Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g00651.C1

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: 4570
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32


Found at i:2741 original size:213 final size:212

Alignment explanation


    Indices: 2396--3443  Score: 1275
    Period size: 213  Copynumber: 4.9  Consensus size: 212

       2386 TCAAGTATTC

                 *          *   *      *        *       *                 *  
       2396 ATAAACTGAAATCTCTCG-AGTATTTCGATCTTCAAGGTTGCTCCAGATTGGAGATTTTCCCTGA
          1 ATAAATTGAAATCTCTTGAAATA-TTCAATCTT-AAAGTTGCTCAAGATTGGAGATTTTCCCAGA

                        *         *     ****           *                **   
       2460 AATCATGGACACTATGGAGAGGTTG-AGGGTTCTTGATTTAAGTGGAACGGCTTTGAAGGGCTTA
         64 AATCATGGACACCATGGAGAGGATGTA-TAAACTTGATTTAAGCGGAACGGCTTTGAAGGAATTA

                          *               *                 *        * *     
       2524 CCATCCTCAATTGATAATCTTATTGGTCTTGAGGATTTGAGATTGAACTACTGTGAAGATCTTGT
        128 CCATCCTCAATTGACAATCTTATTGGTCTTAAGGATTTGAGATTGAACAACTGTGAAAACCTTGT

                        *       
       2589 TTGCCTTCCTAAAAGCTTTT
        193 TTGCCTTCCTAACAGCTTTT

                    *                                      *        *        
       2609 ATAAATTGGAATCTCTTGAAA-ATTTCAATCTTGGAAA-TTGCTCAATATTGGAGACTTTCCCAG
          1 ATAAATTGAAATCTCTTGAAATA-TTCAATCTT--AAAGTTGCTCAAGATTGGAGATTTTCCCAG

                 *     *                                               *     
       2672 AAATCTTGGACGCCATGGAG-GAGATGTATAAACTTGATTTAAGCGGAACGGCTTTGAAAGAATT
         63 AAATCATGGACACCATGGAGAG-GATGTATAAACTTGATTTAAGCGGAACGGCTTTGAAGGAATT

                          *                                        *        *
       2736 ACCATCCTCAATTGCCAATCTTATTGGTCTTAAGGATTTGAGATTGAACAACTGTCAAAACCTTA
        127 ACCATCCTCAATTGACAATCTTATTGGTCTTAAGGATTTGAGATTGAACAACTGTGAAAACCTTG

                         *       
       2801 TTTGCCTTCCTAATAGCTTTT
        192 TTTGCCTTCCTAACAGCTTTT

                               **              *                             
       2822 ATAAATTGAAATCTCTTGAGTTATTCAATCTTGAAGGTTGCTCAAGATTGGAGATTTTCCCAGAA
          1 ATAAATTGAAATCTCTTGAAATATTCAATCTT-AAAGTTGCTCAAGATTGGAGATTTTCCCAGAA

                                 *                       *                   
       2887 ATCATGGACACCATGGAGAGGCTGTATGAAA-TTGATTTAAGCGGGACGGCTTTGAAGGAATTAC
         65 ATCATGGACACCATGGAGAGGATGTAT-AAACTTGATTTAAGCGGAACGGCTTTGAAGGAATTAC

                        *                  **     *                   *      
       2951 CATCCTCAATTGCCAATCTTATTGGTCTTAAATATTTGGGATTGAACAACTGTGAAAATCTTGTT
        129 CATCCTCAATTGACAATCTTATTGGTCTTAAGGATTTGAGATTGAACAACTGTGAAAACCTTGTT

                     *    *    
       3016 TGCCTTCCTGACAGTTTTT
        194 TGCCTTCCTAACAGCTTTT

                               *         *             *                 *   
       3035 ATAAATTGAAATCTCTTGAGATATTCAATGTTAAAGGTTGCTCGAGATTGGAGATTTTCCCTGAA
          1 ATAAATTGAAATCTCTTGAAATATTCAATCTTAAA-GTTGCTCAAGATTGGAGATTTTCCCAGAA

              *              *   *     *             *     *                 
       3100 ATTATGGACACCATGGAAAGGTTGTATGAACTTGATTTAAGTGGAACAGCTTTGAAGGAATTACC
         65 ATCATGGACACCATGGAGAGGATGTATAAACTTGATTTAAGCGGAACGGCTTTGAAGGAATTACC

