Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g01045.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: 2284
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.25


Found at i:239 original size:12 final size:12

Alignment explanation


    Indices: 222--299  Score: 84
    Period size: 12  Copynumber: 6.5  Consensus size: 12

        212 CAGAAACTAC

                        
        222 AGGAAGTGGAAG
          1 AGGAAGTGGAAG

                   *    
        234 AGGAAGTAGAAG
          1 AGGAAGTGGAAG

                *  *    
        246 AGGAGGTTGAAG
          1 AGGAAGTGGAAG

             *    *     
        258 AAGAAGAGGAAG
          1 AGGAAGTGGAAG

            *    *      
        270 TGGAACTGGAAG
          1 AGGAAGTGGAAG

                  *     
        282 AGGAAGAGGAAG
          1 AGGAAGTGGAAG

                  
        294 AGGAAG
          1 AGGAAG

        300 AGGAGGAAGA


Statistics
Matches: 52,  Mismatches: 14, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  12   52  1.00

ACGTcount: A:0.45, C:0.01, G:0.46, T:0.08


Consensus pattern (12 bp):   
AGGAAGTGGAAG

Found at i:312 original size:6 final size:6

Alignment explanation


    Indices: 222--303  Score: 76
    Period size: 6  Copynumber: 13.7  Consensus size: 6

        212 CAGAAACTAC

                   *                         *  **      *           
        222 AGGAAG TGGAAG AGGAAG TA-GAAG AGGAGG TTGAAG AAGAAG AGGAAG
          1 AGGAAG AGGAAG AGGAAG -AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG

            *    * *                               
        270 TGGAAC TGGAAG AGGAAG AGGAAG AGGAAG AGGA
          1 AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG AGGA

        304 GGAAGAGGAG


Statistics
Matches: 61,  Mismatches: 13, Indels: 4
        0.78            0.17        0.05

Matches are distributed among these distances:
   5    1  0.02
   6   59  0.97
   7    1  0.02

ACGTcount: A:0.45, C:0.01, G:0.46, T:0.07


Consensus pattern (6 bp):   
AGGAAG

Found at i:1307 original size:27 final size:27

Alignment explanation


    Indices: 1277--1331  Score: 83
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       1267 AGTGGGAGTG

                             *         
       1277 GGGTTCAACCCTGGAGTTGCTGCTGCT
          1 GGGTTCAACCCTGGAGTGGCTGCTGCT

                 *        *            
       1304 GGGTTTAACCCTGGGGTGGCTGCTGCT
          1 GGGTTCAACCCTGGAGTGGCTGCTGCT

             
       1331 G
          1 G

       1332 CACCAGCTTT


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  27   25  1.00

ACGTcount: A:0.09, C:0.24, G:0.38, T:0.29


Consensus pattern (27 bp):   
GGGTTCAACCCTGGAGTGGCTGCTGCT

Found at i:2203 original size:41 final size:41

Alignment explanation


    Indices: 2158--2237  Score: 151
    Period size: 41  Copynumber: 2.0  Consensus size: 41

       2148 TTTATTTTGA

                               *                     
       2158 AGTTTGAGATTCATTCATTTGAGGTTAAAGGAAAAAAAAGT
          1 AGTTTGAGATTCATTCATTCGAGGTTAAAGGAAAAAAAAGT

                                                   
       2199 AGTTTGAGATTCATTCATTCGAGGTTAAAGGAAAAAAAA
          1 AGTTTGAGATTCATTCATTCGAGGTTAAAGGAAAAAAAA

       2238 TTAACTTTGC


Statistics
Matches: 38,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  41   38  1.00

ACGTcount: A:0.42, C:0.06, G:0.21, T:0.30


Consensus pattern (41 bp):   
AGTTTGAGATTCATTCATTCGAGGTTAAAGGAAAAAAAAGT
Done.