Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2640

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: 6476
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.31


Found at i:220 original size:93 final size:93

Alignment explanation


    Indices: 113--283  Score: 306
    Period size: 93  Copynumber: 1.8  Consensus size: 93

        103 GCCCCTAAGT

                                        * *                                  
        113 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
          1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA

                                        
        178 CGAGTTCGGATGCCTAGTTACATCTCAC
         66 CGAGTTCGGATGCCTAGTTACATCTCAC

                                   *         *                               
        206 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
          1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA

                         
        271 CGAGTTCGGATGC
         66 CGAGTTCGGATGC

        284 TCAACCATCC


Statistics
Matches: 74,  Mismatches: 4, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  93   74  1.00

ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22


Consensus pattern (93 bp):   
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC

Found at i:280 original size:46 final size:46

Alignment explanation


    Indices: 108--280  Score: 217
    Period size: 46  Copynumber: 3.7  Consensus size: 46

         98 AACCCGCCCC

                                        *    * *  *       
        108 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
          1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA

                                                    *  *      
        154 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
          1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA

             *  *                                         
        202 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
          1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA

                                              
        247 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
          1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA

        281 TGCTCAACCA


Statistics
Matches: 108,  Mismatches: 12, Indels: 14
        0.81            0.09        0.10

Matches are distributed among these distances:
  43    6  0.06
  44    2  0.02
  45    2  0.02
  46   61  0.56
  47   29  0.27
  48    2  0.02
  49    2  0.02
  50    4  0.04

ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22


Consensus pattern (46 bp):   
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA

Done.