Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006404.1 Kokia drynarioides strain JFW-HI SEQ_120981, 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: 4427
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35


Found at i:975 original size:24 final size:24

Alignment explanation


    Indices: 889--963  Score: 114
    Period size: 24  Copynumber: 3.1  Consensus size: 24

        879 AGAAATAACC

                 *         *    *   
        889 TTTCAGTTAAACTCTATTTAATTG
          1 TTTCAATTAAACTCTGTTTATTTG

                         *          
        913 TTTCAATTAAACTTTGTTTATTTG
          1 TTTCAATTAAACTCTGTTTATTTG

                                    
        937 TTTCAATTAAACTCTGTTTATTTG
          1 TTTCAATTAAACTCTGTTTATTTG

               
        961 TTT
          1 TTT

        964 GAGTCAAACT


Statistics
Matches: 46,  Mismatches: 5, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  24   46  1.00

ACGTcount: A:0.25, C:0.11, G:0.08, T:0.56


Consensus pattern (24 bp):   
TTTCAATTAAACTCTGTTTATTTG

Found at i:2928 original size:24 final size:23

Alignment explanation


    Indices: 2900--2962  Score: 81
    Period size: 23  Copynumber: 2.7  Consensus size: 23

       2890 AGAAATAATC

                                    
       2900 TTTCAGTTAAACTCTGTTTATTTG
          1 TTTCAGTTAAACTCT-TTTATTTG

                 *     *           
       2924 TTTCAATTAAATTCTTTTATTTG
          1 TTTCAGTTAAACTCTTTTATTTG

               *   *        
       2947 TTTGAGTCAAACTCTT
          1 TTTCAGTTAAACTCTT

       2963 ATTAGTCTAG


Statistics
Matches: 33,  Mismatches: 6, Indels: 1
        0.82            0.15        0.03

Matches are distributed among these distances:
  23   20  0.61
  24   13  0.39

ACGTcount: A:0.24, C:0.13, G:0.10, T:0.54


Consensus pattern (23 bp):   
TTTCAGTTAAACTCTTTTATTTG

Found at i:2946 original size:23 final size:24

Alignment explanation


    Indices: 2900--2949  Score: 75
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       2890 AGAAATAATC

                 *                  
       2900 TTTCAGTTAAACTCTGTTTATTTG
          1 TTTCAATTAAACTCTGTTTATTTG

                       *            
       2924 TTTCAATTAAATTCT-TTTATTTG
          1 TTTCAATTAAACTCTGTTTATTTG

               
       2947 TTT
          1 TTT

       2950 GAGTCAAACT


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  23   11  0.46
  24   13  0.54

ACGTcount: A:0.22, C:0.10, G:0.08, T:0.60


Consensus pattern (24 bp):   
TTTCAATTAAACTCTGTTTATTTG

Found at i:3926 original size:28 final size:28

Alignment explanation


    Indices: 3892--3988  Score: 194
    Period size: 28  Copynumber: 3.5  Consensus size: 28

       3882 ATTATTTATA

                                        
       3892 TAATTAAATAATCTTATATTTCGTCTAC
          1 TAATTAAATAATCTTATATTTCGTCTAC

                                        
       3920 TAATTAAATAATCTTATATTTCGTCTAC
          1 TAATTAAATAATCTTATATTTCGTCTAC

                                        
       3948 TAATTAAATAATCTTATATTTCGTCTAC
          1 TAATTAAATAATCTTATATTTCGTCTAC

                         
       3976 TAATTAAATAATC
          1 TAATTAAATAATC

       3989 AATCTATCTA


Statistics
Matches: 69,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   69  1.00

ACGTcount: A:0.38, C:0.13, G:0.03, T:0.45


Consensus pattern (28 bp):   
TAATTAAATAATCTTATATTTCGTCTAC
Done.