Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g02647.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, 677

Length: 1129
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.24


Found at i:477 original size:228 final size:228

Alignment explanation


    Indices: 68--875  Score: 1001
    Period size: 228  Copynumber: 3.5  Consensus size: 228

         58 AGCCAAAAAA

                  *        *         *                                       
         68 GATGCAGATCTTCGTTAAGA-CTCTAACCGGCAAGACGATCACTCTCGAGGTCGAGAGCTCCGAC
          1 GATGCAAATCTTCGTCAAGACCT-TGACCGGCAAGACGATCACTCTCGAGGTCGAGAGCTCCGAC

                             *              *              *           *     
        132 ACGATCGACAACGTGAAGGCCAAAATCCAAGATAAGGAAGGCATCCCTCCAGACCAGCAGCGTCT
         65 ACGATCGACAACGTGAAAGCCAAAATCCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCT

            *                 *  *                                   *       
        197 GATCTTCGCCGGAAAACAGCTTGAGGACGGCCGGACCTTGGCCGATTACAACATCCAAAAGGAGT
        130 CATCTTCGCCGGAAAACAACTCGAGGACGGCCGGACCTTGGCCGATTACAACATCCAGAAGGAGT

                                        *     
        262 CAACTCTCCACCTCGTCCTCCGTTTGCGCGGTGG
        195 CAACTCTCCACCTCGTCCTCCGTTTGCGAGGTGG

                           *  *                 *                            
        296 GATGCAAATCTTCGTGAAAACCTTGACCGGCAAGACAATCACTCTCGAGGTCGAGAGCTCCGACA
          1 GATGCAAATCTTCGTCAAGACCTTGACCGGCAAGACGATCACTCTCGAGGTCGAGAGCTCCGACA

                         *  *  *  *                       *                  
        361 CGATCGACAACGTTAAGGCGAAGATCCAAGACAAGGAAGGCATCCCCCCAGACCAGCAACGTCTC
         66 CGATCGACAACGTGAAAGCCAAAATCCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTC

                                   *        *           *                    
        426 ATCTTCGCCGGAAAACAACTCGAAGACGGCCGTACCTTGGCCGACTACAACATCCAGAAGGAGTC
        131 ATCTTCGCCGGAAAACAACTCGAGGACGGCCGGACCTTGGCCGATTACAACATCCAGAAGGAGTC

               *        *     *        *  *  
        491 AACGCTCCACCTTGTCCTTCGTTTGCGTGGCGG
        196 AACTCTCCACCTCGTCCTCCGTTTGCGAGGTGG

                           *               *                             *   
        524 GATGCAAATCTTCGTTAAGACGCTT-ACCGGAAAGACGATCACTCTCGAGGTCGAGAGCTCTGAC
          1 GATGCAAATCTTCGTCAAGAC-CTTGACCGGCAAGACGATCACTCTCGAGGTCGAGAGCTCCGAC

                                                           *                 
        588 ACGATCGACAACGTGAAAGCCAAAATCCAAGACAAGGAAGGCATCCCGCCAGACCAGCAACGTCT
         65 ACGATCGACAACGTGAAAGCCAAAATCCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCT

                           *              *     *  *           *           * 
        653 CATCTTCGCCGGAAAGCAACTCGAGGACGGGCGGACTTTAGCCGATTACAATATCCAGAAGGAAT
        130 CATCTTCGCCGGAAAACAACTCGAGGACGGCCGGACCTTGGCCGATTACAACATCCAGAAGGAGT

             *     *  *  *     *               
        718 CGACTCTTCATCTGGTCCTGCGTCTT-CGAGGTGG
        195 CAACTCTCCACCTCGTCCTCCGT-TTGCGAGGTGG

                  *              *        *        *   * *  *  *        *  * 
        752 GATGCAGATCTTCGTCAAGACTTTGACCGGTAAGACGATTACTTTAGAAGTGGAGAGCTCGGATA
          1 GATGCAAATCTTCGTCAAGACCTTGACCGGCAAGACGATCACTCTCGAGGTCGAGAGCTCCGACA

                *  *           *  *  *  *     *     *  *        *      
        817 CGATTGATAACGTGAAAGCGAAGATTCAGGACAAAGAAGGAATTCCACCAGATCAGCAA
         66 CGATCGACAACGTGAAAGCCAAAATCCAAGACAAGGAAGGCATCCCACCAGACCAGCAA

