Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004338.1 Kokia drynarioides strain JFW-HI SEQ_117669, 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: 12940
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32


Found at i:163 original size:13 final size:13

Alignment explanation


    Indices: 145--184  Score: 53
    Period size: 13  Copynumber: 3.1  Consensus size: 13

        135 ATTAAATCAA

                         
        145 ACTTTTCAAAAAC
          1 ACTTTTCAAAAAC

                  *     *
        158 ACTTTTTAAAAAT
          1 ACTTTTCAAAAAC

             *           
        171 ATTTTTCAAAAAC
          1 ACTTTTCAAAAAC

             
        184 A
          1 A

        185 ATGTTAAACT


Statistics
Matches: 22,  Mismatches: 5, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  13   22  1.00

ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38


Consensus pattern (13 bp):   
ACTTTTCAAAAAC

Found at i:6123 original size:33 final size:33

Alignment explanation


    Indices: 6040--6123  Score: 123
    Period size: 33  Copynumber: 2.5  Consensus size: 33

       6030 AGGAGCAATA

                       *     *    *          
       6040 AAACACGAAGAGGAGGAACGGGTAGAAGGAAGC
          1 AAACACGAAGAAGAGGAGCGGGAAGAAGGAAGC

              *                             *
       6073 AAGCACGAAGAAGAGGAGCGGGAAGAAGGAAGT
          1 AAACACGAAGAAGAGGAGCGGGAAGAAGGAAGC

                              
       6106 AAACACGAAGAAGAGGAG
          1 AAACACGAAGAAGAGGAG

       6124 GAAGAAGAAA


Statistics
Matches: 45,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  33   45  1.00

ACGTcount: A:0.48, C:0.11, G:0.39, T:0.02


Consensus pattern (33 bp):   
AAACACGAAGAAGAGGAGCGGGAAGAAGGAAGC

Found at i:6131 original size:33 final size:33

Alignment explanation


    Indices: 6040--6152  Score: 111
    Period size: 33  Copynumber: 3.4  Consensus size: 33

       6030 AGGAGCAATA

                       *     *  * *          
       6040 AAACACGAAGAGGAGGAACGGGTAGAAGGAAGC
          1 AAACACGAAGAAGAGGAGCGAGAAGAAGGAAGC

              *                 *           *
       6073 AAGCACGAAGAAGAGGAGCGGGAAGAAGGAAGT
          1 AAACACGAAGAAGAGGAGCGAGAAGAAGGAAGC

                                        **  * 
       6106 AAACACGAAGAAGAGGAG-GAAGAAGAAACAAAC
          1 AAACACGAAGAAGAGGAGCG-AGAAGAAGGAAGC

                 *        
       6139 AAACATGAAGAAGA
          1 AAACACGAAGAAGA

       6153 AGAAGAAGAG


Statistics
Matches: 67,  Mismatches: 12, Indels: 2
        0.83            0.15        0.02

Matches are distributed among these distances:
  32    1  0.01
  33   66  0.99

ACGTcount: A:0.52, C:0.11, G:0.35, T:0.03


Consensus pattern (33 bp):   
AAACACGAAGAAGAGGAGCGAGAAGAAGGAAGC
Done.