Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004679.1 Kokia drynarioides strain JFW-HI SEQ_118229, 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: 17049
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36


Found at i:1445 original size:2 final size:2

Alignment explanation


    Indices: 1438--1462  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       1428 AGCATGGTGG

                                                 
       1438 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

       1463 GTTTTTGCTG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:8646 original size:29 final size:31

Alignment explanation


    Indices: 8614--8673  Score: 81
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       8604 GTGTCTAAAG

                                           
       8614 TTTTTTT-TGTCC-C-AAATTGATATCTGAA
          1 TTTTTTTCTGTCCACTAAATTGATATCTGAA

                              *       *    
       8642 TTTTTTTCTGTCCACTAATTTGATATTTGAA
          1 TTTTTTTCTGTCCACTAAATTGATATCTGAA

             
       8673 T
          1 T

       8674 CTAACACCAT


Statistics
Matches: 27,  Mismatches: 2, Indels: 3
        0.84            0.06        0.09

Matches are distributed among these distances:
  28    7  0.26
  29    5  0.19
  30    1  0.04
  31   14  0.52

ACGTcount: A:0.23, C:0.13, G:0.10, T:0.53


Consensus pattern (31 bp):   
TTTTTTTCTGTCCACTAAATTGATATCTGAA

Found at i:12898 original size:24 final size:24

Alignment explanation


    Indices: 12866--12933  Score: 66
    Period size: 24  Copynumber: 2.8  Consensus size: 24

      12856 TTAAACTTTG

                *                *  
      12866 TCTGAGCTCGAATGAGCTAACTTA
          1 TCTGGGCTCGAATGAGCTAACATA

                         *           
      12890 TCTGGGCTC-ATAAGAGCTAACATA
          1 TCTGGGCTCGA-ATGAGCTAACATA

               *  *   *         
      12914 TCTAGGTTCGTATGAGCTAA
          1 TCTGGGCTCGAATGAGCTAA

      12934 TTTTGTCTTG


Statistics
Matches: 35,  Mismatches: 7, Indels: 4
        0.76            0.15        0.09

Matches are distributed among these distances:
  23    1  0.03
  24   34  0.97

ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29


Consensus pattern (24 bp):   
TCTGGGCTCGAATGAGCTAACATA

Found at i:13975 original size:23 final size:25

Alignment explanation


    Indices: 13949--13994  Score: 69
    Period size: 25  Copynumber: 1.9  Consensus size: 25

      13939 CCAATTAGGG

                                     
      13949 AATTAT-TGTTTAG-ATTTAATTCA
          1 AATTATCTGTTTAGAATTTAATTCA

                    *              
      13972 AATTATCTTTTTAGAATTTAATT
          1 AATTATCTGTTTAGAATTTAATT

      13995 TGGATCCAAC


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  23    6  0.30
  24    6  0.30
  25    8  0.40

ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54


Consensus pattern (25 bp):   
AATTATCTGTTTAGAATTTAATTCA

Found at i:15128 original size:13 final size:14

Alignment explanation


    Indices: 15092--15121  Score: 51
    Period size: 14  Copynumber: 2.1  Consensus size: 14

      15082 GTTATTTGCA

                  *       
      15092 TTTCTAATTTAATT
          1 TTTCTATTTTAATT

                          
      15106 TTTCTATTTTAATT
          1 TTTCTATTTTAATT

              
      15120 TT
          1 TT

      15122 CTCTTTTCCC


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70


Consensus pattern (14 bp):   
TTTCTATTTTAATT
Done.