Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012396.1 Kokia drynarioides strain JFW-HI SEQ_127400, 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: 1953
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32


Found at i:372 original size:28 final size:27

Alignment explanation


    Indices: 316--396  Score: 90
    Period size: 28  Copynumber: 2.9  Consensus size: 27

        306 CCTTAATCAA

                         *          *   
        316 TCTAGTGTTTACGGTTTAGAGTTTCAAG
          1 TCTAGTGTTTACGATTTAG-GTTTTAAG

                                        
        344 TCTAGTGTTTACGATTTAAGGTTTTAAG
          1 TCTAGTGTTTACGATTT-AGGTTTTAAG

             *   *     **            
        372 TTTAGGGTTTATAATTTAGGTTTTA
          1 TCTAGTGTTTACGATTTAGGTTTTA

        397 GGGTTTAATG


Statistics
Matches: 46,  Mismatches: 6, Indels: 3
        0.84            0.11        0.05

Matches are distributed among these distances:
  27    8  0.17
  28   36  0.78
  29    2  0.04

ACGTcount: A:0.23, C:0.06, G:0.22, T:0.48


Consensus pattern (27 bp):   
TCTAGTGTTTACGATTTAGGTTTTAAG

Found at i:650 original size:21 final size:21

Alignment explanation


    Indices: 624--666  Score: 68
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        614 TAGGGTCCAT

                  *      *       
        624 TTGCCCTGGAGGAGTAGAGTA
          1 TTGCCCGGGAGGAATAGAGTA

                                 
        645 TTGCCCGGGAGGAATAGAGTA
          1 TTGCCCGGGAGGAATAGAGTA

             
        666 T
          1 T

        667 CGCGGTGGCT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.26, C:0.14, G:0.37, T:0.23


Consensus pattern (21 bp):   
TTGCCCGGGAGGAATAGAGTA

Found at i:793 original size:45 final size:45

Alignment explanation


    Indices: 661--797  Score: 168
    Period size: 45  Copynumber: 3.0  Consensus size: 45

        651 GGGAGGAATA

                  *                * * **            *    
        661 GAGTATCGCGGTGGCTCGTCAAACTCATCCTGATATCCTT-CCATT
          1 GAGTATTGCGGTGGCTCGTCAAATTGAGGCTGATATCCTTGGC-TT

            * *     *                            *       
        706 CAATATTGTGGTGGCTCGTCAAATTGAGGCTGATATCATTGGCTT
          1 GAGTATTGCGGTGGCTCGTCAAATTGAGGCTGATATCCTTGGCTT

                                                         
        751 GAGTATTGCGGTGGCTCGTCAAATTGAGGCTGATATCCTTGGCTT
          1 GAGTATTGCGGTGGCTCGTCAAATTGAGGCTGATATCCTTGGCTT

              
        796 GA
          1 GA

        798 TGAGCTATGC


Statistics
Matches: 77,  Mismatches: 14, Indels: 2
        0.83            0.15        0.02

Matches are distributed among these distances:
  45   76  0.99
  46    1  0.01

ACGTcount: A:0.20, C:0.20, G:0.26, T:0.33


Consensus pattern (45 bp):   
GAGTATTGCGGTGGCTCGTCAAATTGAGGCTGATATCCTTGGCTT
Done.