Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010452.1 Kokia drynarioides strain JFW-HI SEQ_125349, 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: 6586
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.33

Warning! 177 characters in sequence are not A, C, G, or T


Found at i:974 original size:4 final size:4

Alignment explanation


    Indices: 954--1019  Score: 62
    Period size: 4  Copynumber: 16.2  Consensus size: 4

        944 AACACATTAC

                       *                     *   *      *               
        954 CTTT CTTT CCTT C-TT CTTT CTTT CCTCT CCTT CTTC CTTT CTTT CTTT
          1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT

                     *            
       1002 CTTT CCTTG CTTT CTTT C
          1 CTTT -CTTT CTTT CTTT C

       1020 CTGTTTATTT


Statistics
Matches: 50,  Mismatches: 9, Indels: 6
        0.77            0.14        0.09

Matches are distributed among these distances:
   3    3  0.06
   4   41  0.82
   5    6  0.12

ACGTcount: A:0.00, C:0.35, G:0.02, T:0.64


Consensus pattern (4 bp):   
CTTT

Found at i:988 original size:17 final size:15

Alignment explanation


    Indices: 954--1019  Score: 66
    Period size: 17  Copynumber: 4.3  Consensus size: 15

        944 AACACATTAC

                           
        954 CTTTCTTTCCTTCTT
          1 CTTTCTTTCCTTCTT

                           
        969 CTTTCTTTCC-TC-T
          1 CTTTCTTTCCTTCTT

             *               
        982 CCTTC-TTCCTTTCTTT
          1 CTTTCTTTCC-TTC-TT

                             
        998 CTTTCTTTCCTTGCTTT
          1 CTTTCTTTCCTT-C-TT

                 
       1015 CTTTC
          1 CTTTC

       1020 CTGTTTATTT


Statistics
Matches: 43,  Mismatches: 2, Indels: 10
        0.78            0.04        0.18

Matches are distributed among these distances:
  12    4  0.09
  13    5  0.12
  14    4  0.09
  15   10  0.23
  16    7  0.16
  17   13  0.30

ACGTcount: A:0.00, C:0.35, G:0.02, T:0.64


Consensus pattern (15 bp):   
CTTTCTTTCCTTCTT

Found at i:1016 original size:29 final size:27

Alignment explanation


    Indices: 954--1017  Score: 76
    Period size: 29  Copynumber: 2.3  Consensus size: 27

        944 AACACATTAC

                                        
        954 CTTTCTTTCCTTCTTCTTTCTTTCCTCT
          1 CTTTC-TTCCTTCTTCTTTCTTTCCTCT

             *                           
        982 CCTTCTTCCTTTCTTTCTTTCTTTCCT-T
          1 CTTTCTTCC-TTC-TTCTTTCTTTCCTCT

                    
       1010 GCTTTCTT
          1 -CTTTCTT

       1018 TCCTGTTTAT


Statistics
Matches: 31,  Mismatches: 2, Indels: 5
        0.82            0.05        0.13

Matches are distributed among these distances:
  27    4  0.13
  28    8  0.26
  29   19  0.61

ACGTcount: A:0.00, C:0.34, G:0.02, T:0.64


Consensus pattern (27 bp):   
CTTTCTTCCTTCTTCTTTCTTTCCTCT

Found at i:4570 original size:19 final size:19

Alignment explanation


    Indices: 4548--4594  Score: 51
    Period size: 19  Copynumber: 2.5  Consensus size: 19

       4538 ATATTATTTG

                               
       4548 ATTTTTTTTAAATGCATAT
          1 ATTTTTTTTAAATGCATAT

                * *   *    *   
       4567 ATTTCTATTATATGCTTAT
          1 ATTTTTTTTAAATGCATAT

                      
       4586 -TTTTTTTTA
          1 ATTTTTTTTA

       4595 CACATTTTTT


Statistics
Matches: 22,  Mismatches: 6, Indels: 1
        0.76            0.21        0.03

Matches are distributed among these distances:
  18    7  0.32
  19   15  0.68

ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64


Consensus pattern (19 bp):   
ATTTTTTTTAAATGCATAT
Done.