Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002877.1 Kokia drynarioides strain JFW-HI SEQ_115288, 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, 618

Length: 1031
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34


Found at i:399 original size:23 final size:21

Alignment explanation


    Indices: 367--465  Score: 87
    Period size: 21  Copynumber: 4.6  Consensus size: 21

        357 GCTGGGGAAA

                 *                
        367 CAGTAAGCACACACAGTGCAAT
          1 CAGTAGGC-CACACAGTGCAAT

                                  
        389 CCAGTAGG-CACACAGTGCAAT
          1 -CAGTAGGCCACACAGTGCAAT

                  *               
        410 CCAGTAAG-CACACAGTGCAAT
          1 -CAGTAGGCCACACAGTGCAAT

                         *  *      
        431 CAGTAGGCGCACATAGCGCAAAT
          1 CAGTAGGC-CACACAGTGC-AAT

              *          
        454 CAATAGG-CACAC
          1 CAGTAGGCCACAC

        466 GAAGTGCGAA


Statistics
Matches: 66,  Mismatches: 7, Indels: 8
        0.81            0.09        0.10

Matches are distributed among these distances:
  20    6  0.09
  21   37  0.56
  22    8  0.12
  23   15  0.23

ACGTcount: A:0.37, C:0.28, G:0.21, T:0.13


Consensus pattern (21 bp):   
CAGTAGGCCACACAGTGCAAT

Found at i:402 original size:21 final size:21

Alignment explanation


    Indices: 376--443  Score: 111
    Period size: 21  Copynumber: 3.3  Consensus size: 21

        366 ACAGTAAGCA

                                 
        376 CACACAGTGCAATCCAGTAGG
          1 CACACAGTGCAATCCAGTAGG

                               * 
        397 CACACAGTGCAATCCAGTAAG
          1 CACACAGTGCAATCCAGTAGG

                                 
        418 CACACAGTGCAAT-CAGTAGG
          1 CACACAGTGCAATCCAGTAGG

             *    
        438 CGCACA
          1 CACACA

        444 TAGCGCAAAT


Statistics
Matches: 44,  Mismatches: 3, Indels: 1
        0.92            0.06        0.02

Matches are distributed among these distances:
  20   11  0.25
  21   33  0.75

ACGTcount: A:0.35, C:0.29, G:0.22, T:0.13


Consensus pattern (21 bp):   
CACACAGTGCAATCCAGTAGG

Found at i:490 original size:23 final size:21

Alignment explanation


    Indices: 339--494  Score: 100
    Period size: 23  Copynumber: 6.9  Consensus size: 21

        329 CGAAGTATTT

                                      
        339 AACAGTAAGCACACAAGTGCTGGGGA
          1 AACAGTAAGCACACAAGTGC-----A

                                  
        365 AACAGTAAGCACACACAGTGCA
          1 AACAGTAAGCACACA-AGTGCA

              *     *             
        387 ATCCAGTAGGCACAC-AGTGCA
          1 A-ACAGTAAGCACACAAGTGCA

              *                   
        408 ATCCAGTAAGCACAC-AGTGCA
          1 A-ACAGTAAGCACACAAGTGCA

             *     *  *       *   
        429 ATCAGTAGGCGCACATAGCGCA
          1 AACAGTAAGCACACA-AGTGCA

                 *  *               
        451 AATCAATAGGCACACGAAGTGCGA
          1 AA-CAGTAAGCACAC-AAGTGC-A

                                
        475 AACAGTAAGCACACGAAGTG
          1 AACAGTAAGCACAC-AAGTG

        495 TGAAATAGTA


Statistics
Matches: 110,  Mismatches: 13, Indels: 17
        0.79            0.09        0.12

Matches are distributed among these distances:
  20   10  0.09
  21   27  0.25
  22    8  0.07
  23   41  0.37
  24    4  0.04
  26   15  0.14
  27    5  0.05

ACGTcount: A:0.39, C:0.24, G:0.24, T:0.12


Consensus pattern (21 bp):   
AACAGTAAGCACACAAGTGCA

Done.