Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011517.1 Kokia drynarioides strain JFW-HI SEQ_126503, 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: 5026
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34


Found at i:3492 original size:22 final size:24

Alignment explanation


    Indices: 3467--3530  Score: 87
    Period size: 24  Copynumber: 2.8  Consensus size: 24

       3457 TTTCTTGAGC

                                    
       3467 GATAT-GTT-ATGGAAGACTTGGT
          1 GATATCGTTAATGGAAGACTTGGT

                  *                 
       3489 GATATCTTTAATGGAAGACTTGGT
          1 GATATCGTTAATGGAAGACTTGGT

               *  *           
       3513 GATTTCTTTAATGGAAGA
          1 GATATCGTTAATGGAAGA

       3531 GCTTACATCT


Statistics
Matches: 38,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
  22    5  0.13
  23    2  0.05
  24   31  0.82

ACGTcount: A:0.30, C:0.06, G:0.27, T:0.38


Consensus pattern (24 bp):   
GATATCGTTAATGGAAGACTTGGT

Found at i:3503 original size:24 final size:24

Alignment explanation


    Indices: 3475--3530  Score: 103
    Period size: 24  Copynumber: 2.3  Consensus size: 24

       3465 GCGATATGTT

                                    
       3475 ATGGAAGACTTGGTGATATCTTTA
          1 ATGGAAGACTTGGTGATATCTTTA

                             *      
       3499 ATGGAAGACTTGGTGATTTCTTTA
          1 ATGGAAGACTTGGTGATATCTTTA

                    
       3523 ATGGAAGA
          1 ATGGAAGA

       3531 GCTTACATCT


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  24   31  1.00

ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36


Consensus pattern (24 bp):   
ATGGAAGACTTGGTGATATCTTTA

Found at i:4419 original size:43 final size:43

Alignment explanation


    Indices: 4358--4446  Score: 151
    Period size: 43  Copynumber: 2.1  Consensus size: 43

       4348 CTTGAAACAA

                         *                             
       4358 GGTCTAGGACATGGCCATGTAAGGGTATTTCGTGTATGCACAC
          1 GGTCTAGGACATGACCATGTAAGGGTATTTCGTGTATGCACAC

                    *                     *            
       4401 GGTCTAGGGCATGACCATGTAAGGGTATTTTGTGTATGCACAC
          1 GGTCTAGGACATGACCATGTAAGGGTATTTCGTGTATGCACAC

               
       4444 GGT
          1 GGT

       4447 TTGGCACAGG


Statistics
Matches: 43,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  43   43  1.00

ACGTcount: A:0.22, C:0.17, G:0.31, T:0.29


Consensus pattern (43 bp):   
GGTCTAGGACATGACCATGTAAGGGTATTTCGTGTATGCACAC

Found at i:4904 original size:15 final size:15

Alignment explanation


    Indices: 4884--4914  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       4874 TGTGAAGAGT

                           
       4884 ATTAATCTAAACTAA
          1 ATTAATCTAAACTAA

                       *   
       4899 ATTAATCTAAATTAA
          1 ATTAATCTAAACTAA

             
       4914 A
          1 A

       4915 ATTGAAAGAT


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

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35


Consensus pattern (15 bp):   
ATTAATCTAAACTAA
Done.