Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010000.1 Kokia drynarioides strain JFW-HI SEQ_124758, 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: 6021
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32


Found at i:321 original size:27 final size:27

Alignment explanation


    Indices: 291--373  Score: 148
    Period size: 27  Copynumber: 3.1  Consensus size: 27

        281 ATAAAATATA

                                       
        291 TAAAAGATTACATAAATAAGGGTAAAT
          1 TAAAAGATTACATAAATAAGGGTAAAT

                                       
        318 TAAAAGATTACATAAATAAGGGTAAAT
          1 TAAAAGATTACATAAATAAGGGTAAAT

                               **      
        345 TAAAAGATTACATAAATAACAGTAAAT
          1 TAAAAGATTACATAAATAAGGGTAAAT

              
        372 TA
          1 TA

        374 CATAAATAAT


Statistics
Matches: 54,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  27   54  1.00

ACGTcount: A:0.57, C:0.05, G:0.12, T:0.27


Consensus pattern (27 bp):   
TAAAAGATTACATAAATAAGGGTAAAT

Found at i:1083 original size:25 final size:24

Alignment explanation


    Indices: 1038--1092  Score: 58
    Period size: 25  Copynumber: 2.2  Consensus size: 24

       1028 CTCAACTCTC

                                    
       1038 ATTTTTTATTAAAATTCTATTA-A
          1 ATTTTTTATTAAAATTCTATTACA

                          **  *       
       1061 GATTTTTTAATTAATTTTTTATTACA
          1 -ATTTTTT-ATTAAAATTCTATTACA

                  
       1087 ATTTTT
          1 ATTTTT

       1093 ATTTCATATT


Statistics
Matches: 26,  Mismatches: 3, Indels: 3
        0.81            0.09        0.09

Matches are distributed among these distances:
  24    7  0.27
  25   18  0.69
  26    1  0.04

ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62


Consensus pattern (24 bp):   
ATTTTTTATTAAAATTCTATTACA

Found at i:4524 original size:24 final size:24

Alignment explanation


    Indices: 4491--4554  Score: 92
    Period size: 24  Copynumber: 2.7  Consensus size: 24

       4481 AAAAAGGTGG

                 *              *   
       4491 ACCATATTCGTAACCAGCTCTACA
          1 ACCATCTTCGTAACCAGCTCCACA

                      *   *         
       4515 ACCATCTTCGCAACTAGCTCCACA
          1 ACCATCTTCGTAACCAGCTCCACA

                            
       4539 ACCATCTTCGTAACCA
          1 ACCATCTTCGTAACCA

       4555 CCTATTCGTA


Statistics
Matches: 34,  Mismatches: 6, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  24   34  1.00

ACGTcount: A:0.31, C:0.38, G:0.08, T:0.23


Consensus pattern (24 bp):   
ACCATCTTCGTAACCAGCTCCACA

Found at i:4848 original size:17 final size:16

Alignment explanation


    Indices: 4807--4848  Score: 50
    Period size: 17  Copynumber: 2.6  Consensus size: 16

       4797 AATATTGTAT

                            
       4807 ATGAAA-TGTTTTTAA
          1 ATGAAATTGTTTTTAA

              *              
       4822 ATAAATATTGTTTTTAA
          1 ATGAA-ATTGTTTTTAA

                      
       4839 ATCGAAATTG
          1 AT-GAAATTG

       4849 GTTGTCATTG


Statistics
Matches: 22,  Mismatches: 2, Indels: 4
        0.79            0.07        0.14

Matches are distributed among these distances:
  15    4  0.18
  16    1  0.05
  17   15  0.68
  18    2  0.09

ACGTcount: A:0.40, C:0.02, G:0.12, T:0.45


Consensus pattern (16 bp):   
ATGAAATTGTTTTTAA
Done.