Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga03g02468.P1

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: 3526
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.30


Found at i:124 original size:2 final size:2

Alignment explanation


    Indices: 117--146  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

        107 CTTTACCTCA

                                                        
        117 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

        147 ACACACACAC


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50


Consensus pattern (2 bp):   
TC

Found at i:2266 original size:33 final size:33

Alignment explanation


    Indices: 2156--2275  Score: 116
    Period size: 33  Copynumber: 3.6  Consensus size: 33

       2146 TAAGAGGCAA

                *         *    *  *           
       2156 GAAGCAGAGGAGCATGAAGGAGCAA-TAAAACAC
          1 GAAGAAGAGGAGCAGGAAGAAGGAAGT-AAACAC

             *         * *  *         *     *
       2189 GTAGAAGAGGAACGGGTAGAAGGAAGCAAACAT
          1 GAAGAAGAGGAGCAGGAAGAAGGAAGTAAACAC

                                             
       2222 GAAGAAGAGGAGCAGGAAGAAGGAAGTAAACAC
          1 GAAGAAGAGGAGCAGGAAGAAGGAAGTAAACAC

                        * *      
       2255 GAAGAAGAGGAGGAAGAAGAA
          1 GAAGAAGAGGAGCAGGAAGAA

       2276 ACAAACAAAC


Statistics
Matches: 68,  Mismatches: 18, Indels: 2
        0.77            0.20        0.02

Matches are distributed among these distances:
  33   68  1.00

ACGTcount: A:0.50, C:0.09, G:0.36, T:0.05


Consensus pattern (33 bp):   
GAAGAAGAGGAGCAGGAAGAAGGAAGTAAACAC

Found at i:2286 original size:33 final size:33

Alignment explanation


    Indices: 2215--2295  Score: 99
    Period size: 33  Copynumber: 2.5  Consensus size: 33

       2205 TAGAAGGAAG

                                 *      **  *
       2215 CAAACATGAAGAAGAGGAGCAGGAAGAAGGAAG
          1 CAAACATGAAGAAGAGGAGCAAGAAGAAACAAA

            *     *            *             
       2248 TAAACACGAAGAAGAGGAGGAAGAAGAAACAAA
          1 CAAACATGAAGAAGAGGAGCAAGAAGAAACAAA

                           
       2281 CAAACATGAAGAAGA
          1 CAAACATGAAGAAGA

       2296 TGAAGAGGCT


Statistics
Matches: 39,  Mismatches: 9, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  33   39  1.00

ACGTcount: A:0.57, C:0.10, G:0.30, T:0.04


Consensus pattern (33 bp):   
CAAACATGAAGAAGAGGAGCAAGAAGAAACAAA

Found at i:2791 original size:15 final size:16

Alignment explanation


    Indices: 2764--2794  Score: 55
    Period size: 15  Copynumber: 2.0  Consensus size: 16

       2754 ATGGTGATGA

                            
       2764 AAACAAGTCTGAAGGT
          1 AAACAAGTCTGAAGGT

                            
       2780 AAACAA-TCTGAAGGT
          1 AAACAAGTCTGAAGGT

       2795 GGTAGCTCGT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    9  0.60
  16    6  0.40

ACGTcount: A:0.45, C:0.13, G:0.23, T:0.19


Consensus pattern (16 bp):   
AAACAAGTCTGAAGGT
Done.