Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008938.1 Kokia drynarioides strain JFW-HI SEQ_123630, 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, 1000

Length: 4534
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.30


Found at i:4355 original size:22 final size:22

Alignment explanation


    Indices: 4298--4377  Score: 106
    Period size: 23  Copynumber: 3.5  Consensus size: 22

       4288 GCTGGGGAAA

                 *                
       4298 CAGTAAGCACACACAGTGCAAT
          1 CAGTAGGCACACACAGTGCAAT

               *                   
       4320 CTAATAGGCACACACAGTGCAAT
          1 C-AGTAGGCACACACAGTGCAAT

                    *    *         
       4343 CAGTAGGCGCACATAGTGCAAAT
          1 CAGTAGGCACACACAGTGC-AAT

                        
       4366 CAGTAGGCACAC
          1 CAGTAGGCACAC

       4378 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:4384 original size:23 final size:23

Alignment explanation


    Indices: 4357--4442  Score: 129
    Period size: 23  Copynumber: 3.7  Consensus size: 23

       4347 AGGCGCACAT

                           *        
       4357 AGTGC-AAATCAGTAGGCACACGA
          1 AGTGCGAAA-CAGTAAGCACACGA

            *                      
       4380 GGTGCGAAACAGTAAGCACACGA
          1 AGTGCGAAACAGTAAGCACACGA

                                   
       4403 AGTGCGAAACAGTAAGCACACGA
          1 AGTGCGAAACAGTAAGCACACGA

             *               
       4426 AATGCGAAACAGTAAGC
          1 AGTGCGAAACAGTAAGC

       4443 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:4416 original size:46 final size:45

Alignment explanation


    Indices: 4294--4442  Score: 151
    Period size: 46  Copynumber: 3.3  Consensus size: 45

       4284 AAGTGCTGGG

                                     *   *                 
       4294 GAAACAGTAAGCACACACAGTGCAATCTAATAGGCACAC-ACAGTGC
          1 GAAACAGTAAGCACACACAGTGCAAAC-AGTAGGCACACGA-AGTGC

               *     *  *    *                       *    
       4340 -AATCAGTAGGCGCACATAGTGCAAATCAGTAGGCACACGAGGTGC
          1 GAAACAGTAAGCACACACAGTGCAAA-CAGTAGGCACACGAAGTGC

                                             *         *   
       4385 GAAACAGTAAGCACACGA-AGTGCGAAACAGTAAGCACACGAAATGC
          1 GAAACAGTAAGCACAC-ACAGTGC-AAACAGTAGGCACACGAAGTGC

                        
       4431 GAAACAGTAAGC
          1 GAAACAGTAAGC

       4443 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.