Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003197.1 Kokia drynarioides strain JFW-HI SEQ_115812, 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: 8085
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31


Found at i:7116 original size:7 final size:7

Alignment explanation


    Indices: 7104--7140  Score: 58
    Period size: 7  Copynumber: 5.4  Consensus size: 7

       7094 TCTTTTCAAT

                   
       7104 CATCATC
          1 CATCATC

                   
       7111 CATCATC
          1 CATCATC

                   
       7118 CATCATC
          1 CATCATC

                 * 
       7125 CATCACC
          1 CATCATC

                   
       7132 CATCA-C
          1 CATCATC

               
       7138 CAT
          1 CAT

       7141 TACCTTTTCC


Statistics
Matches: 29,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
   6    4  0.14
   7   25  0.86

ACGTcount: A:0.30, C:0.46, G:0.00, T:0.24


Consensus pattern (7 bp):   
CATCATC

Found at i:7892 original size:13 final size:13

Alignment explanation


    Indices: 7866--7915  Score: 55
    Period size: 13  Copynumber: 3.6  Consensus size: 13

       7856 ACATTTAATT

                     *    
       7866 TTTATTTTTATTTA
          1 TTTA-TTTTGTTTA

                         
       7880 TTTATTTTGTTTA
          1 TTTATTTTGTTTA

                 *         
       7893 TTTATCTTGTTGTTA
          1 TTTATTTTG-T-TTA

                    
       7908 TTTATTTT
          1 TTTATTTT

       7916 TAGACCATTT


Statistics
Matches: 31,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
  13   16  0.52
  14    5  0.16
  15   10  0.32

ACGTcount: A:0.16, C:0.02, G:0.06, T:0.76


Consensus pattern (13 bp):   
TTTATTTTGTTTA

Found at i:7966 original size:41 final size:40

Alignment explanation


    Indices: 7921--8041  Score: 110
    Period size: 40  Copynumber: 3.1  Consensus size: 40

       7911 ATTTTTAGAC

                          *                          
       7921 CATTTTATTGTTATCTCTTTTATTATTTTTTATTTAATTTA
          1 CATTTTATTGTTATATCTTTT-TTATTTTTTATTTAATTTA

                                *       *             
       7962 CA-TTTATTGTTATTATCTTGTTTATCTATTTATTT-ATTTA
          1 CATTTTATTGTTA-TATCTTTTTTAT-TTTTTATTTAATTTA

                 **        *                         
       8002 TCATTAAATT-TTATGT-TTTTTTA-TTTTTATTTAA-TTA
          1 -CATTTTATTGTTATATCTTTTTTATTTTTTATTTAATTTA

               
       8039 CAT
          1 CAT

       8042 GTTGATTAAT


Statistics
Matches: 67,  Mismatches: 8, Indels: 15
        0.74            0.09        0.17

Matches are distributed among these distances:
  36    3  0.04
  37   11  0.16
  38    1  0.01
  39    6  0.09
  40   21  0.31
  41   21  0.31
  42    4  0.06

ACGTcount: A:0.24, C:0.07, G:0.03, T:0.66


Consensus pattern (40 bp):   
CATTTTATTGTTATATCTTTTTTATTTTTTATTTAATTTA

Done.