Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008672.1 Kokia drynarioides strain JFW-HI SEQ_123354, 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: 21584
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:1435 original size:10 final size:10

Alignment explanation


    Indices: 1405--1455  Score: 54
    Period size: 10  Copynumber: 5.4  Consensus size: 10

       1395 TCAGTCATTT

                      
       1405 GAAAAAGAAA
          1 GAAAAAGAAA

            *    *    
       1415 CAAAATG--A
          1 GAAAAAGAAA

                      
       1423 GAAAAAGAAA
          1 GAAAAAGAAA

                  *   
       1433 GAAAAATAAA
          1 GAAAAAGAAA

                      
       1443 -AAAAAGAAA
          1 GAAAAAGAAA

                
       1452 GAAA
          1 GAAA

       1456 TTTTTGATAA


Statistics
Matches: 32,  Mismatches: 6, Indels: 6
        0.73            0.14        0.14

Matches are distributed among these distances:
   8    6  0.19
   9    8  0.25
  10   18  0.56

ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04


Consensus pattern (10 bp):   
GAAAAAGAAA

Found at i:1438 original size:19 final size:19

Alignment explanation


    Indices: 1405--1455  Score: 68
    Period size: 19  Copynumber: 2.7  Consensus size: 19

       1395 TCAGTCATTT

                       *     * 
       1405 GAAAAAGAAA-CAAAATGA
          1 GAAAAAGAAAGAAAAATAA

                               
       1423 GAAAAAGAAAGAAAAATAA
          1 GAAAAAGAAAGAAAAATAA

            *             
       1442 AAAAAAGAAAGAAA
          1 GAAAAAGAAAGAAA

       1456 TTTTTGATAA


Statistics
Matches: 29,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  18   10  0.34
  19   19  0.66

ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04


Consensus pattern (19 bp):   
GAAAAAGAAAGAAAAATAA

Found at i:5353 original size:6 final size:6

Alignment explanation


    Indices: 5342--5380  Score: 51
    Period size: 6  Copynumber: 6.2  Consensus size: 6

       5332 TTTATAGCAA

                                       *                 
       5342 TTTTTC TTTTTC TTTTCTC TTTTTT TCTTTTC TTTTTC T
          1 TTTTTC TTTTTC TTTT-TC TTTTTC T-TTTTC TTTTTC T

       5381 CATTTAACAT


Statistics
Matches: 29,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
   6   18  0.62
   7   11  0.38

ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82


Consensus pattern (6 bp):   
TTTTTC

Found at i:5368 original size:15 final size:14

Alignment explanation


    Indices: 5348--5378  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 14

       5338 GCAATTTTTC

                           
       5348 TTTTTCTTTTCTCTT
          1 TTTTTCTTTTCT-TT

                          
       5363 TTTTTCTTTTCTTT
          1 TTTTTCTTTTCTTT

              
       5377 TT
          1 TT

       5379 CTCATTTAAC


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    4  0.25
  15   12  0.75

ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84


Consensus pattern (14 bp):   
TTTTTCTTTTCTTT
Done.