Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002862.1 Kokia drynarioides strain JFW-HI SEQ_115265, 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, 894

Length: 1490
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37


Found at i:576 original size:23 final size:23

Alignment explanation


    Indices: 520--602  Score: 87
    Period size: 23  Copynumber: 3.7  Consensus size: 23

        510 TTTCTTTTTA

                *            *     
        520 TACAAAAAATCTTCACTCTT-AT
          1 TACAGAAAATCTTCACTGTTCAT

             * * *       * *       
        542 TGCTGGAAATCTTTATTGTTCAT
          1 TACAGAAAATCTTCACTGTTCAT

              *                    
        565 TATAGAAAATCTTCACTGTTCAT
          1 TACAGAAAATCTTCACTGTTCAT

                           
        588 TACAGAAAATCTTCA
          1 TACAGAAAATCTTCA

        603 ACATTTGTCT


Statistics
Matches: 46,  Mismatches: 14, Indels: 1
        0.75            0.23        0.02

Matches are distributed among these distances:
  22   13  0.28
  23   33  0.72

ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39


Consensus pattern (23 bp):   
TACAGAAAATCTTCACTGTTCAT

Found at i:1022 original size:28 final size:26

Alignment explanation


    Indices: 990--1042  Score: 88
    Period size: 28  Copynumber: 2.0  Consensus size: 26

        980 CAGGTTGAAG

                                        
        990 GATGACGTGGCAAAAATAAATTAAATAA
          1 GATGACGTGGC-AAAAT-AATTAAATAA

                                     
       1018 GATGACGTGGCAAAATAATTAAATA
          1 GATGACGTGGCAAAATAATTAAATA

       1043 CAATAAACCC


Statistics
Matches: 25,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  26    9  0.36
  27    5  0.20
  28   11  0.44

ACGTcount: A:0.51, C:0.08, G:0.19, T:0.23


Consensus pattern (26 bp):   
GATGACGTGGCAAAATAATTAAATAA

Found at i:1239 original size:30 final size:30

Alignment explanation


    Indices: 1198--1267  Score: 104
    Period size: 30  Copynumber: 2.3  Consensus size: 30

       1188 ATTTTTCTAT

                *              *     *    
       1198 ATCCTTAATCCCTTATTCCTAAATCGTGAA
          1 ATCCCTAATCCCTTATTCCCAAATCATGAA

                                          
       1228 ATCCCTAATCCCTTATTCCCAAATCATGAA
          1 ATCCCTAATCCCTTATTCCCAAATCATGAA

                      
       1258 ATCCCATAAT
          1 ATCCC-TAAT

       1268 TTATGGAAAT


Statistics
Matches: 36,  Mismatches: 3, Indels: 1
        0.90            0.08        0.03

Matches are distributed among these distances:
  30   32  0.89
  31    4  0.11

ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33


Consensus pattern (30 bp):   
ATCCCTAATCCCTTATTCCCAAATCATGAA
Done.