CTCTCTTCTCTCTCTCT

     325101 CTGGTCCACA


Statistics
Matches: 33,  Mismatches: 1, Indels: 5
        0.85            0.03        0.13

Matches are distributed among these distances:
  19    6  0.18
  20   22  0.67
  21    2  0.06
  22    3  0.09

ACGTcount: A:0.00, C:0.50, G:0.02, T:0.48


Consensus pattern (21 bp):   
CTCTCTTCTCTCTCTCTGCTC

Found at i:325078 original size:24 final size:20

Alignment explanation


    Indices: 325041--325102  Score: 87
    Period size: 18  Copynumber: 3.3  Consensus size: 20

     325031 TAGAAATTAA

                                
     325041 CTCTCT-CTCTC-TCTCTCT
          1 CTCTCTCCTCTCTTCTCTCT

                                
     325059 CT-TCTCCTC-CTTCTCTCT
          1 CTCTCTCCTCTCTTCTCTCT

               *                
     325077 CTCGCTCCTCTCTTCTCTCT
          1 CTCTCTCCTCTCTTCTCTCT

                  
     325097 CTCTCT
          1 CTCTCT

     325103 GGTCCACAGC


Statistics
Matches: 38,  Mismatches: 2, Indels: 6
        0.83            0.04        0.13

Matches are distributed among these distances:
  17    4  0.11
  18   14  0.37
  19    6  0.16
  20   14  0.37

ACGTcount: A:0.00, C:0.50, G:0.02, T:0.48


Consensus pattern (20 bp):   
CTCTCTCCTCTCTTCTCTCT

Done.