        876 AGGTTGATTT


Statistics
Matches: 504,  Mismatches: 72, Indels: 8
        0.86            0.12        0.01

Matches are distributed among these distances:
 227    2  0.00
 228  495  0.98
 229    7  0.01

ACGTcount: A:0.29, C:0.27, G:0.25, T:0.18


Consensus pattern (228 bp):   
GATGCAAATCTTCGTCAAGACCTTGACCGGCAAGACGATCACTCTCGAGGTCGAGAGCTCCGACA
CGATCGACAACGTGAAAGCCAAAATCCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTC
ATCTTCGCCGGAAAACAACTCGAGGACGGCCGGACCTTGGCCGATTACAACATCCAGAAGGAGTC
AACTCTCCACCTCGTCCTCCGTTTGCGAGGTGG

Found at i:930 original size:228 final size:227

Alignment explanation


    Indices: 68--980  Score: 963
    Period size: 228  Copynumber: 4.0  Consensus size: 227

         58 AGCCAAAAAA

                  *        *         *     *                                 
         68 GATGCAGATCTTCGTTAAGA-CTCTAACCGGCAAGACGATCACTCTCGAGGTCGAGAGCTCCGAC
          1 GATGCAAATCTTCGTCAAGACCT-TGACCGGAAAGACGATCACTCTCGAGGTCGAGAGCTCCGAC

                             *  *  *        *              *           *     
        132 ACGATCGACAACGTGAAGGCCAAAATCCAAGATAAGGAAGGCATCCCTCCAGACCAGCAGCGTCT
         65 ACGATCGACAACGTGAAAGCGAAGATCCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCT

            *           *     *  *  *     *                                  
        197 GATCTTCGCCGGAAAACAGCTTGAGGACGGCCGGACCTTGGCCGATTACAACATCCAAAAGGAGT
        130 CATCTTCG-CGGGAAACAACTCGAAGACGGACGGACCTTGGCCGATTACAACATCCAAAAGGAGT

                         *     *        *     
        262 CAACTCTCCACCTCGTCCTCCGTTTGCGCGGTGG
        194 CAACTCTCCACCTTGTCCTTCGTTTGCGTGGTGG

                           *  *           *     *                            
        296 GATGCAAATCTTCGTGAAAACCTTGACCGGCAAGACAATCACTCTCGAGGTCGAGAGCTCCGACA
          1 GATGCAAATCTTCGTCAAGACCTTGACCGGAAAGACGATCACTCTCGAGGTCGAGAGCTCCGACA

                         *  *                             *                  
        361 CGATCGACAACGTTAAGGCGAAGATCCAAGACAAGGAAGGCATCCCCCCAGACCAGCAACGTCTC
         66 CGATCGACAACGTGAAAGCGAAGATCCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTC

                       *                 *  *           *           *        
        426 ATCTTCGCCGGAAAACAACTCGAAGACGGCCGTACCTTGGCCGACTACAACATCCAGAAGGAGTC
        131 ATCTTCG-CGGGAAACAACTCGAAGACGGACGGACCTTGGCCGATTACAACATCCAAAAGGAGTC

               *                          *  
        491 AACGCTCCACCTTGTCCTTCGTTTGCGTGGCGG
        195 AACTCTCCACCTTGTCCTTCGTTTGCGTGGTGG

                           *                                             *   
        524 GATGCAAATCTTCGTTAAGACGCTT-ACCGGAAAGACGATCACTCTCGAGGTCGAGAGCTCTGAC
          1 GATGCAAATCTTCGTCAAGAC-CTTGACCGGAAAGACGATCACTCTCGAGGTCGAGAGCTCCGAC

                                *  *                       *                 
        588 ACGATCGACAACGTGAAAGCCAAAATCCAAGACAAGGAAGGCATCCCGCCAGACCAGCAACGTCT
         65 ACGATCGACAACGTGAAAGCGAAGATCCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCT

                     *              *     *     *  *           *     *     * 
        653 CATCTTCGCCGGAAAGCAACTCGAGGACGGGCGGACTTTAGCCGATTACAATATCCAGAAGGAAT
        130 CATCTTCGCGGGAAA-CAACTCGAAGACGGACGGACCTTGGCCGATTACAACATCCAAAAGGAGT

