Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011064.1 Kokia drynarioides strain JFW-HI SEQ_126035, 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: 3840
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.29


Found at i:2616 original size:14 final size:14

Alignment explanation


    Indices: 2578--2616  Score: 53
    Period size: 14  Copynumber: 2.8  Consensus size: 14

       2568 GCTTTCCAAC

                 *        
       2578 TTTATGATTTAGGG
          1 TTTATAATTTAGGG

                           
       2592 TTT-TAAGTTTAGGG
          1 TTTATAA-TTTAGGG

                       
       2606 TTTATAATTTA
          1 TTTATAATTTA

       2617 TGTTTTATGG


Statistics
Matches: 22,  Mismatches: 1, Indels: 4
        0.81            0.04        0.15

Matches are distributed among these distances:
  13    2  0.09
  14   17  0.77
  15    3  0.14

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


Consensus pattern (14 bp):   
TTTATAATTTAGGG

Found at i:2877 original size:21 final size:21

Alignment explanation


    Indices: 2851--2893  Score: 68
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2841 TAGGGTCCAT

                  *      *       
       2851 TTGCCCCGGAGGAGTAGAGTA
          1 TTGCCCAGGAGGAATAGAGTA

                                 
       2872 TTGCCCAGGAGGAATAGAGTA
          1 TTGCCCAGGAGGAATAGAGTA

             
       2893 T
          1 T

       2894 CGCGATGACT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.28, C:0.16, G:0.35, T:0.21


Consensus pattern (21 bp):   
TTGCCCAGGAGGAATAGAGTA

Found at i:3018 original size:45 final size:45

Alignment explanation


    Indices: 2888--3024  Score: 168
    Period size: 45  Copynumber: 3.0  Consensus size: 45

       2878 AGGAGGAATA

                  *   *  *               *           **   
       2888 GAGTATCGCGATGACTCGTCAAACT-CAGCCTGATATCCTTCCCTT
          1 GAGTATTGCGGTGGCTCGTCAAACTGC-GGCTGATATCCTTGGCTT

                    *              *  *                  
       2933 GAGTATTGTGGTGGCTCGTCAAATTGAGGCTGATATCCTTGGCTT
          1 GAGTATTGCGGTGGCTCGTCAAACTGCGGCTGATATCCTTGGCTT

                        *                                
       2978 GAGTATTGCGGTTGCTCGTCAAACTGCGGCTGATATCCTTGGCTT
          1 GAGTATTGCGGTGGCTCGTCAAACTGCGGCTGATATCCTTGGCTT

              
       3023 GA
          1 GA

       3025 TGAGCTATGC


Statistics
Matches: 78,  Mismatches: 13, Indels: 2
        0.84            0.14        0.02

Matches are distributed among these distances:
  45   78  1.00

ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32


Consensus pattern (45 bp):   
GAGTATTGCGGTGGCTCGTCAAACTGCGGCTGATATCCTTGGCTT
Done.