Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold575

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: 37597
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:23509 original size:65 final size:65

Alignment explanation


    Indices: 23405--23535  Score: 226
    Period size: 65  Copynumber: 2.0  Consensus size: 65

      23395 AGTCCCATGC

                                *                        *   *               
      23405 ATCAGATAATAATAACATGGCATACAGTAAATAGTAACAGTCAAATATGTATTCAGGTCAACCTT
          1 ATCAGATAATAATAACATGGAATACAGTAAATAGTAACAGTCAAACATGCATTCAGGTCAACCTT

                                   *                                         
      23470 ATCAGATAATAATAACATGGAATGCAGTAAATAGTAACAGTCAAACATGCATTCAGGTCAACCTT
          1 ATCAGATAATAATAACATGGAATACAGTAAATAGTAACAGTCAAACATGCATTCAGGTCAACCTT

             
      23535 A
          1 A

      23536 ACCCTAGGGG


Statistics
Matches: 62,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  65   62  1.00

ACGTcount: A:0.44, C:0.16, G:0.15, T:0.26


Consensus pattern (65 bp):   
ATCAGATAATAATAACATGGAATACAGTAAATAGTAACAGTCAAACATGCATTCAGGTCAACCTT

Found at i:30706 original size:43 final size:43

Alignment explanation


    Indices: 30645--30843  Score: 258
    Period size: 43  Copynumber: 4.6  Consensus size: 43

      30635 AAGTGTGCGA

                      *                    *           
      30645 GTAAGACCACATCTGGGACGTTGGCATCGATTTGTGATTACGT
          1 GTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACGT

                                                    *  
      30688 GTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTATGT
          1 GTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACGT

                          *   *                 *   * *
      30731 GTAAGACCACGTCTAGGATGTTGGCATCGATATGTGTTTATGA
          1 GTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACGT

                         *            *                * 
      30774 GTAAGACC-CTGTTTGGGACAG-TGGGATCGATATGTGATTACAT
          1 GTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATGTGATTACGT

                     *                 
      30817 GTAAGACCATGTCTGGGACGTTGGCAT
          1 GTAAGACCACGTCTGGGACGTTGGCAT

      30844 TGTACGATAT


Statistics
Matches: 134,  Mismatches: 18, Indels: 8
        0.84            0.11        0.05

Matches are distributed among these distances:
  42    2  0.01
  43  131  0.98
  44    1  0.01

ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30


Consensus pattern (43 bp):   
GTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACGT

Done.