Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007723.1 Kokia drynarioides strain JFW-HI SEQ_122356, 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: 7149
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34


Found at i:3244 original size:24 final size:25

Alignment explanation


    Indices: 3217--3269  Score: 63
    Period size: 24  Copynumber: 2.2  Consensus size: 25

       3207 GTATTAAATT

                      *              
       3217 TTTTTTCTTTGTCT-TCTTATGAAA
          1 TTTTTTCTTTATCTATCTTATGAAA

                  *         *      * 
       3241 TTTTTTTTTTATCTATTTTATGACA
          1 TTTTTTCTTTATCTATCTTATGAAA

                
       3266 TTTT
          1 TTTT

       3270 AAAGATTATT


Statistics
Matches: 24,  Mismatches: 4, Indels: 1
        0.83            0.14        0.03

Matches are distributed among these distances:
  24   12  0.50
  25   12  0.50

ACGTcount: A:0.17, C:0.09, G:0.06, T:0.68


Consensus pattern (25 bp):   
TTTTTTCTTTATCTATCTTATGAAA

Found at i:3261 original size:25 final size:25

Alignment explanation


    Indices: 3216--3269  Score: 65
    Period size: 25  Copynumber: 2.2  Consensus size: 25

       3206 TGTATTAAAT

                       *             
       3216 TTTTTTTCTTTGTCTTCTTATGAAA
          1 TTTTTTTCTTTATCTTCTTATGAAA

                             *      * 
       3241 TTTTTTT-TTTATCTATTTTATGACA
          1 TTTTTTTCTTTATCT-TCTTATGAAA

                
       3266 TTTT
          1 TTTT

       3270 AAAGATTATT


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

Matches are distributed among these distances:
  24    6  0.24
  25   19  0.76

ACGTcount: A:0.17, C:0.09, G:0.06, T:0.69


Consensus pattern (25 bp):   
TTTTTTTCTTTATCTTCTTATGAAA

Found at i:5848 original size:31 final size:32

Alignment explanation


    Indices: 5813--5890  Score: 88
    Period size: 31  Copynumber: 2.5  Consensus size: 32

       5803 GTTACAAAAT

                                         *  
       5813 AGTCATTAAACTATTAC-AAAATTGTCATTTA
          1 AGTCATTAAACTATTACGAAAATTGTCATGTA

                      *          *  * *     
       5844 AGTCATTAAATTATT-CGAAAGTTTTTATGTA
          1 AGTCATTAAACTATTACGAAAATTGTCATGTA

                 *          
       5875 AGTCACTAAACTATTA
          1 AGTCATTAAACTATTA

       5891 AGTTTTTTTA


Statistics
Matches: 38,  Mismatches: 7, Indels: 3
        0.79            0.15        0.06

Matches are distributed among these distances:
  30    1  0.03
  31   37  0.97

ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40


Consensus pattern (32 bp):   
AGTCATTAAACTATTACGAAAATTGTCATGTA

Found at i:5999 original size:16 final size:16

Alignment explanation


    Indices: 5971--6009  Score: 53
    Period size: 16  Copynumber: 2.5  Consensus size: 16

       5961 TATAATTGAG

                            
       5971 ATAAAT-ATAAATTTT
          1 ATAAATAATAAATTTT

                     *      
       5986 ATAAATAATTAATTTT
          1 ATAAATAATAAATTTT

              *     
       6002 ATTAATAA
          1 ATAAATAA

       6010 GTGAGATCTG


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15    6  0.29
  16   15  0.71

ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46


Consensus pattern (16 bp):   
ATAAATAATAAATTTT
Done.