Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006231.1 Kokia drynarioides strain JFW-HI SEQ_120802, 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: 27354
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35


Found at i:3349 original size:2 final size:2

Alignment explanation


    Indices: 3342--3385  Score: 88
    Period size: 2  Copynumber: 22.0  Consensus size: 2

       3332 ACCATATTTG

                                                                          
       3342 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

              
       3384 AT
          1 AT

       3386 TCTGACTTGA


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   42  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:14198 original size:20 final size:22

Alignment explanation


    Indices: 14163--14203  Score: 68
    Period size: 20  Copynumber: 2.0  Consensus size: 22

      14153 TTTCTCAACT

                                  
      14163 ATTATTGATAATTTTTATAATA
          1 ATTATTGATAATTTTTATAATA

                                 
      14185 ATTATT-AT-ATTTTTATAAT
          1 ATTATTGATAATTTTTATAAT

      14204 TTAAAATTAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  20   11  0.58
  21    2  0.11
  22    6  0.32

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


Consensus pattern (22 bp):   
ATTATTGATAATTTTTATAATA

Found at i:21749 original size:30 final size:28

Alignment explanation


    Indices: 21707--21764  Score: 80
    Period size: 30  Copynumber: 2.0  Consensus size: 28

      21697 TTTTCAGAGA

                         *              
      21707 AAAATGGAGAAAATTGAATGTTTTTTTT
          1 AAAATGGAGAAAAATGAATGTTTTTTTT

                                 *        
      21735 AAAATGGATTGAAAAATGAATTTTTTTTTT
          1 AAAATGGA--GAAAAATGAATGTTTTTTTT

      21765 TTTTATAACT


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
  28    8  0.31
  30   18  0.69

ACGTcount: A:0.40, C:0.00, G:0.16, T:0.45


Consensus pattern (28 bp):   
AAAATGGAGAAAAATGAATGTTTTTTTT

Found at i:26620 original size:26 final size:26

Alignment explanation


    Indices: 26556--26620  Score: 103
    Period size: 26  Copynumber: 2.5  Consensus size: 26

      26546 AGCATGTATT

                        *             
      26556 TAATAGATATAACTTCATTAAAAAAA
          1 TAATAGATATAATTTCATTAAAAAAA

                 *         *          
      26582 TAATAAATATAATTTTATTAAAAAAA
          1 TAATAGATATAATTTCATTAAAAAAA

                         
      26608 TAATAGATATAAT
          1 TAATAGATATAAT

      26621 ATTACACTAA


Statistics
Matches: 35,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  26   35  1.00

ACGTcount: A:0.58, C:0.03, G:0.03, T:0.35


Consensus pattern (26 bp):   
TAATAGATATAATTTCATTAAAAAAA

Done.