Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_579 ID=scaffold_579-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: 6498
ACGTcount: A:0.27, C:0.17, G:0.09, T:0.32

Warning! 973 characters in sequence are not A, C, G, or T


Found at i:2191 original size:50 final size:50

Alignment explanation


    Indices: 2137--2310  Score: 231
    Period size: 50  Copynumber: 3.5  Consensus size: 50

       2127 TATCCCAAAT

                     *      **      * *      * *              
       2137 ATGGTCTTATATGGGAGTTCTCATATTGGTGCCCATGCCATGTCCCAGAC
          1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC

                       *                        * *           
       2187 ATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACACTATGTCCCAGAC
          1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC

                                                              
       2237 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
          1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC

              *  *             *    
       2287 ATCGTTTTACATGGGACCTTTCAT
          1 ATGGTCTTACATGGGACCTCTCAT

       2311 AATTTCAATA


Statistics
Matches: 108,  Mismatches: 16, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  50  108  1.00

ACGTcount: A:0.21, C:0.29, G:0.22, T:0.29


Consensus pattern (50 bp):   
ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC

Found at i:6405 original size:25 final size:25

Alignment explanation


    Indices: 6377--6461  Score: 134
    Period size: 25  Copynumber: 3.4  Consensus size: 25

       6367 GTATGCTCTC

                     *               
       6377 ACGAGCTGTGAATCGGGAAGCTCAT
          1 ACGAGCTGTAAATCGGGAAGCTCAT

                    *    *           
       6402 ACGAGCTGCAAATTGGGAAGCTCAT
          1 ACGAGCTGTAAATCGGGAAGCTCAT

                           *         
       6427 ACGAGCTGTAAATCGAGAAGCTCAT
          1 ACGAGCTGTAAATCGGGAAGCTCAT

                      
       6452 ACGAGCTGTA
          1 ACGAGCTGTA

       6462 GTGTGTTCGC


Statistics
Matches: 54,  Mismatches: 6, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  25   54  1.00

ACGTcount: A:0.32, C:0.20, G:0.28, T:0.20


Consensus pattern (25 bp):   
ACGAGCTGTAAATCGGGAAGCTCAT
Done.