Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008409.1 Kokia drynarioides strain JFW-HI SEQ_123078, 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: 21994
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31

Warning! 10 characters in sequence are not A, C, G, or T


Found at i:6086 original size:2 final size:2

Alignment explanation


    Indices: 6079--6132  Score: 108
    Period size: 2  Copynumber: 27.0  Consensus size: 2

       6069 CTATGTATGA

                                                                          
       6079 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                             
       6121 TC TC TC TC TC TC
          1 TC TC TC TC TC TC

       6133 ACATGCCATA


Statistics
Matches: 52,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   52  1.00

ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50


Consensus pattern (2 bp):   
TC

Found at i:6245 original size:45 final size:44

Alignment explanation


    Indices: 6194--6286  Score: 109
    Period size: 45  Copynumber: 2.1  Consensus size: 44

       6184 TTTCTTTTGC

                                 *     *                   
       6194 AAAATTTT-AA-TTACTTTTTTTATTGTTTTAGATATTTTTATTTTT
          1 AAAATTTTAAATTTACTTTTTATATTGATTT--AT-TTTTTATTTTT

                            *                            
       6239 AAAATTTTAAATTTTAGTTTTTATATTGATTTATTTTTTATTTTT
          1 AAAATTTTAAA-TTTACTTTTTATATTGATTTATTTTTTATTTTT

               
       6284 AAA
          1 AAA

       6287 TTTCATAATT


Statistics
Matches: 42,  Mismatches: 3, Indels: 6
        0.82            0.06        0.12

Matches are distributed among these distances:
  45   22  0.52
  46    4  0.10
  48   16  0.38

ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65


Consensus pattern (44 bp):   
AAAATTTTAAATTTACTTTTTATATTGATTTATTTTTTATTTTT

Found at i:6605 original size:29 final size:30

Alignment explanation


    Indices: 6559--6617  Score: 93
    Period size: 29  Copynumber: 2.0  Consensus size: 30

       6549 GAATTGGATC

                                          
       6559 AAATCAAAATTTAATGTATAAAATTGCACA
          1 AAATCAAAATTTAATGTATAAAATTGCACA

                    *           *         
       6589 AAATCAAAGTTT-ATGTATACAATTGCACA
          1 AAATCAAAATTTAATGTATAAAATTGCACA

       6618 TTAAACCGTG


Statistics
Matches: 27,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  29   16  0.59
  30   11  0.41

ACGTcount: A:0.49, C:0.12, G:0.08, T:0.31


Consensus pattern (30 bp):   
AAATCAAAATTTAATGTATAAAATTGCACA

Found at i:16440 original size:16 final size:17

Alignment explanation


    Indices: 16421--16456  Score: 56
    Period size: 17  Copynumber: 2.2  Consensus size: 17

      16411 CGAATGAAAC

                       *     
      16421 AAACAATA-AGTGAAGG
          1 AAACAATAGAGGGAAGG

                             
      16437 AAACAATAGAGGGAAGG
          1 AAACAATAGAGGGAAGG

               
      16454 AAA
          1 AAA

      16457 AAAAAAAGAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  16    8  0.44
  17   10  0.56

ACGTcount: A:0.58, C:0.06, G:0.28, T:0.08


Consensus pattern (17 bp):   
AAACAATAGAGGGAAGG

Done.