Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002149.1 Kokia drynarioides strain JFW-HI SEQ_114098, 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: 3653
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.28


Found at i:3038 original size:3 final size:3

Alignment explanation


    Indices: 3025--3072  Score: 64
    Period size: 3  Copynumber: 16.3  Consensus size: 3

       3015 CAGAAGAGGA

                                                               *        
       3025 AAG AA- AAG AAG AAG AAG AAG AAG AAG -AG AAGG AAG AAA AAG AAG
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG AAG AAG

                 
       3069 AAG A
          1 AAG A

       3073 TGTTGCCCTG


Statistics
Matches: 40,  Mismatches: 2, Indels: 6
        0.83            0.04        0.12

Matches are distributed among these distances:
   2    4  0.10
   3   33  0.82
   4    3  0.08

ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00


Consensus pattern (3 bp):   
AAG

Found at i:3045 original size:24 final size:26

Alignment explanation


    Indices: 3017--3072  Score: 71
    Period size: 27  Copynumber: 2.2  Consensus size: 26

       3007 TATTGAGGCA

                 *              *     
       3017 GAAGAGGAA-AGAA-AAGAAGAAGAA
          1 GAAGAAGAAGAGAAGAAGAAAAAGAA

                                       
       3041 GAAGAAGAAGAGAAGGAAGAAAAAGAA
          1 GAAGAAGAAGAGAA-GAAGAAAAAGAA

                 
       3068 GAAGA
          1 GAAGA

       3073 TGTTGCCCTG


Statistics
Matches: 27,  Mismatches: 2, Indels: 3
        0.84            0.06        0.09

Matches are distributed among these distances:
  24    8  0.30
  25    4  0.15
  27   15  0.56

ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00


Consensus pattern (26 bp):   
GAAGAAGAAGAGAAGAAGAAAAAGAA

Found at i:3523 original size:18 final size:18

Alignment explanation


    Indices: 3483--3523  Score: 52
    Period size: 16  Copynumber: 2.4  Consensus size: 18

       3473 GTCATTGCAT

                              
       3483 TTTTA-TTATCTCTA-CA
          1 TTTTATTTATCTCTAGCA

                              
       3499 TTTTATTTATC-CTAGCA
          1 TTTTATTTATCTCTAGCA

                    
       3516 TCTTTATT
          1 T-TTTATT

       3524 GTAGTTGCAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  16    8  0.36
  17    8  0.36
  18    6  0.27

ACGTcount: A:0.22, C:0.17, G:0.02, T:0.59


Consensus pattern (18 bp):   
TTTTATTTATCTCTAGCA
Done.