Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004707.1 Kokia drynarioides strain JFW-HI SEQ_118275, 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: 12763
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:5532 original size:6 final size:6

Alignment explanation


    Indices: 5521--5565  Score: 69
    Period size: 6  Copynumber: 8.0  Consensus size: 6

       5511 ACATACAATT

                                                                   
       5521 ATTTAA ATTTAA A--T-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
          1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA

       5566 TTCCAACTAA


Statistics
Matches: 36,  Mismatches: 0, Indels: 6
        0.86            0.00        0.14

Matches are distributed among these distances:
   3    2  0.06
   4    1  0.03
   5    1  0.03
   6   32  0.89

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (6 bp):   
ATTTAA

Found at i:12174 original size:4 final size:4

Alignment explanation


    Indices: 12161--12198  Score: 53
    Period size: 4  Copynumber: 10.0  Consensus size: 4

      12151 AAAATTGAAG

                                       *                     
      12161 GAAA -AAA GAAA GAAA -AAA GAGA GAAA GAAA GAAA GAAA
          1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA

      12199 TAAGAAGGAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
   3    6  0.20
   4   24  0.80

ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00


Consensus pattern (4 bp):   
GAAA

Found at i:12187 original size:15 final size:16

Alignment explanation


    Indices: 12167--12196  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

      12157 GAAGGAAAAA

                            
      12167 AGAAAGAAA-AAAGAG
          1 AGAAAGAAAGAAAGAG

                           
      12182 AGAAAGAAAGAAAGA
          1 AGAAAGAAAGAAAGA

      12197 AATAAGAAGG


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    9  0.64
  16    5  0.36

ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00


Consensus pattern (16 bp):   
AGAAAGAAAGAAAGAG

Found at i:12191 original size:23 final size:22

Alignment explanation


    Indices: 12161--12224  Score: 76
    Period size: 23  Copynumber: 2.9  Consensus size: 22

      12151 AAAATTGAAG

                                   
      12161 GAAA-AAAGAAAGAAAAAAGAGA
          1 GAAAGAAAGAAAGAAAAAAGA-A

                            *     
      12183 GAAAGAAAGAAAGAAATAAGAA
          1 GAAAGAAAGAAAGAAAAAAGAA

             *     *            
      12205 GGAAGAAGGAGAAGAAAAAA
          1 GAAAGAAAGA-AAGAAAAAA

      12225 AAAATAATGT


Statistics
Matches: 36,  Mismatches: 4, Indels: 3
        0.84            0.09        0.07

Matches are distributed among these distances:
  22   13  0.36
  23   23  0.64

ACGTcount: A:0.72, C:0.00, G:0.27, T:0.02


Consensus pattern (22 bp):   
GAAAGAAAGAAAGAAAAAAGAA

Found at i:12412 original size:12 final size:12

Alignment explanation


    Indices: 12395--12419  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      12385 TTAAGTTTGG

                        
      12395 TTAATTTTAAAA
          1 TTAATTTTAAAA

                        
      12407 TTAATTTTAAAA
          1 TTAATTTTAAAA

             
      12419 T
          1 T

      12420 ATTTTAATTT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (12 bp):   
TTAATTTTAAAA
Done.