Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000489.1 Kokia drynarioides strain JFW-HI SEQ_111364, 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: 10465
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29


Found at i:8112 original size:3 final size:3

Alignment explanation


    Indices: 8104--8160  Score: 57
    Period size: 3  Copynumber: 19.0  Consensus size: 3

       8094 GTAATGAGGT

                                                  *                      
       8104 AGA AGA AGA AGAA AGA A-A AGA AGA AGA AAA AGA AG- AGA AGAA AGA
          1 AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA

                            
       8149 A-A ATGA AGA AGA
          1 AGA A-GA AGA AGA

       8161 TGTTGCCCCA


Statistics
Matches: 46,  Mismatches: 2, Indels: 12
        0.77            0.03        0.20

Matches are distributed among these distances:
   2    6  0.13
   3   32  0.70
   4    8  0.17

ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02


Consensus pattern (3 bp):   
AGA

Found at i:8130 original size:21 final size:24

Alignment explanation


    Indices: 8104--8160  Score: 73
    Period size: 24  Copynumber: 2.4  Consensus size: 24

       8094 GTAATGAGGT

                                     
       8104 AGAAGAAGAAGA-AAGAAAAGAAGA
          1 AGAAGAAGAAGAGAAG-AAAGAAGA

                *                   
       8128 AGAAAAAGAAGAGAAGAAAGAA-A
          1 AGAAGAAGAAGAGAAGAAAGAAGA

                      
       8151 ATGAAGAAGA
          1 A-GAAGAAGA

       8161 TGTTGCCCCA


Statistics
Matches: 29,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  23    2  0.07
  24   24  0.83
  25    3  0.10

ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02


Consensus pattern (24 bp):   
AGAAGAAGAAGAGAAGAAAGAAGA

Found at i:8148 original size:18 final size:17

Alignment explanation


    Indices: 8104--8157  Score: 72
    Period size: 18  Copynumber: 3.1  Consensus size: 17

       8094 GTAATGAGGT

                             *
       8104 AGAAGAAGAAGAAAGAAA
          1 AGAAGAAGAA-AAAGAAG

                             
       8122 AGAAGAAGAAAAAGAAG
          1 AGAAGAAGAAAAAGAAG

                         *    
       8139 AGAAGAAAGAAAATGAAG
          1 AGAAG-AAGAAAAAGAAG

             
       8157 A
          1 A

       8158 AGATGTTGCC


Statistics
Matches: 33,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
  17   11  0.33
  18   22  0.67

ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02


Consensus pattern (17 bp):   
AGAAGAAGAAAAAGAAG

Done.