Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000787.1 Kokia drynarioides strain JFW-HI SEQ_111856, 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, 910

Length: 1517
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35


Found at i:155 original size:30 final size:30

Alignment explanation


    Indices: 119--217  Score: 105
    Period size: 30  Copynumber: 3.3  Consensus size: 30

        109 TAAATCTAGC

                                          
        119 TAATTAATTACCAAAATATAATATAAAAAA
          1 TAATTAATTACCAAAATATAATATAAAAAA

                      *              **** 
        149 TAATTAATTATC-AAA-ATAATAT-CCTCA
          1 TAATTAATTACCAAAATATAATATAAAAAA

                    *                       
        176 TCATATTATTTACCAAAATATAATATAAAAAA
          1 T-A-ATTAATTACCAAAATATAATATAAAAAA

                      
        208 TAATTAATTA
          1 TAATTAATTA

        218 TGAAAATAAT


Statistics
Matches: 52,  Mismatches: 12, Indels: 10
        0.70            0.16        0.14

Matches are distributed among these distances:
  27    2  0.04
  28    8  0.15
  29   11  0.21
  30   21  0.40
  31    8  0.15
  32    2  0.04

ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35


Consensus pattern (30 bp):   
TAATTAATTACCAAAATATAATATAAAAAA

Found at i:164 original size:16 final size:16

Alignment explanation


    Indices: 119--168  Score: 52
    Period size: 16  Copynumber: 3.2  Consensus size: 16

        109 TAAATCTAGC

                      *     
        119 TAATTAATTACCAAAA
          1 TAATTAATTATCAAAA

                        *    
        135 T-A-TAA-TATAAAAAA
          1 TAATTAATTAT-CAAAA

                            
        149 TAATTAATTATCAAAA
          1 TAATTAATTATCAAAA

                
        165 TAAT
          1 TAAT

        169 ATCCTCATCA


Statistics
Matches: 27,  Mismatches: 3, Indels: 8
        0.71            0.08        0.21

Matches are distributed among these distances:
  13    2  0.07
  14    8  0.30
  15    2  0.07
  16   12  0.44
  17    3  0.11

ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34


Consensus pattern (16 bp):   
TAATTAATTATCAAAA

Found at i:189 original size:59 final size:59

Alignment explanation


    Indices: 121--249  Score: 231
    Period size: 59  Copynumber: 2.2  Consensus size: 59

        111 AATCTAGCTA

                *                                               *      
        121 ATTAATTACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCTCATCAT
          1 ATTATTTACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCAT

                                                   *                   
        180 ATTATTTACCAAAATATAATATAAAAAATAATTAATTATGAAAATAATATCCCCATCAT
          1 ATTATTTACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCAT

                       
        239 ATTATTTACCA
          1 ATTATTTACCA

        250 TTTTGTGTCA


Statistics
Matches: 67,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  59   67  1.00

ACGTcount: A:0.52, C:0.12, G:0.01, T:0.35


Consensus pattern (59 bp):   
ATTATTTACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCAT
Done.