Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011275.1 Kokia drynarioides strain JFW-HI SEQ_126254, 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: 1670
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30


Found at i:101 original size:28 final size:27

Alignment explanation


    Indices: 56--136  Score: 83
    Period size: 28  Copynumber: 2.9  Consensus size: 27

         46 CCTTAATCAA

                       * *              
         56 TCTAGTGTTTACGGTTTAGAGTTTTAAG
          1 TCTAGTGTTTATGATTTAG-GTTTTAAG

                                    *   
         84 TCTAGTGTTTATGATTTAGGGTTTCAAG
          1 TCTAGTGTTTATGATTTA-GGTTTTAAG

             *           *            
        112 TTTAAG-GTTTATAATTTAGGTTTTA
          1 TCT-AGTGTTTATGATTTAGGTTTTA

        137 GGGTTTAATG


Statistics
Matches: 45,  Mismatches: 6, Indels: 5
        0.80            0.11        0.09

Matches are distributed among these distances:
  27    6  0.13
  28   36  0.80
  29    3  0.07

ACGTcount: A:0.23, C:0.05, G:0.22, T:0.49


Consensus pattern (27 bp):   
TCTAGTGTTTATGATTTAGGTTTTAAG

Found at i:533 original size:45 final size:45

Alignment explanation


    Indices: 402--538  Score: 143
    Period size: 45  Copynumber: 3.0  Consensus size: 45

        392 GGGAGGAATA

                  *  *      *        *  *  *        **   
        402 GAGTATCGCTGTGGCTCGTCAAACTCAGCCTGATATCCTTTCCTT
          1 GAGTATTGCGGTGGCTTGTCAAACTGAGGCTTATATCCTTGGCTT

            *                       *                      
        447 AAGTATTGCGGTGGCTCT-TCAAATTGAGG-TTGATATCCTTGGCTT
          1 GAGTATTGCGGTGGCT-TGTCAAACTGAGGCTT-ATATCCTTGGCTT

                    *                                    
        492 GAGTATTGTGGTGGCTTGTCAAACTGAGGCTTATATCCTTGGCTT
          1 GAGTATTGCGGTGGCTTGTCAAACTGAGGCTTATATCCTTGGCTT

              
        537 GA
          1 GA

        539 TGAGCTATGC


Statistics
Matches: 75,  Mismatches: 13, Indels: 8
        0.78            0.14        0.08

Matches are distributed among these distances:
  44    2  0.03
  45   71  0.95
  46    2  0.03

ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36


Consensus pattern (45 bp):   
GAGTATTGCGGTGGCTTGTCAAACTGAGGCTTATATCCTTGGCTT

Found at i:805 original size:14 final size:16

Alignment explanation


    Indices: 780--811  Score: 50
    Period size: 15  Copynumber: 2.1  Consensus size: 16

        770 AGCTGTAAAT

                            
        780 TCGGAGTGTACTC-CA
          1 TCGGAGTGTACTCGCA

                            
        795 TCGGA-TGTACTCGCA
          1 TCGGAGTGTACTCGCA

              
        810 TC
          1 TC

        812 ATTCGGTTGT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  14    7  0.44
  15    9  0.56

ACGTcount: A:0.19, C:0.28, G:0.25, T:0.28


Consensus pattern (16 bp):   
TCGGAGTGTACTCGCA
Done.