Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012730.1 Kokia drynarioides strain JFW-HI SEQ_127741, 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, 765

Length: 1276
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35


Found at i:329 original size:22 final size:22

Alignment explanation


    Indices: 272--351  Score: 106
    Period size: 23  Copynumber: 3.5  Consensus size: 22

        262 GCTGGGGAAA

                 *                
        272 CAGTAAGCACACACAGTGCAAT
          1 CAGTAGGCACACACAGTGCAAT

               *                   
        294 CTAATAGGCACACACAGTGCAAT
          1 C-AGTAGGCACACACAGTGCAAT

                    *    *         
        317 CAGTAGGCGCACATAGTGCAAAT
          1 CAGTAGGCACACACAGTGC-AAT

                        
        340 CAGTAGGCACAC
          1 CAGTAGGCACAC

        352 GAGGTGCGAA


Statistics
Matches: 50,  Mismatches: 6, Indels: 3
        0.85            0.10        0.05

Matches are distributed among these distances:
  22   16  0.32
  23   34  0.68

ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15


Consensus pattern (22 bp):   
CAGTAGGCACACACAGTGCAAT

Found at i:358 original size:23 final size:23

Alignment explanation


    Indices: 331--416  Score: 129
    Period size: 23  Copynumber: 3.7  Consensus size: 23

        321 AGGCGCACAT

                           *        
        331 AGTGC-AAATCAGTAGGCACACGA
          1 AGTGCGAAA-CAGTAAGCACACGA

            *                      
        354 GGTGCGAAACAGTAAGCACACGA
          1 AGTGCGAAACAGTAAGCACACGA

                                   
        377 AGTGCGAAACAGTAAGCACACGA
          1 AGTGCGAAACAGTAAGCACACGA

             *               
        400 AATGCGAAACAGTAAGC
          1 AGTGCGAAACAGTAAGC

        417 GTGCTAGCGT


Statistics
Matches: 58,  Mismatches: 4, Indels: 2
        0.91            0.06        0.03

Matches are distributed among these distances:
  23   55  0.95
  24    3  0.05

ACGTcount: A:0.42, C:0.21, G:0.27, T:0.10


Consensus pattern (23 bp):   
AGTGCGAAACAGTAAGCACACGA

Found at i:390 original size:46 final size:45

Alignment explanation


    Indices: 268--416  Score: 151
    Period size: 46  Copynumber: 3.3  Consensus size: 45

        258 AAGTGCTGGG

                                     *   *                 
        268 GAAACAGTAAGCACACACAGTGCAATCTAATAGGCACAC-ACAGTGC
          1 GAAACAGTAAGCACACACAGTGCAAAC-AGTAGGCACACGA-AGTGC

               *     *  *    *                       *    
        314 -AATCAGTAGGCGCACATAGTGCAAATCAGTAGGCACACGAGGTGC
          1 GAAACAGTAAGCACACACAGTGCAAA-CAGTAGGCACACGAAGTGC

                                             *         *   
        359 GAAACAGTAAGCACACGA-AGTGCGAAACAGTAAGCACACGAAATGC
          1 GAAACAGTAAGCACAC-ACAGTGC-AAACAGTAGGCACACGAAGTGC

                        
        405 GAAACAGTAAGC
          1 GAAACAGTAAGC

        417 GTGCTAGCGT


Statistics
Matches: 85,  Mismatches: 13, Indels: 10
        0.79            0.12        0.09

Matches are distributed among these distances:
  45   34  0.40
  46   47  0.55
  47    4  0.05

ACGTcount: A:0.41, C:0.23, G:0.24, T:0.12


Consensus pattern (45 bp):   
GAAACAGTAAGCACACACAGTGCAAACAGTAGGCACACGAAGTGC
Done.