Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009828.1 Kokia drynarioides strain JFW-HI SEQ_124549, 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: 25023
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32


Found at i:18465 original size:14 final size:15

Alignment explanation


    Indices: 18437--18465  Score: 51
    Period size: 14  Copynumber: 2.0  Consensus size: 15

      18427 TTCAAATAAC

                           
      18437 TTTTAAAAAATAATG
          1 TTTTAAAAAATAATG

                           
      18452 TTTT-AAAAATAATG
          1 TTTTAAAAAATAATG

      18466 AATTAAAATT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14   10  0.71
  15    4  0.29

ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41


Consensus pattern (15 bp):   
TTTTAAAAAATAATG

Found at i:18582 original size:4 final size:4

Alignment explanation


    Indices: 18573--18618  Score: 74
    Period size: 4  Copynumber: 11.2  Consensus size: 4

      18563 CGTGGTCATG

                                              *                      
      18573 TGTA TGTA TGTA TGTA TGTA TGTTA TGTC TGTA TGTA TGTA TGTA T
          1 TGTA TGTA TGTA TGTA TGTA TG-TA TGTA TGTA TGTA TGTA TGTA T

      18619 ACACACTCAT


Statistics
Matches: 39,  Mismatches: 2, Indels: 2
        0.91            0.05        0.05

Matches are distributed among these distances:
   4   35  0.90
   5    4  0.10

ACGTcount: A:0.22, C:0.02, G:0.24, T:0.52


Consensus pattern (4 bp):   
TGTA

Found at i:18599 original size:21 final size:22

Alignment explanation


    Indices: 18570--18616  Score: 78
    Period size: 21  Copynumber: 2.2  Consensus size: 22

      18560 TAACGTGGTC

                                  
      18570 ATGTGTATGTATGTATGTATGT
          1 ATGTGTATGTATGTATGTATGT

                      *           
      18592 ATGT-TATGTCTGTATGTATGT
          1 ATGTGTATGTATGTATGTATGT

                
      18613 ATGT
          1 ATGT

      18617 ATACACACTC


Statistics
Matches: 24,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  21   20  0.83
  22    4  0.17

ACGTcount: A:0.21, C:0.02, G:0.26, T:0.51


Consensus pattern (22 bp):   
ATGTGTATGTATGTATGTATGT

Found at i:24415 original size:18 final size:18

Alignment explanation


    Indices: 24378--24416  Score: 51
    Period size: 18  Copynumber: 2.2  Consensus size: 18

      24368 CATGAATTAC

                  *       *   
      24378 ATTTAATGAAATAATAGT
          1 ATTTAACGAAATAACAGT

                           *  
      24396 ATTTAACGAAATAACGGT
          1 ATTTAACGAAATAACAGT

               
      24414 ATT
          1 ATT

      24417 ATTTTCAAAT


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.46, C:0.05, G:0.13, T:0.36


Consensus pattern (18 bp):   
ATTTAACGAAATAACAGT
Done.