Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011596.1 Kokia drynarioides strain JFW-HI SEQ_126586, 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: 276558
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34

Warning! 84 characters in sequence are not A, C, G, or T


File 2 of 2

Found at i:254959 original size:23 final size:23

Alignment explanation


    Indices: 254909--254960  Score: 77
    Period size: 23  Copynumber: 2.2  Consensus size: 23

     254899 TTCTTTCAAC

                                  **
     254909 ATTGAGTAAGTCAACATATTCGTG
          1 ATTG-GTAAGTCAACATATTCGCA

                                   
     254933 ATTGGTAAGTCAACATATTCGCA
          1 ATTGGTAAGTCAACATATTCGCA

                 
     254956 ATTGG
          1 ATTGG

     254961 ACATCTGCCT


Statistics
Matches: 26,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  23   22  0.85
  24    4  0.15

ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33


Consensus pattern (23 bp):   
ATTGGTAAGTCAACATATTCGCA

Found at i:260278 original size:20 final size:20

Alignment explanation


    Indices: 260253--260293  Score: 73
    Period size: 20  Copynumber: 2.0  Consensus size: 20

     260243 TTAAGGTATG

                  *             
     260253 TGAGTCTGAGTAAAATTCCT
          1 TGAGTCGGAGTAAAATTCCT

                                
     260273 TGAGTCGGAGTAAAATTCCT
          1 TGAGTCGGAGTAAAATTCCT

             
     260293 T
          1 T

     260294 TACTGTTGGT


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34


Consensus pattern (20 bp):   
TGAGTCGGAGTAAAATTCCT

Found at i:261249 original size:39 final size:39

Alignment explanation


    Indices: 261205--261316  Score: 152
    Period size: 39  Copynumber: 2.9  Consensus size: 39

     261195 CCACATTAGG

                                                   
     261205 AATATACTGAACTGGTAGTGACACTGTAAACACTACGAT
          1 AATATACTGAACTGGTAGTGACACTGTAAACACTACGAT

            *     *        *                  **   
     261244 GATATATTGAACTGGCAGTGACACTGTAAACACTGGGAT
          1 AATATACTGAACTGGTAGTGACACTGTAAACACTACGAT

              *  *                   *        
     261283 AACATTCTGAACTGGTAGTGACACTATAAACACT
          1 AATATACTGAACTGGTAGTGACACTGTAAACACT

     261317 GAAGTTGCTA


Statistics
Matches: 62,  Mismatches: 11, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  39   62  1.00

ACGTcount: A:0.37, C:0.18, G:0.20, T:0.26


Consensus pattern (39 bp):   
AATATACTGAACTGGTAGTGACACTGTAAACACTACGAT

Found at i:266391 original size:29 final size:29

Alignment explanation


    Indices: 266359--266435  Score: 75
    Period size: 29  Copynumber: 2.6  Consensus size: 29

     266349 ATTTTTTACC

                                          
     266359 AAAATGTTTAAATGAAGATCAAACA-TCTT
          1 AAAATGTTTAAAT-AAGATCAAACATTCTT

                  * *        * *       *  
     266388 AAAATGATCAAATAAAGGTTAAACATTTTT
          1 AAAATGTTTAAAT-AAGATCAAACATTCTT

                              
     266418 AAAAGTGTTTAAATAAGA
          1 AAAA-TGTTTAAATAAGA

     266436 ACTTTTCAAA


Statistics
Matches: 37,  Mismatches: 9, Indels: 3
        0.76            0.18        0.06

Matches are distributed among these distances:
  29   20  0.54
  30   10  0.27
  31    7  0.19

ACGTcount: A:0.51, C:0.06, G:0.12, T:0.31


Consensus pattern (29 bp):   
AAAATGTTTAAATAAGATCAAACATTCTT

Found at i:271691 original size:12 final size:12

Alignment explanation


    Indices: 271669--271718  Score: 55
    Period size: 12  Copynumber: 4.2  Consensus size: 12

     271659 ATGTTCATGA

                *       
     271669 ATAATCTCGTTT
          1 ATAAGCTCGTTT

             *          
     271681 AAAAGCTCGTTT
          1 ATAAGCTCGTTT

              **    *   
     271693 ATTGGCTCATTT
          1 ATAAGCTCGTTT

                        
     271705 ATAAGCTCGTTT
          1 ATAAGCTCGTTT

              
     271717 AT
          1 AT

     271719 TGACTCGTTT


Statistics
Matches: 29,  Mismatches: 9, Indels: 0
        0.76            0.24        0.00

Matches are distributed among these distances:
  12   29  1.00

ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44


Consensus pattern (12 bp):   
ATAAGCTCGTTT

Found at i:271710 original size:24 final size:24

Alignment explanation


    Indices: 271678--271730  Score: 79
    Period size: 24  Copynumber: 2.2  Consensus size: 24

     271668 AATAATCTCG

                *              *    
     271678 TTTAAAAGCTCGTTTATTGGCTCA
          1 TTTATAAGCTCGTTTATTGACTCA

                                   *
     271702 TTTATAAGCTCGTTTATTGACTCG
          1 TTTATAAGCTCGTTTATTGACTCA

                 
     271726 TTTAT
          1 TTTAT

     271731 TTATTAATGA


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  24   26  1.00

ACGTcount: A:0.23, C:0.15, G:0.15, T:0.47


Consensus pattern (24 bp):   
TTTATAAGCTCGTTTATTGACTCA

Found at i:271882 original size:23 final size:24

Alignment explanation


    Indices: 271832--271885  Score: 83
    Period size: 24  Copynumber: 2.3  Consensus size: 24

     271822 ACATTTTTCG

                                    
     271832 TGAACATGTTCAATTATATATTCA
          1 TGAACATGTTCAATTATATATTCA

                        *      *    
     271856 TGAACATGTTCATTTA-ATGTTCA
          1 TGAACATGTTCAATTATATATTCA

                   
     271879 TGAACAT
          1 TGAACAT

     271886 TAAACAAACA


Statistics
Matches: 28,  Mismatches: 2, Indels: 1
        0.90            0.06        0.03

Matches are distributed among these distances:
  23   13  0.46
  24   15  0.54

ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41


Consensus pattern (24 bp):   
TGAACATGTTCAATTATATATTCA

Done.