Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014623.1 Kokia drynarioides strain JFW-HI SEQ_129662, 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: 20391
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:6803 original size:15 final size:15

Alignment explanation


    Indices: 6783--6813  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       6773 GTAAAGAGTA

                           
       6783 AATAACTTAAAATCC
          1 AATAACTTAAAATCC

                           
       6798 AATAACTTAAAATCC
          1 AATAACTTAAAATCC

             
       6813 A
          1 A

       6814 TAGAGAAGTC


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.55, C:0.19, G:0.00, T:0.26


Consensus pattern (15 bp):   
AATAACTTAAAATCC

Found at i:17402 original size:26 final size:26

Alignment explanation


    Indices: 17353--17401  Score: 73
    Period size: 25  Copynumber: 1.9  Consensus size: 26

      17343 AAAAGTTATC

                        *             
      17353 AAATTCAAGGACTAACATGAAAAACA
          1 AAATTCAAGGACCAACATGAAAAACA

                           *        
      17379 AAATT-AAGGACCAAGATGAAAAA
          1 AAATTCAAGGACCAACATGAAAAA

      17402 AAATGCAAAT


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  25   16  0.76
  26    5  0.24

ACGTcount: A:0.59, C:0.12, G:0.14, T:0.14


Consensus pattern (26 bp):   
AAATTCAAGGACCAACATGAAAAACA

Found at i:17636 original size:2 final size:2

Alignment explanation


    Indices: 17629--17668  Score: 73
    Period size: 2  Copynumber: 20.5  Consensus size: 2

      17619 GGAAAATGGA

                                                                         
      17629 AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      17669 AACAGTAAAA


Statistics
Matches: 37,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   36  0.97

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


Consensus pattern (2 bp):   
AT

Found at i:19104 original size:17 final size:17

Alignment explanation


    Indices: 19082--19144  Score: 99
    Period size: 17  Copynumber: 3.7  Consensus size: 17

      19072 TTGGAAATTG

                             
      19082 AATTTAAATTTATTTTA
          1 AATTTAAATTTATTTTA

                           * 
      19099 AATTTAAATTTATTTGA
          1 AATTTAAATTTATTTTA

                          *  
      19116 AATTTAAATTTATTATA
          1 AATTTAAATTTATTTTA

              *         
      19133 AAATTAAATTTA
          1 AATTTAAATTTA

      19145 GAAAAGTCCA


Statistics
Matches: 42,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  17   42  1.00

ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52


Consensus pattern (17 bp):   
AATTTAAATTTATTTTA

Found at i:19120 original size:7 final size:6

Alignment explanation


    Indices: 19082--19144  Score: 55
    Period size: 6  Copynumber: 11.0  Consensus size: 6

      19072 TTGGAAATTG

                           *                                        
      19082 AATTTA AATTT- ATTTTA AATTTA AATTT- -ATTTGA AATTTA AATTT-
          1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA AATTTA

                      *          
      19127 -ATTATA AAATTA AATTTA
          1 AATT-TA AATTTA AATTTA

      19145 GAAAAGTCCA


Statistics
Matches: 46,  Mismatches: 4, Indels: 14
        0.72            0.06        0.22

Matches are distributed among these distances:
   4    7  0.15
   5    5  0.11
   6   28  0.61
   7    6  0.13

ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52


Consensus pattern (6 bp):   
AATTTA

Found at i:19220 original size:15 final size:15

Alignment explanation


    Indices: 19181--19230  Score: 55
    Period size: 15  Copynumber: 3.3  Consensus size: 15

      19171 AAACAAAAGT

                            
      19181 CCAAATAACAAATGGC
          1 CCAAAT-ACAAATGGC

               **    *     
      19197 CCAGTTACAGATGGC
          1 CCAAATACAAATGGC

                          *
      19212 CCAAATACAAATGGT
          1 CCAAATACAAATGGC

                
      19227 CCAA
          1 CCAA

      19231 TTATAAAGTG


Statistics
Matches: 27,  Mismatches: 7, Indels: 1
        0.77            0.20        0.03

Matches are distributed among these distances:
  15   23  0.85
  16    4  0.15

ACGTcount: A:0.42, C:0.26, G:0.16, T:0.16


Consensus pattern (15 bp):   
CCAAATACAAATGGC
Done.