Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2359

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: 10812
ACGTcount: A:0.18, C:0.29, G:0.33, T:0.20


Found at i:9517 original size:62 final size:60

Alignment explanation


    Indices: 9323--9525  Score: 182
    Period size: 62  Copynumber: 3.2  Consensus size: 60

       9313 CGGCAACTGT

                            *                                               
       9323 GCGCACCCGGTGCTCCCCACGGTGTGCGCCGCGACCGCCCCC-ACCCCAGGGGGCGGGAAGGGC
          1 GCGCA-CC-GTGCTCCGCACGG-GTGCGCCGCGACCGCCCCCGACCCCAGGGGGCGGG-AGGGC

                                              *                          *   
       9386 GCGCACCGTGCTCCTGGC-CGGGTGCGTGCCGCGGCCG-CCCCGCACCCCCCAGGGTGG-GCGA-
          1 GCGCACCGTGCTCC--GCACGGGTGC--GCCGCGACCGCCCCCG-A--CCCCAGGG-GGCGGGAG

               
       9447 GGC
         58 GGC

                             *          *  *                              
       9450 GCGCACCGTGCTCCGCATGGCGTGCGCCCCGCCCGCCCCCGACCCCAGGGGGCGGGATGGGC
          1 GCGCACCGTGCTCCGCACGG-GTGCGCCGCGACCGCCCCCGACCCCAGGGGGCGGGA-GGGC

                     *    
       9512 GCGCACCGTTCTCC
          1 GCGCACCGTGCTCC

       9526 CGCCCGCAGC


Statistics
Matches: 117,  Mismatches: 8, Indels: 31
        0.75            0.05        0.20

Matches are distributed among these distances:
  59    2  0.02
  60   11  0.09
  61   11  0.09
  62   36  0.31
  63   22  0.19
  64   22  0.19
  65    1  0.01
  66   10  0.09
  67    2  0.02

ACGTcount: A:0.08, C:0.45, G:0.38, T:0.09


Consensus pattern (60 bp):   
GCGCACCGTGCTCCGCACGGGTGCGCCGCGACCGCCCCCGACCCCAGGGGGCGGGAGGGC

Found at i:9614 original size:102 final size:102

Alignment explanation


    Indices: 9436--9622  Score: 315
    Period size: 102  Copynumber: 1.8  Consensus size: 102

       9426 CGCACCCCCC

                                                         *           *       
       9436 AGGGTGGGCGAGGCGCGCACCGTGCTCCGCATGGCGTGCGCCCCGCCCGCCCCCGACCCCAGGGG
          1 AGGGTGGGCGAGGCGCGCACCGTGCTCCGCATGGCGTGCGCCCCGACCGCCCCCGACACCAGGGG

                                                 
       9501 GCGGGATGGGCGCGCACCGTTCTCCCGCCCGCAGCCG
         66 GCGGGATGGGCGCGCACCGTTCTCCCGCCCGCAGCCG

                                               *                             
       9538 AGGGTGGGCGAGGCGCGCACCGGTGCTCCGCATGGTGTGCGCCCCGACCGCCCCC-ACACCAGGG
          1 AGGGTGGGCGAGGCGCGCACC-GTGCTCCGCATGGCGTGCGCCCCGACCGCCCCCGACACCAGGG

                                  
       9602 GGCGGGCA-GGGCGCGCACCGT
         65 GGCGGG-ATGGGCGCGCACCGT

       9623 GCACCTGGCC


Statistics
Matches: 80,  Mismatches: 3, Indels: 4
        0.92            0.03        0.05

Matches are distributed among these distances:
 102   48  0.60
 103   32  0.40

ACGTcount: A:0.10, C:0.41, G:0.41, T:0.09


Consensus pattern (102 bp):   
AGGGTGGGCGAGGCGCGCACCGTGCTCCGCATGGCGTGCGCCCCGACCGCCCCCGACACCAGGGG
GCGGGATGGGCGCGCACCGTTCTCCCGCCCGCAGCCG
Done.