Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_435 ID=scaffold_435-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: 8093
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.29

Warning! 1048 characters in sequence are not A, C, G, or T


Found at i:6084 original size:43 final size:42

Alignment explanation


    Indices: 6017--6187  Score: 172
    Period size: 43  Copynumber: 4.0  Consensus size: 42

       6007 ACATAGTATT

                         *                             
       6017 TCGATATGTGTTTTCATGTAAGACCACGTCTGGGACGTTGGCA
          1 TCGAT-TGTGTTTACATGTAAGACCACGTCTGGGACGTTGGCA

                           *          *     *   *  *   
       6060 TCGACTTGTGTTTACGTGTAAGACCATGTCTGAGACATTTGCA
          1 TCGA-TTGTGTTTACATGTAAGACCACGTCTGGGACGTTGGCA

                            *                             
       6103 TCGTATT-TGATTT--GTGTAAGACC-CTGTCTGGGACAG-TGGCA
          1 TCG-ATTGTG-TTTACATGTAAGACCAC-GTCTGGGAC-GTTGGCA

                      *                                
       6144 TCGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCA
          1 TCGAT-TGTGTTTACATGTAAGACCACGTCTGGGACGTTGGCA

             
       6187 T
          1 T

       6188 TGTACAAGTC


Statistics
Matches: 105,  Mismatches: 12, Indels: 22
        0.76            0.09        0.16

Matches are distributed among these distances:
  40    2  0.02
  41   28  0.27
  42    5  0.05
  43   67  0.64
  44    3  0.03

ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33


Consensus pattern (42 bp):   
TCGATTGTGTTTACATGTAAGACCACGTCTGGGACGTTGGCA

Done.