Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001455.1 Kokia drynarioides strain JFW-HI SEQ_112974, 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: 9059
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:85 original size:21 final size:20

Alignment explanation


    Indices: 61--153  Score: 62
    Period size: 21  Copynumber: 4.5  Consensus size: 20

         51 CCACTCCCCT

                *                
         61 CCTCTACCAGTGCACTCACCA
          1 CCTCCACCAGT-CACTCACCA

                                  
         82 CCTCCACCTA-TCTACTCACCA
          1 CCTCCACC-AGTC-ACTCACCA

              *              *   
        103 CCACCACCAGTCCACTCTCCA
          1 CCTCCACCAGT-CACTCACCA

              *    *      *  *   
        124 CCCCCACTAGTACAATCTCCA
          1 CCTCCACCAGT-CACTCACCA

                *    
        145 CCTCTACCA
          1 CCTCCACCA

        154 ATTCCATCTC


Statistics
Matches: 58,  Mismatches: 10, Indels: 8
        0.76            0.13        0.11

Matches are distributed among these distances:
  20    2  0.03
  21   54  0.93
  22    2  0.03

ACGTcount: A:0.25, C:0.52, G:0.04, T:0.19


Consensus pattern (20 bp):   
CCTCCACCAGTCACTCACCA

Found at i:1206 original size:24 final size:24

Alignment explanation


    Indices: 1170--1225  Score: 64
    Period size: 23  Copynumber: 2.4  Consensus size: 24

       1160 CAATAGTTTT

                             *        
       1170 CCCAAA-AATTATC-TTTTATCCAAA
          1 CCCAAACAATTATCATTATAT--AAA

                                    
       1194 CCCAAACAA-TATCATTATATAAA
          1 CCCAAACAATTATCATTATATAAA

                     
       1217 CCCAAACAA
          1 CCCAAACAA

       1226 AAAATTAAAA


Statistics
Matches: 29,  Mismatches: 1, Indels: 5
        0.83            0.03        0.14

Matches are distributed among these distances:
  23   12  0.41
  24   10  0.34
  25    7  0.24

ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25


Consensus pattern (24 bp):   
CCCAAACAATTATCATTATATAAA

Found at i:4229 original size:17 final size:19

Alignment explanation


    Indices: 4202--4240  Score: 55
    Period size: 18  Copynumber: 2.2  Consensus size: 19

       4192 GAAATGAGAC

                           *   
       4202 AAAAATGAGAA-TGATGTG
          1 AAAAATGAGAATTGAAGTG

                               
       4220 AAAAAT-AGAATTGAAGTG
          1 AAAAATGAGAATTGAAGTG

               
       4238 AAA
          1 AAA

       4241 TTTGTTTTTT


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  17    4  0.21
  18   15  0.79

ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21


Consensus pattern (19 bp):   
AAAAATGAGAATTGAAGTG
Done.