Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002225.1 Kokia drynarioides strain JFW-HI SEQ_114223, whole genome shotgun sequence

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: 7535
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30


Found at i:69 original size:6 final size:6

Alignment explanation


    Indices: 58--117  Score: 63
    Period size: 6  Copynumber: 10.5  Consensus size: 6

         48 GACTTTAAGA

                               *            *       *              
         58 TAAATT TAAATT TAAA-A TAAATT TAAACT TAAA-A TAAATT TAAATT
          1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT

                 *           
        104 TAAA-A TAAATT TAA
          1 TAAATT TAAATT TAA

        118 TTTGGTTTAA


Statistics
Matches: 44,  Mismatches: 7, Indels: 6
        0.77            0.12        0.11

Matches are distributed among these distances:
   5   12  0.27
   6   32  0.73

ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40


Consensus pattern (6 bp):   
TAAATT

Found at i:77 original size:17 final size:17

Alignment explanation


    Indices: 51--117  Score: 116
    Period size: 17  Copynumber: 3.9  Consensus size: 17

         41 TAATTTGGAC

                 *           
         51 TTTAAGATAAATTTAAA
          1 TTTAAAATAAATTTAAA

                             
         68 TTTAAAATAAATTTAAA
          1 TTTAAAATAAATTTAAA

            *                
         85 CTTAAAATAAATTTAAA
          1 TTTAAAATAAATTTAAA

                            
        102 TTTAAAATAAATTTAA
          1 TTTAAAATAAATTTAA

        118 TTTGGTTTAA


Statistics
Matches: 47,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   47  1.00

ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40


Consensus pattern (17 bp):   
TTTAAAATAAATTTAAA

Found at i:78 original size:11 final size:12

Alignment explanation


    Indices: 64--117  Score: 51
    Period size: 11  Copynumber: 4.8  Consensus size: 12

         54 AAGATAAATT

                        
         64 TAAATTTAAA-A
          1 TAAATTTAAACA

                       *
         75 TAAATTTAAACT
          1 TAAATTTAAACA

                 *    **
         87 TAAA-ATAAATT
          1 TAAATTTAAACA

                        
         98 TAAATTTAAA-A
          1 TAAATTTAAACA

                     
        109 TAAATTTAA
          1 TAAATTTAA

        118 TTTGGTTTAA


Statistics
Matches: 36,  Mismatches: 5, Indels: 4
        0.80            0.11        0.09

Matches are distributed among these distances:
  11   28  0.78
  12    8  0.22

ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39


Consensus pattern (12 bp):   
TAAATTTAAACA

Done.