Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002440.1 Kokia drynarioides strain JFW-HI SEQ_114552, 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, 651

Length: 1085
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.29


Found at i:725 original size:60 final size:60

Alignment explanation


    Indices: 599--780  Score: 249
    Period size: 60  Copynumber: 3.0  Consensus size: 60

        589 AGAAGTTCAA

                                               *                         
        599 GGGTCAAAATATGATTTTGGAAAAGTTTGAGGGGTCAAAATGTAATTTTGGAAAAGTTTAG
          1 GGGTCAAAATATGATTTTGGAAAAGTTT-AGGGGTTAAAATGTAATTTTGGAAAAGTTTAG

            *            *                        *                   * 
        660 AGGTCAAAATATGCTTTTGGAAAAGTTTAGGGGTTAAATTGTAATTTTGGAAAAGTTTGG
          1 GGGTCAAAATATGATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTGGAAAAGTTTAG

                      * *                 * *               *     *     
        720 GGGTCAAAATGTAATTTTGGAAAAGTTT-GTGTTTAAAATGTAATTTTAGAAAAATTTAG
          1 GGGTCAAAATATGATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTGGAAAAGTTTAG

              
        779 GG
          1 GG

        781 ACCTCTTAAG


Statistics
Matches: 106,  Mismatches: 15, Indels: 2
        0.86            0.12        0.02

Matches are distributed among these distances:
  59   27  0.25
  60   53  0.50
  61   26  0.25

ACGTcount: A:0.36, C:0.03, G:0.26, T:0.36


Consensus pattern (60 bp):   
GGGTCAAAATATGATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTGGAAAAGTTTAG

Found at i:771 original size:29 final size:30

Alignment explanation


    Indices: 599--780  Score: 222
    Period size: 30  Copynumber: 6.1  Consensus size: 30

        589 AGAAGTTCAA

                      * *                  
        599 GGGTCAAAATATGATTTTGGAAAAGTTTGAG
          1 GGGTCAAAATGTAATTTTGGAAAAGTTT-AG

                                          
        630 GGGTCAAAATGTAATTTTGGAAAAGTTTAG
          1 GGGTCAAAATGTAATTTTGGAAAAGTTTAG

            *         * **                
        660 AGGTCAAAATATGCTTTTGGAAAAGTTTAG
          1 GGGTCAAAATGTAATTTTGGAAAAGTTTAG

                *   *                   * 
        690 GGGTTAAATTGTAATTTTGGAAAAGTTTGG
          1 GGGTCAAAATGTAATTTTGGAAAAGTTTAG

                                          
        720 GGGTCAAAATGTAATTTTGGAAAAGTTT-G
          1 GGGTCAAAATGTAATTTTGGAAAAGTTTAG

            * * *             *     *     
        749 TGTTTAAAATGTAATTTTAGAAAAATTTAG
          1 GGGTCAAAATGTAATTTTGGAAAAGTTTAG

              
        779 GG
          1 GG

        781 ACCTCTTAAG


Statistics
Matches: 129,  Mismatches: 21, Indels: 3
        0.84            0.14        0.02

Matches are distributed among these distances:
  29   24  0.19
  30   79  0.61
  31   26  0.20

ACGTcount: A:0.36, C:0.03, G:0.26, T:0.36


Consensus pattern (30 bp):   
GGGTCAAAATGTAATTTTGGAAAAGTTTAG
Done.