Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga13g00445.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: 2787
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.28


Found at i:243 original size:6 final size:6

Alignment explanation


    Indices: 234--292  Score: 73
    Period size: 6  Copynumber: 9.8  Consensus size: 6

        224 GCCACCCTCA

                *      *      *                        *           
        234 CCGCTG CCGCTG CCGCTG CCGCCG CCGCCG CCGCCG CTGCCG CCGCCG
          1 CCGCCG CCGCCG CCGCCG CCGCCG CCGCCG CCGCCG CCGCCG CCGCCG

                *       
        282 CCGCTG CCGCC
          1 CCGCCG CCGCC

        293 ACCTCCTTTT


Statistics
Matches: 48,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   6   48  1.00

ACGTcount: A:0.00, C:0.59, G:0.32, T:0.08


Consensus pattern (6 bp):   
CCGCCG

Found at i:251 original size:12 final size:12

Alignment explanation


    Indices: 234--292  Score: 82
    Period size: 12  Copynumber: 4.9  Consensus size: 12

        224 GCCACCCTCA

                      * 
        234 CCGCTGCCGCTG
          1 CCGCTGCCGCCG

                        
        246 CCGCTGCCGCCG
          1 CCGCTGCCGCCG

                *       
        258 CCGCCGCCGCCG
          1 CCGCTGCCGCCG

             *  *       
        270 CTGCCGCCGCCG
          1 CCGCTGCCGCCG

                       
        282 CCGCTGCCGCC
          1 CCGCTGCCGCC

        293 ACCTCCTTTT


Statistics
Matches: 42,  Mismatches: 5, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  12   42  1.00

ACGTcount: A:0.00, C:0.59, G:0.32, T:0.08


Consensus pattern (12 bp):   
CCGCTGCCGCCG

Found at i:263 original size:15 final size:15

Alignment explanation


    Indices: 234--292  Score: 79
    Period size: 15  Copynumber: 4.1  Consensus size: 15

        224 GCCACCCTCA

                *          
        234 CCGCTGCCGCTGCCG
          1 CCGCCGCCGCTGCCG

             *             
        249 CTGCCG-C-C-GCCG
          1 CCGCCGCCGCTGCCG

                           
        261 CCGCCGCCGCTGCCG
          1 CCGCCGCCGCTGCCG

                           
        276 CCGCCGCCGCTGCCG
          1 CCGCCGCCGCTGCCG

              
        291 CC
          1 CC

        293 ACCTCCTTTT


Statistics
Matches: 38,  Mismatches: 3, Indels: 6
        0.81            0.06        0.13

Matches are distributed among these distances:
  12    9  0.24
  13    2  0.05
  14    2  0.05
  15   25  0.66

ACGTcount: A:0.00, C:0.59, G:0.32, T:0.08


Consensus pattern (15 bp):   
CCGCCGCCGCTGCCG

Found at i:2542 original size:25 final size:25

Alignment explanation


    Indices: 2514--2563  Score: 91
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       2504 ATTGGAGTTT

                                     
       2514 CTCAAGATTCAGCAACCACAAAAAG
          1 CTCAAGATTCAGCAACCACAAAAAG

                              *      
       2539 CTCAAGATTCAGCAACCATAAAAAG
          1 CTCAAGATTCAGCAACCACAAAAAG

       2564 AAAGGTATTT


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  25   24  1.00

ACGTcount: A:0.48, C:0.26, G:0.12, T:0.14


Consensus pattern (25 bp):   
CTCAAGATTCAGCAACCACAAAAAG
Done.