Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002987.1 Kokia drynarioides strain JFW-HI SEQ_115474, 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: 4943
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.40


Found at i:1864 original size:22 final size:20

Alignment explanation


    Indices: 1833--1872  Score: 53
    Period size: 22  Copynumber: 1.9  Consensus size: 20

       1823 AGGTATAAAA

                 *                
       1833 TTTATTTTAAATATTCTTAATT
          1 TTTATCTTAAA-ATT-TTAATT

                              
       1855 TTTATCTTAAAATTTTAA
          1 TTTATCTTAAAATTTTAA

       1873 AGTTATTTAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    4  0.24
  21    3  0.18
  22   10  0.59

ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60


Consensus pattern (20 bp):   
TTTATCTTAAAATTTTAATT

Found at i:3207 original size:30 final size:30

Alignment explanation


    Indices: 3173--3239  Score: 109
    Period size: 30  Copynumber: 2.2  Consensus size: 30

       3163 AAAGATAGTT

                                           
       3173 TTATATTAATTATATTAT-GAGAAAGTATGG
          1 TTATATTAATTATATTATGGA-AAAGTATGG

                                         *
       3203 TTATATTAATTATATTATGGAAAAGTATGT
          1 TTATATTAATTATATTATGGAAAAGTATGG

                   
       3233 TTATATT
          1 TTATATT

       3240 TTGATATTCT


Statistics
Matches: 35,  Mismatches: 1, Indels: 2
        0.92            0.03        0.05

Matches are distributed among these distances:
  30   33  0.94
  31    2  0.06

ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48


Consensus pattern (30 bp):   
TTATATTAATTATATTATGGAAAAGTATGG

Found at i:3247 original size:29 final size:29

Alignment explanation


    Indices: 3173--3247  Score: 91
    Period size: 30  Copynumber: 2.5  Consensus size: 29

       3163 AAAGATAGTT

                                          
       3173 TTATATTAATTATATTATGAGAAAGTATGG
          1 TTATATT-ATTATATTATGAGAAAGTATGG

                                          *
       3203 TTATATTAATTATATTATG-GAAAAGTATGT
          1 TTATATT-ATTATATTATGAG-AAAGTATGG

                            
       3233 TTATATT-TTGATATT
          1 TTATATTATT-ATATT

       3248 CTCCATATTC


Statistics
Matches: 42,  Mismatches: 1, Indels: 5
        0.88            0.02        0.10

Matches are distributed among these distances:
  28    2  0.05
  29    6  0.14
  30   34  0.81

ACGTcount: A:0.37, C:0.00, G:0.13, T:0.49


Consensus pattern (29 bp):   
TTATATTATTATATTATGAGAAAGTATGG
Done.