Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008504.1 Kokia drynarioides strain JFW-HI SEQ_123180, 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: 7786
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:2956 original size:31 final size:31

Alignment explanation


    Indices: 2850--2943  Score: 129
    Period size: 30  Copynumber: 3.1  Consensus size: 31

       2840 AATAGTCCAA

                                        *  
       2850 TGACTTAAATG-AAACTTTTGAATAGTTCAG
          1 TGACTTAAATGAAAACTTTTGAATAGTTTAG

                                *    *     
       2880 TGACTTAAATGAAAACTTTTAAATAATTTAG
          1 TGACTTAAATGAAAACTTTTGAATAGTTTAG

             *             *               
       2911 TTACTTAAAT-AAAATTTTTGAATAGTTTAG
          1 TGACTTAAATGAAAACTTTTGAATAGTTTAG

               
       2941 TGA
          1 TGA

       2944 TCAAAATGAA


Statistics
Matches: 55,  Mismatches: 8, Indels: 2
        0.85            0.12        0.03

Matches are distributed among these distances:
  30   30  0.55
  31   25  0.45

ACGTcount: A:0.40, C:0.06, G:0.13, T:0.40


Consensus pattern (31 bp):   
TGACTTAAATGAAAACTTTTGAATAGTTTAG

Found at i:7227 original size:23 final size:22

Alignment explanation


    Indices: 7145--7248  Score: 102
    Period size: 23  Copynumber: 4.5  Consensus size: 22

       7135 CGAAGTACTT

                     *                
       7145 AACAGTAAGTACACAAGTGCTGGGGA
          1 AACAGTAAGCACACAAGTGC----GA

                *                  
       7171 AACATTAAGCACACACAGTGC-A
          1 AACAGTAAGCACACA-AGTGCGA

             *     *               
       7193 ATCAGTAGGCACACAAGGTGCGA
          1 AACAGTAAGCACACAA-GTGCGA

                                   
       7216 AACAGTAAGCACACGAAGTGCGA
          1 AACAGTAAGCACAC-AAGTGCGA

                      
       7239 AACAGTAAGC
          1 AACAGTAAGC

       7249 GCGCTAGCGT


Statistics
Matches: 67,  Mismatches: 7, Indels: 11
        0.79            0.08        0.13

Matches are distributed among these distances:
  21    1  0.01
  22   17  0.25
  23   29  0.43
  24    2  0.03
  26   13  0.19
  27    5  0.07

ACGTcount: A:0.41, C:0.21, G:0.25, T:0.12


Consensus pattern (22 bp):   
AACAGTAAGCACACAAGTGCGA
Done.