Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005915.1 Kokia drynarioides strain JFW-HI SEQ_120281, 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: 6126
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40


Found at i:1936 original size:25 final size:25

Alignment explanation


    Indices: 1890--1938  Score: 62
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       1880 TTGATTTTCT

                       **            
       1890 TTTTTAAAATTTTACCCATTTATTC
          1 TTTTTAAAATTAAACCCATTTATTC

                          *  *      
       1915 TTTTTAAAATTAAATCCTTTTATT
          1 TTTTTAAAATTAAACCCATTTATT

       1939 TGTATTTTTT


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  25   20  1.00

ACGTcount: A:0.31, C:0.12, G:0.00, T:0.57


Consensus pattern (25 bp):   
TTTTTAAAATTAAACCCATTTATTC

Found at i:1966 original size:32 final size:31

Alignment explanation


    Indices: 1910--2026  Score: 114
    Period size: 32  Copynumber: 3.8  Consensus size: 31

       1900 TTTACCCATT

                *           *  *           
       1910 TATTCTTTTTAAAATTAAATCCTTTTATTTG
          1 TATTTTTTTTAAAATTTAACCCTTTTATTTG

                                           *
       1941 TATTTTTTGTTAAAATTTAACCCTTTTATTTT
          1 TATTTTTT-TTAAAATTTAACCCTTTTATTTG

                 *                        *
       1973 TATTTCTTTTAAAA-TT-ACCCTTTTA-TTC
          1 TATTTTTTTTAAAATTTAACCCTTTTATTTG

                 *     * *     *      
       2001 TATTTCTTTTATATTTTAATCCTTTT
          1 TATTTTTTTTAAAATTTAACCCTTTT

       2027 GTATTTTTTA


Statistics
Matches: 74,  Mismatches: 9, Indels: 7
        0.82            0.10        0.08

Matches are distributed among these distances:
  28   14  0.19
  29   11  0.15
  30    9  0.12
  31   13  0.18
  32   27  0.36

ACGTcount: A:0.25, C:0.12, G:0.02, T:0.62


Consensus pattern (31 bp):   
TATTTTTTTTAAAATTTAACCCTTTTATTTG

Found at i:2011 original size:28 final size:30

Alignment explanation


    Indices: 1916--2011  Score: 115
    Period size: 32  Copynumber: 3.2  Consensus size: 30

       1906 CATTTATTCT

                         *          *     *
       1916 TTTTAAAATTAAATCCTTTTATTTGTATTTT
          1 TTTTAAAATT-AACCCTTTTATTTCTATTTC

                                     *      
       1947 TTGTTAAAATTTAACCCTTTTATTTTTATTTC
          1 TT-TTAAAA-TTAACCCTTTTATTTCTATTTC

                                          
       1979 TTTTAAAATT-ACCCTTTTA-TTCTATTTC
          1 TTTTAAAATTAACCCTTTTATTTCTATTTC

                 
       2007 TTTTA
          1 TTTTA

       2012 TATTTTAATC


Statistics
Matches: 59,  Mismatches: 4, Indels: 7
        0.84            0.06        0.10

Matches are distributed among these distances:
  28   13  0.22
  29    9  0.15
  30    2  0.03
  31    8  0.14
  32   25  0.42
  33    2  0.03

ACGTcount: A:0.26, C:0.11, G:0.02, T:0.60


Consensus pattern (30 bp):   
TTTTAAAATTAACCCTTTTATTTCTATTTC

Found at i:3988 original size:10 final size:10

Alignment explanation


    Indices: 3973--4008  Score: 72
    Period size: 10  Copynumber: 3.6  Consensus size: 10

       3963 ATTTTAAACC

                      
       3973 AAAAAATTAA
          1 AAAAAATTAA

                      
       3983 AAAAAATTAA
          1 AAAAAATTAA

                      
       3993 AAAAAATTAA
          1 AAAAAATTAA

                  
       4003 AAAAAA
          1 AAAAAA

       4009 ATCTAATTAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   26  1.00

ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17


Consensus pattern (10 bp):   
AAAAAATTAA
Done.