Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_592 ID=scaffold_592-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, 1000

Length: 5618
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.34

Warning! 234 characters in sequence are not A, C, G, or T


Found at i:1874 original size:17 final size:18

Alignment explanation


    Indices: 1845--1881  Score: 58
    Period size: 17  Copynumber: 2.1  Consensus size: 18

       1835 CTTTTTTATT

                              
       1845 TTATATAGATATAAATAC
          1 TTATATAGATATAAATAC

                         *    
       1863 TTATAT-GATATATATAC
          1 TTATATAGATATAAATAC

              
       1880 TT
          1 TT

       1882 TACACTTTAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  17   12  0.67
  18    6  0.33

ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46


Consensus pattern (18 bp):   
TTATATAGATATAAATAC

Found at i:3933 original size:40 final size:40

Alignment explanation


    Indices: 3812--3943  Score: 135
    Period size: 40  Copynumber: 3.4  Consensus size: 40

       3802 TTCTTCGATT

                                 *   *              *
       3812 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATT
          1 CGATGAGACACTGGGTGTCAAATTATTACTTCGGATT-ATC

                   *   *       *              *   * 
       3853 CGATGAGGCACAGGGTG-CCAA-T-TTACTTCGGTTTAGC
          1 CGATGAGACACTGGGTGTCAAATTATTACTTCGGATTATC

                                           * *      
       3890 CGATGAGACACTGGGTGTCAAATTATTACTTTGAATTATC
          1 CGATGAGACACTGGGTGTCAAATTATTACTTCGGATTATC

                   *      
       3930 CGATGAGGCACTGG
          1 CGATGAGACACTGG

       3944 ATGCCAAACT


Statistics
Matches: 72,  Mismatches: 16, Indels: 7
        0.76            0.17        0.07

Matches are distributed among these distances:
  37   16  0.22
  38   13  0.18
  39    2  0.03
  40   26  0.36
  41   15  0.21

ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30


Consensus pattern (40 bp):   
CGATGAGACACTGGGTGTCAAATTATTACTTCGGATTATC
Done.