Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011998.1 Kokia drynarioides strain JFW-HI SEQ_126996, 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: 11811
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:2931 original size:30 final size:29

Alignment explanation


    Indices: 2895--2986  Score: 96
    Period size: 30  Copynumber: 3.1  Consensus size: 29

       2885 CCTTCATCCA

                                          
       2895 TGCTCGCAACATGAGTGTTCACAACATCAG
          1 TGCTCGCAACAT-AGTGTTCACAACATCAG

                    *            *      *  
       2925 TGCTCGCAGC-TCCAGTGTTCGCAACATGAG
          1 TGCTCGCAACAT--AGTGTTCACAACATCAG

                     *                 *  
       2955 TGCTCGCAATACTAGTGTTCACAACATTAG
          1 TGCTCGCAACA-TAGTGTTCACAACATCAG

              
       2985 TG
          1 TG

       2987 TTAGTAGCTC


Statistics
Matches: 51,  Mismatches: 8, Indels: 6
        0.78            0.12        0.09

Matches are distributed among these distances:
  29    1  0.02
  30   49  0.96
  32    1  0.02

ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26


Consensus pattern (29 bp):   
TGCTCGCAACATAGTGTTCACAACATCAG

Found at i:2996 original size:60 final size:60

Alignment explanation


    Indices: 2895--3031  Score: 186
    Period size: 60  Copynumber: 2.3  Consensus size: 60

       2885 CCTTCATCCA

                                               *         *               
       2895 TGCTCGCAACA-TGAGTGTTCACAACATCAGTGCTCGCAGCTCCAGTGTTCGCAACATGAG
          1 TGCTCGCAACACT-AGTGTTCACAACATCAGTGCTAGCAGCTCCAATGTTCGCAACATGAG

                     *                 *    *   *                       
       2955 TGCTCGCAATACTAGTGTTCACAACATTAGTGTTAGTAGCTCCAATGTTCGCAACATGAG
          1 TGCTCGCAACACTAGTGTTCACAACATCAGTGCTAGCAGCTCCAATGTTCGCAACATGAG

              *   *          
       3015 TGTTCGTAACACTAGTG
          1 TGCTCGCAACACTAGTG

       3032 CTCGCATCTT


Statistics
Matches: 67,  Mismatches: 9, Indels: 2
        0.86            0.12        0.03

Matches are distributed among these distances:
  60   66  0.99
  61    1  0.01

ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28


Consensus pattern (60 bp):   
TGCTCGCAACACTAGTGTTCACAACATCAGTGCTAGCAGCTCCAATGTTCGCAACATGAG

Found at i:3031 original size:15 final size:15

Alignment explanation


    Indices: 2898--3025  Score: 73
    Period size: 15  Copynumber: 8.5  Consensus size: 15

       2888 TCATCCATGC

                           
       2898 TCGCAACATGAGTGT
          1 TCGCAACATGAGTGT

              *      *    *
       2913 TCACAACATCAGTGC
          1 TCGCAACATGAGTGT

                 *    *     
       2928 TCGCAGC-TCCAGTGT
          1 TCGCAACAT-GAGTGT

                          *
       2943 TCGCAACATGAGTGC
          1 TCGCAACATGAGTGT

                  *         
       2958 TCGCAATACT-AGTGT
          1 TCGCAACA-TGAGTGT

              *      *     
       2973 TCACAACATTAGTGT
          1 TCGCAACATGAGTGT

             * * *    * *   
       2988 TAGTAGC-TCCAATGT
          1 TCGCAACAT-GAGTGT

                           
       3003 TCGCAACATGAGTGT
          1 TCGCAACATGAGTGT

               *    
       3018 TCGTAACA
          1 TCGCAACA

       3026 CTAGTGCTCG


Statistics
Matches: 82,  Mismatches: 25, Indels: 12
        0.69            0.21        0.10

Matches are distributed among these distances:
  14    3  0.04
  15   76  0.93
  16    3  0.04

ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27


Consensus pattern (15 bp):   
TCGCAACATGAGTGT

Found at i:3037 original size:30 final size:30

Alignment explanation


    Indices: 2938--3037  Score: 101
    Period size: 30  Copynumber: 3.3  Consensus size: 30

       2928 TCGCAGCTCC

                               *   *  *   
       2938 AGTGTTCGCAACATGAGTGCTCGCAATACT
          1 AGTGTTCGCAACATGAGTGTTCGTAACACT

                   *      *      *   * * *
       2968 AGTGTTCACAACATTAGTGTTAGTAGCTCC
          1 AGTGTTCGCAACATGAGTGTTCGTAACACT

             *                            
       2998 AATGTTCGCAACATGAGTGTTCGTAACACT
          1 AGTGTTCGCAACATGAGTGTTCGTAACACT

                *     
       3028 AGTGCTCGCA
          1 AGTGTTCGCA

       3038 TCTTCCAAGC


Statistics
Matches: 52,  Mismatches: 18, Indels: 0
        0.74            0.26        0.00

Matches are distributed among these distances:
  30   52  1.00

ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29


Consensus pattern (30 bp):   
AGTGTTCGCAACATGAGTGTTCGTAACACT

Found at i:8460 original size:21 final size:22

Alignment explanation


    Indices: 8436--8477  Score: 68
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       8426 TGTATAATTT

                            *     
       8436 AGGTTTT-GTTATTTCTTTTCA
          1 AGGTTTTAGTTATTTCGTTTCA

                                 
       8457 AGGTTTTAGTTATTTCGTTTC
          1 AGGTTTTAGTTATTTCGTTTC

       8478 GTTATTATTT


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  21    7  0.37
  22   12  0.63

ACGTcount: A:0.14, C:0.10, G:0.17, T:0.60


Consensus pattern (22 bp):   
AGGTTTTAGTTATTTCGTTTCA

Done.