Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002758.1 Kokia drynarioides strain JFW-HI SEQ_115075, 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: 20521
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.31


Found at i:4308 original size:18 final size:19

Alignment explanation


    Indices: 4274--4315  Score: 52
    Period size: 18  Copynumber: 2.3  Consensus size: 19

       4264 TACATATATC

                    *          
       4274 AATTTTTATAATATTTA-A
          1 AATTTTTAGAATATTTATA

                                
       4292 AATTTTTAGAACT-TTTATA
          1 AATTTTTAGAA-TATTTATA

                 
       4311 AATTT
          1 AATTT

       4316 GCATCCATCT


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  18   14  0.67
  19    7  0.33

ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55


Consensus pattern (19 bp):   
AATTTTTAGAATATTTATA

Found at i:6094 original size:25 final size:23

Alignment explanation


    Indices: 6043--6097  Score: 60
    Period size: 22  Copynumber: 2.4  Consensus size: 23

       6033 ATAGTGTGTG

                                   
       6043 ATATA-ATATTATATAATGAAAT
          1 ATATATATATTATATAATGAAAT

                              *   *  
       6065 A-ATATATATTATAAGTATTGATAT
          1 ATATATATATTAT-A-TAATGAAAT

                     
       6089 ATATATATA
          1 ATATATATA

       6098 ACTATTATTA


Statistics
Matches: 27,  Mismatches: 2, Indels: 5
        0.79            0.06        0.15

Matches are distributed among these distances:
  21    3  0.11
  22    8  0.30
  23    1  0.04
  24    8  0.30
  25    7  0.26

ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44


Consensus pattern (23 bp):   
ATATATATATTATATAATGAAAT

Found at i:9144 original size:15 final size:15

Alignment explanation


    Indices: 9124--9156  Score: 66
    Period size: 15  Copynumber: 2.2  Consensus size: 15

       9114 GAACTATGAA

                           
       9124 ACTTAAGGTGCAAAT
          1 ACTTAAGGTGCAAAT

                           
       9139 ACTTAAGGTGCAAAT
          1 ACTTAAGGTGCAAAT

               
       9154 ACT
          1 ACT

       9157 ATTAAGTCAG


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27


Consensus pattern (15 bp):   
ACTTAAGGTGCAAAT

Found at i:18975 original size:14 final size:14

Alignment explanation


    Indices: 18956--18985  Score: 51
    Period size: 14  Copynumber: 2.1  Consensus size: 14

      18946 GGTTCGGGTT

                          
      18956 AGGTTTAGGTCAAA
          1 AGGTTTAGGTCAAA

                  *       
      18970 AGGTTTGGGTCAAA
          1 AGGTTTAGGTCAAA

              
      18984 AG
          1 AG

      18986 TTCGGTTTGG


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.33, C:0.07, G:0.33, T:0.27


Consensus pattern (14 bp):   
AGGTTTAGGTCAAA
Done.