Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014380.1 Kokia drynarioides strain JFW-HI SEQ_129418, 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: 6871
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36


Found at i:718 original size:17 final size:17

Alignment explanation


    Indices: 696--751  Score: 64
    Period size: 17  Copynumber: 3.3  Consensus size: 17

        686 CTTTCATCTT

                             
        696 TTAACTTTCCATCTTCC
          1 TTAACTTTCCATCTTCC

                               
        713 TTAAC-TTCC-T-TTGACC
          1 TTAACTTTCCATCTT--CC

                              
        729 TTTAACTTTCCATCTTCC
          1 -TTAACTTTCCATCTTCC

                 
        747 TTAAC
          1 TTAAC

        752 CTCCCTTAAT


Statistics
Matches: 33,  Mismatches: 0, Indels: 12
        0.73            0.00        0.27

Matches are distributed among these distances:
  14    2  0.06
  15    1  0.03
  16    6  0.18
  17   15  0.45
  18    6  0.18
  19    1  0.03
  20    2  0.06

ACGTcount: A:0.20, C:0.32, G:0.02, T:0.46


Consensus pattern (17 bp):   
TTAACTTTCCATCTTCC

Found at i:733 original size:34 final size:34

Alignment explanation


    Indices: 695--778  Score: 123
    Period size: 34  Copynumber: 2.5  Consensus size: 34

        685 CCTTTCATCT

                                   *   *  *   
        695 TTTAACTTTCCATCTTCCTTAACTTCCTTTGACC
          1 TTTAACTTTCCATCTTCCTTAACCTCCCTTAACC

                                            * 
        729 TTTAACTTTCCATCTTCCTTAACCTCCCTTAATC
          1 TTTAACTTTCCATCTTCCTTAACCTCCCTTAACC

                  *         
        763 TTTAACGTTCCATCTT
          1 TTTAACTTTCCATCTT

        779 TTTTAGCTTT


Statistics
Matches: 45,  Mismatches: 5, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  34   45  1.00

ACGTcount: A:0.19, C:0.32, G:0.02, T:0.46


Consensus pattern (34 bp):   
TTTAACTTTCCATCTTCCTTAACCTCCCTTAACC

Found at i:1636 original size:24 final size:24

Alignment explanation


    Indices: 1600--1679  Score: 142
    Period size: 24  Copynumber: 3.3  Consensus size: 24

       1590 ACACTAGTAA

                    *               
       1600 TCGTGGTCGAGGACATGGCCGTGG
          1 TCGTGGTCAAGGACATGGCCGTGG

                                    
       1624 TCGTGGTCAAGGACATGGCCGTGG
          1 TCGTGGTCAAGGACATGGCCGTGG

                                    
       1648 TCGTGGTCAAGGACATGGCCGTGG
          1 TCGTGGTCAAGGACATGGCCGTGG

              *     
       1672 TCATGGTC
          1 TCGTGGTC

       1680 GTGGTCGCGA


Statistics
Matches: 54,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   54  1.00

ACGTcount: A:0.15, C:0.21, G:0.41, T:0.23


Consensus pattern (24 bp):   
TCGTGGTCAAGGACATGGCCGTGG

Found at i:5885 original size:34 final size:33

Alignment explanation


    Indices: 5847--5937  Score: 110
    Period size: 34  Copynumber: 2.7  Consensus size: 33

       5837 AACCTTTCAT

                                     *    * * 
       5847 CTTTTAACCTTCCATCTTCCTTAACTTCCTTTGA
          1 CTTTTAACCTTCCATCTTCCTTAACCTCC-CTCA

                            *                
       5881 CTTTTAACCTTCCATCCTCCTTAACCTCCCTCA
          1 CTTTTAACCTTCCATCTTCCTTAACCTCCCTCA

            *  *                    
       5914 ATCGTTAACCTTCCATCTTCCTTA
          1 CT-TTTAACCTTCCATCTTCCTTA

       5938 GCTTTTCATA


Statistics
Matches: 49,  Mismatches: 7, Indels: 2
        0.84            0.12        0.03

Matches are distributed among these distances:
  33    3  0.06
  34   46  0.94

ACGTcount: A:0.19, C:0.37, G:0.02, T:0.42


Consensus pattern (33 bp):   
CTTTTAACCTTCCATCTTCCTTAACCTCCCTCA

Found at i:5904 original size:17 final size:17

Alignment explanation


    Indices: 5884--5937  Score: 56
    Period size: 17  Copynumber: 3.2  Consensus size: 17

       5874 CCTTTGACTT

                         *   
       5884 TTAACCTTCCATCCTCC
          1 TTAACCTTCCATCATCC

                      *      *
       5901 TTAACC-TCCCTCAATCG
          1 TTAACCTTCCATC-ATCC

                         *   
       5918 TTAACCTTCCATCTTCC
          1 TTAACCTTCCATCATCC

               
       5935 TTA
          1 TTA

       5938 GCTTTTCATA


Statistics
Matches: 29,  Mismatches: 6, Indels: 4
        0.74            0.15        0.10

Matches are distributed among these distances:
  16    5  0.17
  17   19  0.66
  18    5  0.17

ACGTcount: A:0.20, C:0.41, G:0.02, T:0.37


Consensus pattern (17 bp):   
TTAACCTTCCATCATCC
Done.