Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000748.1 Kokia drynarioides strain JFW-HI SEQ_111785, 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: 3219
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38


Found at i:2534 original size:12 final size:13

Alignment explanation


    Indices: 2519--2554  Score: 56
    Period size: 14  Copynumber: 2.8  Consensus size: 13

       2509 AAATTGAAGG

                         
       2519 AAAAAAGAAAA-A
          1 AAAAAAGAAAAGA

                          
       2531 AAAAAAGAGAAAGA
          1 AAAAAAGA-AAAGA

                      
       2545 AAAAAAGAAA
          1 AAAAAAGAAA

       2555 GAAGAAGGAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  12    8  0.36
  13    5  0.23
  14    9  0.41

ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00


Consensus pattern (13 bp):   
AAAAAAGAAAAGA

Found at i:2543 original size:18 final size:18

Alignment explanation


    Indices: 2522--2556  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       2512 TTGAAGGAAA

                              
       2522 AAAGAAAAAAAAAAAGAG
          1 AAAGAAAAAAAAAAAGAG

                       *     
       2540 AAAGAAAAAAAGAAAGA
          1 AAAGAAAAAAAAAAAGA

       2557 AGAAGGAAGA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00


Consensus pattern (18 bp):   
AAAGAAAAAAAAAAAGAG

Found at i:2555 original size:12 final size:12

Alignment explanation


    Indices: 2519--2557  Score: 51
    Period size: 13  Copynumber: 3.1  Consensus size: 12

       2509 AAATTGAAGG

                       * 
       2519 AAAAAAGAAAAAA
          1 AAAAAAG-AAAGA

                         
       2532 AAAAAGAGAAAGA
          1 AAAAA-AGAAAGA

                        
       2545 AAAAAAGAAAGA
          1 AAAAAAGAAAGA

             
       2557 A
          1 A

       2558 GAAGGAAGAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  12    8  0.33
  13   14  0.58
  14    2  0.08

ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00


Consensus pattern (12 bp):   
AAAAAAGAAAGA

Found at i:2980 original size:20 final size:21

Alignment explanation


    Indices: 2939--2981  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       2929 TAATTTATTT

                                 
       2939 TAATTTAATTTTGCTAGTTAG
          1 TAATTTAATTTTGCTAGTTAG

                  *        *     
       2960 TAATTTTATTTTG-TTGTTAG
          1 TAATTTAATTTTGCTAGTTAG

              
       2980 TA
          1 TA

       2982 GTAGTAAGTA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20    8  0.40
  21   12  0.60

ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58


Consensus pattern (21 bp):   
TAATTTAATTTTGCTAGTTAG
Done.