Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005699.1 Kokia drynarioides strain JFW-HI SEQ_119909, 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: 12025
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33


Found at i:162 original size:24 final size:24

Alignment explanation


    Indices: 117--162  Score: 65
    Period size: 24  Copynumber: 1.9  Consensus size: 24

        107 TCATTAACAT

                       *    *       
        117 TGTTCGTGAACGTGTTTAATTATA
          1 TGTTCGTGAACATGTTCAATTATA

                             *    
        141 TGTTCGTGAACATGTTCGATTA
          1 TGTTCGTGAACATGTTCAATTA

        163 AGTTAAATGA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  24   19  1.00

ACGTcount: A:0.24, C:0.11, G:0.22, T:0.43


Consensus pattern (24 bp):   
TGTTCGTGAACATGTTCAATTATA

Found at i:191 original size:23 final size:23

Alignment explanation


    Indices: 147--192  Score: 58
    Period size: 23  Copynumber: 2.0  Consensus size: 23

        137 TATATGTTCG

                          *  *     
        147 TGAACATGTTCGATTAAGTTAAA
          1 TGAACATGTTCGATGAAATTAAA

                                    
        170 TGAACATGTTC-ATGAACATTAAA
          1 TGAACATGTTCGATGAA-ATTAAA

        193 CAAACGAACA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  22    4  0.20
  23   16  0.80

ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33


Consensus pattern (23 bp):   
TGAACATGTTCGATGAAATTAAA

Found at i:10570 original size:18 final size:18

Alignment explanation


    Indices: 10529--10573  Score: 56
    Period size: 20  Copynumber: 2.4  Consensus size: 18

      10519 ATTAAATAAA

                               
      10529 AATTATTAAAAATGTTGAC
          1 AATTATTAAAAATGTT-AC

                      *        
      10548 AATTATGTAATAATGTT-C
          1 AATTAT-TAAAAATGTTAC

                    
      10566 AATTATTA
          1 AATTATTA

      10574 TTTTTTTTAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 4
        0.83            0.03        0.14

Matches are distributed among these distances:
  17    2  0.08
  18    7  0.29
  19    6  0.25
  20    9  0.38

ACGTcount: A:0.44, C:0.04, G:0.09, T:0.42


Consensus pattern (18 bp):   
AATTATTAAAAATGTTAC
Done.