Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005304.1 Kokia drynarioides strain JFW-HI SEQ_119233, 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: 3100
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35


Found at i:1119 original size:29 final size:31

Alignment explanation


    Indices: 1056--1119  Score: 78
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       1046 AAATTGATTT

                                        * *
       1056 TGAACTATTCAAATGTTTTCATTTAAATTAT
          1 TGAACTATTCAAATGTTTTCATTTAAATCAC

                                      *  * 
       1087 TGAACTATTCAAAT-TTTT-ATTTAAGTCCC
          1 TGAACTATTCAAATGTTTTCATTTAAATCAC

                
       1116 TGAA
          1 TGAA

       1120 TTGTTATGTG


Statistics
Matches: 29,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
  29   11  0.38
  30    4  0.14
  31   14  0.48

ACGTcount: A:0.34, C:0.12, G:0.08, T:0.45


Consensus pattern (31 bp):   
TGAACTATTCAAATGTTTTCATTTAAATCAC

Found at i:2266 original size:28 final size:28

Alignment explanation


    Indices: 2210--2266  Score: 71
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       2200 ATCCAAAAAA

                                *   *   
       2210 TCAAATCCGAAAAACTTCGAGCCTGAAT
          1 TCAAATCCGAAAAACTTCGAACCTAAAT

                                   *     
       2238 TCAAATCCGAAAAAACTT-GAACTTAAAT
          1 TCAAATCCG-AAAAACTTCGAACCTAAAT

             
       2266 T
          1 T

       2267 AATTTAAATC


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  28   17  0.68
  29    8  0.32

ACGTcount: A:0.44, C:0.21, G:0.11, T:0.25


Consensus pattern (28 bp):   
TCAAATCCGAAAAACTTCGAACCTAAAT

Found at i:2863 original size:18 final size:18

Alignment explanation


    Indices: 2842--2887  Score: 51
    Period size: 18  Copynumber: 2.6  Consensus size: 18

       2832 AAATTAATGA

                          *   
       2842 AAATTAATAAATTGTAAT
          1 AAATTAATAAATTGCAAT

                             * 
       2860 AAATTTAA-AAATTGCATT
          1 AAA-TTAATAAATTGCAAT

                       
       2878 AAATT-ATAAA
          1 AAATTAATAAA

       2888 AACTTACAAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 5
        0.77            0.06        0.16

Matches are distributed among these distances:
  16    1  0.04
  17    5  0.21
  18   14  0.58
  19    4  0.17

ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37


Consensus pattern (18 bp):   
AAATTAATAAATTGCAAT
Done.