Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012047.1 Kokia drynarioides strain JFW-HI SEQ_127045, 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: 2900
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.34


Found at i:2431 original size:26 final size:24

Alignment explanation


    Indices: 2386--2433  Score: 60
    Period size: 26  Copynumber: 1.9  Consensus size: 24

       2376 AGAGAAATGT

                        *           
       2386 AAATGTGATATATGAAATTATGAG
          1 AAATGTGATATAAGAAATTATGAG

                             *      
       2410 AAATGATGAATATAAGAGATTATG
          1 AAATG-TG-ATATAAGAAATTATG

       2434 CCCGTGTAGA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  24    5  0.25
  25    2  0.10
  26   13  0.65

ACGTcount: A:0.48, C:0.00, G:0.21, T:0.31


Consensus pattern (24 bp):   
AAATGTGATATAAGAAATTATGAG

Found at i:2527 original size:23 final size:23

Alignment explanation


    Indices: 2497--2572  Score: 68
    Period size: 23  Copynumber: 3.3  Consensus size: 23

       2487 CGCTAGCGCA

                              *     
       2497 CTTACTGTTCAGCA-TTGTGTGTG
          1 CTTACTGTTCAGCACTT-CGTGTG

                     **            
       2520 CTTACTGTTTTGCACTTCGTGTG
          1 CTTACTGTTCAGCACTTCGTGTG

                                     
       2543 CTTACTGTTTC-GCA-TCTCGTGTG
          1 CTTACTG-TTCAGCACT-TCGTGTG

             *     
       2566 CCTACTG
          1 CTTACTG

       2573 ATTTGCGCTA


Statistics
Matches: 45,  Mismatches: 5, Indels: 6
        0.80            0.09        0.11

Matches are distributed among these distances:
  22    1  0.02
  23   40  0.89
  24    4  0.09

ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43


Consensus pattern (23 bp):   
CTTACTGTTCAGCACTTCGTGTG

Found at i:2565 original size:46 final size:44

Alignment explanation


    Indices: 2514--2642  Score: 129
    Period size: 46  Copynumber: 2.9  Consensus size: 44

       2504 TTCAGCATTG

                   *     *                                
       2514 TGTGTGCTTACTGTTTTGCACT-TCGTGTGCTTACTGTTTCGCATC
          1 TGTGTGCCTACTGATTTGCACTAT-GTGTGCTTACTGTTTCGCA-C

                                *       *  *     *       
       2559 TCGTGTGCCTACTGATTTGCGCTATGTGCGCCTACTGATT-GCAC
          1 T-GTGTGCCTACTGATTTGCACTATGTGTGCTTACTGTTTCGCAC

                                   *            *    
       2603 TGTGTGCCTACTGGA-TTGCACTGTGTGTGCTTACTATTTC
          1 TGTGTGCCTACT-GATTTGCACTATGTGTGCTTACTGTTTC

       2643 CCCAGCACTT


Statistics
Matches: 68,  Mismatches: 12, Indels: 9
        0.76            0.13        0.10

Matches are distributed among these distances:
  43   29  0.43
  44    4  0.06
  45    4  0.06
  46   30  0.44
  47    1  0.01

ACGTcount: A:0.12, C:0.23, G:0.24, T:0.41


Consensus pattern (44 bp):   
TGTGTGCCTACTGATTTGCACTATGTGTGCTTACTGTTTCGCAC

Found at i:2637 original size:23 final size:21

Alignment explanation


    Indices: 2514--2637  Score: 97
    Period size: 23  Copynumber: 5.6  Consensus size: 21

       2504 TTCAGCATTG

                   *      *       
       2514 TGTGTGCTTACTGTTTTGCACT
          1 TGTGTGCCTACTG-ATTGCACT

                    *     *         
       2536 TCGTGTGCTTACTGTTTCGCATCT
          1 T-GTGTGCCTACTGATT-GCA-CT

            *                  *  
       2560 CGTGTGCCTACTGATTTGCGCT
          1 TGTGTGCCTACTGA-TTGCACT

                 *                
       2582 ATGTGCGCCTACTGATTGCAC-
          1 -TGTGTGCCTACTGATTGCACT

                                  
       2603 TGTGTGCCTACTGGATTGCACT
          1 TGTGTGCCTACT-GATTGCACT

                    *    
       2625 GTGTGTGCTTACT
          1 -TGTGTGCCTACT

       2638 ATTTCCCCAG


Statistics
Matches: 85,  Mismatches: 9, Indels: 15
        0.78            0.08        0.14

Matches are distributed among these distances:
  20   11  0.13
  21    8  0.09
  22   11  0.13
  23   51  0.60
  24    4  0.05

ACGTcount: A:0.11, C:0.23, G:0.25, T:0.40


Consensus pattern (21 bp):   
TGTGTGCCTACTGATTGCACT
Done.