Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000690.1 Kokia drynarioides strain JFW-HI SEQ_111690, 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: 17559
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32


Found at i:2069 original size:15 final size:15

Alignment explanation


    Indices: 2040--2070  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       2030 TTCTTCTGTA

                           
       2040 TCTTTCTCTTCTCTT
          1 TCTTTCTCTTCTCTT

                 *         
       2055 TCTTTGTCTTCTCTT
          1 TCTTTCTCTTCTCTT

             
       2070 T
          1 T

       2071 TCTCTTTTTC


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.00, C:0.29, G:0.03, T:0.68


Consensus pattern (15 bp):   
TCTTTCTCTTCTCTT

Found at i:3749 original size:13 final size:14

Alignment explanation


    Indices: 3731--3781  Score: 50
    Period size: 14  Copynumber: 3.6  Consensus size: 14

       3721 ATTCCTACAG

                          
       3731 AAAATT-AAAGAAA
          1 AAAATTAAAAGAAA

                          
       3744 AAAATTAAAAGAAA
          1 AAAATTAAAAGAAA

                 **      * 
       3758 AGAAAAGAAAAGACA
          1 A-AAATTAAAAGAAA

                *    
       3773 AAAAGTAAA
          1 AAAATTAAA

       3782 TATAAAGATT


Statistics
Matches: 31,  Mismatches: 5, Indels: 3
        0.79            0.13        0.08

Matches are distributed among these distances:
  13    6  0.19
  14   14  0.45
  15   11  0.35

ACGTcount: A:0.76, C:0.02, G:0.12, T:0.10


Consensus pattern (14 bp):   
AAAATTAAAAGAAA

Found at i:6838 original size:18 final size:18

Alignment explanation


    Indices: 6798--6840  Score: 50
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       6788 CATGTGGTTT

                   *          
       6798 CATCTGATTATATGACTA
          1 CATCTGAGTATATGACTA

            *          *     *
       6816 AATCTGAGTATGTGACTG
          1 CATCTGAGTATATGACTA

                   
       6834 CATCTGA
          1 CATCTGA

       6841 TCAGGCTGCG


Statistics
Matches: 20,  Mismatches: 5, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35


Consensus pattern (18 bp):   
CATCTGAGTATATGACTA

Found at i:11122 original size:52 final size:52

Alignment explanation


    Indices: 10981--11216  Score: 307
    Period size: 52  Copynumber: 4.6  Consensus size: 52

      10971 CAAGAGTTTG

                             *              *      *     *      
      10981 ATACTCACGATGACACAAAGTCATCGGACCT-TTAATCCATAAAGAATTCAT
          1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT

                                                                
      11032 ATACTCACGATGACAC--AGTCATCGGACCTCATAATCCGTAAAGGATTCAT
          1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT

               * *  *               *                   *   *   
      11082 ATATTGACTATGACACATAGTCATTGGACCTCATAATCCGTAAAAGATCCAT
          1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT

              *     *          *     *  *                       
      11134 ATGCTCACAATGACACATAATCATCAGATCTCATAATCCGTAAAGGATTCAT
          1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT

                                      *    
      11186 ATACTCACGATGACACATAGTCATCGAACCT
          1 ATACTCACGATGACACATAGTCATCGGACCT

      11217 ATTTCATTTA


Statistics
Matches: 157,  Mismatches: 25, Indels: 5
        0.84            0.13        0.03

Matches are distributed among these distances:
  49   13  0.08
  50   30  0.19
  51   16  0.10
  52   98  0.62

ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26


Consensus pattern (52 bp):   
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT

Found at i:16562 original size:6 final size:6

Alignment explanation


    Indices: 16551--16581  Score: 53
    Period size: 6  Copynumber: 5.0  Consensus size: 6

      16541 CATTCACAAT

                                               
      16551 TATAAA TATAAA TATAAA TATATAA TATAAA
          1 TATAAA TATAAA TATAAA TATA-AA TATAAA

      16582 GTCTATAATT


Statistics
Matches: 24,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
   6   18  0.75
   7    6  0.25

ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35


Consensus pattern (6 bp):   
TATAAA

Found at i:16588 original size:14 final size:13

Alignment explanation


    Indices: 16551--16594  Score: 56
    Period size: 13  Copynumber: 3.5  Consensus size: 13

      16541 CATTCACAAT

                         
      16551 TATAAATATA-AA
          1 TATAAATATATAA

                         
      16563 TATAAATATATAA
          1 TATAAATATATAA

                    *     
      16576 TATAAAGTCTATAA
          1 TATAAA-TATATAA

                  
      16590 T-TAAA
          1 TATAAA

      16595 ATAAAATAAC


Statistics
Matches: 29,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  12   10  0.34
  13   12  0.41
  14    7  0.24

ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36


Consensus pattern (13 bp):   
TATAAATATATAA
Done.