Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001709.1 Kokia drynarioides strain JFW-HI SEQ_113403, 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, 714

Length: 1191
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36


Found at i:551 original size:28 final size:28

Alignment explanation


    Indices: 515--584  Score: 97
    Period size: 28  Copynumber: 2.5  Consensus size: 28

        505 CCCTCCTTAA

                                        
        515 TCAA-TCTAGTGTTTACGATTTAGAGTT
          1 TCAAGTCTAGTGTTTACGATTTAGAGTT

                                    *   
        542 TCAAGTCTAGTGTTTACGATTTAGGGTT
          1 TCAAGTCTAGTGTTTACGATTTAGAGTT

             *    *   *    
        570 TTAAGTTTAGGGTTT
          1 TCAAGTCTAGTGTTT

        585 TAAGTTTAGG


Statistics
Matches: 38,  Mismatches: 4, Indels: 1
        0.88            0.09        0.02

Matches are distributed among these distances:
  27    4  0.11
  28   34  0.89

ACGTcount: A:0.23, C:0.09, G:0.23, T:0.46


Consensus pattern (28 bp):   
TCAAGTCTAGTGTTTACGATTTAGAGTT

Found at i:606 original size:14 final size:14

Alignment explanation


    Indices: 561--599  Score: 71
    Period size: 14  Copynumber: 2.9  Consensus size: 14

        551 GTGTTTACGA

                          
        561 TTTAGGGTTTTAAG
          1 TTTAGGGTTTTAAG

                          
        575 TTTAGGGTTTTAAG
          1 TTTAGGGTTTTAAG

                        
        589 TTTA-GGTTTTA
          1 TTTAGGGTTTTA

        600 GGGTTTAATG


Statistics
Matches: 25,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  13    7  0.28
  14   18  0.72

ACGTcount: A:0.21, C:0.00, G:0.26, T:0.54


Consensus pattern (14 bp):   
TTTAGGGTTTTAAG

Found at i:853 original size:21 final size:21

Alignment explanation


    Indices: 827--871  Score: 72
    Period size: 21  Copynumber: 2.1  Consensus size: 21

        817 TAAGGTCCAT

                         *       
        827 TTGCCCCGGAGGAGTAGAGTA
          1 TTGCCCCGGAGGAATAGAGTA

                  *              
        848 TTGCCCGGGAGGAATAGAGTA
          1 TTGCCCCGGAGGAATAGAGTA

               
        869 TTG
          1 TTG

        872 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:994 original size:45 final size:45

Alignment explanation


    Indices: 864--1000  Score: 193
    Period size: 45  Copynumber: 3.0  Consensus size: 45

        854 GGGAGGAATA

                                     *  *           **   
        864 GAGTATTGTGGTGGCTCGTCAAACTCAGCCTGATATCCTTCCCTT
          1 GAGTATTGTGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT

                     *             *     *               
        909 GAGTATTGTAGTGGCTCGTCAAATTGAGGTTGATATCCTTGGCTT
          1 GAGTATTGTGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT

                   **                                    
        954 GAGTATTACGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
          1 GAGTATTGTGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT

              
        999 GA
          1 GA

       1001 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.