Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013199.1 Kokia drynarioides strain JFW-HI SEQ_128218, 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: 4909
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:828 original size:31 final size:33

Alignment explanation


    Indices: 790--862  Score: 98
    Period size: 31  Copynumber: 2.3  Consensus size: 33

        780 CAAATGATTT

                          *      *            
        790 TAAAATTATTAAATTTTTTTTTAAA-AA-AA-TA
          1 TAAAATTATTAAA-ATTTTTTAAAATAATAATTA

                                             
        821 TAAAATTATTAAAATTTTTTAAAATAATAATTA
          1 TAAAATTATTAAAATTTTTTAAAATAATAATTA

                     
        854 TAAAATTAT
          1 TAAAATTAT

        863 ATATATATAT


Statistics
Matches: 37,  Mismatches: 2, Indels: 4
        0.86            0.05        0.09

Matches are distributed among these distances:
  30    9  0.24
  31   15  0.41
  32    2  0.05
  33   11  0.30

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (33 bp):   
TAAAATTATTAAAATTTTTTAAAATAATAATTA

Found at i:856 original size:33 final size:31

Alignment explanation


    Indices: 790--877  Score: 97
    Period size: 31  Copynumber: 2.7  Consensus size: 31

        780 CAAATGATTT

                          *      *         
        790 TAAAATTATTAAATTTTTTTTTAAAAAAATA
          1 TAAAATTATTAAATATTTTTTAAAAAAAATA

                                              
        821 TAAAATTATTAAA-ATTTTTTAAAATAATAATTA
          1 TAAAATTATTAAATATTTTTTAAAA-AA-AA-TA

                                    
        854 TAAAATTATATATATATATTTTTT
          1 TAAAATTAT-TA-A-ATATTTTTT

        878 GAGATTAACA


Statistics
Matches: 48,  Mismatches: 2, Indels: 8
        0.83            0.03        0.14

Matches are distributed among these distances:
  30    9  0.19
  31   15  0.31
  32    2  0.04
  33   11  0.23
  34    2  0.04
  35    1  0.02
  36    1  0.02
  37    7  0.15

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


Consensus pattern (31 bp):   
TAAAATTATTAAATATTTTTTAAAAAAAATA

Found at i:3305 original size:14 final size:14

Alignment explanation


    Indices: 3286--3312  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

       3276 GATAATATAA

                          
       3286 TACCAAATGTTGCT
          1 TACCAAATGTTGCT

                         
       3300 TACCAAATGTTGC
          1 TACCAAATGTTGC

       3313 CGTGCGAAAA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33


Consensus pattern (14 bp):   
TACCAAATGTTGCT
Done.