Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002185.1 Kokia drynarioides strain JFW-HI SEQ_114155, 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: 17051
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32


Found at i:12 original size:3 final size:3

Alignment explanation


    Indices: 5--45  Score: 64
    Period size: 3  Copynumber: 13.7  Consensus size: 3

          1 TGGA

                                    *         *                   
          5 GGT GGT GGT GGT GGT GGT AGT GGT GGC GGT GGT GGT GGT GG
          1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GG

         46 AGGGGCACAT


Statistics
Matches: 34,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
   3   34  1.00

ACGTcount: A:0.02, C:0.02, G:0.66, T:0.29


Consensus pattern (3 bp):   
GGT

Found at i:8978 original size:23 final size:23

Alignment explanation


    Indices: 8952--8998  Score: 94
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       8942 CATTGTATCA

                                   
       8952 ATAAATTTAATACAATTGAAATT
          1 ATAAATTTAATACAATTGAAATT

                                   
       8975 ATAAATTTAATACAATTGAAATT
          1 ATAAATTTAATACAATTGAAATT

             
       8998 A
          1 A

       8999 GGAGTTGATG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   24  1.00

ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38


Consensus pattern (23 bp):   
ATAAATTTAATACAATTGAAATT

Found at i:10526 original size:32 final size:32

Alignment explanation


    Indices: 10490--10560  Score: 97
    Period size: 32  Copynumber: 2.2  Consensus size: 32

      10480 TTTTTAGAGG

                          *                 
      10490 TTGATTAATACAAATACTCAAAGAAATTAGGA
          1 TTGATTAATACAAACACTCAAAGAAATTAGGA

                           *  **            
      10522 TTGATTAATACAAACCCTTGAAGAAATTAGGA
          1 TTGATTAATACAAACACTCAAAGAAATTAGGA

              *    
      10554 TTTATTA
          1 TTGATTA

      10561 GAAATTTAGC


Statistics
Matches: 34,  Mismatches: 5, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  32   34  1.00

ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32


Consensus pattern (32 bp):   
TTGATTAATACAAACACTCAAAGAAATTAGGA

Found at i:16475 original size:25 final size:25

Alignment explanation


    Indices: 16445--16494  Score: 66
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      16435 TTTAAAGAAA

                  *                   
      16445 TAAATACAT-TAATTTATTTATATAT
          1 TAAATAAATATAA-TTATTTATATAT

                               *     
      16470 TAAATAAATATAATTATTTTTATAT
          1 TAAATAAATATAATTATTTATATAT

      16495 GCAATATATA


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  25   19  0.86
  26    3  0.14

ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52


Consensus pattern (25 bp):   
TAAATAAATATAATTATTTATATAT
Done.