Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold592

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: 11008
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32


Found at i:5643 original size:39 final size:39

Alignment explanation


    Indices: 5523--5736  Score: 310
    Period size: 38  Copynumber: 5.5  Consensus size: 39

       5513 ACAAAGCATG

                               *   *           *     
       5523 CGGGACTTTAAGCCCGGATGTAATACCAGCAC-AAAGCCTT
          1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT

              *                                     
       5563 C-AGACTTAGCCCCGGATATAACACCAGCACGAATGCC-T
          1 CGGGACTTAG-CCCGGATATAACACCAGCACGAATGCCTT

                           *                       
       5601 CGGGACTTAGCCCGGGTATAACACCAGCACGAATGCCTT
          1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT

                                                   
       5640 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
          1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT

                        *                          
       5679 C-GGACTTAGCCTGGATATAACACCAGCACGAATGCCTT
          1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT

                 *              
       5717 CGGGAATTAGCCCGGATATA
          1 CGGGACTTAGCCCGGATATA

       5737 TATCTCACAC


Statistics
Matches: 159,  Mismatches: 10, Indels: 11
        0.88            0.06        0.06

Matches are distributed among these distances:
  37    2  0.01
  38   85  0.53
  39   71  0.45
  40    1  0.01

ACGTcount: A:0.29, C:0.29, G:0.23, T:0.19


Consensus pattern (39 bp):   
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT

Found at i:5666 original size:77 final size:78

Alignment explanation


    Indices: 5523--5736  Score: 310
    Period size: 77  Copynumber: 2.8  Consensus size: 78

       5513 ACAAAGCATG

                               *   *           *       *                     
       5523 CGGGACTTTAAGCCCGGATGTAATACCAGCAC-AAAGCCTTC-AGACTTAGCCCCGGATATAACA
          1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTTAG-CCCGGATATAACA

                            
       5586 CCAGCACGAATGCC-T
         63 CCAGCACGAATGCCTT

                           *                                                 
       5601 CGGGACTTAGCCCGGGTATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAACACCA
          1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAACACCA

                         
       5666 GCACGAATGCCTT
         66 GCACGAATGCCTT

                        *                               *              
       5679 C-GGACTTAGCCTGGATATAACACCAGCACGAATGCCTTCGGGAATTAGCCCGGATATA
          1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGATATA

       5737 TATCTCACAC


Statistics
Matches: 125,  Mismatches: 8, Indels: 7
        0.89            0.06        0.05

Matches are distributed among these distances:
  76   19  0.15
  77   91  0.73
  78   15  0.12

ACGTcount: A:0.29, C:0.29, G:0.23, T:0.19


Consensus pattern (78 bp):   
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAACACCA
GCACGAATGCCTT
Done.