Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004866.1 Kokia drynarioides strain JFW-HI SEQ_118534, 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: 6197
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36


Found at i:701 original size:49 final size:49

Alignment explanation


    Indices: 622--719  Score: 169
    Period size: 49  Copynumber: 2.0  Consensus size: 49

        612 TTATTTAAAG

                                 *                           
        622 GTTGAAAAACCTTATTCTAATTAATATCAAATAGAAAAAGTGTAGTAAT
          1 GTTGAAAAACCTTATTCTAATCAATATCAAATAGAAAAAGTGTAGTAAT

                     *               *                       
        671 GTTGAAAAATCTTATTCTAATCAATCTCAAATAGAAAAAGTGTAGTAAT
          1 GTTGAAAAACCTTATTCTAATCAATATCAAATAGAAAAAGTGTAGTAAT

        720 ATATGGATTT


Statistics
Matches: 46,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  49   46  1.00

ACGTcount: A:0.46, C:0.09, G:0.12, T:0.33


Consensus pattern (49 bp):   
GTTGAAAAACCTTATTCTAATCAATATCAAATAGAAAAAGTGTAGTAAT

Found at i:6007 original size:4 final size:4

Alignment explanation


    Indices: 5998--6056  Score: 77
    Period size: 4  Copynumber: 14.8  Consensus size: 4

       5988 CAAATAAACG

                                                                *        
       5998 AGAA AGAA AGAA AGGAA AGAA AGAA AGAA AG-A AGAA AGAGA GGAA AGAA
          1 AGAA AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AGAA AGA-A AGAA AGAA

                         
       6047 AG-A AGAA AGA
          1 AGAA AGAA AGA

       6057 GGGAAAGATA


Statistics
Matches: 49,  Mismatches: 2, Indels: 8
        0.83            0.03        0.14

Matches are distributed among these distances:
   3    6  0.12
   4   36  0.73
   5    7  0.14

ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00


Consensus pattern (4 bp):   
AGAA

Found at i:6017 original size:13 final size:13

Alignment explanation


    Indices: 5999--6050  Score: 68
    Period size: 13  Copynumber: 3.8  Consensus size: 13

       5989 AAATAAACGA

                         
       5999 GAAAGAAAGAAAG
          1 GAAAGAAAGAAAG

                         
       6012 GAAAGAAAGAAAG
          1 GAAAGAAAGAAAG

             *          *  
       6025 AAAGAAGAAAGAGAG
          1 -GA-AAGAAAGAAAG

                       
       6040 GAAAGAAAGAA
          1 GAAAGAAAGAA

       6051 GAAAGAGGGA


Statistics
Matches: 33,  Mismatches: 4, Indels: 4
        0.80            0.10        0.10

Matches are distributed among these distances:
  13   21  0.64
  14    2  0.06
  15   10  0.30

ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00


Consensus pattern (13 bp):   
GAAAGAAAGAAAG

Found at i:6064 original size:28 final size:28

Alignment explanation


    Indices: 6001--6056  Score: 96
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       5991 ATAAACGAGA

                                        
       6001 AAGAAAGAAAGGAAAGAAAGAAAGAAAG
          1 AAGAAAGAAAGGAAAGAAAGAAAGAAAG

                    *                   
       6029 AAGAAAGAGAGGAAAGAAAG-AAGAAAG
          1 AAGAAAGAAAGGAAAGAAAGAAAGAAAG

             
       6056 A
          1 A

       6057 GGGAAAGATA


Statistics
Matches: 27,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  27    8  0.30
  28   19  0.70

ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00


Consensus pattern (28 bp):   
AAGAAAGAAAGGAAAGAAAGAAAGAAAG

Found at i:6137 original size:19 final size:18

Alignment explanation


    Indices: 6103--6147  Score: 54
    Period size: 19  Copynumber: 2.4  Consensus size: 18

       6093 GTATGATATC

                             * 
       6103 TTTTTAAAATTGTATTTTA
          1 TTTTT-AAATTGTATTTAA

                       *       
       6122 TTTATTAAATTTTATTTAA
          1 TTT-TTAAATTGTATTTAA

                   
       6141 TTTTTAA
          1 TTTTTAA

       6148 CAGATTTATT


Statistics
Matches: 23,  Mismatches: 2, Indels: 3
        0.82            0.07        0.11

Matches are distributed among these distances:
  18    4  0.17
  19   17  0.74
  20    2  0.09

ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64


Consensus pattern (18 bp):   
TTTTTAAATTGTATTTAA
Done.