Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001878.1 Kokia drynarioides strain JFW-HI SEQ_113647, 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: 10050
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36


Found at i:337 original size:77 final size:79

Alignment explanation


    Indices: 245--409  Score: 307
    Period size: 77  Copynumber: 2.1  Consensus size: 79

        235 ATGCTTGTTA

                                                                             
        245 CACACAAAACAACTTTTAAATACCAAAAGTATCAAAGCACATGAG-TCTTAACACTCTCCTTATT
          1 CACACAAAACAACTTTTAAATACCAAAAGTATCAAAGCACATGAGTTCTTAACACTCTCCTTATT

                          
        309 CAAACACAAA-CCT
         66 CAAACACAAACCCT

                                                                       *     
        322 CACACAAAACAACTTTTAAATACCAAAAGTATCAAAGCACATGAGTTCTTAACACTCTCGTTATT
          1 CACACAAAACAACTTTTAAATACCAAAAGTATCAAAGCACATGAGTTCTTAACACTCTCCTTATT

                          
        387 CAAACACAAACCCT
         66 CAAACACAAACCCT

                     
        401 CACACAAAA
          1 CACACAAAA

        410 GCATACATTA


Statistics
Matches: 85,  Mismatches: 1, Indels: 2
        0.97            0.01        0.02

Matches are distributed among these distances:
  77   45  0.53
  78   28  0.33
  79   12  0.14

ACGTcount: A:0.45, C:0.27, G:0.05, T:0.22


Consensus pattern (79 bp):   
CACACAAAACAACTTTTAAATACCAAAAGTATCAAAGCACATGAGTTCTTAACACTCTCCTTATT
CAAACACAAACCCT

Found at i:4464 original size:16 final size:16

Alignment explanation


    Indices: 4440--4482  Score: 77
    Period size: 16  Copynumber: 2.7  Consensus size: 16

       4430 CGCCATGAAT

                *           
       4440 ACTGTAGCTTCGCGCA
          1 ACTGCAGCTTCGCGCA

                            
       4456 ACTGCAGCTTCGCGCA
          1 ACTGCAGCTTCGCGCA

                       
       4472 ACTGCAGCTTC
          1 ACTGCAGCTTC

       4483 CTTAACGTTT


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  16   26  1.00

ACGTcount: A:0.19, C:0.35, G:0.23, T:0.23


Consensus pattern (16 bp):   
ACTGCAGCTTCGCGCA

Found at i:6034 original size:22 final size:23

Alignment explanation


    Indices: 6009--6054  Score: 58
    Period size: 22  Copynumber: 2.0  Consensus size: 23

       5999 TTTATAAACA

                  *                
       6009 TAAATAGCTATATTTATTT-TTT
          1 TAAATAACTATATTTATTTGTTT

                   * *             
       6031 TAAATAATTGTATTTATTTGTTT
          1 TAAATAACTATATTTATTTGTTT

             
       6054 T
          1 T

       6055 TTAATACTTC


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  22   16  0.80
  23    4  0.20

ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61


Consensus pattern (23 bp):   
TAAATAACTATATTTATTTGTTT
Done.