Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008082.1 Kokia drynarioides strain JFW-HI SEQ_122738, 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: 3885
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34


Found at i:2920 original size:17 final size:17

Alignment explanation


    Indices: 2879--2959  Score: 63
    Period size: 17  Copynumber: 4.8  Consensus size: 17

       2869 TCATATGAAC

                             
       2879 TAACAGTTTATACCAAA
          1 TAACAGTTTATACCAAA

             * *       *    *
       2896 TGAGAGTTTATTCCAAT
          1 TAACAGTTTATACCAAA

                    *   *  * 
       2913 TAACAGTTCATAACACA
          1 TAACAGTTTATACCAAA

                    *  * *   
       2930 TAACAGTTCATGCAAAA
          1 TAACAGTTTATACCAAA

                    *    
       2947 TAACAGTTCATAC
          1 TAACAGTTTATAC

       2960 TCCATCATAA


Statistics
Matches: 48,  Mismatches: 16, Indels: 0
        0.75            0.25        0.00

Matches are distributed among these distances:
  17   48  1.00

ACGTcount: A:0.42, C:0.19, G:0.10, T:0.30


Consensus pattern (17 bp):   
TAACAGTTTATACCAAA

Found at i:3613 original size:29 final size:29

Alignment explanation


    Indices: 3555--3622  Score: 84
    Period size: 29  Copynumber: 2.3  Consensus size: 29

       3545 ACATATATAG

                                  *      
       3555 CACGCATATATATTTTATAACCCCAAACT
          1 CACGCATATATATTTTATAACCACAAACT

                              *       *   
       3584 CACGCATATATA-TTTATCACCTACAGACT
          1 CACGCATATATATTTTATAACC-ACAAACT

               *      
       3613 CACACATATA
          1 CACGCATATA

       3623 ATATAATGTA


Statistics
Matches: 34,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  28    8  0.24
  29   26  0.76

ACGTcount: A:0.38, C:0.28, G:0.04, T:0.29


Consensus pattern (29 bp):   
CACGCATATATATTTTATAACCACAAACT
Done.