Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000003.1 Kokia drynarioides strain JFW-HI SEQ_1859, 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, 773

Length: 1289
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39


Found at i:169 original size:18 final size:18

Alignment explanation


    Indices: 146--231  Score: 68
    Period size: 18  Copynumber: 4.6  Consensus size: 18

        136 TATGACTATA

                              
        146 TAAATAAAATTCTTTAAT
          1 TAAATAAAATTCTTTAAT

                                  
        164 TAAATAAAA-TCATTGTAATTT
          1 TAAATAAAATTC-TT-TAA--T

              *   *     **     
        185 TAGATACAATATGATT-AT
          1 TAAATAAAAT-TCTTTAAT

                               
        203 ATAAATAAAATTCTTTAAT
          1 -TAAATAAAATTCTTTAAT

                      
        222 TAAATAAAAT
          1 TAAATAAAAT

        232 CATAATTTTT


Statistics
Matches: 52,  Mismatches: 8, Indels: 16
        0.68            0.11        0.21

Matches are distributed among these distances:
  17    2  0.04
  18   25  0.48
  19   13  0.25
  20    1  0.02
  21    9  0.17
  22    1  0.02
  23    1  0.02

ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41


Consensus pattern (18 bp):   
TAAATAAAATTCTTTAAT

Found at i:208 original size:58 final size:58

Alignment explanation


    Indices: 118--234  Score: 225
    Period size: 58  Copynumber: 2.0  Consensus size: 58

        108 TTATTAGAGT

                                                                      
        118 TTGTAATTTTAGATACAATATGACTATATAAATAAAATTCTTTAATTAAATAAAATCA
          1 TTGTAATTTTAGATACAATATGACTATATAAATAAAATTCTTTAATTAAATAAAATCA

                                   *                                  
        176 TTGTAATTTTAGATACAATATGATTATATAAATAAAATTCTTTAATTAAATAAAATCA
          1 TTGTAATTTTAGATACAATATGACTATATAAATAAAATTCTTTAATTAAATAAAATCA

             
        234 T
          1 T

        235 AATTTTTTAC


Statistics
Matches: 58,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  58   58  1.00

ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41


Consensus pattern (58 bp):   
TTGTAATTTTAGATACAATATGACTATATAAATAAAATTCTTTAATTAAATAAAATCA
Done.