Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g00323.F1

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: 1874
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.33


Found at i:189 original size:12 final size:12

Alignment explanation


    Indices: 154--197  Score: 52
    Period size: 12  Copynumber: 3.7  Consensus size: 12

        144 TTTCCACTAC

                      * 
        154 CTTCTTCATCGT
          1 CTTCTTCATCTT

                *       
        166 CTTCATCATCTT
          1 CTTCTTCATCTT

                   *    
        178 CTTCTTCTTCTT
          1 CTTCTTCATCTT

             *      
        190 CCTCTTCA
          1 CTTCTTCA

        198 CCATTTTCTT


Statistics
Matches: 26,  Mismatches: 6, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  12   26  1.00

ACGTcount: A:0.09, C:0.36, G:0.02, T:0.52


Consensus pattern (12 bp):   
CTTCTTCATCTT

Found at i:968 original size:15 final size:15

Alignment explanation


    Indices: 937--993  Score: 60
    Period size: 15  Copynumber: 3.8  Consensus size: 15

        927 CGTCATCACT

                  *        
        937 GTCATCATCGTCGTC
          1 GTCATCGTCGTCGTC

               *        *  
        952 GTCGTCGTCGTCATC
          1 GTCATCGTCGTCGTC

                   *     * 
        967 GTCATCGCCGTCGCC
          1 GTCATCGTCGTCGTC

            *           
        982 TTCATCGTCGTC
          1 GTCATCGTCGTC

        994 ATCATCGTCT


Statistics
Matches: 33,  Mismatches: 9, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  15   33  1.00

ACGTcount: A:0.09, C:0.37, G:0.23, T:0.32


Consensus pattern (15 bp):   
GTCATCGTCGTCGTC

Found at i:1095 original size:3 final size:3

Alignment explanation


    Indices: 1089--1113  Score: 50
    Period size: 3  Copynumber: 8.3  Consensus size: 3

       1079 TCCTCCTCTC

                                             
       1089 CGT CGT CGT CGT CGT CGT CGT CGT C
          1 CGT CGT CGT CGT CGT CGT CGT CGT C

       1114 ATCTTCGCCT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   22  1.00

ACGTcount: A:0.00, C:0.36, G:0.32, T:0.32


Consensus pattern (3 bp):   
CGT

Done.