Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010235.1 Kokia drynarioides strain JFW-HI SEQ_125066, 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, 631

Length: 1053
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36


Found at i:45 original size:23 final size:23

Alignment explanation


    Indices: 16--178  Score: 146
    Period size: 23  Copynumber: 7.4  Consensus size: 23

          6 AGTGCTGGGC

                                   
         16 AACAGAGAGCACACAAAGTGCTA
          1 AACAGAGAGCACACAAAGTGCTA

                     *             
         39 AACAGAGAGTACACAAA--G-T-
          1 AACAGAGAGCACACAAAGTGCTA

                 *         *       
         58 -AC--TGAGCACACACAGTGCTA
          1 AACAGAGAGCACACAAAGTGCTA

             *                      
         78 ATCAGAGGAGCACAC--AGTGCTA
          1 AACAGA-GAGCACACAAAGTGCTA

             *            *        
        100 ATCAGAGAGCACACGAAGTGCTA
          1 AACAGAGAGCACACAAAGTGCTA

             *            *     *  
        123 ATCAGAGAGCACACGAAGTGTTA
          1 AACAGAGAGCACACAAAGTGCTA

                       *   *       
        146 AACAGAGAGCATACACAGTGCTA
          1 AACAGAGAGCACACAAAGTGCTA

             *        
        169 ATCAGAGAGC
          1 AACAGAGAGC

        179 GCGCTAGTGT


Statistics
Matches: 117,  Mismatches: 13, Indels: 20
        0.78            0.09        0.13

Matches are distributed among these distances:
  16    9  0.08
  18    3  0.03
  19    1  0.01
  20    1  0.01
  21   10  0.09
  22   13  0.11
  23   72  0.62
  24    8  0.07

ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13


Consensus pattern (23 bp):   
AACAGAGAGCACACAAAGTGCTA

Found at i:166 original size:46 final size:44

Alignment explanation


    Indices: 16--178  Score: 167
    Period size: 46  Copynumber: 3.8  Consensus size: 44

          6 AGTGCTGGGC

                           *        *       *     **    
         16 AACAGAGAGCACACAAAGTGCTAAACAGAGAGTACACAAAG-T-
          1 AACAGAGAGCACACACAGTGCTAATCAGAGAGCACACAGTGCTA

                 *                                       
         58 -AC--TGAGCACACACAGTGCTAATCAGAGGAGCACACAGTGCTA
          1 AACAGAGAGCACACACAGTGCTAATCAGA-GAGCACACAGTGCTA

             *                                          *  
        100 ATCAGAGAGCACACGA-AGTGCTAATCAGAGAGCACACGAAGTGTTA
          1 AACAGAGAGCACAC-ACAGTGCTAATCAGAGAGCACAC--AGTGCTA

                       *                     
        146 AACAGAGAGCATACACAGTGCTAATCAGAGAGC
          1 AACAGAGAGCACACACAGTGCTAATCAGAGAGC

        179 GCGCTAGTGT


Statistics
Matches: 100,  Mismatches: 11, Indels: 16
        0.79            0.09        0.13

Matches are distributed among these distances:
  39   21  0.21
  40    9  0.09
  41    3  0.03
  43    1  0.01
  44    8  0.08
  45   22  0.22
  46   36  0.36

ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13


Consensus pattern (44 bp):   
AACAGAGAGCACACACAGTGCTAATCAGAGAGCACACAGTGCTA

Found at i:279 original size:24 final size:26

Alignment explanation


    Indices: 241--288  Score: 66
    Period size: 24  Copynumber: 1.9  Consensus size: 26

        231 TCTACATGGG

                                       
        241 CATAATCTCTCATAT-TCATCATTTCT
          1 CATAATCTCTCATATATCA-CATTTCT

                                    
        267 CATAAT-T-TCATATATCACATTT
          1 CATAATCTCTCATATATCACATTT

        289 ACATTTCTCT


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  24   11  0.52
  25    4  0.19
  26    6  0.29

ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46


Consensus pattern (26 bp):   
CATAATCTCTCATATATCACATTTCT
Done.