Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014706.1 Kokia drynarioides strain JFW-HI SEQ_129745, 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: 313676
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34

Warning! 64 characters in sequence are not A, C, G, or T


File 2 of 2

Found at i:296473 original size:24 final size:24

Alignment explanation


    Indices: 296437--296592  Score: 152
    Period size: 24  Copynumber: 6.5  Consensus size: 24

     296427 ACATCAAACT

                                    
     296437 GCGTAAACGTGTGCAAGCTGACGA
          1 GCGTAAACGTGTGCAAGCTGACGA

                    *        *      
     296461 GCGTAAACATGTGCAAGTTGACGA
          1 GCGTAAACGTGTGCAAGCTGACGA

              *   **  * **   *      
     296485 GCATAATTGTATATAAGTTGAC-A
          1 GCGTAAACGTGTGCAAGCTGACGA

                   *    **  *       
     296508 GCGTAAATGTGTATAAACTGACGA
          1 GCGTAAACGTGTGCAAGCTGACGA

                   *         *   *  
     296532 GCGTAAATGTGTGCAAGTTGAAGA
          1 GCGTAAACGTGTGCAAGCTGACGA

                                 *  
     296556 GCGTAAACGTGTGCAAGCTGAAGA
          1 GCGTAAACGTGTGCAAGCTGACGA

                         
     296580 GCGTAAACGTGTG
          1 GCGTAAACGTGTG

     296593 AAAGTTGATA


Statistics
Matches: 110,  Mismatches: 21, Indels: 2
        0.83            0.16        0.02

Matches are distributed among these distances:
  23   18  0.16
  24   92  0.84

ACGTcount: A:0.33, C:0.14, G:0.29, T:0.23


Consensus pattern (24 bp):   
GCGTAAACGTGTGCAAGCTGACGA

Found at i:296638 original size:25 final size:25

Alignment explanation


    Indices: 296609--296693  Score: 64
    Period size: 25  Copynumber: 3.2  Consensus size: 25

     296599 GATAAGTTTT

                                     
     296609 AACATATACAAGATGTTGAATATCA
          1 AACATATACAAGATGTTGAATATCA

                 *  *       *            **
     296634 AACATGTATAAGTAAAAGTT-AATAAGTTTT
          1 AACATATACAAG---ATGTTGAAT-A--TCA

                                     
     296664 AACATATACAAGATGTTGAATATCA
          1 AACATATACAAGATGTTGAATATCA

                 
     296689 AACAT
          1 AACAT

     296694 GTATAAGTAG


Statistics
Matches: 43,  Mismatches: 10, Indels: 14
        0.64            0.15        0.21

Matches are distributed among these distances:
  25   16  0.37
  27    8  0.19
  28    8  0.19
  30   11  0.26

ACGTcount: A:0.48, C:0.09, G:0.12, T:0.31


Consensus pattern (25 bp):   
AACATATACAAGATGTTGAATATCA

Found at i:296660 original size:55 final size:55

Alignment explanation


    Indices: 296593--296707  Score: 212
    Period size: 55  Copynumber: 2.1  Consensus size: 55

     296583 TAAACGTGTG

                  *                                                
     296593 AAAGTTGATAAGTTTTAACATATACAAGATGTTGAATATCAAACATGTATAAGTA
          1 AAAGTTAATAAGTTTTAACATATACAAGATGTTGAATATCAAACATGTATAAGTA

                                                                   
     296648 AAAGTTAATAAGTTTTAACATATACAAGATGTTGAATATCAAACATGTATAAGTA
          1 AAAGTTAATAAGTTTTAACATATACAAGATGTTGAATATCAAACATGTATAAGTA

            *    
     296703 GAAGT
          1 AAAGT

     296708 GCACAAATGT


Statistics
Matches: 58,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  55   58  1.00

ACGTcount: A:0.46, C:0.07, G:0.15, T:0.32


Consensus pattern (55 bp):   
AAAGTTAATAAGTTTTAACATATACAAGATGTTGAATATCAAACATGTATAAGTA

Found at i:313607 original size:15 final size:16

Alignment explanation


    Indices: 313575--313607  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

     313565 AGTCTCTTGG

                            
     313575 GTTGATTATAGTGGAA
          1 GTTGATTATAGTGGAA

                   *        
     313591 GTTGATTTTAG-GGAA
          1 GTTGATTATAGTGGAA

              
     313606 GT
          1 GT

     313608 GTACAACTGG


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  15    6  0.38
  16   10  0.62

ACGTcount: A:0.27, C:0.00, G:0.33, T:0.39


Consensus pattern (16 bp):   
GTTGATTATAGTGGAA

Done.