Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000541.1 Kokia drynarioides strain JFW-HI SEQ_111441, 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: 33718
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36


Found at i:2207 original size:23 final size:22

Alignment explanation


    Indices: 2181--2231  Score: 68
    Period size: 22  Copynumber: 2.3  Consensus size: 22

       2171 CATTAATAAT

                          *        
       2181 TAATTAATTATTTTTATTTAAAA
          1 TAATTAATT-TTTTAATTTAAAA

                              *   
       2204 TAATTAATTTTTTAATTTTAAA
          1 TAATTAATTTTTTAATTTAAAA

                   
       2226 -AATTAA
          1 TAATTAA

       2232 AAAATTTAAT


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
  21    6  0.23
  22   11  0.42
  23    9  0.35

ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55


Consensus pattern (22 bp):   
TAATTAATTTTTTAATTTAAAA

Found at i:2217 original size:21 final size:24

Alignment explanation


    Indices: 2181--2231  Score: 65
    Period size: 21  Copynumber: 2.3  Consensus size: 24

       2171 CATTAATAAT

                                    
       2181 TAATTAATTATTTTT-ATTTAAAA
          1 TAATTAATTATTTTTAATTTAAAA

                                *   
       2204 TAATTAA-T-TTTTTAATTTTAAA
          1 TAATTAATTATTTTTAATTTAAAA

                   
       2226 -AATTAA
          1 TAATTAA

       2232 AAAATTTAAT


Statistics
Matches: 26,  Mismatches: 1, Indels: 4
        0.84            0.03        0.13

Matches are distributed among these distances:
  21   11  0.42
  22    8  0.31
  23    7  0.27

ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55


Consensus pattern (24 bp):   
TAATTAATTATTTTTAATTTAAAA

Found at i:8453 original size:4 final size:4

Alignment explanation


    Indices: 8444--8472  Score: 58
    Period size: 4  Copynumber: 7.2  Consensus size: 4

       8434 AGAATCATTC

                                                
       8444 TTTG TTTG TTTG TTTG TTTG TTTG TTTG T
          1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG T

       8473 GTTCACCCTT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   25  1.00

ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76


Consensus pattern (4 bp):   
TTTG

Found at i:22447 original size:19 final size:19

Alignment explanation


    Indices: 22402--22447  Score: 56
    Period size: 19  Copynumber: 2.4  Consensus size: 19

      22392 AAAATTAAAA

                     *   *     
      22402 AAAAAAAATCATATTTTAT
          1 AAAAAAAATAATAATTTAT

             * *               
      22421 ATATAAAATAATAATTTAT
          1 AAAAAAAATAATAATTTAT

                    
      22440 AAAAAAAA
          1 AAAAAAAA

      22448 AAAAAATCCA


Statistics
Matches: 21,  Mismatches: 6, Indels: 0
        0.78            0.22        0.00

Matches are distributed among these distances:
  19   21  1.00

ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33


Consensus pattern (19 bp):   
AAAAAAAATAATAATTTAT

Found at i:32901 original size:20 final size:21

Alignment explanation


    Indices: 32869--32913  Score: 67
    Period size: 21  Copynumber: 2.2  Consensus size: 21

      32859 TTAAAAAAAA

                                 
      32869 TTTATGAACTA-TTTATAATT
          1 TTTATGAACTATTTTATAATT

                                  
      32889 TTTATTGAA-TATTTTATAATT
          1 TTTA-TGAACTATTTTATAATT

                
      32910 TTTA
          1 TTTA

      32914 AATTATTTAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  20    6  0.26
  21   17  0.74

ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60


Consensus pattern (21 bp):   
TTTATGAACTATTTTATAATT

Found at i:33673 original size:17 final size:17

Alignment explanation


    Indices: 33651--33718  Score: 100
    Period size: 17  Copynumber: 3.9  Consensus size: 17

      33641 CATACTCCTT

                             
      33651 TTAAATTTATTTTAAAA
          1 TTAAATTTATTTTAAAA

                    *   *    
      33668 TTAAATTTGTTTAAAAA
          1 TTAAATTTATTTTAAAA

                             *
      33685 TTTAAATTTATTTTAAAT
          1 -TTAAATTTATTTTAAAA

                            
      33703 TTAAATTTATTTTAAA
          1 TTAAATTTATTTTAAA


Statistics
Matches: 45,  Mismatches: 5, Indels: 2
        0.87            0.10        0.04

Matches are distributed among these distances:
  17   31  0.69
  18   14  0.31

ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54


Consensus pattern (17 bp):   
TTAAATTTATTTTAAAA
Done.