Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007966.1 Kokia drynarioides strain JFW-HI SEQ_122614, 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: 9933
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36


Found at i:3182 original size:20 final size:20

Alignment explanation


    Indices: 3145--3182  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       3135 TTATTTTTTT

                         *      
       3145 TATATATACACAGGCATATA
          1 TATATATACACAGACATATA

                      *       
       3165 TATATATACATAGACATA
          1 TATATATACACAGACATA

       3183 CATTCTGATT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32


Consensus pattern (20 bp):   
TATATATACACAGACATATA

Found at i:5333 original size:10 final size:10

Alignment explanation


    Indices: 5300--5332  Score: 59
    Period size: 10  Copynumber: 3.4  Consensus size: 10

       5290 TAAGTGAAAG

                      
       5300 AAAATCATGA
          1 AAAATCATGA

                      
       5310 AAAATCATGA
          1 AAAATCATGA

                      
       5320 AAAATCAT-A
          1 AAAATCATGA

                
       5329 AAAA
          1 AAAA

       5333 ACTTATAAAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   9    5  0.22
  10   18  0.78

ACGTcount: A:0.67, C:0.09, G:0.06, T:0.18


Consensus pattern (10 bp):   
AAAATCATGA

Found at i:5412 original size:18 final size:18

Alignment explanation


    Indices: 5381--5432  Score: 52
    Period size: 18  Copynumber: 2.9  Consensus size: 18

       5371 ATAAGTTCTA

                 *   *        
       5381 ATAAATTATAAAAAAATG
          1 ATAAAATATTAAAAAATG

                           * *
       5399 ATAAAATATTAAAAATTT
          1 ATAAAATATTAAAAAATG

                             
       5417 ATAAAAT-TTATAAAAA
          1 ATAAAATATTA-AAAAA

       5433 AACTCTTTTA


Statistics
Matches: 28,  Mismatches: 5, Indels: 2
        0.80            0.14        0.06

Matches are distributed among these distances:
  17    3  0.11
  18   25  0.89

ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33


Consensus pattern (18 bp):   
ATAAAATATTAAAAAATG

Found at i:5413 original size:9 final size:9

Alignment explanation


    Indices: 5399--5431  Score: 50
    Period size: 9  Copynumber: 3.7  Consensus size: 9

       5389 TAAAAAAATG

                      
       5399 ATAAAATATT
          1 ATAAAAT-TT

                     
       5409 A-AAAATTT
          1 ATAAAATTT

                     
       5417 ATAAAATTT
          1 ATAAAATTT

                  
       5426 ATAAAA
          1 ATAAAA

       5432 AAACTCTTTT


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
   8    3  0.14
   9   18  0.82
  10    1  0.05

ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36


Consensus pattern (9 bp):   
ATAAAATTT
Done.