             *     *  *  *     *         *     
        718 CGACTCTTCATCTGGTCCTGCGTCTT-CGAGGTGG
        194 CAACTCTCCACCTTGTCCTTCGT-TTGCGTGGTGG

                  *              *        *        *   * *  *  *        *  * 
        752 GATGCAGATCTTCGTCAAGACTTTGACCGGTAAGACGATTACTTTAGAAGTGGAGAGCTCGGATA
          1 GATGCAAATCTTCGTCAAGACCTTGACCGGAAAGACGATCACTCTCGAGGTCGAGAGCTCCGACA

                *  *                 *  *     *     *  *        *       *    
        817 CGATTGATAACGTGAAAGCGAAGATTCAGGACAAAGAAGGAATTCCACCAGATCAGCAAAGGT-T
         66 CGATCGACAACGTGAAAGCGAAGATCCAAGACAAGGAAGGCATCCCACCAGACCAGC-AACGTCT

            *  *  *              *         *    *     *        *  *          
        881 GATTTTTGCTGGGAAACAACTGGAAGACGGAAGGACTTTGGCTGATTACAATATTCAAAAGGAGT
        130 CATCTTCGC-GGGAAACAACTCGAAGACGGACGGACCTTGGCCGATTACAACATCCAAAAGGAGT

             *     *        *                  
        946 CCACTCTTCACCTTGTTCTTCGTCTT-CGTGGTGG
        194 CAACTCTCCACCTTGTCCTTCGT-TTGCGTGGTGG

             
        980 G
          1 G

        981 TTCTAAGCCT


Statistics
Matches: 585,  Mismatches: 93, Indels: 14
        0.85            0.13        0.02

Matches are distributed among these distances:
 227    7  0.01
 228  562  0.96
 229   16  0.03

ACGTcount: A:0.29, C:0.26, G:0.25, T:0.20


Consensus pattern (227 bp):   
GATGCAAATCTTCGTCAAGACCTTGACCGGAAAGACGATCACTCTCGAGGTCGAGAGCTCCGACA
CGATCGACAACGTGAAAGCGAAGATCCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTC
ATCTTCGCGGGAAACAACTCGAAGACGGACGGACCTTGGCCGATTACAACATCCAAAAGGAGTCA
ACTCTCCACCTTGTCCTTCGTTTGCGTGGTGG

Found at i:945 original size:456 final size:456

Alignment explanation


    Indices: 68--976  Score: 1149
    Period size: 456  Copynumber: 2.0  Consensus size: 456

         58 AGCCAAAAAA

                  *              *        *                                  
         68 GATGCAGATCTTCGTTAAGACTCTAACCGGCAAGACGATCACTCTCGAGGTCGAGAGCTCCGACA
          1 GATGCAAATCTTCGTTAAGACGCTAACCGGAAAGACGATCACTCTCGAGGTCGAGAGCTCCGACA

                            *              *              *           *     *
        133 CGATCGACAACGTGAAGGCCAAAATCCAAGATAAGGAAGGCATCCCTCCAGACCAGCAGCGTCTG
         66 CGATCGACAACGTGAAAGCCAAAATCCAAGACAAGGAAGGCATCCCGCCAGACCAGCAACGTCTC

                             *  *                 *                       *  
        198 ATCTTCGCCGGAAAACAGCTTGAGGACGGCCGGACCTTGGCCGATTACAACATCCAAAAGGAGTC
        131 ATCTTCGCCGGAAAACAACTCGAGGACGGCCGGACCTTAGCCGATTACAACATCCAAAAGGAATC

                                       *                    *                
        263 AACTCTCCACCTCGTCCTCCGTTTGCGCGGTGGGATGCAAATCTTCGTGAAAACCTTGACCGGCA
        196 AACTCTCCACCTCGTCCTCCGTTTGCGAGGTGGGATGCAAATCTTCGTCAAAACCTTGACCGGCA

                         *  *                             *  *               
        328 AGACAATCACTCTCGAGGTCGAGAGCTCCGACACGATCGACAACGTTAAGGCGAAGATCCAAGAC
        261 AGACAATCACTCTAGAAGTCGAGAGCTCCGACACGATCGACAACGTGAAAGCGAAGATCCAAGAC

              *     *     *                                               ** 
        393 AAGGAAGGCATCCCCCCAGACCAGCAACGTCTCATCTTCGCCGGAAAACAACTCGAAGACGGCCG
        326 AAAGAAGGAATCCCACCAGACCAGCAACGTCTCATCTTCGCCGGAAAACAACTCGAAGACGGAAG