                       *          *             *                        *   
       3165 ATCCTCAATTGGCAATCTTATTAGTCTTAAGGATTTCAGATTGAACAACTGTGAAAACCTTATTT
        130 ATCCTCAATTGACAATCTTATTGGTCTTAAGGATTTGAGATTGAACAACTGTGAAAACCTTGTTT

            **           *    
       3230 ATCTTCCTAACAGTTTTT
        195 GCCTTCCTAACAGCTTTT

                    *                                            *     *     
       3248 ATAAATTGCAATCTCTTGAGAA-ATTCAATCTTAAAGGTTGCTCAAGATTGGAAATTTTTCCAGA
          1 ATAAATTGAAATCTCTTGA-AATATTCAATCTTAAA-GTTGCTCAAGATTGGAGATTTTCCCAGA

                                         *              *    * *   *         
       3312 AATCATGGACACCATGGAG-GGATTGTATGAACTTGATTTAAGCAGAACAGTTTTAAAGGAATTA
         64 AATCATGGACACCATGGAGAGGA-TGTATAAACTTGATTTAAGCGGAACGGCTTTGAAGGAATTA

                          *   *                             *                
       3376 CCATCCTCAATTGATAATTTTATTGGTCTTAAGGATTTGAGATTGAACGACTGTGAAAACCTTGT
        128 CCATCCTCAATTGACAATCTTATTGGTCTTAAGGATTTGAGATTGAACAACTGTGAAAACCTTGT

               
       3441 TTG
        193 TTG

       3444 TAGTAATTCA


Statistics
Matches: 726,  Mismatches: 97, Indels: 24
        0.86            0.11        0.03

Matches are distributed among these distances:
 212   10  0.01
 213  706  0.97
 214   10  0.01

ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34


Consensus pattern (212 bp):   
ATAAATTGAAATCTCTTGAAATATTCAATCTTAAAGTTGCTCAAGATTGGAGATTTTCCCAGAAA
TCATGGACACCATGGAGAGGATGTATAAACTTGATTTAAGCGGAACGGCTTTGAAGGAATTACCA
TCCTCAATTGACAATCTTATTGGTCTTAAGGATTTGAGATTGAACAACTGTGAAAACCTTGTTTG
CCTTCCTAACAGCTTTT

Found at i:3116 original size:426 final size:424

Alignment explanation


    Indices: 2396--3443  Score: 1406
    Period size: 426  Copynumber: 2.5  Consensus size: 424

       2386 TCAAGTATTC

                 *          *         *     *          *                 *   
       2396 ATAAACTGAAATCTCTCGAGTATTTCGATCTTCAAGGTTGCTCCAGATTGGAGATTTTCCCTGAA
          1 ATAAATTGAAATCTCTTGAGTA-TTCAATCTTAAAGGTTGCTCAAGATTGGAGATTTTCCCAGAA

                       *               * **           *                **    
       2461 ATCATGGACACTATGGAGAGGTTG-AGGGTTCTTGATTTAAGTGGAACGGCTTTGAAGGGCTTAC
         65 ATCATGGACACCATGGAGAGGTTGTA-TGAACTTGATTTAAGCGGAACGGCTTTGAAGGAATTAC

                                         *                 *        *        
       2525 CATCCTCAATTGATAATCTTATTGGTCTTGAGGATTTGAGATTGAACTACTGTGAAGATCTTGTT
        129 CATCCTCAATTGATAATCTTATTGGTCTTAAGGATTTGAGATTGAACAACTGTGAAAATCTTGTT

                                       *                                    *
       2590 TGCCTTCCTAAAAGCTTTTATAAATTGGAATCTCTTGAAAATTTCAATCTTGGAAATTGCTCAAT
        194 TGCCTTCCTAAAAGCTTTTATAAATTGAAATCTCTTGAAAATTTCAATCTT-GAAATTGCTCAAG

                                        *        *                           
       2655 ATTGGAGACTTTCCCAGAAATCTTGGACGCCATGG-AGGAGATGTATAAACTTGATTTAAGCGGA
        258 ATTGGAGACTTTCCCAGAAATCTTGGACACCATGGAAAG-GATGTATAAACTTGATTTAAGCGGA

              *                                       *             *        
       2719 ACGGCTTTGAAAGAATTACCATCCTCAATTGCCAATCTTATTGGTCTTAAGGATTTGAGATTGAA
        322 ACAGCTTTGAAAGAATTACCATCCTCAATTGCCAATCTTATTAGTCTTAAGGATTTCAGATTGAA

