Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold4000

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, 365

Length: 609
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.25


Found at i:95 original size:14 final size:14

Alignment explanation


    Indices: 41--97  Score: 53
    Period size: 15  Copynumber: 3.9  Consensus size: 14

         31 CCAAAACATT

                          
         41 AAACCCC-AACCCC
          1 AAACCCCAAACCCC

                    *   *   
         54 TAAACCCTAAAAACCC
          1 -AAACCC-CAAACCCC

            *              
         70 TAACCCCAAAACCCC
          1 AAACCCC-AAACCCC

                         
         85 AAACCCCAAACCC
          1 AAACCCCAAACCC

         98 AAAAAGAAAC


Statistics
Matches: 34,  Mismatches: 6, Indels: 6
        0.74            0.13        0.13

Matches are distributed among these distances:
  14   12  0.35
  15   17  0.50
  16    5  0.15

ACGTcount: A:0.44, C:0.51, G:0.00, T:0.05


Consensus pattern (14 bp):   
AAACCCCAAACCCC

Found at i:100 original size:6 final size:7

Alignment explanation


    Indices: 41--97  Score: 53
    Period size: 7  Copynumber: 7.9  Consensus size: 7

         31 CCAAAACATT

                   
         41 AAACCCC
          1 AAACCCC

                   
         48 -AACCCC
          1 AAACCCC

                    *
         54 TAAACCCTA
          1 -AAACCC-C

               *   
         63 AAAACCC
          1 AAACCCC

            *      
         70 TAACCCC
          1 AAACCCC

                    
         77 AAAACCCC
          1 -AAACCCC

                   
         85 AAACCCC
          1 AAACCCC

                  
         92 AAACCC
          1 AAACCC

         98 AAAAAGAAAC


Statistics
Matches: 40,  Mismatches: 6, Indels: 8
        0.74            0.11        0.15

Matches are distributed among these distances:
   6    6  0.15
   7   18  0.45
   8   16  0.40

ACGTcount: A:0.44, C:0.51, G:0.00, T:0.05


Consensus pattern (7 bp):   
AAACCCC

Found at i:365 original size:31 final size:32

Alignment explanation


    Indices: 330--392  Score: 92
    Period size: 31  Copynumber: 2.0  Consensus size: 32

        320 GATATTCCTA

                           *                
        330 GAATAGCTTAATTCATGTTAGGATAT-CCTGG
          1 GAATAGCTTAATTCACGTTAGGATATACCTGG

                         *     *            
        361 GAATAGCTTAATTGACGTTGGGATATACCTGG
          1 GAATAGCTTAATTCACGTTAGGATATACCTGG

        393 AAAACCTCTC


Statistics
Matches: 28,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  31   23  0.82
  32    5  0.18

ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33


Consensus pattern (32 bp):   
GAATAGCTTAATTCACGTTAGGATATACCTGG
Done.