Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g00341.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: 2702
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25


Found at i:1066 original size:36 final size:35

Alignment explanation


    Indices: 989--1067  Score: 97
    Period size: 36  Copynumber: 2.2  Consensus size: 35

        979 GAACACTCAG

                            *                   
        989 AAAGTACCCAAGGAACCAACCTGAGTGAAAACAATC
          1 AAAGT-CCCAAGGAACAAACCTGAGTGAAAACAATC

            *                           *        
       1025 TAAGTCCACAAGGAACAAACCTGAGTGAGAACACA-C
          1 AAAGTCC-CAAGGAACAAACCTGAGTGAAAACA-ATC

                   
       1061 AAAGTCC
          1 AAAGTCC

       1068 TTCAGAGATT


Statistics
Matches: 37,  Mismatches: 4, Indels: 4
        0.82            0.09        0.09

Matches are distributed among these distances:
  35    2  0.05
  36   34  0.92
  37    1  0.03

ACGTcount: A:0.46, C:0.25, G:0.18, T:0.11


Consensus pattern (35 bp):   
AAAGTCCCAAGGAACAAACCTGAGTGAAAACAATC

Found at i:1250 original size:108 final size:108

Alignment explanation


    Indices: 1162--1399  Score: 280
    Period size: 108  Copynumber: 2.2  Consensus size: 108

       1152 TGGCAATGAT

                           * *       *   *                        **         
       1162 GACACACAAAGTCCTCAGAAGAGAAGCCATGATGCAAACATGAGTAGTCCTCAATGTATAAA-CA
          1 GACACACAAAGTCCTAAAAAGAGAAACCACGATGCAAACATGAGTAGTCCTCAACATATAAATC-

                                                        
       1226 ATAATGAAGATGCACAAAAACCTCAAGATATAATCTGGAATGGA
         65 ATAATGAAGATGCACAAAAACCTCAAGATATAATCTGGAATGGA

             **                         *      *                            *
       1270 GGTACACAAAGTCCTAAAAAGAGAAACCGCGATGCTAACATGAGTAGTCCTCAACATATAAATCC
          1 GACACACAAAGTCCTAAAAAGAGAAACCACGATGCAAACATGAGTAGTCCTCAACATATAAATCA

                               *   *    *   * *      * 
       1335 TAATGAAGATGCACAAAAAGCTCGAGATGTAAACCGGAATGAA
         66 TAATGAAGATGCACAAAAACCTCAAGATATAATCTGGAATGGA

              *     *      *      
       1378 GATACACACAGTCCTCAAAAGA
          1 GACACACAAAGTCCTAAAAAGA

       1400 TAAGCCGCAA


Statistics
Matches: 109,  Mismatches: 20, Indels: 2
        0.83            0.15        0.02

Matches are distributed among these distances:
 108  108  0.99
 109    1  0.01

ACGTcount: A:0.44, C:0.20, G:0.18, T:0.18


Consensus pattern (108 bp):   
GACACACAAAGTCCTAAAAAGAGAAACCACGATGCAAACATGAGTAGTCCTCAACATATAAATCA
TAATGAAGATGCACAAAAACCTCAAGATATAATCTGGAATGGA
Done.