Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013076.1 Kokia drynarioides strain JFW-HI SEQ_128094, 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: 4096
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30


Found at i:614 original size:21 final size:21

Alignment explanation


    Indices: 588--630  Score: 68
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        578 AGCCATCTGG

                    *            
        588 ATACTCTATTCCTCCCGGGCA
          1 ATACTCTACTCCTCCCGGGCA

                           *     
        609 ATACTCTACTCCTCCGGGGCA
          1 ATACTCTACTCCTCCCGGGCA

             
        630 A
          1 A

        631 ATGGACCCTA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.21, C:0.37, G:0.16, T:0.26


Consensus pattern (21 bp):   
ATACTCTACTCCTCCCGGGCA

Found at i:3968 original size:4 final size:4

Alignment explanation


    Indices: 3959--4024  Score: 80
    Period size: 4  Copynumber: 16.2  Consensus size: 4

       3949 AAATAAACGG

                                                 *      *                
       3959 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA GGAA GAAG GAAA GGAAA GAAA
          1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GAAA -GAAA GAAA

                    *            
       4009 GAAA -AAG GAAA GAAA G
          1 GAAA GAAA GAAA GAAA G

       4025 GTAATGTGTT


Statistics
Matches: 53,  Mismatches: 6, Indels: 6
        0.82            0.09        0.09

Matches are distributed among these distances:
   3    2  0.04
   4   43  0.81
   5    8  0.15

ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00


Consensus pattern (4 bp):   
GAAA

Found at i:3988 original size:25 final size:25

Alignment explanation


    Indices: 3959--4024  Score: 84
    Period size: 25  Copynumber: 2.7  Consensus size: 25

       3949 AAATAAACGG

                                     
       3959 GAAAGAAAGAAAGGAAAGAAAGAAA
          1 GAAAGAAAGAAAGGAAAGAAAGAAA

                 *                    
       3984 GAAAGGAAG-AAGGAAAGGAAAGAAA
          1 GAAAGAAAGAAAGGAAA-GAAAGAAA

                   *          
       4009 GAAA-AAGGAAA-GAAAG
          1 GAAAGAAAGAAAGGAAAG

       4025 GTAATGTGTT


Statistics
Matches: 36,  Mismatches: 3, Indels: 6
        0.80            0.07        0.13

Matches are distributed among these distances:
  23    1  0.03
  24   13  0.36
  25   22  0.61

ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00


Consensus pattern (25 bp):   
GAAAGAAAGAAAGGAAAGAAAGAAA

Found at i:4025 original size:29 final size:31

Alignment explanation


    Indices: 3958--4025  Score: 101
    Period size: 29  Copynumber: 2.4  Consensus size: 31

       3948 CAAATAAACG

                                           
       3958 GGAAAGAAA-GAAAGGAAAGAAAGAAAGAAA
          1 GGAAAGAAAGGAAAGGAAAGAAAGAAAGAAA

                                           
       3988 GG-AAG-AAGGAAAGGAAAGAAAG-AA-AAA
          1 GGAAAGAAAGGAAAGGAAAGAAAGAAAGAAA

                       
       4015 GGAAAGAAAGG
          1 GGAAAGAAAGG

       4026 TAATGTGTTT


Statistics
Matches: 35,  Mismatches: 0, Indels: 7
        0.83            0.00        0.17

Matches are distributed among these distances:
  27    5  0.14
  28    7  0.20
  29   21  0.60
  30    2  0.06

ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00


Consensus pattern (31 bp):   
GGAAAGAAAGGAAAGGAAAGAAAGAAAGAAA
Done.