Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_1022 ID=scaffold_1022-JGI_221_v2.0

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, 919

Length: 1532
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.23

Warning! 100 characters in sequence are not A, C, G, or T


Found at i:1118 original size:303 final size:303

Alignment explanation


    Indices: 431--1532  Score: 1807
    Period size: 303  Copynumber: 3.6  Consensus size: 303

        421 NNNNNNNNNN

                              **                          *   *              
        431 CATCCTAGTACTACTCTCAACCAAGCACGCTTAACTGCGGAGTTCTAATGCGATCCGGTGCATTA
          1 CATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTA

                 *             * *             *   *                    *    
        496 GTGCTAGTATGATCGCACCAGTCAACTCTTGCGCATTCTGTTCATATAAAGGCTGCCCCTGATCG
         66 GTGCTGGTATGATCGCACCCGCCAACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCG

              *         *                     *         *      *             
        561 CACTTGCGCCTCGAATTTAAATGCAAATTCGACCGAATATCGTTCCAAATTATTTATTTCACAAA
        131 CAGTTGCGCCTCAAATTTAAATGCAAATTCGACCAAATATCGTTTCAAATTGTTTATTTCACAAA

               *                                                             
        626 ACGAAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAACT-AAAAAAACATTATATGAAAT
        196 ACGCAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAACTAAAAAAAACATTATATGAAAT

                                       *               
        690 AAAATGGGAGGGGTGCAACACGAGGACCTCCCAGGAGGTCACC
        261 AAAATGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACC

                                               *                             
        733 CATCCTAGTACTACTCTCGCCCAAGCACGCTTAACAGCGGAGTTCTGCA-GGGATCCGGTGCATT
          1 CATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTG-ATGGGATCCGGTGCATT

                                                                 *           
        797 AGTGCTGGTATGATCGCACCCGCCAACTCTTGCGCAATCTATTCATATAAAGGATGCCCCTTATC
         65 AGTGCTGGTATGATCGCACCCGCCAACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATC

                                                                             
        862 GCAGTTGCGCCTCAAATTTAAATGCAAATTCGACCAAATATCGTTTCAAATTGTTTATTTCACAA
        130 GCAGTTGCGCCTCAAATTTAAATGCAAATTCGACCAAATATCGTTTCAAATTGTTTATTTCACAA

              *                                       *                      
        927 AATGCAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAGCTAAAAAAAACATTATATGAAA
        195 AACGCAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAACTAAAAAAAACATTATATGAAA

                                                       *
        992 TAAAATGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACG
        260 TAAAATGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACC

              *               *              *                               
       1036 CAACCTAGTACTACTCTCCCCCAAGCACGCTTAGCTGCGGAGTTCTGATGGGATCCGGTGCATTA
          1 CATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTA

              *                  *                           *               
       1101 GTACTGGTATGATCGCACCCGTCAACTCTTGCGCAATCTATTCATATAAGGGCTGCCCCTTATCG
         66 GTGCTGGTATGATCGCACCCGCCAACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCG

                        *                                                    
       1166 CAGTTGCGCCTCGAATTTAAATGCAAATTCGACCAAATATCGTTTCAAATTGTTTATTTCACAAA
        131 CAGTTGCGCCTCAAATTTAAATGCAAATTCGACCAAATATCGTTTCAAATTGTTTATTTCACAAA

                         *                                                   
       1231 ACGCAAATAACGATTGAGTTACACCACGTCGAGAAAATGCAACTAAAAAAAACATTATATGAAAT
        196 ACGCAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAACTAAAAAAAACATTATATGAAAT

                                              *          
       1296 AAAATGGGGAGGGGGTGCAACACGAGGACTTCCCGGGAGGTCACC
        261 AAAAT-GGGA-GGGGTGCAACACGAGGACTTCCCAGGAGGTCACC

                   *               *     *        *                *         
       1341 CATCCTATTACTACTCTCGCCCAGGCACGATTAACTGCAGAGTTCTGATGGGATCGGGTGCATTA
          1 CATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTA

                                                   *                         
       1406 GTGCTGGTATGATCGCACCCGCCAACTTCTTGCGCAATCCATTCATATAAAGGCTGCCCCTTATC
         66 GTGCTGGTATGATCGCACCCGCCAAC-TCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATC

                                                                            
       1471 GCAGTTGCGCCTCAAATTTAAATGCAAATTCGACC-AATATCGTTTC-AATTGTTTATTTCACA
        130 GCAGTTGCGCCTCAAATTTAAATGCAAATTCGACCAAATATCGTTTCAAATTGTTTATTTCACA


Statistics
Matches: 745,  Mismatches: 49, Indels: 10
        0.93            0.06        0.01

Matches are distributed among these distances:
 302  218  0.29
 303  313  0.42
 304   20  0.03
 305  124  0.17
 306   70  0.09

ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25


Consensus pattern (303 bp):   
CATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTA
GTGCTGGTATGATCGCACCCGCCAACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCG
CAGTTGCGCCTCAAATTTAAATGCAAATTCGACCAAATATCGTTTCAAATTGTTTATTTCACAAA
ACGCAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAACTAAAAAAAACATTATATGAAAT
AAAATGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACC
Done.