Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000960.1 Kokia drynarioides strain JFW-HI SEQ_112135, 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: 16504
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33


Found at i:3759 original size:26 final size:26

Alignment explanation


    Indices: 3725--3778  Score: 108
    Period size: 26  Copynumber: 2.1  Consensus size: 26

       3715 ATGATTTCCT

                                      
       3725 ATCAAATATTATTGAAGATTTAAAAA
          1 ATCAAATATTATTGAAGATTTAAAAA

                                      
       3751 ATCAAATATTATTGAAGATTTAAAAA
          1 ATCAAATATTATTGAAGATTTAAAAA

              
       3777 AT
          1 AT

       3779 TCATGAGAAA


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:0.54, C:0.04, G:0.07, T:0.35


Consensus pattern (26 bp):   
ATCAAATATTATTGAAGATTTAAAAA

Found at i:9700 original size:41 final size:41

Alignment explanation


    Indices: 9655--9791  Score: 238
    Period size: 41  Copynumber: 3.3  Consensus size: 41

       9645 TTGTTCGTAA

                     * *                             
       9655 AGAATTCTTATCAAGGTGGAGATTGTTAGAATTGCGTGATT
          1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGCGTGATT

                                               *     
       9696 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGCATGATT
          1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGCGTGATT

                                              *      
       9737 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGATT
          1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGCGTGATT

                          
       9778 AGAATTCTTGTTAA
          1 AGAATTCTTGTTAA

       9792 AATAAAATTC


Statistics
Matches: 91,  Mismatches: 5, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  41   91  1.00

ACGTcount: A:0.29, C:0.05, G:0.27, T:0.39


Consensus pattern (41 bp):   
AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGCGTGATT

Found at i:12328 original size:18 final size:19

Alignment explanation


    Indices: 12291--12328  Score: 51
    Period size: 18  Copynumber: 2.1  Consensus size: 19

      12281 CTTTTTAATC

                           *   
      12291 AAATTTAAAATCACATAAT
          1 AAATTTAAAATCACACAAT

                     *         
      12310 AAATTT-AATTCACACAAT
          1 AAATTTAAAATCACACAAT

             
      12328 A
          1 A

      12329 TGAAAATTCA


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  18   11  0.65
  19    6  0.35

ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32


Consensus pattern (19 bp):   
AAATTTAAAATCACACAAT

Found at i:14462 original size:77 final size:77

Alignment explanation


    Indices: 14253--14489  Score: 381
    Period size: 76  Copynumber: 3.1  Consensus size: 77

      14243 TACTTTTCGT

                                                                             
      14253 TTATATAAATGTCACACTATGACTAAAAATGTTATTGAAAAACTTTGATTTTAAACTAATTTAAA
          1 TTATATAAATGTCACACTATGACT-AAAATGTTATTGAAAAACTTTGATTTTAAACTAATTTAAA

                         
      14318 CTTTGATTTTCAA
         65 CTTTGATTTTCAA

                  *  *    *                                    *             
      14331 TTATATCAACGTCAAAC-ACTGAC-AAAATGTTATTGAAAAACTTTGATTTAAAACTAATTT-AA
          1 TTATATAAATGTCACACTA-TGACTAAAATGTTATTGAAAAACTTTGATTTTAAACTAATTTAAA

                         
      14393 CTTTGATTTTCAA
         65 CTTTGATTTTCAA

                                                                             
      14406 TTATATAAATGTCACACTATGACTAAAATTGTTATTGAAAAACTTTGATTTTAAACTAATTTAAA
          1 TTATATAAATGTCACACTATGACTAAAA-TGTTATTGAAAAACTTTGATTTTAAACTAATTTAAA

                    *    
      14471 CTTTGATTCTCAA
         65 CTTTGATTTTCAA

                  
      14484 TTATAT
          1 TTATAT

      14490 GCATCATCAA


Statistics
Matches: 145,  Mismatches: 9, Indels: 10
        0.88            0.05        0.06

Matches are distributed among these distances:
  75   33  0.23
  76   41  0.28
  77   33  0.23
  78   38  0.26

ACGTcount: A:0.41, C:0.11, G:0.08, T:0.41


Consensus pattern (77 bp):   
TTATATAAATGTCACACTATGACTAAAATGTTATTGAAAAACTTTGATTTTAAACTAATTTAAAC
TTTGATTTTCAA
Done.