Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014225.1 Kokia drynarioides strain JFW-HI SEQ_129258, 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: 9461
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36


Found at i:1530 original size:151 final size:151

Alignment explanation


    Indices: 1256--1558  Score: 606
    Period size: 151  Copynumber: 2.0  Consensus size: 151

       1246 ATTATTTGTT

                                                                             
       1256 TGCTTATTTATAAATAAAATACTCTATTAAAAATTTTTAAAAATATAGAAATAAAAATATTCATA
          1 TGCTTATTTATAAATAAAATACTCTATTAAAAATTTTTAAAAATATAGAAATAAAAATATTCATA

                                                                             
       1321 TATGCAATGGATGTGTATAGTTTGATGAACATGATTAAAAACATTAAATAAAATATTTATATATG
         66 TATGCAATGGATGTGTATAGTTTGATGAACATGATTAAAAACATTAAATAAAATATTTATATATG

                                 
       1386 CATTAAAAGTGTATAGTTTGG
        131 CATTAAAAGTGTATAGTTTGG

                                                                             
       1407 TGCTTATTTATAAATAAAATACTCTATTAAAAATTTTTAAAAATATAGAAATAAAAATATTCATA
          1 TGCTTATTTATAAATAAAATACTCTATTAAAAATTTTTAAAAATATAGAAATAAAAATATTCATA

                                                                             
       1472 TATGCAATGGATGTGTATAGTTTGATGAACATGATTAAAAACATTAAATAAAATATTTATATATG
         66 TATGCAATGGATGTGTATAGTTTGATGAACATGATTAAAAACATTAAATAAAATATTTATATATG

                                 
       1537 CATTAAAAGTGTATAGTTTGG
        131 CATTAAAAGTGTATAGTTTGG

             
       1558 T
          1 T

       1559 AATATGATTG


Statistics
Matches: 152,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
 151  152  1.00

ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38


Consensus pattern (151 bp):   
TGCTTATTTATAAATAAAATACTCTATTAAAAATTTTTAAAAATATAGAAATAAAAATATTCATA
TATGCAATGGATGTGTATAGTTTGATGAACATGATTAAAAACATTAAATAAAATATTTATATATG
CATTAAAAGTGTATAGTTTGG

Found at i:5043 original size:23 final size:22

Alignment explanation


    Indices: 5017--5066  Score: 66
    Period size: 23  Copynumber: 2.2  Consensus size: 22

       5007 AACAAATACA

                                    
       5017 TATATTTATATA-ACTAAAATATT
          1 TATATTT-TATACA-TAAAATATT

                                   
       5040 TATATTTTATACTATAAAATATT
          1 TATATTTTATAC-ATAAAATATT

                
       5063 TATA
          1 TATA

       5067 AATTTTAATA


Statistics
Matches: 25,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
  22    4  0.16
  23   20  0.80
  24    1  0.04

ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50


Consensus pattern (22 bp):   
TATATTTTATACATAAAATATT

Found at i:6258 original size:48 final size:48

Alignment explanation


    Indices: 6187--6279  Score: 186
    Period size: 48  Copynumber: 1.9  Consensus size: 48

       6177 ACTTCAGAAA

                                                            
       6187 TCTTGAAGTGCTCCAACATCCTTAACATTGAACTTGTTGAGAATACTG
          1 TCTTGAAGTGCTCCAACATCCTTAACATTGAACTTGTTGAGAATACTG

                                                         
       6235 TCTTGAAGTGCTCCAACATCCTTAACATTGAACTTGTTGAGAATA
          1 TCTTGAAGTGCTCCAACATCCTTAACATTGAACTTGTTGAGAATA

       6280 GTAATGCTGG


Statistics
Matches: 45,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  48   45  1.00

ACGTcount: A:0.30, C:0.20, G:0.16, T:0.33


Consensus pattern (48 bp):   
TCTTGAAGTGCTCCAACATCCTTAACATTGAACTTGTTGAGAATACTG

Found at i:8993 original size:17 final size:17

Alignment explanation


    Indices: 8960--8993  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       8950 AAAAAAATTT

                    *        
       8960 ATTTAAATGTTAGTTAA
          1 ATTTAAATATTAGTTAA

                        *    
       8977 ATTTAAATATTATTTAA
          1 ATTTAAATATTAGTTAA

       8994 TCATGTAAAA


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50


Consensus pattern (17 bp):   
ATTTAAATATTAGTTAA

Found at i:9337 original size:2 final size:2

Alignment explanation


    Indices: 9332--9376  Score: 81
    Period size: 2  Copynumber: 22.5  Consensus size: 2

       9322 GTTTTTTTAA

                                              *                           
       9332 AT AT AT AT AT AT AT AT AT AT AT AA 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 AT AT AT AT AT

                
       9374 AT A
          1 AT A

       9377 AAATTCAATT


Statistics
Matches: 41,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   41  1.00

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Done.