Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001708.1 Kokia drynarioides strain JFW-HI SEQ_113402, 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, 706

Length: 1177
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36


Found at i:585 original size:28 final size:28

Alignment explanation


    Indices: 522--575  Score: 90
    Period size: 28  Copynumber: 1.9  Consensus size: 28

        512 TAATCAATCT

                                        
        522 AGTGTTTACGATTTAGAGTTTCAAGTCC
          1 AGTGTTTACGATTTAGAGTTTCAAGTCC

                            *    *    
        550 AGTGTTTACGATTTAGGGTTTTAAGT
          1 AGTGTTTACGATTTAGAGTTTCAAGT

        576 TTAGGTTTTA


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  28   24  1.00

ACGTcount: A:0.24, C:0.09, G:0.24, T:0.43


Consensus pattern (28 bp):   
AGTGTTTACGATTTAGAGTTTCAAGTCC

Found at i:839 original size:21 final size:21

Alignment explanation


    Indices: 813--857  Score: 72
    Period size: 21  Copynumber: 2.1  Consensus size: 21

        803 TAAGGTCCAT

                         *       
        813 TTGCCCCGGAGGAGTAGAGTA
          1 TTGCCCCGGAGGAATAGAGTA

                  *              
        834 TTGCCCGGGAGGAATAGAGTA
          1 TTGCCCCGGAGGAATAGAGTA

               
        855 TTG
          1 TTG

        858 TGGTGGCTCG


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.24, C:0.16, G:0.38, T:0.22


Consensus pattern (21 bp):   
TTGCCCCGGAGGAATAGAGTA

Found at i:980 original size:45 final size:45

Alignment explanation


    Indices: 850--986  Score: 193
    Period size: 45  Copynumber: 3.0  Consensus size: 45

        840 GGGAGGAATA

                                     *  *           **   
        850 GAGTATTGTGGTGGCTCGTCAAACTCAGCCTGATATCCTTCCCTT
          1 GAGTATTGTGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT

                     *             *     *               
        895 GAGTATTGTAGTGGCTCGTCAAATTGAGGTTGATATCCTTGGCTT
          1 GAGTATTGTGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT

                   **                                    
        940 GAGTATTACGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
          1 GAGTATTGTGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT

              
        985 GA
          1 GA

        987 TGAGCTATGC


Statistics
Matches: 80,  Mismatches: 12, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  45   80  1.00

ACGTcount: A:0.20, C:0.20, G:0.27, T:0.34


Consensus pattern (45 bp):   
GAGTATTGTGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
Done.