Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga06g01862.M6

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: 4653
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30


Found at i:959 original size:369 final size:366

Alignment explanation


    Indices: 197--1077  Score: 1446
    Period size: 369  Copynumber: 2.4  Consensus size: 366

        187 GCAAAAGGGA

                                                                             
        197 AACAAAGATTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGGCAGATGACTCCTAAATGTG
          1 AACAAAGATTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGGCAGATGACTCCTAAATGTG

                               *             *                  *       *    
        262 ATGGTACTTCACAAAGTGGTTGTAAAGAGGCTGGGGATTCATGCCTTCCCTTTCCCAAAATTGGT
         66 ATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCTTCCCTTACCCAAAACTGGT

                 *                                           *               
        327 TCTCAACAGTCATCTGTGAGTATGATGTTTGAAAGTCCAACGCCGATTTTAGTTTACAGGAGGAA
        131 TCTCAGCAGTCATCTGTGAGTATGATGTTTGAAAGTCCAACGCCGATTTCAGTTTACAGGAGGAA

                         *          *                         *              
        392 GAAACGGTGGGGCTGCAGCAGCAGTGCTAGTGCTGTTGTTGCCAACTTTTGTGCACAGGAGCTGG
        196 GAAACGGTGGGGCAGCAGCAGCAGCGCTAGTGCTGTTGTTGCCAACTTTTATGCACAGGAGCTGG

                            * *       *                                      
        457 TTAATTCAAAGAGAAGTGTGGATTGTTTTTCTGTTCTTAGTTCTAATGCACTTTCAGAGGCAGTT
        261 TTAATTCAAAGAGAAGGGCGGATTGTCTTTCTGTTCTTAGTTCTAATGCACTTTCAGAGGCAGTT

                                  *                  
        522 ATGGAGCAAAAGGGAGTTTCTCGAGTTGAACATGAAACTGC
        326 ATGGAGCAAAAGGGAGTTTCTCAAGTTGAACATGAAACTGC

                    *                                            *           
        563 AACAAAGACTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGGCAGATGATTCCTAAATGTG
          1 AACAAAGATTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGGCAGATGACTCCTAAATGTG

                                                                             
        628 ATGGTACTTCAC-AAGCTGGATGTAAAGAGGCTGAGGATTCATGCCTTCCCTTACCCAAAACTGG
         66 ATGGTACTTCACAAAG-TGGATGTAAAGAGGCTGAGGATTCATGCCTTCCCTTACCCAAAACTGG

                      *           *                * *                      *
        692 TTCTCAGCAGCCATCTGTGAGTGTGATGTTTGAAAGTCCTATGCCGATTTCAGTTTACAGTAGGG
        130 TTCTCAGCAGTCATCTGTGAGTATGATGTTTGAAAGTCCAACGCCGATTTCAGTTTAC---AGGA

                                                                         *   
        757 GGAAGAAACGGTGGGGCAGCAGCAGCAGCGCTAGCT-CTGTTGTTGCCAACTTTTATGCACGGGA
        192 GGAAGAAACGGTGGGGCAGCAGCAGCAGCGCTAG-TGCTGTTGTTGCCAACTTTTATGCACAGGA

                                                     *        *          *   
        821 GCAT-GTTAATTCAAAGAGAAGGGCGGATTGTCTTTCTGTTGTTAGTTCTGATGCACTTTCGGAG
        256 GC-TGGTTAATTCAAAGAGAAGGGCGGATTGTCTTTCTGTTCTTAGTTCTAATGCACTTTCAGAG

                         *                                 
        885 GCAGTTATGGAGCGAAAGGGAGTTTCTCAAGTTGAACATGAAACTGC
        320 GCAGTTATGGAGCAAAAGGGAGTTTCTCAAGTTGAACATGAAACTGC

                                                                             
        932 AACAAAGATTTCTTTATGTGATTGGATGTCTGGTAATGAAACTT-GCAAGATGACTCCTAAATGT
          1 AACAAAGATTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGGC-AGATGACTCCTAAATGT

                                                                             
        996 GATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCTTCCCTTACCCAAAACTGG
         65 GATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCTTCCCTTACCCAAAACTGG

