Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_257 ID=scaffold_257-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: 8888
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34


Found at i:3165 original size:2 final size:2

Alignment explanation


    Indices: 3146--3193  Score: 69
    Period size: 2  Copynumber: 23.5  Consensus size: 2

       3136 TAAAATTTAG

                      *  *                                                 
       3146 TA TA TA TG TG TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                   
       3189 TA TA T
          1 TA TA T

       3194 GGTAATGTTA


Statistics
Matches: 43,  Mismatches: 2, Indels: 2
        0.91            0.04        0.04

Matches are distributed among these distances:
   2   41  0.95
   3    2  0.05

ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:5760 original size:7 final size:7

Alignment explanation


    Indices: 5749--5780  Score: 55
    Period size: 7  Copynumber: 4.6  Consensus size: 7

       5739 GCTACTACAC

                  *
       5749 TGCTCTC
          1 TGCTCTT

                   
       5756 TGCTCTT
          1 TGCTCTT

                   
       5763 TGCTCTT
          1 TGCTCTT

                   
       5770 TGCTCTT
          1 TGCTCTT

                
       5777 TGCT
          1 TGCT

       5781 GGTTCCCTCT


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   7   24  1.00

ACGTcount: A:0.00, C:0.31, G:0.16, T:0.53


Consensus pattern (7 bp):   
TGCTCTT

Found at i:6753 original size:13 final size:13

Alignment explanation


    Indices: 6732--6782  Score: 75
    Period size: 13  Copynumber: 3.9  Consensus size: 13

       6722 ACACTCAAAT

                         
       6732 TTCTCAAAAGCAC
          1 TTCTCAAAAGCAC

              *          
       6745 TTTTCAAAAGCAC
          1 TTCTCAAAAGCAC

                *     *  
       6758 TTCTGAAAAGTAC
          1 TTCTCAAAAGCAC

                        
       6771 TTCTCAAAAGCA
          1 TTCTCAAAAGCA

       6783 ATGAAAAACT


Statistics
Matches: 32,  Mismatches: 6, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  13   32  1.00

ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27


Consensus pattern (13 bp):   
TTCTCAAAAGCAC

Done.