Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007406.1 Kokia drynarioides strain JFW-HI SEQ_122025, 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: 3601
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.35


Found at i:994 original size:30 final size:30

Alignment explanation


    Indices: 958--1022  Score: 112
    Period size: 30  Copynumber: 2.2  Consensus size: 30

        948 TAACTTAACA

                    *  *                  
        958 AACAAATGTCTTTAAAATAATAACAAAATT
          1 AACAAATGCCTCTAAAATAATAACAAAATT

                                          
        988 AACAAATGCCTCTAAAATAATAACAAAATT
          1 AACAAATGCCTCTAAAATAATAACAAAATT

                 
       1018 AACAA
          1 AACAA

       1023 TAAAATAAGT


Statistics
Matches: 33,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  30   33  1.00

ACGTcount: A:0.58, C:0.14, G:0.03, T:0.25


Consensus pattern (30 bp):   
AACAAATGCCTCTAAAATAATAACAAAATT

Found at i:3417 original size:34 final size:34

Alignment explanation


    Indices: 3374--3460  Score: 129
    Period size: 34  Copynumber: 2.6  Consensus size: 34

       3364 ATATGAAAAA

                       *             *   *  * 
       3374 TTAAGGAAGATAGAAGGTTAAAGATTAAAGGAGG
          1 TTAAGGAAGATGGAAGGTTAAAGATCAAAAGAAG

                                              
       3408 TTAAGGAAGATGGAAGGTTAAAGATCAAAAGAAG
          1 TTAAGGAAGATGGAAGGTTAAAGATCAAAAGAAG

                    *          
       3442 TTAAGGAATATGGAAGGTT
          1 TTAAGGAAGATGGAAGGTT

       3461 GAACATCCAT


Statistics
Matches: 48,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  34   48  1.00

ACGTcount: A:0.46, C:0.01, G:0.31, T:0.22


Consensus pattern (34 bp):   
TTAAGGAAGATGGAAGGTTAAAGATCAAAAGAAG

Found at i:3425 original size:17 final size:17

Alignment explanation


    Indices: 3374--3428  Score: 51
    Period size: 17  Copynumber: 3.2  Consensus size: 17

       3364 ATATGAAAAA

                       *     
       3374 TTAAGGAAGATAGAAGG
          1 TTAAGGAAGATGGAAGG

                *       *      
       3391 TTAAAGATTA-AAGG-AGG
          1 TTAAGGA--AGATGGAAGG

                             
       3408 TTAAGGAAGATGGAAGG
          1 TTAAGGAAGATGGAAGG

                
       3425 TTAA
          1 TTAA

       3429 AGATCAAAAG


Statistics
Matches: 29,  Mismatches: 5, Indels: 8
        0.69            0.12        0.19

Matches are distributed among these distances:
  15    1  0.03
  16    3  0.10
  17   22  0.76
  18    2  0.07
  19    1  0.03

ACGTcount: A:0.45, C:0.00, G:0.33, T:0.22


Consensus pattern (17 bp):   
TTAAGGAAGATGGAAGG
Done.