Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005347.1 Kokia drynarioides strain JFW-HI SEQ_119310, 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: 2109
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.35


Found at i:1379 original size:10 final size:10

Alignment explanation


    Indices: 1364--1395  Score: 50
    Period size: 10  Copynumber: 3.4  Consensus size: 10

       1354 TTAAAAATTT

                      
       1364 AAATTTTAAA
          1 AAATTTTAAA

                      
       1374 AAATTTT--A
          1 AAATTTTAAA

                      
       1382 AAATTTTAAA
          1 AAATTTTAAA

                
       1392 AAAT
          1 AAAT

       1396 GTATAACTTT


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

Matches are distributed among these distances:
   8    8  0.40
  10   12  0.60

ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41


Consensus pattern (10 bp):   
AAATTTTAAA

Found at i:1385 original size:18 final size:17

Alignment explanation


    Indices: 1351--1409  Score: 66
    Period size: 18  Copynumber: 3.4  Consensus size: 17

       1341 CTTTAAATTT

                *            
       1351 TTTTTAAAAA-TTTAAA
          1 TTTTAAAAAATTTTAAA

                              
       1367 TTTTAAAAAATTTTAAAA
          1 TTTTAAAAAATTTT-AAA

                         *   *
       1385 TTTTAAAAAATGTATAAC
          1 TTTTAAAAAAT-TTTAAA

                   
       1403 TTTTAAA
          1 TTTTAAA

       1410 GATGTTTTAA


Statistics
Matches: 37,  Mismatches: 3, Indels: 4
        0.84            0.07        0.09

Matches are distributed among these distances:
  16    9  0.24
  17    3  0.08
  18   23  0.62
  19    2  0.05

ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46


Consensus pattern (17 bp):   
TTTTAAAAAATTTTAAA

Found at i:1781 original size:17 final size:17

Alignment explanation


    Indices: 1760--1854  Score: 127
    Period size: 17  Copynumber: 5.4  Consensus size: 17

       1750 TTTGGGCTTT

                       *     
       1760 ATTTAAATTTATAATAA
          1 ATTTAAATTTAAAATAA

            *                 
       1777 TTTTAAATTTGAAAATAA
          1 ATTTAAATTT-AAAATAA

                   *         
       1795 ATTTAAACTTAAAATAA
          1 ATTTAAATTTAAAATAA

                     *       
       1812 ATTTAAATTCAAAATAA
          1 ATTTAAATTTAAAATAA

                               
       1829 ATTTAAATTTTTAAAATAA
          1 ATTTAAA--TTTAAAATAA

                   
       1848 ATTTAAA
          1 ATTTAAA

       1855 GGGAGTTTGG


Statistics
Matches: 68,  Mismatches: 7, Indels: 4
        0.86            0.09        0.05

Matches are distributed among these distances:
  17   38  0.56
  18   14  0.21
  19   16  0.24

ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42


Consensus pattern (17 bp):   
ATTTAAATTTAAAATAA

Found at i:1799 original size:35 final size:34

Alignment explanation


    Indices: 1760--1854  Score: 127
    Period size: 35  Copynumber: 2.7  Consensus size: 34

       1750 TTTGGGCTTT

                       *     *         *       
       1760 ATTTAAATTTATAATAATTTTAAATTTGAAAATAA
          1 ATTTAAATTTAAAATAAATTTAAA-TTCAAAATAA

                   *                          
       1795 ATTTAAACTTAAAATAAATTTAAATTCAAAATAA
          1 ATTTAAATTTAAAATAAATTTAAATTCAAAATAA

                                      
       1829 ATTTAAATTTTTAAAATAAATTTAAA
          1 ATTTAAA--TTTAAAATAAATTTAAA

       1855 GGGAGTTTGG


Statistics
Matches: 53,  Mismatches: 5, Indels: 3
        0.87            0.08        0.05

Matches are distributed among these distances:
  34   16  0.30
  35   21  0.40
  36   16  0.30

ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42


Consensus pattern (34 bp):   
ATTTAAATTTAAAATAAATTTAAATTCAAAATAA

Found at i:1854 original size:6 final size:6

Alignment explanation


    Indices: 1760--1838  Score: 51
    Period size: 6  Copynumber: 13.7  Consensus size: 6

       1750 TTTGGGCTTT

                                  *                *            *    
       1760 ATTTAA ATTTATA A--TAA TTTTAA ATTTGAA A-ATAA ATTTAA ACTTAA
          1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTT-AA ATTTAA ATTTAA ATTTAA

              *              *     *               
       1807 A-ATAA ATTTAA ATTCAA A-ATAA ATTTAA ATTT
          1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT

       1839 TTAAAATAAA


Statistics
Matches: 55,  Mismatches: 11, Indels: 14
        0.69            0.14        0.17

Matches are distributed among these distances:
   4    1  0.02
   5   12  0.22
   6   37  0.67
   7    5  0.09

ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43


Consensus pattern (6 bp):   
ATTTAA
Done.