Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1013

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: 5608
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.28


Found at i:2013 original size:10 final size:10

Alignment explanation


    Indices: 1998--2151  Score: 75
    Period size: 10  Copynumber: 15.4  Consensus size: 10

       1988 CTTCCACAAT

                      
       1998 ATTCTAGAAC
          1 ATTCTAGAAC

                       
       2008 ATTCTAGAATC
          1 ATTCTAGAA-C

                *     
       2019 -TTCCAGAAC
          1 ATTCTAGAAC

            *   * *  *
       2028 CTTCCATAAT
          1 ATTCTAGAAC

                      
       2038 ATTCTAGAAC
          1 ATTCTAGAAC

                       
       2048 ATTCTAGAATC
          1 ATTCTAGAA-C

                *   * 
       2059 -TTCCAGAGC
          1 ATTCTAGAAC

            *   *     *
       2068 CTTCCACG-AT
          1 ATTCTA-GAAC

                      
       2078 ATTCTAGAAC
          1 ATTCTAGAAC

                       
       2088 ATTCTAGAATC
          1 ATTCTAGAA-C

                *   * 
       2099 -TTCCAGAGC
          1 ATTCTAGAAC

            *   *     *
       2108 CTTCCACG-AT
          1 ATTCTA-GAAC

                     *
       2118 ATTCTAGAAT
          1 ATTCTAGAAC

                *     
       2128 ATTCCAGAAC
          1 ATTCTAGAAC

                      
       2138 ATTCTAGAAC
          1 ATTCTAGAAC

                
       2148 ATTC
          1 ATTC

       2152 CAAAGTGTTC


Statistics
Matches: 111,  Mismatches: 23, Indels: 20
        0.72            0.15        0.13

Matches are distributed among these distances:
   9    5  0.05
  10  101  0.91
  11    5  0.05

ACGTcount: A:0.33, C:0.25, G:0.10, T:0.31


Consensus pattern (10 bp):   
ATTCTAGAAC

Found at i:2042 original size:40 final size:40

Alignment explanation


    Indices: 1987--2153  Score: 237
    Period size: 40  Copynumber: 4.2  Consensus size: 40

       1977 AGTTCTAGAG

                                                    
       1987 CCTTCCACAATATTCTAGAACATTCTAGAATCTTCCAGAA
          1 CCTTCCACAATATTCTAGAACATTCTAGAATCTTCCAGAA

                   *                               *
       2027 CCTTCCATAATATTCTAGAACATTCTAGAATCTTCCAGAG
          1 CCTTCCACAATATTCTAGAACATTCTAGAATCTTCCAGAA

                    *                              *
       2067 CCTTCCACGATATTCTAGAACATTCTAGAATCTTCCAGAG
          1 CCTTCCACAATATTCTAGAACATTCTAGAATCTTCCAGAA

                    *           *    *          *    
       2107 CCTTCCACGATATTCTAGAATATTCCAGAA-CATTCTAGAA
          1 CCTTCCACAATATTCTAGAACATTCTAGAATC-TTCCAGAA

             *     
       2147 CATTCCA
          1 CCTTCCA

       2154 AAGTGTTCTA


Statistics
Matches: 117,  Mismatches: 9, Indels: 2
        0.91            0.07        0.02

Matches are distributed among these distances:
  39    1  0.01
  40  116  0.99

ACGTcount: A:0.33, C:0.27, G:0.10, T:0.31


Consensus pattern (40 bp):   
CCTTCCACAATATTCTAGAACATTCTAGAATCTTCCAGAA

Done.