Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2424

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, 568

Length: 948
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26


Found at i:548 original size:303 final size:300

Alignment explanation


    Indices: 1--948  Score: 1352
    Period size: 303  Copynumber: 3.2  Consensus size: 300

                              *                    *                     *   
          1 ATTAGTGCTGGTATGATCGCACCCGTCAACTCTTGCGCACCTTATTCATATAAAGGCTGTCTCTT
          1 ATTAGTGCTGGTATGATCACACCCGTCAACTCTTGCGCATC-TATTCATATAAAGGCTG-CCCTT

               *                                                             
         66 ATCTTACTTGAGCCTCGATTTTGAATACAAATTCAACAAAATATCGTTTCAAATTATTTATTTCA
         64 ATCATACTTGAGCCTCGATTTTGAATACAAATTCAACAAAATATCGTTTCAAATTATTTATTTCA

            *    *                                                           
        131 GAAAAGGAAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAACTAAAAAAAACATTATATG
        129 CAAAACGAAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAACT-AAAAAAACATTATATG

                                       *                               *     
        196 AAATAAAATGGGAGGGGTGCAACACGATGACTTCCCAGGAGGTCACCCATCCTAGTACTGCTCTC
        193 AAATAAAATGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTC

                                *                      
        261 GCCCAAGCACGCTTAACTGCTGAGTTCTGATGGGATCCGGTGC
        258 GCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGC

                               *    *                                       *
        304 ATTAGTGCTGGTATGATCATACCCATCAACTCTTGCGCAATCTATTCATATAAAGGCTGCACCTG
          1 ATTAGTGCTGGTATGATCACACCCGTCAACTCTTGCGC-ATCTATTCATATAAAGGCTGC-CCTT

                *     *       *   *   *          **         *                
        369 ATCACACTTGCGCCTCGAATTTAAATGCAAATTCAACCGAATATCGTTCCAAATTATTTATTTCA
         64 ATCATACTTGAGCCTCGATTTTGAATACAAATTCAACAAAATATCGTTTCAAATTATTTATTTCA

                                                                             
        434 CAAAACGAAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAACTAAAGAAAACATTATATG
        129 CAAAACGAAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAACTAAA-AAAACATTATATG

                                                 *                          *
        499 AAATAAAATGGGAGGGGTGCAACACGAGGACTTCCCAAGAGGTCACCCATCCTAGTACTACTCTT
        193 AAATAAAATGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTC

                                                       
        564 GCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGC
        258 GCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGC

                  *  *                                  * *                  
        607 ATTAGTTCTAGTATGAT-----CC--C-AC-C--G-G--TC-ATACTTATAAAGGCTGCCTCTTA
          1 ATTAGTGCTGGTATGATCACACCCGTCAACTCTTGCGCATCTATTCATATAAAGGCTGCC-CTTA

              *                         *  * *                               
        657 TCGTACTTGAGCCTCGATTTTGAATACACATACGACAAAATATCGTTTCAAATTATTTATTTCAC
         65 TCATACTTGAGCCTCGATTTTGAATACAAATTCAACAAAATATCGTTTCAAATTATTTATTTCAC

            *     *                                                          
        722 TAAACGCAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAACTAAAAAAACATTATATGAA
        130 AAAACGAAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAACTAAAAAAACATTATATGAA

                                                                             
        787 ATAAAATGGGCA-GGGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCG
        195 ATAAAATGGG-AGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCG

                  *                       *           
        851 CCCAAGGACGCTTAACTGCGGAGTTCTGATAGGATCCGGTGC
        259 CCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGC

                *  *      *   *                           *         
        893 ATTATTGGTGGTATTATCGCACCCGTCAACTCTTGCGCAATCTATTTATATAAAGG
          1 ATTAGTGCTGGTATGATCACACCCGTCAACTCTTGCGC-ATCTATTCATATAAAGG


Statistics
Matches: 571,  Mismatches: 53, Indels: 43
        0.86            0.08        0.06

Matches are distributed among these distances:
 286  128  0.22
 287  120  0.21
 288    2  0.00
 291    3  0.01
 292    1  0.00
 293    1  0.00
 294    3  0.01
 295    3  0.01
 296    1  0.00
 297    1  0.00
 298    3  0.01
 301    2  0.00
 302   14  0.02
 303  287  0.50
 304    2  0.00

ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26


Consensus pattern (300 bp):   
ATTAGTGCTGGTATGATCACACCCGTCAACTCTTGCGCATCTATTCATATAAAGGCTGCCCTTAT
CATACTTGAGCCTCGATTTTGAATACAAATTCAACAAAATATCGTTTCAAATTATTTATTTCACA
AAACGAAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAACTAAAAAAACATTATATGAAA
TAAAATGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCC
CAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGC

Done.