Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000666.1 Kokia drynarioides strain JFW-HI SEQ_111654, 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: 10987
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31


Found at i:1476 original size:24 final size:24

Alignment explanation


    Indices: 1389--1467  Score: 113
    Period size: 24  Copynumber: 3.3  Consensus size: 24

       1379 ACTCTGCCTG

                        *    *   * *
       1389 GGCTCGTAAGAGATAACTATTATG
          1 GGCTCGTAAGAGCTAACCATTCTA

                            *       
       1413 GGCTCGTAAGAGCTAATCATTCTA
          1 GGCTCGTAAGAGCTAACCATTCTA

                                    
       1437 GGCTCGTAAGAGCTAACCATTCTA
          1 GGCTCGTAAGAGCTAACCATTCTA

                   
       1461 GGCTCGT
          1 GGCTCGT

       1468 GTAGGCTAAA


Statistics
Matches: 49,  Mismatches: 6, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  24   49  1.00

ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28


Consensus pattern (24 bp):   
GGCTCGTAAGAGCTAACCATTCTA

Found at i:10116 original size:6 final size:6

Alignment explanation


    Indices: 10092--10168  Score: 79
    Period size: 6  Copynumber: 13.0  Consensus size: 6

      10082 TTTAATTTAT

                                                    *       *       
      10092 TTTAAA TTTAAGA -TT-AA TTTAAA TTTAAA TTTAGA TTT-AT TTTAAA
          1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA

                                *        *     
      10138 TTTAAA TTTAAAA TTTAAT TTTAAA ATTAAA
          1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA

      10169 AAGTCCATTA


Statistics
Matches: 59,  Mismatches: 7, Indels: 10
        0.78            0.09        0.13

Matches are distributed among these distances:
   4    1  0.02
   5    6  0.10
   6   45  0.76
   7    7  0.12

ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51


Consensus pattern (6 bp):   
TTTAAA

Found at i:10122 original size:23 final size:24

Alignment explanation


    Indices: 10082--10168  Score: 108
    Period size: 23  Copynumber: 3.7  Consensus size: 24

      10072 GGGCCCCCTT

                      *             
      10082 TTTAATTT-ATTTTAAATTTAAGA
          1 TTTAATTTAAATTTAAATTTAAGA

                                    
      10105 -TTAATTTAAATTTAAATTT-AGA
          1 TTTAATTTAAATTTAAATTTAAGA

                *                 * 
      10127 TTTATTTTAAATTTAAATTTAAAA
          1 TTTAATTTAAATTTAAATTTAAGA

                        *     
      10151 TTTAATTTTAAAATTAAA
          1 TTTAA-TTTAAATTTAAA

      10169 AAGTCCATTA


Statistics
Matches: 55,  Mismatches: 5, Indels: 6
        0.83            0.08        0.09

Matches are distributed among these distances:
  22   10  0.18
  23   28  0.51
  24    6  0.11
  25   11  0.20

ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53


Consensus pattern (24 bp):   
TTTAATTTAAATTTAAATTTAAGA

Found at i:10135 original size:17 final size:17

Alignment explanation


    Indices: 10115--10147  Score: 57
    Period size: 17  Copynumber: 1.9  Consensus size: 17

      10105 TTAATTTAAA

                      *      
      10115 TTTAAATTTAGATTTAT
          1 TTTAAATTTAAATTTAT

                            
      10132 TTTAAATTTAAATTTA
          1 TTTAAATTTAAATTTA

      10148 AAATTTAATT


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

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58


Consensus pattern (17 bp):   
TTTAAATTTAAATTTAT

Found at i:10265 original size:45 final size:45

Alignment explanation


    Indices: 10192--10286  Score: 149
    Period size: 45  Copynumber: 2.1  Consensus size: 45

      10182 ATGTCCAAAA

                             *             *             
      10192 TACAAAGGGCCCAAAGATTAGCTCAATGACCTAATTACACCCAAT
          1 TACAAAGGGCCCAAAGACTAGCTCAATGACCCAATTACACCCAAT

                                                          
      10237 TACAAAGGGCCCAAAGACTAG-TCTAATGACCCAATTACACCCAAT
          1 TACAAAGGGCCCAAAGACTAGCTC-AATGACCCAATTACACCCAAT

                  
      10282 T-CAAA
          1 TACAAA

      10287 CCCATTACAT


Statistics
Matches: 47,  Mismatches: 2, Indels: 3
        0.90            0.04        0.06

Matches are distributed among these distances:
  44    6  0.13
  45   41  0.87

ACGTcount: A:0.41, C:0.27, G:0.13, T:0.19


Consensus pattern (45 bp):   
TACAAAGGGCCCAAAGACTAGCTCAATGACCCAATTACACCCAAT
Done.