Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012233.1 Kokia drynarioides strain JFW-HI SEQ_127234, 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: 5499
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.26


Found at i:4054 original size:26 final size:27

Alignment explanation


    Indices: 3998--4057  Score: 68
    Period size: 26  Copynumber: 2.2  Consensus size: 27

       3988 CAATTTTCAA

                             *          
       3998 TTAATGATTGTTTCCTTTGACCCTCCCT
          1 TTAAT-ATTGTTTCCTTCGACCCTCCCT

                               *    ** 
       4026 TTAATATTGTTT-CTTCGATCCTCTTT
          1 TTAATATTGTTTCCTTCGACCCTCCCT

                  
       4052 TTAATA
          1 TTAATA

       4058 GAATTCTTGG


Statistics
Matches: 28,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  26   16  0.57
  27    7  0.25
  28    5  0.18

ACGTcount: A:0.18, C:0.22, G:0.08, T:0.52


Consensus pattern (27 bp):   
TTAATATTGTTTCCTTCGACCCTCCCT

Found at i:5454 original size:17 final size:17

Alignment explanation


    Indices: 5432--5497  Score: 89
    Period size: 17  Copynumber: 3.9  Consensus size: 17

       5422 CATACTCCCT

                             
       5432 TTAAATTTATTTTAAAA
          1 TTAAATTTATTTTAAAA

                     *       
       5449 TTAAATTT-GTTTAAAA
          1 TTAAATTTATTTTAAAA

                             *
       5465 TTTAAATTTATTTTAAAT
          1 -TTAAATTTATTTTAAAA

                     *     
       5483 TTAAATTTAATTTAA
          1 TTAAATTTATTTTAA

       5498 GT


Statistics
Matches: 43,  Mismatches: 4, Indels: 4
        0.84            0.08        0.08

Matches are distributed among these distances:
  16    7  0.16
  17   30  0.70
  18    6  0.14

ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55


Consensus pattern (17 bp):   
TTAAATTTATTTTAAAA

Found at i:5484 original size:7 final size:6

Alignment explanation


    Indices: 5431--5497  Score: 54
    Period size: 6  Copynumber: 11.8  Consensus size: 6

       5421 CCATACTCCC

                        *        *           *                     *
       5431 TTTAAA TTT-AT TTTAAA ATTAAA TTT--G TTTAAAA TTTAAA TTT-AT
          1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA

                                      
       5476 TTTAAA TTTAAA TTT-AA TTTAA
          1 TTTAAA TTTAAA TTTAAA TTTAA

       5498 GT


Statistics
Matches: 47,  Mismatches: 8, Indels: 12
        0.70            0.12        0.18

Matches are distributed among these distances:
   4    3  0.06
   5   13  0.28
   6   28  0.60
   7    3  0.06

ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55


Consensus pattern (6 bp):   
TTTAAA
Done.