Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003243.1 Kokia drynarioides strain JFW-HI SEQ_115893, 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: 6100
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33


Found at i:4052 original size:11 final size:14

Alignment explanation


    Indices: 4019--4045  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

       4009 AAGGAGTTCG

                          
       4019 AATAAAGAAGAAAC
          1 AATAAAGAAGAAAC

                         
       4033 AATAAAGAAGAAA
          1 AATAAAGAAGAAA

       4046 AAAAGAACAG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.74, C:0.04, G:0.15, T:0.07


Consensus pattern (14 bp):   
AATAAAGAAGAAAC

Found at i:4111 original size:11 final size:11

Alignment explanation


    Indices: 4087--4130  Score: 54
    Period size: 11  Copynumber: 4.1  Consensus size: 11

       4077 AAAAGGTTCG

                      *
       4087 AAAAG-AAAAG
          1 AAAAGAAAAAA

                       
       4097 AAAAGAAAAAA
          1 AAAAGAAAAAA

                  *    
       4108 AAAAGAGAAAA
          1 AAAAGAAAAAA

             *         
       4119 AGAAGAAAAAA
          1 AAAAGAAAAAA

             
       4130 A
          1 A

       4131 TGGTTGCTTA


Statistics
Matches: 29,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  10    5  0.17
  11   24  0.83

ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00


Consensus pattern (11 bp):   
AAAAGAAAAAA

Found at i:4939 original size:23 final size:23

Alignment explanation


    Indices: 4861--4941  Score: 108
    Period size: 23  Copynumber: 3.5  Consensus size: 23

       4851 CTGACGTGGT

                 *    *            
       4861 GTCCAATCAGTAGCTTCTAGAAG
          1 GTCCAGTCAGCAGCTTCTAGAAG

                     *  *          
       4884 GTCCAGTCAACAACTTCTAGAAG
          1 GTCCAGTCAGCAGCTTCTAGAAG

                 *                 
       4907 GTCCAATCAGCAGCTTCTAGAAG
          1 GTCCAGTCAGCAGCTTCTAGAAG

               *        
       4930 GTCTAGTCAGCA
          1 GTCCAGTCAGCA

       4942 AGGATGGAAG


Statistics
Matches: 49,  Mismatches: 9, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  23   49  1.00

ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23


Consensus pattern (23 bp):   
GTCCAGTCAGCAGCTTCTAGAAG

Found at i:5791 original size:17 final size:17

Alignment explanation


    Indices: 5769--5802  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       5759 AGGCTGATAC

                             
       5769 TTAAATTGAGTTTCTTT
          1 TTAAATTGAGTTTCTTT

                   * *       
       5786 TTAAATTTATTTTCTTT
          1 TTAAATTGAGTTTCTTT

       5803 AAATTCTTAG


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.24, C:0.06, G:0.06, T:0.65


Consensus pattern (17 bp):   
TTAAATTGAGTTTCTTT
Done.