Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002224.1 Kokia drynarioides strain JFW-HI SEQ_114222, 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: 7552
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--134  Score: 81
    Period size: 6  Copynumber: 13.5  Consensus size: 6

         48 GACTTTAAGA

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

                 *                    *           
        104 TAAA-A TAAATT TAAATT TAAA-A TAAATT TAA
          1 TAAATT TAAATT TAAATT TAAATT TAAATT TAA

        135 TTTGGTTTAA


Statistics
Matches: 58,  Mismatches: 9, Indels: 8
        0.77            0.12        0.11

Matches are distributed among these distances:
   5   16  0.28
   6   42  0.72

ACGTcount: A:0.58, C:0.01, 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--134  Score: 150
    Period size: 17  Copynumber: 4.9  Consensus size: 17

         41 TAATTTGGAC

                 *           
         51 TTTAAGATAAATTTAAA
          1 TTTAAAATAAATTTAAA

                             
         68 TTTAAAATAAATTTAAA
          1 TTTAAAATAAATTTAAA

                             
         85 TTTAAAATAAATTTAAA
          1 TTTAAAATAAATTTAAA

            *                
        102 CTTAAAATAAATTTAAA
          1 TTTAAAATAAATTTAAA

                            
        119 TTTAAAATAAATTTAA
          1 TTTAAAATAAATTTAA

        135 TTTGGTTTAA


Statistics
Matches: 64,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  17   64  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:11

Alignment explanation


    Indices: 64--134  Score: 55
    Period size: 11  Copynumber: 6.8  Consensus size: 11

         54 AAGATAAATT

                       
         64 TAAATTTAAAA
          1 TAAATTTAAAA

                       
         75 TAAATTT----
          1 TAAATTTAAAA

                       
         82 -AAATTTAAAA
          1 TAAATTTAAAA

                       *
         92 TAAATTTAAACT
          1 TAAATTTAAA-A

                 *     *
        104 TAAA-ATAAATT
          1 TAAATTTAAA-A

                       
        115 TAAATTTAAAA
          1 TAAATTTAAAA

                     
        126 TAAATTTAA
          1 TAAATTTAA

        135 TTTGGTTTAA


Statistics
Matches: 48,  Mismatches: 5, Indels: 14
        0.72            0.07        0.21

Matches are distributed among these distances:
   6    6  0.12
  11   34  0.71
  12    8  0.17

ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39


Consensus pattern (11 bp):   
TAAATTTAAAA

Done.