Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004077.1 Kokia drynarioides strain JFW-HI SEQ_117244, 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: 1738
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39


Found at i:73 original size:6 final size:6

Alignment explanation


    Indices: 62--105  Score: 79
    Period size: 6  Copynumber: 7.3  Consensus size: 6

         52 TTGACCTCCC

                                                    *          
         62 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTC CTTTTT CT
          1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CT

        106 CTCTATCTTC


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   6   36  1.00

ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80


Consensus pattern (6 bp):   
CTTTTT

Found at i:983 original size:6 final size:5

Alignment explanation


    Indices: 949--996  Score: 60
    Period size: 5  Copynumber: 9.0  Consensus size: 5

        939 TGACTTTTCC

                                     *                              
        949 TTCTT TTCTT TTCTT TTCTT TGCTT TTCTTT TTCTTT TTCCTT TTCTT
          1 TTCTT TTCTT TTCTT TTCTT TTCTT TTC-TT TTC-TT TT-CTT TTCTT

        997 GGGTTTTAAG


Statistics
Matches: 39,  Mismatches: 2, Indels: 4
        0.87            0.04        0.09

Matches are distributed among these distances:
   5   24  0.62
   6   14  0.36
   7    1  0.03

ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77


Consensus pattern (5 bp):   
TTCTT

Found at i:1087 original size:22 final size:22

Alignment explanation


    Indices: 1042--1093  Score: 61
    Period size: 22  Copynumber: 2.4  Consensus size: 22

       1032 CTTAACCCTT

                      *        *  
       1042 TTCTTTTTCTTTTTTTCTTTCC
          1 TTCTTTTTCTCTTTTTCTTACC

                                   
       1064 TTCTTTTTCCTCTTTTT-TTACC
          1 TTCTTTTT-CTCTTTTTCTTACC

              *     
       1086 TTTTTTTT
          1 TTCTTTTT

       1094 TGATAACACG


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  22   19  0.73
  23    7  0.27

ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77


Consensus pattern (22 bp):   
TTCTTTTTCTCTTTTTCTTACC

Found at i:1091 original size:12 final size:11

Alignment explanation


    Indices: 1038--1094  Score: 53
    Period size: 12  Copynumber: 5.0  Consensus size: 11

       1028 TCATCTTAAC

                        
       1038 CCTTTTCTTTTT
          1 CCTTTT-TTTTT

             *          
       1050 CTTTTTTTCTTT
          1 CCTTTTTT-TTT

                 *     
       1062 CC-TTCTTTTT
          1 CCTTTTTTTTT

                       *
       1072 CCTCTTTTTTTA
          1 CCT-TTTTTTTT

                       
       1084 CCTTTTTTTTT
          1 CCTTTTTTTTT

       1095 GATAACACGT


Statistics
Matches: 36,  Mismatches: 6, Indels: 7
        0.73            0.12        0.14

Matches are distributed among these distances:
  10    5  0.14
  11   13  0.36
  12   18  0.50

ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75


Consensus pattern (11 bp):   
CCTTTTTTTTT
Done.