Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005322.1 Kokia drynarioides strain JFW-HI SEQ_119260, 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: 1883
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.39


Found at i:847 original size:16 final size:18

Alignment explanation


    Indices: 828--861  Score: 54
    Period size: 16  Copynumber: 2.0  Consensus size: 18

        818 TAATATTTTA

                              
        828 TTTATAA-TAATA-ATAT
          1 TTTATAAGTAATATATAT

                              
        844 TTTATAAGTAATATATAT
          1 TTTATAAGTAATATATAT

        862 ATCATCTTTC


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16    7  0.44
  17    5  0.31
  18    4  0.25

ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50


Consensus pattern (18 bp):   
TTTATAAGTAATATATAT

Found at i:1638 original size:6 final size:6

Alignment explanation


    Indices: 1627--1684  Score: 55
    Period size: 6  Copynumber: 9.8  Consensus size: 6

       1617 TTTAAATATG

                          *       *          *             *      *
       1627 AAATGA AAATGA TAATG- ATATGA AAATGG AAATGA AAATGG AAATGG
          1 AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA

                 *      
       1674 AAATGG AAATG
          1 AAATGA AAATG

       1685 TAATGGATGT


Statistics
Matches: 44,  Mismatches: 7, Indels: 2
        0.83            0.13        0.04

Matches are distributed among these distances:
   5    3  0.07
   6   41  0.93

ACGTcount: A:0.55, C:0.00, G:0.24, T:0.21


Consensus pattern (6 bp):   
AAATGA

Found at i:1660 original size:17 final size:17

Alignment explanation


    Indices: 1624--1684  Score: 70
    Period size: 18  Copynumber: 3.5  Consensus size: 17

       1614 TGATTTAAAT

                              
       1624 ATGAAATGAAAAT-GATA
          1 ATGAAATGAAAATGGA-A

                *            
       1641 ATGATATGAAAATGGAA
          1 ATGAAATGAAAATGGAA

                     *        
       1658 ATGAAAATGGAAATGGAA
          1 ATG-AAATGAAAATGGAA

                     
       1676 ATGGAAATG
          1 AT-GAAATG

       1685 TAATGGATGT


Statistics
Matches: 38,  Mismatches: 3, Indels: 5
        0.83            0.07        0.11

Matches are distributed among these distances:
  17   16  0.42
  18   21  0.55
  19    1  0.03

ACGTcount: A:0.54, C:0.00, G:0.25, T:0.21


Consensus pattern (17 bp):   
ATGAAATGAAAATGGAA

Found at i:1661 original size:12 final size:12

Alignment explanation


    Indices: 1627--1684  Score: 73
    Period size: 12  Copynumber: 4.9  Consensus size: 12

       1617 TTTAAATATG

                 *      
       1627 AAATGAAAATGA
          1 AAATGGAAATGA

            *      *    
       1639 TAAT-GATATGA
          1 AAATGGAAATGA

                        
       1650 AAATGGAAATGA
          1 AAATGGAAATGA

                       *
       1662 AAATGGAAATGG
          1 AAATGGAAATGA

                       
       1674 AAATGGAAATG
          1 AAATGGAAATG

       1685 TAATGGATGT


Statistics
Matches: 39,  Mismatches: 6, Indels: 2
        0.83            0.13        0.04

Matches are distributed among these distances:
  11    8  0.21
  12   31  0.79

ACGTcount: A:0.55, C:0.00, G:0.24, T:0.21


Consensus pattern (12 bp):   
AAATGGAAATGA

Done.