Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012677.1 Kokia drynarioides strain JFW-HI SEQ_127688, 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: 21076
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32

Warning! 2 characters in sequence are not A, C, G, or T


Found at i:1177 original size:2 final size:2

Alignment explanation


    Indices: 1170--1200  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       1160 ATTTAAACTC

                                                          
       1170 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G

       1201 CACATGCTTC


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

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


Consensus pattern (2 bp):   
GA

Found at i:2076 original size:47 final size:47

Alignment explanation


    Indices: 2025--2121  Score: 185
    Period size: 47  Copynumber: 2.1  Consensus size: 47

       2015 TAAATAAGAA

                                                           
       2025 ATGCATGCATAATTTGACTGGGTAGGGAAAAATGTGGTTAAGAGGAG
          1 ATGCATGCATAATTTGACTGGGTAGGGAAAAATGTGGTTAAGAGGAG

                             *                             
       2072 ATGCATGCATAATTTGATTGGGTAGGGAAAAATGTGGTTAAGAGGAG
          1 ATGCATGCATAATTTGACTGGGTAGGGAAAAATGTGGTTAAGAGGAG

               
       2119 ATG
          1 ATG

       2122 AAAGAGGGCA


Statistics
Matches: 49,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  47   49  1.00

ACGTcount: A:0.34, C:0.05, G:0.34, T:0.27


Consensus pattern (47 bp):   
ATGCATGCATAATTTGACTGGGTAGGGAAAAATGTGGTTAAGAGGAG

Found at i:3453 original size:32 final size:33

Alignment explanation


    Indices: 3412--3487  Score: 102
    Period size: 32  Copynumber: 2.3  Consensus size: 33

       3402 TTATTCAATA

                               *             
       3412 TTGTTATTTTATTAATTTTGTTTTGACT-AAAT
          1 TTGTTATTTTATTAATTTTATTTTGACTGAAAT

                      *               *      
       3444 TTGTTATTTTCTTAATTTTATTTTGATTGAAAT
          1 TTGTTATTTTATTAATTTTATTTTGACTGAAAT

                        
       3477 TAT-TTATTTTA
          1 T-TGTTATTTTA

       3488 AGTAAATAGG


Statistics
Matches: 38,  Mismatches: 4, Indels: 3
        0.84            0.09        0.07

Matches are distributed among these distances:
  32   25  0.66
  33   12  0.32
  34    1  0.03

ACGTcount: A:0.25, C:0.03, G:0.08, T:0.64


Consensus pattern (33 bp):   
TTGTTATTTTATTAATTTTATTTTGACTGAAAT

Found at i:10473 original size:12 final size:12

Alignment explanation


    Indices: 10456--10489  Score: 50
    Period size: 12  Copynumber: 2.8  Consensus size: 12

      10446 GAAATCGGGC

                        
      10456 AAAGAAGGGAAA
          1 AAAGAAGGGAAA

                  *     
      10468 AAAGAAAGGAAA
          1 AAAGAAGGGAAA

                      
      10480 AATAGAAGGG
          1 AA-AGAAGGG

      10490 GGAAAAGAAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  12   13  0.68
  13    6  0.32

ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03


Consensus pattern (12 bp):   
AAAGAAGGGAAA

Found at i:21054 original size:18 final size:19

Alignment explanation


    Indices: 21030--21076  Score: 62
    Period size: 18  Copynumber: 2.6  Consensus size: 19

      21020 CCATACTCCC

                       *       
      21030 TTTAAATTTATTTTAAAAA
          1 TTTAAATTTATCTTAAAAA

                      *        
      21049 -TTAAATTT-GCTTAAAAA
          1 TTTAAATTTATCTTAAAAA

                       
      21066 TTTAAATTTAT
          1 TTTAAATTTAT


Statistics
Matches: 23,  Mismatches: 3, Indels: 4
        0.77            0.10        0.13

Matches are distributed among these distances:
  17    7  0.30
  18   16  0.70

ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51


Consensus pattern (19 bp):   
TTTAAATTTATCTTAAAAA
Done.