Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_91 ID=scaffold_91-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: 14988
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32

Warning! 254 characters in sequence are not A, C, G, or T


Found at i:1732 original size:15 final size:16

Alignment explanation


    Indices: 1714--1750  Score: 58
    Period size: 15  Copynumber: 2.4  Consensus size: 16

       1704 ATAATAAATT

                   *        
       1714 ATAAATGTAAGAA-AA
          1 ATAAATGGAAGAATAA

                            
       1729 ATAAATGGAAGAATAA
          1 ATAAATGGAAGAATAA

                  
       1745 ATAAAT
          1 ATAAAT

       1751 AAATAAATAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  15   12  0.60
  16    8  0.40

ACGTcount: A:0.65, C:0.00, G:0.14, T:0.22


Consensus pattern (16 bp):   
ATAAATGGAAGAATAA

Found at i:2887 original size:45 final size:45

Alignment explanation


    Indices: 2803--2888  Score: 109
    Period size: 45  Copynumber: 1.9  Consensus size: 45

       2793 TAGCTTATAG

                                                         
       2803 CTTCAATCTGTCCCACTGCAACTTCAAGGAAATAAGACTTGCTAT
          1 CTTCAATCTGTCCCACTGCAACTTCAAGGAAATAAGACTTGCTAT

                 *     *      *  *    *   *   *      
       2848 CTTCAGTCTGTTCCACTGTAATTTCAGGGAGATAGGACTTG
          1 CTTCAATCTGTCCCACTGCAACTTCAAGGAAATAAGACTTG

       2889 TGGCTCTAAT


Statistics
Matches: 34,  Mismatches: 7, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  45   34  1.00

ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31


Consensus pattern (45 bp):   
CTTCAATCTGTCCCACTGCAACTTCAAGGAAATAAGACTTGCTAT

Found at i:4093 original size:7 final size:7

Alignment explanation


    Indices: 4081--4113  Score: 57
    Period size: 7  Copynumber: 4.7  Consensus size: 7

       4071 TTGGCTCTCC

                   
       4081 TTTTTCT
          1 TTTTTCT

                   
       4088 TTTTTCT
          1 TTTTTCT

                *  
       4095 TTTTCCT
          1 TTTTTCT

                   
       4102 TTTTTCT
          1 TTTTTCT

                 
       4109 TTTTT
          1 TTTTT

       4114 TGACCCAAAG


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   7   24  1.00

ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85


Consensus pattern (7 bp):   
TTTTTCT

Done.