Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004353.1 Kokia drynarioides strain JFW-HI SEQ_117694, 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: 18817
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--32  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

                                                           
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

         33 TAGTTTCAAT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:4303 original size:21 final size:20

Alignment explanation


    Indices: 4260--4304  Score: 54
    Period size: 20  Copynumber: 2.2  Consensus size: 20

       4250 AATTTTCATA

                            * * 
       4260 TATTTTTAATAGTTTATATT
          1 TATTTTTAATAGTTTAGAAT

                        *        
       4280 TATTTTTAATATTTTTAGAAT
          1 TATTTTTAATA-GTTTAGAAT

                
       4301 TATT
          1 TATT

       4305 GTTGAGAAAA


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  20   11  0.52
  21   10  0.48

ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64


Consensus pattern (20 bp):   
TATTTTTAATAGTTTAGAAT

Found at i:11969 original size:19 final size:18

Alignment explanation


    Indices: 11939--12054  Score: 151
    Period size: 18  Copynumber: 6.3  Consensus size: 18

      11929 TTAGCTCATA

                *             
      11939 AGAGTATACTGGCTCGTT
          1 AGAGCATACTGGCTCGTT

                               
      11957 AGAGCATTACTGGCTCGTT
          1 AGAGCA-TACTGGCTCGTT

                              *
      11976 AGAGCATTACTGGCTCGTA
          1 AGAGCA-TACTGGCTCGTT

                *      *      
      11995 AGAGAATACTGACTCGTT
          1 AGAGCATACTGGCTCGTT

               *      *      *
      12013 AGACCATACTAGCTCGTA
          1 AGAGCATACTGGCTCGTT

                              
      12031 AGAGCATACTGGCTCGTT
          1 AGAGCATACTGGCTCGTT

                  
      12049 AGAGCA
          1 AGAGCA

      12055 ATATATTGTT


Statistics
Matches: 84,  Mismatches: 13, Indels: 2
        0.85            0.13        0.02

Matches are distributed among these distances:
  18   49  0.58
  19   35  0.42

ACGTcount: A:0.28, C:0.21, G:0.25, T:0.27


Consensus pattern (18 bp):   
AGAGCATACTGGCTCGTT

Done.