            *                       *                                        
        458 TACCTTGGCCGACTACAACATCCAGAAGGAGTCAACGCTCCACCTTGTCCTTCGT-TTGCGTGGC
        391 GACCTTGGCCGACTACAACATCCAAAAGGAGTCAACGCTCCACCTTGTCCTTCGTCTT-CGTGGC

              
        522 GG
        455 GG

                                    *                                   *    
        524 GATGCAAATCTTCGTTAAGACGCTTACCGGAAAGACGATCACTCTCGAGGTCGAGAGCTCTGACA
          1 GATGCAAATCTTCGTTAAGACGCTAACCGGAAAGACGATCACTCTCGAGGTCGAGAGCTCCGACA

                                                                             
        589 CGATCGACAACGTGAAAGCCAAAATCCAAGACAAGGAAGGCATCCCGCCAGACCAGCAACGTCTC
         66 CGATCGACAACGTGAAAGCCAAAATCCAAGACAAGGAAGGCATCCCGCCAGACCAGCAACGTCTC

                          *              *     *              *     *        
        654 ATCTTCGCCGGAAAGCAACTCGAGGACGGGCGGACTTTAGCCGATTACAATATCCAGAAGGAATC
        131 ATCTTCGCCGGAAAACAACTCGAGGACGGCCGGACCTTAGCCGATTACAACATCCAAAAGGAATC

            *     *  *  *     *                     *           *  *        *
        719 GACTCTTCATCTGGTCCTGCGTCTT-CGAGGTGGGATGCAGATCTTCGTCAAGACTTTGACCGGT
        196 AACTCTCCACCTCGTCCTCCGT-TTGCGAGGTGGGATGCAAATCTTCGTCAAAACCTTGACCGGC

                 *  *   *       *        *  *     *  *                 *  *  
        783 AAGACGATTACTTTAGAAGTGGAGAGCTCGGATACGATTGATAACGTGAAAGCGAAGATTCAGGA
        260 AAGACAATCACTCTAGAAGTCGAGAGCTCCGACACGATCGACAACGTGAAAGCGAAGATCCAAGA

                        *        *       *    *  *  *  *  *        *         
        848 CAAAGAAGGAATTCCACCAGATCAGCAAAGGT-TGATTTTTGCTGGGAAACAACTGGAAGACGGA
        325 CAAAGAAGGAATCCCACCAGACCAGC-AACGTCTCATCTTCGCCGGAAAACAACTCGAAGACGGA

                 *     *  *     *  *           *  *  *        *              
        912 AGGACTTTGGCTGATTACAATATTCAAAAGGAGTCCACTCTTCACCTTGTTCTTCGTCTTCGTGG
        389 AGGACCTTGGCCGACTACAACATCCAAAAGGAGTCAACGCTCCACCTTGTCCTTCGTCTTCGTGG

        977 TGGGTTCTAA


Statistics
Matches: 381,  Mismatches: 69, Indels: 6
        0.84            0.15        0.01

Matches are distributed among these distances:
 456  373  0.98
 457    8  0.02

ACGTcount: A:0.29, C:0.27, G:0.25, T:0.20


Consensus pattern (456 bp):   
GATGCAAATCTTCGTTAAGACGCTAACCGGAAAGACGATCACTCTCGAGGTCGAGAGCTCCGACA
CGATCGACAACGTGAAAGCCAAAATCCAAGACAAGGAAGGCATCCCGCCAGACCAGCAACGTCTC
ATCTTCGCCGGAAAACAACTCGAGGACGGCCGGACCTTAGCCGATTACAACATCCAAAAGGAATC
AACTCTCCACCTCGTCCTCCGTTTGCGAGGTGGGATGCAAATCTTCGTCAAAACCTTGACCGGCA
AGACAATCACTCTAGAAGTCGAGAGCTCCGACACGATCGACAACGTGAAAGCGAAGATCCAAGAC
AAAGAAGGAATCCCACCAGACCAGCAACGTCTCATCTTCGCCGGAAAACAACTCGAAGACGGAAG
GACCTTGGCCGACTACAACATCCAAAAGGAGTCAACGCTCCACCTTGTCCTTCGTCTTCGTGGCG
G
Done.