                             
       1061 TTCTCAGCAGTCATCTG
        130 TTCTCAGCAGTCATCTG

       1078 AGCTGGTTAA


Statistics
Matches: 479,  Mismatches: 28, Indels: 13
        0.92            0.05        0.03

Matches are distributed among these distances:
 365    3  0.01
 366  171  0.36
 368    2  0.00
 369  298  0.62
 370    5  0.01

ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30


Consensus pattern (366 bp):   
AACAAAGATTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGGCAGATGACTCCTAAATGTG
ATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCTTCCCTTACCCAAAACTGGT
TCTCAGCAGTCATCTGTGAGTATGATGTTTGAAAGTCCAACGCCGATTTCAGTTTACAGGAGGAA
GAAACGGTGGGGCAGCAGCAGCAGCGCTAGTGCTGTTGTTGCCAACTTTTATGCACAGGAGCTGG
TTAATTCAAAGAGAAGGGCGGATTGTCTTTCTGTTCTTAGTTCTAATGCACTTTCAGAGGCAGTT
ATGGAGCAAAAGGGAGTTTCTCAAGTTGAACATGAAACTGC

Found at i:1282 original size:258 final size:258

Alignment explanation


    Indices: 825--1335  Score: 869
    Period size: 258  Copynumber: 2.0  Consensus size: 258

        815 ACGGGAGCAT

                             *                 *                    *        
        825 GTTAATTCAAAGAGAAGGGCGGATTGTCTTTCTGTTGTTAGTTCTGATGCACTTTCGGAGGCAGT
          1 GTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTCGTTAGTTCTGATGCACTTTCAGAGGCAGT

                                                                             
        890 TATGGAGCGAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAAAGATTTCTTTATGTGATT
         66 TATGGAGCGAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAAAGATTTCTTTATGTGATT

                *    *                                  *            *       
        955 GGATGTCTGGTAATGAAACTTGCAAGATGACTCCTAAATGTGATGGTACTTCACAAAGTGGATGT
        131 GGATATCTGATAATGAAACTTGCAAGATGACTCCTAAATGTGATAGTACTTCACAAACTGGATGT

                              *                                            
       1020 AAAGAGGCTGAGGATTCATGCCTTCCCTTACCCAAAACTGGTTCTCAGCAGTCATCTGAGCTG
        196 AAAGAGGCTGAGGATTCACGCCTTCCCTTACCCAAAACTGGTTCTCAGCAGTCATCTGAGCTG

                                                              *              
       1083 GTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTCGTTAGTTCTGATGCGCTTTCAGAGGCAGT
          1 GTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTCGTTAGTTCTGATGCACTTTCAGAGGCAGT

                                          *                                  
       1148 TATGGAGCGAAAGGGAGTTTCTCAAGTTGATCATGAAACTGCAACAAAGATTTCTTTATGTGATT
         66 TATGGAGCGAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAAAGATTTCTTTATGTGATT

                                 * **                               *        
       1213 GGATATCTGATAATGAAACTTTCCGGATGACTCCTAAATGTGATAGTACTTCACAACCTGGATGT
        131 GGATATCTGATAATGAAACTTGCAAGATGACTCCTAAATGTGATAGTACTTCACAAACTGGATGT

                                             *               *  *     
       1278 AAAGAGGCTGAGGATTCACGCCTTCCCTTACCCGAAACTGGTTCTCAGCGGTTATCTG
        196 AAAGAGGCTGAGGATTCACGCCTTCCCTTACCCAAAACTGGTTCTCAGCAGTCATCTG

       1336 TGAGTGTGAT


Statistics
Matches: 236,  Mismatches: 17, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
 258  236  1.00

ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31


Consensus pattern (258 bp):   
GTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTCGTTAGTTCTGATGCACTTTCAGAGGCAGT
TATGGAGCGAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAAAGATTTCTTTATGTGATT
GGATATCTGATAATGAAACTTGCAAGATGACTCCTAAATGTGATAGTACTTCACAAACTGGATGT
AAAGAGGCTGAGGATTCACGCCTTCCCTTACCCAAAACTGGTTCTCAGCAGTCATCTGAGCTG
Done.