Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000143.1 Kokia drynarioides strain JFW-HI SEQ_110797, 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: 3213
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36

Warning! 11 characters in sequence are not A, C, G, or T


Found at i:1350 original size:48 final size:48

Alignment explanation


    Indices: 1292--1388  Score: 194
    Period size: 48  Copynumber: 2.0  Consensus size: 48

       1282 AATATATATG

                                                            
       1292 TATATATAAAATGATAAATGTTTACGTTTGGTAAAATAAATTTTAAAA
          1 TATATATAAAATGATAAATGTTTACGTTTGGTAAAATAAATTTTAAAA

                                                            
       1340 TATATATAAAATGATAAATGTTTACGTTTGGTAAAATAAATTTTAAAA
          1 TATATATAAAATGATAAATGTTTACGTTTGGTAAAATAAATTTTAAAA

             
       1388 T
          1 T

       1389 TAGAATAATA


Statistics
Matches: 49,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  48   49  1.00

ACGTcount: A:0.47, C:0.02, G:0.10, T:0.40


Consensus pattern (48 bp):   
TATATATAAAATGATAAATGTTTACGTTTGGTAAAATAAATTTTAAAA

Found at i:2119 original size:6 final size:6

Alignment explanation


    Indices: 2110--2189  Score: 78
    Period size: 6  Copynumber: 13.8  Consensus size: 6

       2100 GATTTATTTC

                           * *                    *                
       2110 TAAATT TAAA-T TCATTT TAAATT TAAATT T-ATTT TAAATT TAAATT
          1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT

               *                    *                
       2156 T-AGTT TAAATT TAAATT T-AGTT TAAATT TGAAAT
          1 TAAATT TAAATT TAAATT TAAATT TAAATT T-AAAT

       2190 AATTTTAAAC


Statistics
Matches: 59,  Mismatches: 10, Indels: 9
        0.76            0.13        0.12

Matches are distributed among these distances:
   5   15  0.25
   6   40  0.68
   7    4  0.07

ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53


Consensus pattern (6 bp):   
TAAATT

Found at i:2132 original size:17 final size:17

Alignment explanation


    Indices: 2096--2204  Score: 139
    Period size: 17  Copynumber: 6.4  Consensus size: 17

       2086 TAAATTAATT

                *             
       2096 TTTAGATTTATTTCTAAA
          1 TTTAAATTTATTT-TAAA

                    *        
       2114 TTTAAATTCATTTTAAA
          1 TTTAAATTTATTTTAAA

                             
       2131 TTTAAATTTATTTTAAA
          1 TTTAAATTTATTTTAAA

                      *      
       2148 TTTAAATTTAGTTTAAA
          1 TTTAAATTTATTTTAAA

                      *      
       2165 TTTAAATTTAGTTTAAA
          1 TTTAAATTTATTTTAAA

                     *        
       2182 TTTGAAA-TAATTTTAAA
          1 TTT-AAATTTATTTTAAA

            *     
       2199 CTTAAA
          1 TTTAAA

       2205 ACTTTAAAAT


Statistics
Matches: 83,  Mismatches: 7, Indels: 4
        0.88            0.07        0.04

Matches are distributed among these distances:
  16    3  0.04
  17   66  0.80
  18   14  0.17

ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52


Consensus pattern (17 bp):   
TTTAAATTTATTTTAAA

Found at i:2960 original size:3 final size:3

Alignment explanation


    Indices: 2858--2948  Score: 83
    Period size: 3  Copynumber: 28.7  Consensus size: 3

       2848 TTTCAAAAAT

                                                                        * 
       2858 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAAA TAA TTTA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA T-AA TAA -TAA

                     *    *            *         * *                
       2906 TAA TAA TGA TAT TAA TAA GTAT TAA TAA CAG TAA TTAA TAA TA
          1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA -TAA TAA TA

       2949 CCTATTAATA


Statistics
Matches: 72,  Mismatches: 12, Indels: 8
        0.78            0.13        0.09

Matches are distributed among these distances:
   3   58  0.81
   4   14  0.19

ACGTcount: A:0.59, C:0.01, G:0.03, T:0.36


Consensus pattern (3 bp):   
TAA

Found at i:3039 original size:17 final size:16

Alignment explanation


    Indices: 3017--3064  Score: 78
    Period size: 17  Copynumber: 2.9  Consensus size: 16

       3007 TTTGACTTAA

                            
       3017 ATTTAAATTTAAATTG
          1 ATTTAAATTTAAATTG

                             
       3033 ATATTAAATTTAAATTG
          1 AT-TTAAATTTAAATTG

                *          
       3050 ATTTTAATTTAAATT
          1 ATTTAAATTTAAATT

       3065 AAAAAGTCCA


Statistics
Matches: 30,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  16   14  0.47
  17   16  0.53

ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52


Consensus pattern (16 bp):   
ATTTAAATTTAAATTG
Done.