Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga03g02046.F4

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: 3547
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29


Found at i:1255 original size:144 final size:143

Alignment explanation


    Indices: 986--1561  Score: 767
    Period size: 144  Copynumber: 4.0  Consensus size: 143

        976 CTCCTGATAT

                    *      *       *  *     *     *                     *    
        986 AGAAAAGGTTTCTCCCCCACTGGGAGCTTCTGATATTGGAAGTGAAATTACAACTGAATCGGCTC
          1 AGAAAAGGCTTCTCCTCCACTGGAAGTTTCTGCTATTGAAAGTGAAATTACAACTGAATCAGCTC

                      **   ***                                  *         *  
       1051 CTTCAGAGTCTGGTTTGGAAAGTGAAGTTCCCCACAGTGTTAAGTTGGAAGAAGAAGAAAACGCT
         66 CTTCAGAGTCCAGTTCCAAAAGTGAAGTTCCCCACAGTGTTAAGTTGGAAGAGGAAGAAAACACT

                         
       1116 GGTGCTGAGGAAA
        131 GGTGCTGAGGAAA

                       * * *      *                                     *    
       1129 ATGAAAAGGCTGCGCTTCCACTTGAAGTTTCTGCTATTGAAAGTGAAATTACAACTGAATTAGCT
          1 A-GAAAAGGCTTCTCCTCCACTGGAAGTTTCTGCTATTGAAAGTGAAATTACAACTGAATCAGCT

                                                                    *     ** 
       1194 CCTTCAGAGTCCAGTTCCAAAAGTGAAGTTCCCCACAGTGTTAAGTTGGAAGAGGATGAAAATGC
         65 CCTTCAGAGTCCAGTTCCAAAAGTGAAGTTCCCCACAGTGTTAAGTTGGAAGAGGAAGAAAACAC

                           
       1259 TGGTGCTGAGGAAAA
        130 TGGTGCTGAGG-AAA

                                                            *        *  *    
       1274 AGAAAAGGCTTCTCCTCCACTGGAAGCTTT-TGCTATTGAAAGTGAAACTACAACTGCATTAGCT
          1 AGAAAAGGCTTCTCCTCCACTGGAAG-TTTCTGCTATTGAAAGTGAAATTACAACTGAATCAGCT

                                    *          *      *        *          *  
       1338 CCTTCAGAGTCCAGTTCCAAAAGTAAAGTTCCCCAGAGTGTTCAGTTGGAAAAGGAAGAAAATAC
         65 CCTTCAGAGTCCAGTTCCAAAAGTGAAGTTCCCCACAGTGTTAAGTTGGAAGAGGAAGAAAACAC

                           
       1403 TGGTGCTGAGGAAGA
        130 TGGTGCTGAGGAA-A

                                      *      *                               
       1418 AGAAAAGGCTTCTCCTCCACTGGAAGCTTCTGCCATTGAAAGTGAAATTACAACTGAATCAGCTC
          1 AGAAAAGGCTTCTCCTCCACTGGAAGTTTCTGCTATTGAAAGTGAAATTACAACTGAATCAGCTC

               *       *               *      *                        *     
       1483 CTTTAGAGTCCGGTTCCAAAAGTGAAGATCCCCAGAGTGTTAAGTTGGAAGAGGAAGAAGACACT
         66 CTTCAGAGTCCAGTTCCAAAAGTGAAGTTCCCCACAGTGTTAAGTTGGAAGAGGAAGAAAACACT

            *            
       1548 AGTGCTGAGGAAA
        131 GGTGCTGAGGAAA

             
       1561 A
          1 A

       1562 AGGTGAAAGA


Statistics
Matches: 382,  Mismatches: 46, Indels: 10
        0.87            0.11        0.02

Matches are distributed among these distances:
 143    7  0.02
 144  368  0.96
 145    7  0.02

ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24


Consensus pattern (143 bp):   
AGAAAAGGCTTCTCCTCCACTGGAAGTTTCTGCTATTGAAAGTGAAATTACAACTGAATCAGCTC
CTTCAGAGTCCAGTTCCAAAAGTGAAGTTCCCCACAGTGTTAAGTTGGAAGAGGAAGAAAACACT
GGTGCTGAGGAAA

Found at i:1792 original size:216 final size:216

Alignment explanation


    Indices: 1418--1833  Score: 521
    Period size: 216  Copynumber: 1.9  Consensus size: 216

       1408 CTGAGGAAGA

                                        *      *           *                 
       1418 AGAAAAGGCTTCTCCTCCACTGGAAGCTTCTGCCATTGAAAGTGAAATTACAACTGAATCAGCTC
          1 AGAAAAGGCTTCTCCTCCACTGGAAGCTCCTGCCAGTGAAAGTGAAACTACAACTGAATCAGCTC

                       *          *           *                        *     
       1483 CTTTAGAGTCCGGTTCCAAAAGTGAAGATCCCCAGAGTGTTAAGTTGGAAGAGGAAGAAGACACT
         66 CTTTAGAGTCCAGTTCCAAAAGCGAAGATCCCCACAGTGTTAAGTTGGAAGAGGAAGAAAACACT

                 *                           *    **                   *     
       1548 AGTGCTGAGGAAAAAGGTGAAAGAATTGGTAAATTTGAGTGTACTACTTCGAATATGGAGTCTAA
        131 AGTGCCGAGGAAAAAGGTGAAAGAATTGGTAAAATTGAAAGTACTACTTCGAATATGGAATCTAA

                                 
       1613 GATGGCTTTAGTTCCTGATTT
        196 GATGGCTTTAGTTCCTGATTT

                               *             *    *           *        *    *
       1634 AGAAAAGGCTTCTCCTCCATTGGAAGCTCCTGCTAGTGGAAGTGAAACTAGAACTGAATTAGCTT
          1 AGAAAAGGCTTCTCCTCCACTGGAAGCTCCTGCCAGTGAAAGTGAAACTACAACTGAATCAGCTC

                       *                * * *                  *           * 
       1699 CTTTAGAG-CTTAGTTCCAAAAGCGAAGTTTCTCACAGTGTTAA-TCTGGAGGAGGAAGAAAATA
         66 CTTTAGAGTC-CAGTTCCAAAAGCGAAGATCCCCACAGTGTTAAGT-TGGAAGAGGAAGAAAACA

            * *      *      *     *                      *     *             
       1762 GTGGTGCCGGGGAAAATGGTGAGAGAATTGGTAAAATTGAAAGTATTACTTTGAATATGGAATCT
        129 CTAGTGCCGAGGAAAAAGGTGAAAGAATTGGTAAAATTGAAAGTACTACTTCGAATATGGAATCT

                   
       1827 AAGATGG
        194 AAGATGG

       1834 ACTTAGCAGT


Statistics
Matches: 167,  Mismatches: 31, Indels: 4
        0.83            0.15        0.02

Matches are distributed among these distances:
 215    2  0.01
 216  165  0.99

ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27


Consensus pattern (216 bp):   
AGAAAAGGCTTCTCCTCCACTGGAAGCTCCTGCCAGTGAAAGTGAAACTACAACTGAATCAGCTC
CTTTAGAGTCCAGTTCCAAAAGCGAAGATCCCCACAGTGTTAAGTTGGAAGAGGAAGAAAACACT
AGTGCCGAGGAAAAAGGTGAAAGAATTGGTAAAATTGAAAGTACTACTTCGAATATGGAATCTAA
GATGGCTTTAGTTCCTGATTT
Done.