Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001366.1 Kokia drynarioides strain JFW-HI SEQ_112825, 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: 7883
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35


Found at i:2437 original size:19 final size:19

Alignment explanation


    Indices: 2413--2457  Score: 56
    Period size: 19  Copynumber: 2.4  Consensus size: 19

       2403 GTATTTCATA

                    *           
       2413 AAAAATTTTATAAATATTT-
          1 AAAAATTTAATAAAT-TTTC

                       *       
       2432 AAAAATTTAATGAATTTTC
          1 AAAAATTTAATAAATTTTC

                   
       2451 AAAAATT
          1 AAAAATT

       2458 CATAATTTTT


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  18    3  0.13
  19   20  0.87

ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42


Consensus pattern (19 bp):   
AAAAATTTAATAAATTTTC

Found at i:4501 original size:21 final size:23

Alignment explanation


    Indices: 4461--4506  Score: 69
    Period size: 21  Copynumber: 2.1  Consensus size: 23

       4451 TTTTCTCTCA

                         *         
       4461 TTTTCTCTCTTGCCAAACACCAT
          1 TTTTCTCTCTTGCAAAACACCAT

                                   
       4484 TTTTCT-TCTT-CAAAACACCAT
          1 TTTTCTCTCTTGCAAAACACCAT

              
       4505 TT
          1 TT

       4507 ATAAAAAACC


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  21   12  0.55
  22    4  0.18
  23    6  0.27

ACGTcount: A:0.24, C:0.30, G:0.02, T:0.43


Consensus pattern (23 bp):   
TTTTCTCTCTTGCAAAACACCAT

Found at i:7107 original size:24 final size:24

Alignment explanation


    Indices: 7050--7111  Score: 90
    Period size: 24  Copynumber: 2.6  Consensus size: 24

       7040 TGCATAGTAG

                  *       *         
       7050 GTATCGCTAGATCTATTCATAGAA
          1 GTATCGGTAGATCTGTTCATAGAA

                 *                  
       7074 GTATCAGTAGATCTGTTCATAGAA
          1 GTATCGGTAGATCTGTTCATAGAA

                           
       7098 GTATCGGTAG-TCTG
          1 GTATCGGTAGATCTG

       7112 GGTGCTTATA


Statistics
Matches: 34,  Mismatches: 4, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  23    4  0.12
  24   30  0.88

ACGTcount: A:0.29, C:0.15, G:0.23, T:0.34


Consensus pattern (24 bp):   
GTATCGGTAGATCTGTTCATAGAA
Done.