                                *         *       
       2784 CAACTGTCAAAACCTTATTTGCCTTCCTAATAGCTTTT
        387 CAACTGTCAAAACCTTATTTACCTTCCTAACAGCTTTT

                                            *                                
       2822 ATAAATTGAAATCTCTTGAGTTATTCAATCTTGAAGGTTGCTCAAGATTGGAGATTTTCCCAGAA
          1 ATAAATTGAAATCTCTTGAG-TATTCAATCTTAAAGGTTGCTCAAGATTGGAGATTTTCCCAGAA

                                 *        *             *                    
       2887 ATCATGGACACCATGGAGAGGCTGTATGAAATTGATTTAAGCGGGACGGCTTTGAAGGAATTACC
         65 ATCATGGACACCATGGAGAGGTTGTATGAACTTGATTTAAGCGGAACGGCTTTGAAGGAATTACC

                       **                 **     *                           
       2952 ATCCTCAATTGCCAATCTTATTGGTCTTAAATATTTGGGATTGAACAACTGTGAAAATCTTGTTT
        130 ATCCTCAATTGATAATCTTATTGGTCTTAAGGATTTGAGATTGAACAACTGTGAAAATCTTGTTT

                    * *  *                        *         *              * 
       3017 GCCTTCCTGACAGTTTTTATAAATTGAAATCTCTTG-AGATATTCAATGTT-AAAGGTTGCTCGA
        195 GCCTTCCTAAAAGCTTTTATAAATTGAAATCTCTTGAAAAT-TTCAATCTTGAAA--TTGCTCAA

                     *      *                         *     *             *  
       3080 GATTGGAGATTTTCCCTGAAAT-TATGGACACCATGGAAAGGTTGTATGAACTTGATTTAAGTGG
        257 GATTGGAGACTTTCCCAGAAATCT-TGGACACCATGGAAAGGATGTATAAACTTGATTTAAGCGG

                        *                   *                                
       3144 AACAGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTAGTCTTAAGGATTTCAGATTGA
        321 AACAGCTTTGAAAGAATTACCATCCTCAATTGCCAATCTTATTAGTCTTAAGGATTTCAGATTGA

                    *             *           *    
       3209 ACAACTGTGAAAACCTTATTTATCTTCCTAACAGTTTTT
        386 ACAACTGTCAAAACCTTATTTACCTTCCTAACAGCTTTT

                    *            *                              *     *      
       3248 ATAAATTGCAATCTCTTGAGAAATTCAATCTTAAAGGTTGCTCAAGATTGGAAATTTTTCCAGAA
          1 ATAAATTGAAATCTCTTGAG-TATTCAATCTTAAAGGTTGCTCAAGATTGGAGATTTTCCCAGAA

                                                       *    * *   *          
       3313 ATCATGGACACCATGGAG-GGATTGTATGAACTTGATTTAAGCAGAACAGTTTTAAAGGAATTAC
         65 ATCATGGACACCATGGAGAGG-TTGTATGAACTTGATTTAAGCGGAACGGCTTTGAAGGAATTAC

                             *                             *          *      
       3377 CATCCTCAATTGATAATTTTATTGGTCTTAAGGATTTGAGATTGAACGACTGTGAAAACCTTGTT
        129 CATCCTCAATTGATAATCTTATTGGTCTTAAGGATTTGAGATTGAACAACTGTGAAAATCTTGTT

              
       3442 TG
        194 TG

       3444 TAGTAATTCA


Statistics
Matches: 544,  Mismatches: 70, Indels: 16
        0.86            0.11        0.03

Matches are distributed among these distances:
 424    3  0.01
 425    6  0.01
 426  530  0.97
 427    5  0.01

ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34


Consensus pattern (424 bp):   
ATAAATTGAAATCTCTTGAGTATTCAATCTTAAAGGTTGCTCAAGATTGGAGATTTTCCCAGAAA
TCATGGACACCATGGAGAGGTTGTATGAACTTGATTTAAGCGGAACGGCTTTGAAGGAATTACCA
TCCTCAATTGATAATCTTATTGGTCTTAAGGATTTGAGATTGAACAACTGTGAAAATCTTGTTTG
CCTTCCTAAAAGCTTTTATAAATTGAAATCTCTTGAAAATTTCAATCTTGAAATTGCTCAAGATT
GGAGACTTTCCCAGAAATCTTGGACACCATGGAAAGGATGTATAAACTTGATTTAAGCGGAACAG
CTTTGAAAGAATTACCATCCTCAATTGCCAATCTTATTAGTCTTAAGGATTTCAGATTGAACAAC
TGTCAAAACCTTATTTACCTTCCTAACAGCTTTT
Done.