Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003454.1 Kokia drynarioides strain JFW-HI SEQ_116245, 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: 2237
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.29


Found at i:1854 original size:29 final size:29

Alignment explanation


    Indices: 1821--1993  Score: 122
    Period size: 30  Copynumber: 5.8  Consensus size: 29

       1811 CATTAAAATC

                      *            *     
       1821 GGGTCAAATTTAATTTTTGGAAACTTC-A
          1 GGGTCAAATTAAATTTTTGGAAAATTCGA

                      *   *               
       1849 GGGGTCAAATCAAAATTTTGGAAAATTCGA
          1 -GGGTCAAATTAAATTTTTGGAAAATTCGA

                       *                  *
       1879 GGGTCAAATTGGAATTTTTGGAAAAGTT-GG
          1 GGGTCAAATT-AAATTTTTGGAAAA-TTCGA

                 *     *                   
       1909 GGGTCGAATTGGAATTTTTGGAAAATAT--A
          1 GGGTCAAATT-AAATTTTTGGAAAAT-TCGA

                                  *      ** 
       1938 GGGATCAAATTCCAAATTTTTGAAAAATTTAA
          1 GGG-TCAAATT--AAATTTTTGGAAAATTCGA

                   *                 
       1970 GGGTCAATTTCAAATTTTT-GAAAA
          1 GGGTCAAATT-AAATTTTTGGAAAA

       1994 GTTTGGAGGT


Statistics
Matches: 120,  Mismatches: 16, Indels: 16
        0.79            0.11        0.11

Matches are distributed among these distances:
  29   40  0.33
  30   55  0.46
  31   21  0.17
  32    4  0.03

ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34


Consensus pattern (29 bp):   
GGGTCAAATTAAATTTTTGGAAAATTCGA

Found at i:1959 original size:31 final size:30

Alignment explanation


    Indices: 1921--1993  Score: 87
    Period size: 31  Copynumber: 2.4  Consensus size: 30

       1911 GTCGAATTGG

                                            
       1921 AATTTTTGGAAAATAT-AGGGATCAAATTCCA
          1 AATTTTTGGAAAATATAAGGG-TC-AATTCCA

                    *     *            *  
       1952 AATTTTTGAAAAATTTAAGGGTCAATTTCA
          1 AATTTTTGGAAAATATAAGGGTCAATTCCA

                         
       1982 AATTTTT-GAAAA
          1 AATTTTTGGAAAA

       1994 GTTTGGAGGT


Statistics
Matches: 37,  Mismatches: 4, Indels: 4
        0.82            0.09        0.09

Matches are distributed among these distances:
  29    4  0.11
  30   13  0.35
  31   16  0.43
  32    4  0.11

ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37


Consensus pattern (30 bp):   
AATTTTTGGAAAATATAAGGGTCAATTCCA

Done.