Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005283.1 Kokia drynarioides strain JFW-HI SEQ_119205, 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: 25644
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:5689 original size:42 final size:42

Alignment explanation


    Indices: 5620--5706  Score: 129
    Period size: 42  Copynumber: 2.1  Consensus size: 42

       5610 AATTTAATTT

                *             *   *         *         
       5620 TCAATGCCATGAATTGATTCTTTCTGATTTTTCAAAGCTGTC
          1 TCAAGGCCATGAATTGATGCTTGCTGATTTTTAAAAGCTGTC

                                                 *    
       5662 TCAAGGCCATGAATTGATGCTTGCTGATTTTTAAAAGTTGTC
          1 TCAAGGCCATGAATTGATGCTTGCTGATTTTTAAAAGCTGTC

               
       5704 TCA
          1 TCA

       5707 TTGTTTTGTA


Statistics
Matches: 40,  Mismatches: 5, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  42   40  1.00

ACGTcount: A:0.25, C:0.17, G:0.17, T:0.40


Consensus pattern (42 bp):   
TCAAGGCCATGAATTGATGCTTGCTGATTTTTAAAAGCTGTC

Found at i:7031 original size:12 final size:14

Alignment explanation


    Indices: 7001--7032  Score: 50
    Period size: 12  Copynumber: 2.4  Consensus size: 14

       6991 AACAAAAGAG

                          
       7001 AAAATTAGAATAGA
          1 AAAATTAGAATAGA

                          
       7015 AAAATTA-AATA-A
          1 AAAATTAGAATAGA

                  
       7027 AAAATT
          1 AAAATT

       7033 GAAAAATTAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  12    7  0.39
  13    4  0.22
  14    7  0.39

ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25


Consensus pattern (14 bp):   
AAAATTAGAATAGA

Found at i:16315 original size:18 final size:17

Alignment explanation


    Indices: 16273--16315  Score: 50
    Period size: 18  Copynumber: 2.4  Consensus size: 17

      16263 CTAATATAAC

                    *   *    
      16273 TTTTTTTCTTTTTTTCT
          1 TTTTTTTCATTTCTTCT

                              
      16290 TTTCTTTTCATTTCTTCT
          1 TTT-TTTTCATTTCTTCT

                    
      16308 TCTTTTTT
          1 T-TTTTTT

      16316 TTATATGTGA


Statistics
Matches: 22,  Mismatches: 2, Indels: 3
        0.81            0.07        0.11

Matches are distributed among these distances:
  17    3  0.14
  18   17  0.77
  19    2  0.09

ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81


Consensus pattern (17 bp):   
TTTTTTTCATTTCTTCT
Done.