Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2598

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: 7231
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32


Found at i:1892 original size:46 final size:45

Alignment explanation


    Indices: 1733--1891  Score: 191
    Period size: 46  Copynumber: 3.5  Consensus size: 45

       1723 GGGTTGTGCG

                              *     *                    
       1733 CGGAC-CAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACT
          1 CGGACTCAACTCAACGAGTTCGGCATTCGCATCCATAAGTGAACT

                                      *        *    *  *     
       1777 CGGACTCAACTCAACGAGTTCGG-ATGC-CTAGTTACATTCA-CGAACT
          1 CGGACTCAACTCAACGAGTTCGGCATTCGC-A--TCCA-TAAGTGAACT

                                                          
       1823 CGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACT
          1 CGGACTCAACTCAACGAGTTCGG-CATTCGCATCCATAAGTGAACT

                                   
       1869 CGGACTCAACTCAACGAGTTCGG
          1 CGGACTCAACTCAACGAGTTCGG

       1892 ATGCTCAACC


Statistics
Matches: 96,  Mismatches: 10, Indels: 16
        0.79            0.08        0.13

Matches are distributed among these distances:
  43    1  0.01
  44    8  0.08
  45   18  0.19
  46   62  0.65
  47    2  0.02
  48    4  0.04
  49    1  0.01

ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21


Consensus pattern (45 bp):   
CGGACTCAACTCAACGAGTTCGGCATTCGCATCCATAAGTGAACT

Found at i:2348 original size:30 final size:30

Alignment explanation


    Indices: 2314--2373  Score: 93
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       2304 ATTTAATACG

                                          
       2314 AACTTTGGAAAAATTACACTTTTGCCCCTA
          1 AACTTTGGAAAAATTACACTTTTGCCCCTA

                  * * *                   
       2344 AACTTTTGCATAATTACACTTTTGCCCCTA
          1 AACTTTGGAAAAATTACACTTTTGCCCCTA

       2374 GGCTCGGGAA


Statistics
Matches: 27,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  30   27  1.00

ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37


Consensus pattern (30 bp):   
AACTTTGGAAAAATTACACTTTTGCCCCTA
Done.