Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002246.1 Kokia drynarioides strain JFW-HI SEQ_114253, 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: 11698
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34


Found at i:4957 original size:33 final size:33

Alignment explanation


    Indices: 4915--4981  Score: 134
    Period size: 33  Copynumber: 2.0  Consensus size: 33

       4905 TAGGCTCAAC

                                             
       4915 TACATCAACACATCTTAGCAACACCTAATCCTT
          1 TACATCAACACATCTTAGCAACACCTAATCCTT

                                             
       4948 TACATCAACACATCTTAGCAACACCTAATCCTT
          1 TACATCAACACATCTTAGCAACACCTAATCCTT

             
       4981 T
          1 T

       4982 CTTCTCTTAT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  33   34  1.00

ACGTcount: A:0.36, C:0.33, G:0.03, T:0.28


Consensus pattern (33 bp):   
TACATCAACACATCTTAGCAACACCTAATCCTT

Found at i:8934 original size:24 final size:24

Alignment explanation


    Indices: 8902--8951  Score: 66
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       8892 CTTTTTTTAT

                             *       
       8902 TTATTATTAATT-ATTCGTCTATTA
          1 TTATTATT-ATTAATTCATCTATTA

                              *     
       8926 TTATTATTATTAATTCATTTATTA
          1 TTATTATTATTAATTCATCTATTA

              
       8950 TT
          1 TT

       8952 CAATAAACAC


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  23    3  0.13
  24   20  0.87

ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62


Consensus pattern (24 bp):   
TTATTATTATTAATTCATCTATTA

Found at i:9728 original size:17 final size:17

Alignment explanation


    Indices: 9708--9762  Score: 83
    Period size: 17  Copynumber: 3.2  Consensus size: 17

       9698 AAATTATATC

                     *       
       9708 AAATTTAAACTAAATTT
          1 AAATTTAAAATAAATTT

                     *       
       9725 AAATTTAAAGTAAATTT
          1 AAATTTAAAATAAATTT

                              
       9742 AAATTTAGAAATAAATTT
          1 AAATTTA-AAATAAATTT

               
       9760 AAA
          1 AAA

       9763 ACTAATCTAA


Statistics
Matches: 35,  Mismatches: 2, Indels: 1
        0.92            0.05        0.03

Matches are distributed among these distances:
  17   23  0.66
  18   12  0.34

ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38


Consensus pattern (17 bp):   
AAATTTAAAATAAATTT

Found at i:9729 original size:6 final size:6

Alignment explanation


    Indices: 9674--9762  Score: 60
    Period size: 6  Copynumber: 15.3  Consensus size: 6

       9664 TTGGACTTTG

                    *       *     *       *    *   *            *  
       9674 AATTTA ATTTTA AAGTTA AGTTTA AAATTA TA-TCA AATTTA AA-CTA
          1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA

                             *                     *            
       9720 AATTTA AATTTA AA-GTA AATTTA AATTTA GAA-ATA AATTTA AA
          1 AATTTA AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AA

       9763 ACTAATCTAA


Statistics
Matches: 61,  Mismatches: 17, Indels: 10
        0.69            0.19        0.11

Matches are distributed among these distances:
   5   13  0.21
   6   46  0.75
   7    2  0.03

ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42


Consensus pattern (6 bp):   
AATTTA

Found at i:11579 original size:16 final size:16

Alignment explanation


    Indices: 11558--11589  Score: 64
    Period size: 16  Copynumber: 2.0  Consensus size: 16

      11548 TTTCTATTGA

                            
      11558 AAATATACTAATTAAG
          1 AAATATACTAATTAAG

                            
      11574 AAATATACTAATTAAG
          1 AAATATACTAATTAAG

      11590 GAATCAGCCA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.56, C:0.06, G:0.06, T:0.31


Consensus pattern (16 bp):   
AAATATACTAATTAAG
Done.