Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold86

Parameters: 2 7 7 80 10 50 500

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500

Length: 1697160
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30

Warning! 169504 characters in sequence are not A, C, G, or T


File 7 of 6

Found at i:1692476 original size:30 final size:30

Alignment explanation


    Indices: 1692436--1692524  Score: 160
    Period size: 30  Copynumber: 3.0  Consensus size: 30

    1692426 TGCTGGATAT

                 *                        
    1692436 CCAGGACAAGGCGGTTACCCAGGGCAACAA
          1 CCAGGTCAAGGCGGTTACCCAGGGCAACAA

                       *                  
    1692466 CCAGGTCAAGGTGGTTACCCAGGGCAACAA
          1 CCAGGTCAAGGCGGTTACCCAGGGCAACAA

                                         
    1692496 CCAGGTCAAGGCGGTTACCCAGGGCAACA
          1 CCAGGTCAAGGCGGTTACCCAGGGCAACA

    1692525 GCCTCCACCA


Statistics
Matches: 56,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  30   56  1.00

ACGTcount: A:0.30, C:0.29, G:0.30, T:0.10


Consensus pattern (30 bp):   
CCAGGTCAAGGCGGTTACCCAGGGCAACAA

Found at i:1694246 original size:12 final size:12

Alignment explanation


    Indices: 1694229--1694268  Score: 71
    Period size: 12  Copynumber: 3.3  Consensus size: 12

    1694219 TGGTTTCACC

                        
    1694229 CTGTCCGTCTGT
          1 CTGTCCGTCTGT

                     *  
    1694241 CTGTCCGTCCGT
          1 CTGTCCGTCTGT

                        
    1694253 CTGTCCGTCTGT
          1 CTGTCCGTCTGT

                
    1694265 CTGT
          1 CTGT

    1694269 AGACGCAACT


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  12   26  1.00

ACGTcount: A:0.00, C:0.35, G:0.25, T:0.40


Consensus pattern (12 bp):   
CTGTCCGTCTGT

Found at i:1694258 original size:8 final size:8

Alignment explanation


    Indices: 1694229--1694265  Score: 56
    Period size: 8  Copynumber: 4.6  Consensus size: 8

    1694219 TGGTTTCACC

                    
    1694229 CTGTCCGT
          1 CTGTCCGT

                 *  
    1694237 CTGTCTGT
          1 CTGTCCGT

             *      
    1694245 CCGTCCGT
          1 CTGTCCGT

                    
    1694253 CTGTCCGT
          1 CTGTCCGT

                 
    1694261 CTGTC
          1 CTGTC

    1694266 TGTAGACGCA


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
   8   25  1.00

ACGTcount: A:0.00, C:0.38, G:0.24, T:0.38


Consensus pattern (8 bp):   
CTGTCCGT

Done.