Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3409

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, 450

Length: 751
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26


Found at i:543 original size:301 final size:300

Alignment explanation


    Indices: 1--751  Score: 1243
    Period size: 301  Copynumber: 2.5  Consensus size: 300

                       *                             * *  *    **      *     
          1 ACTTCCCAGGATGTCACCCATCCTAGTACTACTCTCGCCCAGGGACACTTATCTGCGGAATTCTG
          1 ACTTCCCAGGAAGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAAGTGCGGAGTTCTG

               *                                      *  *                   
         66 ATATGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCAACTGTTGCGCAATCTATTCATAT
         66 AT-GGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCAGCTCTTGCGCAATCTATTCATAT

              *  * *  *                *        *                            
        131 AAGGGTTGCCTCTTATCGCACTTGCGCGTCGAATTTGAATACAAATTCGACAAAATATCGTTTCA
        130 AAAGGCTCCCCCTTATCGCACTTGCGCCTCGAATTTAAATACAAATTCGACAAAATATCGTTTCA

                                                                             
        196 AATTATTTATTTCACAAAACGCAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAACTAAA
        195 AATTATTTATTTCACAAAACGCAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAACTAAA

                                                     
        261 AAAAATTATATGAAATAAAATGGGAGGAGTGCAACACGTGG
        260 AAAAATTATATGAAATAAAATGGGAGGAGTGCAACACGTGG

                                                   *                      *  
        302 ACTTCCCAGGAAGTCACCCATCCTAGTACTACTCTCGCCGAAGCACGCTTAAGTGCGGAGTTTTG
          1 ACTTCCCAGGAAGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAAGTGCGGAGTTCTG

                                                                             
        367 ATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCAGCTCTTGCGCAATCTATTCATAT
         66 AT-GGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCAGCTCTTGCGCAATCTATTCATAT

                                                    *          *             
        432 AAAGGCTCCCCCTTATCGCACTTGCGCCTCGAATTTAAATGCAAATTCGACCAAATATCGTTTCA
        130 AAAGGCTCCCCCTTATCGCACTTGCGCCTCGAATTTAAATACAAATTCGACAAAATATCGTTTCA

                                                                             
        497 AATTATTTATTTCACAAAACGCAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAACTAAA
        195 AATTATTTATTTCACAAAACGCAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAACTAAA

                                                     
        562 AAAAATTATATGAAATAAAATGGGAGGAGTGCAACACGTGG
        260 AAAAATTATATGAAATAAAATGGGAGGAGTGCAACACGTGG

                                            *                                
        603 ACTTCCCAGGAAGTCACCCATCCTAGTACTACCCTCGCCCAAGCACGCTT-AGCTGCGGAGTTCT
          1 ACTTCCCAGGAAGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAAG-TGCGGAGTTCT

                              *               *   *                          
        667 GATGGACTCCGGTGCATTTGTGCTGGTATGATCGTACCGGTCAGCTCTTGCGCAATCTATTCATA
         65 GATGGA-TCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCAGCTCTTGCGCAATCTATTCATA

                                
        732 TAAAGGCTCCCCCTTATCGC
        129 TAAAGGCTCCCCCTTATCGC


Statistics
Matches: 421,  Mismatches: 27, Indels: 4
        0.93            0.06        0.01

Matches are distributed among these distances:
 300    5  0.01
 301  416  0.99

ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26


Consensus pattern (300 bp):   
ACTTCCCAGGAAGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAAGTGCGGAGTTCTG
ATGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCAGCTCTTGCGCAATCTATTCATATA
AAGGCTCCCCCTTATCGCACTTGCGCCTCGAATTTAAATACAAATTCGACAAAATATCGTTTCAA
ATTATTTATTTCACAAAACGCAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAACTAAAA
AAAATTATATGAAATAAAATGGGAGGAGTGCAACACGTGG
Done.