Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007054.1 Kokia drynarioides strain JFW-HI SEQ_121662, 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: 13154
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34


Found at i:6193 original size:24 final size:24

Alignment explanation


    Indices: 6161--6206  Score: 74
    Period size: 24  Copynumber: 1.9  Consensus size: 24

       6151 TATCAATCCT

                                    
       6161 CAATTCAATCCGAAAATGAGTTAA
          1 CAATTCAATCCGAAAATGAGTTAA

                         * *      
       6185 CAATTCAATCCGATACTGAGTT
          1 CAATTCAATCCGAAAATGAGTT

       6207 GAGCAATTAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  24   20  1.00

ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28


Consensus pattern (24 bp):   
CAATTCAATCCGAAAATGAGTTAA

Found at i:8792 original size:2 final size:2

Alignment explanation


    Indices: 8785--8831  Score: 78
    Period size: 2  Copynumber: 24.0  Consensus size: 2

       8775 AAGTACCCAA

                                                                     *    
       8785 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT TT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                    
       8826 AT AT AT
          1 AT AT AT

       8832 GTATTGATGT


Statistics
Matches: 42,  Mismatches: 2, Indels: 2
        0.91            0.04        0.04

Matches are distributed among these distances:
   1    1  0.02
   2   41  0.98

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
AT

Found at i:12876 original size:18 final size:18

Alignment explanation


    Indices: 12847--12900  Score: 56
    Period size: 18  Copynumber: 2.9  Consensus size: 18

      12837 TTTAAGATGC

                        *       
      12847 CATAATTATATTTTACTAAA
          1 CATAA-TATATTATA-TAAA

                              
      12867 -ATAATATATTATATAAA
          1 CATAATATATTATATAAA

             *               
      12884 CTTAATATATTAATATA
          1 CATAATATATT-ATATA

      12901 TCATATTATA


Statistics
Matches: 30,  Mismatches: 2, Indels: 5
        0.81            0.05        0.14

Matches are distributed among these distances:
  17    4  0.13
  18   17  0.57
  19    9  0.30

ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44


Consensus pattern (18 bp):   
CATAATATATTATATAAA

Found at i:13074 original size:22 final size:23

Alignment explanation


    Indices: 13052--13093  Score: 70
    Period size: 23  Copynumber: 1.9  Consensus size: 23

      13042 TTAAATTTTA

                                   
      13052 AAATT-TT-AAAATAAAAATATT
          1 AAATTCTTAAAAATAAAAATATT

                                 
      13073 AAATTCTTAAAAATAAAAATA
          1 AAATTCTTAAAAATAAAAATA

      13094 AAATGAATTA


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  21    5  0.26
  22    2  0.11
  23   12  0.63

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


Consensus pattern (23 bp):   
AAATTCTTAAAAATAAAAATATT

Found at i:13074 original size:29 final size:29

Alignment explanation


    Indices: 13040--13121  Score: 89
    Period size: 29  Copynumber: 2.8  Consensus size: 29

      13030 TAACAGTTGA

                                         
      13040 AATTAAATTTTAAAATTTTAAAATAAAA-
          1 AATTAAATTTTAAAATTTTAAAATAAAAT

                              * *          
      13068 ATATTAAATTCTTAAAA-ATAAAAATAAAAT
          1 A-ATTAAATT-TTAAAATTTTAAAATAAAAT

                                     
      13098 GAATTAAATTTT-AAATTTATAAAA
          1 -AATTAAATTTTAAAATTT-TAAAA

      13122 AGTAGAAATA


Statistics
Matches: 44,  Mismatches: 4, Indels: 10
        0.76            0.07        0.17

Matches are distributed among these distances:
  28    4  0.09
  29   21  0.48
  30   18  0.41
  31    1  0.02

ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38


Consensus pattern (29 bp):   
AATTAAATTTTAAAATTTTAAAATAAAAT

Done.