Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_409 ID=scaffold_409-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: 7383
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32


Found at i:536 original size:84 final size:84

Alignment explanation


    Indices: 391--571  Score: 247
    Period size: 84  Copynumber: 2.2  Consensus size: 84

        381 ATCGACCGAA

                       *    *     *   *     *   *                            
        391 AACAGCAGTCCATT-GGCGCCATCTTTTACTTGAGGTGTCGCCCTCCCAAGCTGTAGAAGGTTTC
          1 AACAGCAGTCCGTTCGTC-CCACCTTGTACTTCAGGCGTCGCCCTCCCAAGCTGTAGAAGGTTTC

                                
        455 CTGTAGATTCAAGGCTGGAC
         65 CTGTAGATTCAAGGCTGGAC

               *                                            *     *         *
        475 AACGGCAGTCCGTTCGTCCCACCTTGTACTTCAGGCGTCGCCCTCCCAGGCTGTCGAAGGTTTCT
          1 AACAGCAGTCCGTTCGTCCCACCTTGTACTTCAGGCGTCGCCCTCCCAAGCTGTAGAAGGTTTCC

                     *         
        540 TGTAGATTCCAGGCTGGAC
         66 TGTAGATTCAAGGCTGGAC

                         
        559 AACAGCAGTCCGT
          1 AACAGCAGTCCGT

        572 CCGCGCTAGT


Statistics
Matches: 84,  Mismatches: 12, Indels: 2
        0.86            0.12        0.02

Matches are distributed among these distances:
  84   82  0.98
  85    2  0.02

ACGTcount: A:0.19, C:0.29, G:0.25, T:0.26


Consensus pattern (84 bp):   
AACAGCAGTCCGTTCGTCCCACCTTGTACTTCAGGCGTCGCCCTCCCAAGCTGTAGAAGGTTTCC
TGTAGATTCAAGGCTGGAC

Done.