Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001741.1 Kokia drynarioides strain JFW-HI SEQ_113452, 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: 6461
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36


Found at i:265 original size:14 final size:13

Alignment explanation


    Indices: 240--264  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

        230 TTTTTCACCA

                         
        240 CACTTTTTAAAAG
          1 CACTTTTTAAAAG

                        
        253 CACTTTTTAAAA
          1 CACTTTTTAAAA

        265 ACAATGTTAA


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:0.40, C:0.16, G:0.04, T:0.40


Consensus pattern (13 bp):   
CACTTTTTAAAAG

Found at i:1876 original size:24 final size:24

Alignment explanation


    Indices: 1835--1927  Score: 75
    Period size: 24  Copynumber: 3.9  Consensus size: 24

       1825 CAATTACACT

                  *      *           
       1835 GTAGTGACACTATTACTTTTCATC-
          1 GTAGTGCCACTATCACTTTTCA-CA

                       *       *    
       1859 GTAGTGCCACTGTCAC-TTGCACA
          1 GTAGTGCCACTATCACTTTTCACA

                      *             *
       1882 GTAGTGCCACCATCACTTTGT-ACG
          1 GTAGTGCCACTATCACTTT-TCACA

                    *  *          
       1906 GTAGTGCCTCTGTCACTTTTCA
          1 GTAGTGCCACTATCACTTTTCA

       1928 TATTGGCATA


Statistics
Matches: 54,  Mismatches: 11, Indels: 8
        0.74            0.15        0.11

Matches are distributed among these distances:
  22    1  0.02
  23   19  0.35
  24   34  0.63

ACGTcount: A:0.20, C:0.27, G:0.18, T:0.34


Consensus pattern (24 bp):   
GTAGTGCCACTATCACTTTTCACA

Found at i:1889 original size:23 final size:23

Alignment explanation


    Indices: 1859--1923  Score: 76
    Period size: 24  Copynumber: 2.8  Consensus size: 23

       1849 ACTTTTCATC

                                   
       1859 GTAGTGCCACTGTCACTTGCACA
          1 GTAGTGCCACTGTCACTTGCACA

                      **        *  *
       1882 GTAGTGCCACCATCACTTTGTACG
          1 GTAGTGCCACTGTCAC-TTGCACA

                    *         
       1906 GTAGTGCCTCTGTCACTT
          1 GTAGTGCCACTGTCACTT

       1924 TTCATATTGG


Statistics
Matches: 34,  Mismatches: 7, Indels: 2
        0.79            0.16        0.05

Matches are distributed among these distances:
  23   16  0.47
  24   18  0.53

ACGTcount: A:0.18, C:0.29, G:0.22, T:0.31


Consensus pattern (23 bp):   
GTAGTGCCACTGTCACTTGCACA

Found at i:1900 original size:47 final size:47

Alignment explanation


    Indices: 1813--1923  Score: 120
    Period size: 47  Copynumber: 2.4  Consensus size: 47

       1803 TACTTACATT

                           *      *          *  *            
       1813 GTAGTGCCTCTG-CAATTACACTGTAGTGACACTATTACTTT-TCATC-
          1 GTAGTGCCTCTGTCACTTACACAGTAGTGACACCATCACTTTGT-A-CG

                    *         *          *                 
       1859 GTAGTGCCACTGTCACTTGCACAGTAGTGCCACCATCACTTTGTACG
          1 GTAGTGCCTCTGTCACTTACACAGTAGTGACACCATCACTTTGTACG

                              
       1906 GTAGTGCCTCTGTCACTT
          1 GTAGTGCCTCTGTCACTT

       1924 TTCATATTGG


Statistics
Matches: 54,  Mismatches: 8, Indels: 5
        0.81            0.12        0.07

Matches are distributed among these distances:
  46   12  0.22
  47   41  0.76
  48    1  0.02

ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33


Consensus pattern (47 bp):   
GTAGTGCCTCTGTCACTTACACAGTAGTGACACCATCACTTTGTACG
Done.