Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005070.1 Kokia drynarioides strain JFW-HI SEQ_118873, 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: 11636
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34


Found at i:1489 original size:18 final size:18

Alignment explanation


    Indices: 1478--1512  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       1468 AGCTCGTCAC

                              
       1478 TTTATGTGAGCTCACCAA
          1 TTTATGTGAGCTCACCAA

                     *       
       1496 TTTATGTGACCTCACCA
          1 TTTATGTGAGCTCACCA

       1513 CTCCGGATGA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34


Consensus pattern (18 bp):   
TTTATGTGAGCTCACCAA

Found at i:6007 original size:18 final size:18

Alignment explanation


    Indices: 5984--6047  Score: 71
    Period size: 18  Copynumber: 3.7  Consensus size: 18

       5974 TAAAAGTTAA

                   *          
       5984 TGAGCTCGCCACTTTATG
          1 TGAGCTCACCACTTTATG

                   *          
       6002 TGAGCTCGCCA--TT-TG
          1 TGAGCTCACCACTTTATG

                  *    *      
       6017 TGAGCTTACCAATTTATG
          1 TGAGCTCACCACTTTATG

                         
       6035 TGAGCTCACCACT
          1 TGAGCTCACCACT

       6048 CCAGATGAGC


Statistics
Matches: 39,  Mismatches: 4, Indels: 6
        0.80            0.08        0.12

Matches are distributed among these distances:
  15   11  0.28
  16    2  0.05
  17    2  0.05
  18   24  0.62

ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33


Consensus pattern (18 bp):   
TGAGCTCACCACTTTATG

Found at i:6909 original size:15 final size:16

Alignment explanation


    Indices: 6891--6927  Score: 58
    Period size: 16  Copynumber: 2.4  Consensus size: 16

       6881 AGACCTAATA

                       *    
       6891 ACCCAA-AACCTTTTG
          1 ACCCAATAACCATTTG

                            
       6906 ACCCAATAACCATTTG
          1 ACCCAATAACCATTTG

                  
       6922 ACCCAA
          1 ACCCAA

       6928 GTCCAAACCT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  15    6  0.30
  16   14  0.70

ACGTcount: A:0.38, C:0.35, G:0.05, T:0.22


Consensus pattern (16 bp):   
ACCCAATAACCATTTG

Found at i:6975 original size:22 final size:22

Alignment explanation


    Indices: 6949--6990  Score: 68
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       6939 AACCAAGTCA

                                   
       6949 AACCGTTGA-TCGATCGTTGATC
          1 AACCGTTGACT-GATCGTTGATC

                                
       6971 AACCGTTGACTGATCGTTGA
          1 AACCGTTGACTGATCGTTGA

       6991 CCGACTATTG


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  22   18  0.95
  23    1  0.05

ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31


Consensus pattern (22 bp):   
AACCGTTGACTGATCGTTGATC
Done.