Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010734.1 Kokia drynarioides strain JFW-HI SEQ_125687, 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: 3578
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29


Found at i:2344 original size:29 final size:28

Alignment explanation


    Indices: 2298--2640  Score: 237
    Period size: 28  Copynumber: 11.9  Consensus size: 28

       2288 AGCAACTCAA

                                        
       2298 GGGTAAAATGGTAATTTTT-GAAGTTCG
          1 GGGTAAAATGGTAATTTTTGGAAGTTCG

                                          
       2325 GGGATAAAATGGTAATTTTTGGAAGATTCG
          1 GGG-TAAAATGGTAATTTTTGGAAG-TTCG

                          *                
       2355 GGGTTAAAAATGG-GATTTTTGGAAGTTCGG
          1 GGG-T-AAAATGGTAATTTTTGGAAGTTC-G

                  *                      
       2385 GGGTAAGATGGTAA-TTTTGGAAGCTTCG
          1 GGGTAAAATGGTAATTTTTGGAAG-TTCG

                          *                
       2413 GGGTCAAAAATGG-GATTTTTGGGAA-TTCG
          1 GGGT--AAAATGGTAATTTTT-GGAAGTTCG

                     **                   
       2442 GGAGTAAAACAGTAA-TTTTGGAAAGTTCG
          1 GG-GTAAAATGGTAATTTTTGG-AAGTTCG

                         *                 
       2471 GGGTCAAAATGG-GATTTTTGGGAA-TTCGG
          1 GGGT-AAAATGGTAATTTTT-GGAAGTTC-G

                    *                    
       2500 GGGTAAAACGGTAA-TTTTGGAAGGTTCG
          1 GGGTAAAATGGTAATTTTTGGAA-GTTCG

            *             *                
       2528 AGGTCAAAAATGG-GATTTTTGGGAA-TTCG
          1 GGGT--AAAATGGTAATTTTT-GGAAGTTCG

                                           
       2557 AGGGTAAAACT-GTAATTTTTGGAAGGTTCG
          1 -GGGTAAAA-TGGTAATTTTTGGAA-GTTCG

            **            *                 
       2587 AAGTCAAAAATGG-GATTTTTGGGAA-TTCGG
          1 GGGT--AAAATGGTAATTTTT-GGAAGTTC-G

                    * *             
       2617 GGGTAAAACGATAATTTTTGGAAG
          1 GGGTAAAATGGTAATTTTTGGAAG

       2641 GTTCAGGGAC


Statistics
Matches: 251,  Mismatches: 27, Indels: 74
        0.71            0.08        0.21

Matches are distributed among these distances:
  27    9  0.04
  28   85  0.34
  29   69  0.27
  30   64  0.25
  31   24  0.10

ACGTcount: A:0.30, C:0.06, G:0.32, T:0.31


Consensus pattern (28 bp):   
GGGTAAAATGGTAATTTTTGGAAGTTCG

Found at i:2641 original size:59 final size:58

Alignment explanation


    Indices: 2321--2644  Score: 454
    Period size: 58  Copynumber: 5.6  Consensus size: 58

       2311 ATTTTTGAAG

                   *     *               *        *                    
       2321 TTCGGGGATAAAATGGTAATTTTTGGAAGATTCGGGGTTAAAAATGGGATTTTT-GGAA
          1 TTCGGGGGTAAAACGGTAA-TTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGGAA

                        * *              *                             
       2379 GTTCGGGGGTAAGATGGTAATTTTGGAAGCTTCGGGGTCAAAAATGGGATTTTTGGGAA
          1 -TTCGGGGGTAAAACGGTAATTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGGAA

                  *       *            *                              
       2438 TTCGGGAGTAAAACAGTAATTTTGGAAAGTTCGGGGTC-AAAATGGGATTTTTGGGAA
          1 TTCGGGGGTAAAACGGTAATTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGGAA

                                             *                        
       2495 TTCGGGGGTAAAACGGTAATTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGGAA
          1 TTCGGGGGTAAAACGGTAATTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGGAA

                *         *                   **                       
       2553 TTCGAGGGTAAAACTGTAATTTTTGGAAGGTTCGAAGTCAAAAATGGGATTTTTGGGAA
          1 TTCGGGGGTAAAACGGTAA-TTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGGAA

                           *                 
       2612 TTCGGGGGTAAAACGATAATTTTTGGAAGGTTC
          1 TTCGGGGGTAAAACGGTAA-TTTTGGAAGGTTC

       2645 AGGGACCTCC


Statistics
Matches: 242,  Mismatches: 20, Indels: 6
        0.90            0.07        0.02

Matches are distributed among these distances:
  57   53  0.22
  58  100  0.41
  59   89  0.37

ACGTcount: A:0.30, C:0.06, G:0.32, T:0.31


Consensus pattern (58 bp):   
TTCGGGGGTAAAACGGTAATTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGGAA
Done.