Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01015049.1 Kokia drynarioides strain JFW-HI SEQ_130093, 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: 16520
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34


Found at i:2215 original size:16 final size:15

Alignment explanation


    Indices: 2188--2232  Score: 58
    Period size: 14  Copynumber: 3.1  Consensus size: 15

       2178 TAAAAAATAT

                           
       2188 ATATAAAG-TTTATA
          1 ATATAAAGTTTTATA

                            
       2202 ATATACAAGTTTTATA
          1 ATATA-AAGTTTTATA

                  *        
       2218 A-ATAAGGTTTTATA
          1 ATATAAAGTTTTATA

             
       2232 A
          1 A

       2233 ATTGTTCAAT


Statistics
Matches: 28,  Mismatches: 1, Indels: 4
        0.85            0.03        0.12

Matches are distributed among these distances:
  14   15  0.54
  15    6  0.21
  16    7  0.25

ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42


Consensus pattern (15 bp):   
ATATAAAGTTTTATA

Found at i:2596 original size:36 final size:37

Alignment explanation


    Indices: 2520--2607  Score: 88
    Period size: 36  Copynumber: 2.4  Consensus size: 37

       2510 TAGGACTTAA

                   *   *   * *                   
       2520 ATAATATAATTGTTTGTTATATAACTTTATAAAATAT
          1 ATAATATCATTTTTTATAATATAACTTTATAAAATAT

                   *                *   *  *   * 
       2557 ATAA-ATTATTTTTTATAATATAATTTTTTAGAATTT
          1 ATAATATCATTTTTTATAATATAACTTTATAAAATAT

                           
       2593 ATAATATCATTTTTT
          1 ATAATATCATTTTTT

       2608 TTTTACCATA


Statistics
Matches: 41,  Mismatches: 9, Indels: 2
        0.79            0.17        0.04

Matches are distributed among these distances:
  36   28  0.68
  37   13  0.32

ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55


Consensus pattern (37 bp):   
ATAATATCATTTTTTATAATATAACTTTATAAAATAT

Found at i:11800 original size:17 final size:17

Alignment explanation


    Indices: 11778--11812  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      11768 GACTTTTCGT

                              
      11778 TTTTAT-TTTCTATTTTA
          1 TTTTATCTTT-TATTTTA

                             
      11795 TTTTATCTTTTATTTTA
          1 TTTTATCTTTTATTTTA

             
      11812 T
          1 T

      11813 GCTTTTAAAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  17   14  0.82
  18    3  0.18

ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77


Consensus pattern (17 bp):   
TTTTATCTTTTATTTTA

Found at i:11819 original size:13 final size:12

Alignment explanation


    Indices: 11778--11819  Score: 57
    Period size: 12  Copynumber: 3.4  Consensus size: 12

      11768 GACTTTTCGT

                     * *
      11778 TTTTATTTTCTA
          1 TTTTATTTTATC

                        
      11790 TTTTATTTTATC
          1 TTTTATTTTATC

                         
      11802 TTTTATTTTATGC
          1 TTTTATTTTAT-C

                 
      11815 TTTTA
          1 TTTTA

      11820 AAATCCAATC


Statistics
Matches: 27,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  12   21  0.78
  13    6  0.22

ACGTcount: A:0.17, C:0.07, G:0.02, T:0.74


Consensus pattern (12 bp):   
TTTTATTTTATC

Found at i:12116 original size:13 final size:13

Alignment explanation


    Indices: 12100--12124  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      12090 GTGTGAAGGA

                         
      12100 TATTAATCTAAAG
          1 TATTAATCTAAAG

                        
      12113 TATTAATCTAAA
          1 TATTAATCTAAA

      12125 CTAAAATAAT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40


Consensus pattern (13 bp):   
TATTAATCTAAAG
Done.