Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006201.1 Kokia drynarioides strain JFW-HI SEQ_120771, 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: 4169
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36


Found at i:3393 original size:48 final size:48

Alignment explanation


    Indices: 3339--3506  Score: 264
    Period size: 48  Copynumber: 3.5  Consensus size: 48

       3329 TTATGCTTTG

                *      *                       *          * 
       3339 TTAAGTGTTTTTTTTGTTAAATGCATCTTTGTTTAATAATCTGCATCA
          1 TTAACTGTTTTGTTTGTTAAATGCATCTTTGTTTAGTAATCTGCATTA

                *                     *                     
       3387 TTAAGTGTTTTGTTTGTTAAATGCATATTTGTTTAGTAATCTGCATTA
          1 TTAACTGTTTTGTTTGTTAAATGCATCTTTGTTTAGTAATCTGCATTA

                                                    *       
       3435 TTAACTGTTTTGTTTGTTAAATGCATCTTTGTTTAGTAATATGCATTA
          1 TTAACTGTTTTGTTTGTTAAATGCATCTTTGTTTAGTAATCTGCATTA

                 *                  
       3483 TTAACAGTTTTGTTTGTTAAATGC
          1 TTAACTGTTTTGTTTGTTAAATGC

       3507 CTTGCATTAA


Statistics
Matches: 112,  Mismatches: 8, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  48  112  1.00

ACGTcount: A:0.25, C:0.08, G:0.15, T:0.52


Consensus pattern (48 bp):   
TTAACTGTTTTGTTTGTTAAATGCATCTTTGTTTAGTAATCTGCATTA

Found at i:4044 original size:79 final size:79

Alignment explanation


    Indices: 3940--4104  Score: 242
    Period size: 79  Copynumber: 2.1  Consensus size: 79

       3930 TTCATTAAGG

                    *            *       **                          **   *  
       3940 AGAAA-TATCATGCCTTTTCAGCTACATCGGATCCTAATGAAGAGACACGACTCATTGGCTTTCC
          1 AGAAATTACCATGCCTTTTCAACTACATCAAATCCTAATGAAGAGACACGACTCATTAACTTCCC

                          
       4004 TACAAGAGTTAAAA
         66 TACAAGAGTTAAAA

            *                  *                                             
       4018 TGAAATTACCATGCCTTTTTAACTACATCAAATCCTAATGAAGAGACACGACTCATTAACTTCCC
          1 AGAAATTACCATGCCTTTTCAACTACATCAAATCCTAATGAAGAGACACGACTCATTAACTTCCC

                          
       4083 TACAAGAGTTAAAA
         66 TACAAGAGTTAAAA

                    
       4097 AGAAATTA
          1 AGAAATTA

       4105 GTGTTTGTAT


Statistics
Matches: 76,  Mismatches: 10, Indels: 1
        0.87            0.11        0.01

Matches are distributed among these distances:
  78    4  0.05
  79   72  0.95

ACGTcount: A:0.38, C:0.21, G:0.13, T:0.27


Consensus pattern (79 bp):   
AGAAATTACCATGCCTTTTCAACTACATCAAATCCTAATGAAGAGACACGACTCATTAACTTCCC
TACAAGAGTTAAAA
Done.