Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006987.1 Kokia drynarioides strain JFW-HI SEQ_121593, 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, 669

Length: 1116
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28


Found at i:407 original size:59 final size:58

Alignment explanation


    Indices: 343--608  Score: 254
    Period size: 59  Copynumber: 4.5  Consensus size: 58

        333 TTAGTCATTC

                                                                          
        343 GGGGGT-AAAA-GGGTAATTTT-GAGAGTTTTGAGGTTAAAAATGGAGATTTTTGGAAGTAT
          1 GGGGGTAAAAATGGG-AATTTTGGA-AGTTTTGAGGTTAAAAATGG-GATTTTTGGAAGT-T

                          *               *     *        *              
        402 GGGGGTAAAAAT-GAAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTT
          1 GGGGGTAAAAATGGGAA-TTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAG-TT

                            *           **    * *                     
        461 GGGGGTAAAAATGGGATTTTTGGAAGTTCAG-GGGTGAAAATGGGATTTTTGGAAGTT
          1 GGGGGTAAAAATGGGAATTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTT

              *  *           *              * *                        
        518 CGAGGATAAAAATGGGATTTTTGGAAGTTTTGCGATTAAAAATGGGATTTTTGGAAGTT
          1 -GGGGGTAAAAATGGGAATTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTT

                    *      *  *             
        577 CGTGGGGTGAAAATGAGATTTTTGGACAGTTT
          1 -G-GGGGTAAAAATGGGAATTTTGGA-AGTTT

        609 AGGGACCTCC


Statistics
Matches: 174,  Mismatches: 23, Indels: 18
        0.81            0.11        0.08

Matches are distributed among these distances:
  57    2  0.01
  58   47  0.27
  59   69  0.40
  60   49  0.28
  61    7  0.04

ACGTcount: A:0.31, C:0.03, G:0.33, T:0.34


Consensus pattern (58 bp):   
GGGGGTAAAAATGGGAATTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTT

Found at i:421 original size:29 final size:28

Alignment explanation


    Indices: 377--607  Score: 228
    Period size: 29  Copynumber: 7.8  Consensus size: 28

        367 GTTTTGAGGT

                                          
        377 TAAAAATGGAGATTTTTGGAAGTATGGGGG
          1 TAAAAATGG-GATTTTTGGAAGT-TGGGGG

                    **              * *  
        407 TAAAAATGAAATTTTTGGAAGTTTCGAGG
          1 TAAAAATGGGATTTTTGGAAG-TTGGGGG

                      *                   
        436 TCAAAAATGGAATTTTTGGAAGTTTGGGGG
          1 T-AAAAATGGGATTTTTGGAAG-TTGGGGG

                                    *    
        466 TAAAAATGGGATTTTTGGAAGTTCAGGGG
          1 TAAAAATGGGATTTTTGGAAGTT-GGGGG

             *                       *  *
        495 TGAAAATGGGATTTTTGGAAGTTCGAGGA
          1 TAAAAATGGGATTTTTGGAAGTT-GGGGG

                                      * **
        524 TAAAAATGGGATTTTTGGAAGTTTTGCGAT
          1 TAAAAATGGGATTTTTGGAAG--TTGGGGG

                                          
        554 TAAAAATGGGATTTTTGGAAGTTCGTGGGG
          1 TAAAAATGGGATTTTTGGAAGTT-G-GGGG

             *      *               
        584 TGAAAATGAGATTTTTGGACAGTT
          1 TAAAAATGGGATTTTTGGA-AGTT

        608 TAGGGACCTC


Statistics
Matches: 171,  Mismatches: 22, Indels: 15
        0.82            0.11        0.07

Matches are distributed among these distances:
  28    4  0.02
  29   85  0.50
  30   76  0.44
  31    6  0.04

ACGTcount: A:0.32, C:0.03, G:0.32, T:0.34


Consensus pattern (28 bp):   
TAAAAATGGGATTTTTGGAAGTTGGGGG
Done.