Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005896.1 Kokia drynarioides strain JFW-HI SEQ_120237, 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: 12034
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34


Found at i:447 original size:16 final size:16

Alignment explanation


    Indices: 426--456  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

        416 CAATAAATTT

                            
        426 AATTTTAAAAATTTTG
          1 AATTTTAAAAATTTTG

                   *       
        442 AATTTTATAAATTTT
          1 AATTTTAAAAATTTT

        457 AAATACTTTT


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

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55


Consensus pattern (16 bp):   
AATTTTAAAAATTTTG

Found at i:3163 original size:3 final size:3

Alignment explanation


    Indices: 3155--3214  Score: 93
    Period size: 3  Copynumber: 19.7  Consensus size: 3

       3145 AATGAACTAT

                         *   *                                             
       3155 AGA AGA AGA ATA AAA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
          1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA

                           
       3203 AGA AGA ATGA AG
          1 AGA AGA A-GA AG

       3215 GGTTTAATTT


Statistics
Matches: 53,  Mismatches: 3, Indels: 2
        0.91            0.05        0.03

Matches are distributed among these distances:
   3   50  0.94
   4    3  0.06

ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03


Consensus pattern (3 bp):   
AGA

Found at i:4218 original size:20 final size:20

Alignment explanation


    Indices: 4193--4231  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       4183 CATCAAAATT

                                 
       4193 AAAATGATATC-GATACTTTG
          1 AAAATGAT-TCTGATACTTTG

                  *            
       4213 AAAATGGTTCTGATACTTT
          1 AAAATGATTCTGATACTTT

       4232 ATGAAAGGTA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19    2  0.12
  20   15  0.88

ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38


Consensus pattern (20 bp):   
AAAATGATTCTGATACTTTG

Found at i:10616 original size:50 final size:50

Alignment explanation


    Indices: 10557--10656  Score: 200
    Period size: 50  Copynumber: 2.0  Consensus size: 50

      10547 TACTTTGAAA

                                                              
      10557 GCATTTACTCAAATACTTTGTGAGCATTGCTTTCTTGTGGCTTTTTTGTT
          1 GCATTTACTCAAATACTTTGTGAGCATTGCTTTCTTGTGGCTTTTTTGTT

                                                              
      10607 GCATTTACTCAAATACTTTGTGAGCATTGCTTTCTTGTGGCTTTTTTGTT
          1 GCATTTACTCAAATACTTTGTGAGCATTGCTTTCTTGTGGCTTTTTTGTT

      10657 CTCTCTTTGC


Statistics
Matches: 50,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  50   50  1.00

ACGTcount: A:0.16, C:0.16, G:0.18, T:0.50


Consensus pattern (50 bp):   
GCATTTACTCAAATACTTTGTGAGCATTGCTTTCTTGTGGCTTTTTTGTT
Done.