Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008633.1 Kokia drynarioides strain JFW-HI SEQ_123313, 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: 23753
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32


Found at i:3405 original size:42 final size:42

Alignment explanation


    Indices: 3358--3439  Score: 164
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       3348 AGCTTGGCGC

                                                      
       3358 AATGAAGATATGCAAGATGGACATTCTTTTGCATTCTATGCT
          1 AATGAAGATATGCAAGATGGACATTCTTTTGCATTCTATGCT

                                                    
       3400 AATGAAGATATGCAAGATGGACATTCTTTTGCATTCTATG
          1 AATGAAGATATGCAAGATGGACATTCTTTTGCATTCTATG

       3440 TTTTCTTGGA


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  42   40  1.00

ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35


Consensus pattern (42 bp):   
AATGAAGATATGCAAGATGGACATTCTTTTGCATTCTATGCT

Found at i:5176 original size:25 final size:26

Alignment explanation


    Indices: 5129--5177  Score: 66
    Period size: 25  Copynumber: 1.9  Consensus size: 26

       5119 AAAATGTTTA

                              *       
       5129 ATTTTTATATAAAATATATTAATCAT
          1 ATTTTTATATAAAATATAATAATCAT

                                     
       5155 ATTTTTAT-T-AAATATTAATAATC
          1 ATTTTTATATAAAATA-TAATAATC

       5178 TTTAAAAAAT


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  24    5  0.24
  25    8  0.38
  26    8  0.38

ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51


Consensus pattern (26 bp):   
ATTTTTATATAAAATATAATAATCAT

Found at i:15021 original size:11 final size:11

Alignment explanation


    Indices: 15005--15034  Score: 60
    Period size: 11  Copynumber: 2.7  Consensus size: 11

      14995 ATGTTAAATC

                       
      15005 ATCAAGAATAA
          1 ATCAAGAATAA

                       
      15016 ATCAAGAATAA
          1 ATCAAGAATAA

                    
      15027 ATCAAGAA
          1 ATCAAGAA

      15035 CAAAACTAAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   19  1.00

ACGTcount: A:0.63, C:0.10, G:0.10, T:0.17


Consensus pattern (11 bp):   
ATCAAGAATAA

Found at i:15318 original size:26 final size:26

Alignment explanation


    Indices: 15289--15342  Score: 108
    Period size: 26  Copynumber: 2.1  Consensus size: 26

      15279 CTAGAGTATC

                                      
      15289 TACACATATTTATCCCATACTTTATT
          1 TACACATATTTATCCCATACTTTATT

                                      
      15315 TACACATATTTATCCCATACTTTATT
          1 TACACATATTTATCCCATACTTTATT

              
      15341 TA
          1 TA

      15343 ATAATTAAAA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   28  1.00

ACGTcount: A:0.31, C:0.22, G:0.00, T:0.46


Consensus pattern (26 bp):   
TACACATATTTATCCCATACTTTATT

Found at i:16855 original size:23 final size:25

Alignment explanation


    Indices: 16801--16857  Score: 73
    Period size: 25  Copynumber: 2.4  Consensus size: 25

      16791 AAATGACAAG

                              ***    
      16801 AAATATTGTAATTCAATATTTTCTA
          1 AAATATTGTAATTCAATAAAATCTA

                                     
      16826 AAATATTGTAATT-AATAAAATC-A
          1 AAATATTGTAATTCAATAAAATCTA

                     
      16849 AAATATTGT
          1 AAATATTGT

      16858 TAAAATACAA


Statistics
Matches: 29,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  23   10  0.34
  24    6  0.21
  25   13  0.45

ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42


Consensus pattern (25 bp):   
AAATATTGTAATTCAATAAAATCTA

Found at i:16879 original size:15 final size:16

Alignment explanation


    Indices: 16859--16895  Score: 51
    Period size: 15  Copynumber: 2.4  Consensus size: 16

      16849 AAATATTGTT

                             
      16859 AAAATACAAAA-TT-AA
          1 AAAATA-AAAATTTCAA

                            
      16874 AAAATAAAAATTTCAA
          1 AAAATAAAAATTTCAA

                  
      16890 AAAATA
          1 AAAATA

      16896 TATCTAAATT


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  14    4  0.20
  15    8  0.40
  16    8  0.40

ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22


Consensus pattern (16 bp):   
AAAATAAAAATTTCAA

Found at i:19079 original size:27 final size:27

Alignment explanation


    Indices: 19025--19146  Score: 82
    Period size: 27  Copynumber: 4.5  Consensus size: 27

      19015 AAAGTCAAAA

                 *          * *  * *   
      19025 TCAACGGGTCGGGTCGATCAAATTGGG
          1 TCAACAGGTCGGGTCGGTTAACTCGGG

             *       *    *            
      19052 TTAACAGGTTGGGTAGGTTAACTCGGG
          1 TCAACAGGTCGGGTCGGTTAACTCGGG

                *    *  *   *        * 
      19079 TCAATAGGTTGGATCGATTAACTCGAG
          1 TCAACAGGTCGGGTCGGTTAACTCGGG

                 *    **            *  
      19106 TCAACGGGTCAAGTCGGTTAACTCAGG
          1 TCAACAGGTCGGGTCGGTTAACTCGGG

             *            
      19133 TTAACAGGTCGGGT
          1 TCAACAGGTCGGGT

      19147 TTGGGTCAAT


Statistics
Matches: 68,  Mismatches: 27, Indels: 0
        0.72            0.28        0.00

Matches are distributed among these distances:
  27   68  1.00

ACGTcount: A:0.25, C:0.16, G:0.33, T:0.26


Consensus pattern (27 bp):   
TCAACAGGTCGGGTCGGTTAACTCGGG
Done.