Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011219.1 Kokia drynarioides strain JFW-HI SEQ_126197, 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: 3580
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31


Found at i:2915 original size:6 final size:6

Alignment explanation


    Indices: 2894--2950  Score: 75
    Period size: 6  Copynumber: 9.8  Consensus size: 6

       2884 TTTAATTTAT

                       *                                            
       2894 TTTAAA TTT-GA TTTAAA TTTAAA TTTAAA -TT-AA TCTTAAA TTTAAA
          1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA

                        
       2940 TTTAAA TTTAA
          1 TTTAAA TTTAA

       2951 TTACAAAATA


Statistics
Matches: 45,  Mismatches: 2, Indels: 8
        0.82            0.04        0.15

Matches are distributed among these distances:
   4    2  0.04
   5    6  0.13
   6   34  0.76
   7    3  0.07

ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51


Consensus pattern (6 bp):   
TTTAAA

Found at i:2916 original size:17 final size:17

Alignment explanation


    Indices: 2884--2950  Score: 75
    Period size: 17  Copynumber: 3.9  Consensus size: 17

       2874 CTGGGCCCTT

                      *      
       2884 TTTAATTT-ATTTTAAA
          1 TTTAATTTAAATTTAAA

               *             
       2900 TTTGATTTAAATTTAAA
          1 TTTAATTTAAATTTAAA

                 *            
       2917 TTTAAATT-AATCTTAAA
          1 TTTAATTTAAAT-TTAAA

                             
       2934 TTTAAATTTAAATTTAA
          1 TTT-AATTTAAATTTAA

       2951 TTACAAAATA


Statistics
Matches: 42,  Mismatches: 5, Indels: 6
        0.79            0.09        0.11

Matches are distributed among these distances:
  16   10  0.24
  17   21  0.50
  18    8  0.19
  19    3  0.07

ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54


Consensus pattern (17 bp):   
TTTAATTTAAATTTAAA

Found at i:2922 original size:23 final size:24

Alignment explanation


    Indices: 2894--2951  Score: 93
    Period size: 23  Copynumber: 2.5  Consensus size: 24

       2884 TTTAATTTAT

                     *              
       2894 TTTAAATTTGAT-TTAAATTTAAA
          1 TTTAAATTTAATCTTAAATTTAAA

                                    
       2917 TTTAAA-TTAATCTTAAATTTAAA
          1 TTTAAATTTAATCTTAAATTTAAA

                        
       2940 TTTAAATTTAAT
          1 TTTAAATTTAAT

       2952 TACAAAATAA


Statistics
Matches: 32,  Mismatches: 1, Indels: 3
        0.89            0.03        0.08

Matches are distributed among these distances:
  22    4  0.12
  23   23  0.72
  24    5  0.16

ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52


Consensus pattern (24 bp):   
TTTAAATTTAATCTTAAATTTAAA

Found at i:2952 original size:11 final size:11

Alignment explanation


    Indices: 2887--2952  Score: 80
    Period size: 11  Copynumber: 5.8  Consensus size: 11

       2877 GGCCCTTTTT

                  *    
       2887 AATTTATTTTA
          1 AATTTAATTTA

                 *     
       2898 AATTTGATTTA
          1 AATTTAATTTA

                        
       2909 AATTTAAATTTA
          1 AATTT-AATTTA

                        
       2921 AA-TTAATCTTA
          1 AATTTAAT-TTA

                        
       2932 AATTTAAATTTA
          1 AATTT-AATTTA

                     
       2944 AATTTAATT
          1 AATTTAATT

       2953 ACAAAATAAA


Statistics
Matches: 48,  Mismatches: 3, Indels: 8
        0.81            0.05        0.14

Matches are distributed among these distances:
  10    3  0.06
  11   25  0.52
  12   17  0.35
  13    3  0.06

ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53


Consensus pattern (11 bp):   
AATTTAATTTA

Found at i:3028 original size:15 final size:15

Alignment explanation


    Indices: 3008--3044  Score: 58
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       2998 GCTCAATGAG

                            
       3008 ACCCAAA-TTCAAATA
          1 ACCCAAACTT-AAATA

                           
       3023 ACCCAAACTTAAATA
          1 ACCCAAACTTAAATA

                   
       3038 ACCCAAA
          1 ACCCAAA

       3045 ACGGCCCAAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  15   19  0.90
  16    2  0.10

ACGTcount: A:0.54, C:0.30, G:0.00, T:0.16


Consensus pattern (15 bp):   
ACCCAAACTTAAATA
Done.