Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014702.1 Kokia drynarioides strain JFW-HI SEQ_129741, 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: 6935
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:3095 original size:16 final size:17

Alignment explanation


    Indices: 3074--3106  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       3064 GACCAAATTG

                             
       3074 TATG-TTTGTTTAGCTA
          1 TATGTTTTGTTTAGCTA

                    *        
       3090 TATGTTTTTTTTAGCTA
          1 TATGTTTTGTTTAGCTA

       3107 AGTGACCAGA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  16    4  0.27
  17   11  0.73

ACGTcount: A:0.18, C:0.06, G:0.15, T:0.61


Consensus pattern (17 bp):   
TATGTTTTGTTTAGCTA

Found at i:3350 original size:25 final size:25

Alignment explanation


    Indices: 3305--3357  Score: 65
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       3295 TTTAATTAGT

                          *           
       3305 AAATATATTTATTTTTAAAATTTATA
          1 AAATATATTTATTTATAAAATTT-TA

                                      
       3331 AAATATA-TTATTTA-ATAAATTTTA
          1 AAATATATTTATTTATA-AAATTTTA

               
       3355 AAA
          1 AAA

       3358 AATAAACACA


Statistics
Matches: 25,  Mismatches: 1, Indels: 4
        0.83            0.03        0.13

Matches are distributed among these distances:
  24    6  0.24
  25   12  0.48
  26    7  0.28

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (25 bp):   
AAATATATTTATTTATAAAATTTTA

Found at i:3358 original size:25 final size:26

Alignment explanation


    Indices: 3305--3361  Score: 71
    Period size: 26  Copynumber: 2.2  Consensus size: 26

       3295 TTTAATTAGT

                          *           
       3305 AAATATATTTATTTTTAAAATTTATA
          1 AAATATATTTATTTATAAAATTTATA

                                *    * 
       3331 AAATATA-TTATTTAATAAATTTTAAA
          1 AAATATATTTATTT-ATAAAATTTATA

                 
       3357 AAATA
          1 AAATA

       3362 AACACATAAA


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  25    6  0.22
  26   21  0.78

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


Consensus pattern (26 bp):   
AAATATATTTATTTATAAAATTTATA

Found at i:4469 original size:19 final size:19

Alignment explanation


    Indices: 4447--4491  Score: 56
    Period size: 19  Copynumber: 2.4  Consensus size: 19

       4437 TTTTATTAGG

                                
       4447 ATTTAATATTTAAGATAT-T
          1 ATTTAATATTTAA-ATATGT

                 *         *   
       4466 ATTTATTATTTAAATTTGT
          1 ATTTAATATTTAAATATGT

                   
       4485 ATTTAAT
          1 ATTTAAT

       4492 TTATGTTTAT


Statistics
Matches: 22,  Mismatches: 3, Indels: 2
        0.81            0.11        0.07

Matches are distributed among these distances:
  18    3  0.14
  19   19  0.86

ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58


Consensus pattern (19 bp):   
ATTTAATATTTAAATATGT

Found at i:6637 original size:21 final size:18

Alignment explanation


    Indices: 6620--6654  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       6610 TATGATGATT

                              
       6620 ATGTGGCCCAAGTAGATG
          1 ATGTGGCCCAAGTAGATG

            *                
       6638 CTGTGGCCCAAGTAGAT
          1 ATGTGGCCCAAGTAGAT

       6655 CGAGAGCCCC


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:0.26, C:0.20, G:0.31, T:0.23


Consensus pattern (18 bp):   
ATGTGGCCCAAGTAGATG
Done.