Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005310.1 Kokia drynarioides strain JFW-HI SEQ_119239, 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: 12832
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33


Found at i:473 original size:24 final size:24

Alignment explanation


    Indices: 446--502  Score: 60
    Period size: 24  Copynumber: 2.4  Consensus size: 24

        436 AAGCCTAATT

                 *           *      
        446 CTAATCAATACAAAATATATTATG
          1 CTAATAAATACAAAATAAATTATG

                     * *           *
        470 CTAATAAATTCTAAATAAATTATA
          1 CTAATAAATACAAAATAAATTATG

               *     
        494 CTACTAAAT
          1 CTAATAAAT

        503 CTTCTAGAAA


Statistics
Matches: 27,  Mismatches: 6, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  24   27  1.00

ACGTcount: A:0.51, C:0.12, G:0.02, T:0.35


Consensus pattern (24 bp):   
CTAATAAATACAAAATAAATTATG

Found at i:4884 original size:24 final size:24

Alignment explanation


    Indices: 4857--4913  Score: 69
    Period size: 24  Copynumber: 2.4  Consensus size: 24

       4847 AATCCTAATT

                 *                  
       4857 CTAATCAATACAAAATATATTATG
          1 CTAATAAATACAAAATATATTATG

                     * *           *
       4881 CTAATAAATGCTAAATATATTATA
          1 CTAATAAATACAAAATATATTATG

               *     
       4905 CTACTAAAT
          1 CTAATAAAT

       4914 CTTCTAGAGA


Statistics
Matches: 28,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  24   28  1.00

ACGTcount: A:0.49, C:0.12, G:0.04, T:0.35


Consensus pattern (24 bp):   
CTAATAAATACAAAATATATTATG

Found at i:7620 original size:25 final size:25

Alignment explanation


    Indices: 7586--7638  Score: 79
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       7576 CCACTTCAAT

                                     
       7586 TATTTTATAAAATAAATCTATTAAA
          1 TATTTTATAAAATAAATCTATTAAA

                       *   * *       
       7611 TATTTTATAAAGTAACTTTATTAAA
          1 TATTTTATAAAATAAATCTATTAAA

               
       7636 TAT
          1 TAT

       7639 ATATTATTCA


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  25   25  1.00

ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47


Consensus pattern (25 bp):   
TATTTTATAAAATAAATCTATTAAA

Found at i:10079 original size:101 final size:102

Alignment explanation


    Indices: 9884--10084  Score: 350
    Period size: 101  Copynumber: 2.0  Consensus size: 102

       9874 GAGCAACTTA

                                        *                                    
       9884 TTTGCTTAAAATCTTAAGGGCTCTAACCGAAGGAACCGAATAAGTAAAAACATCAACTCATGGAA
          1 TTTGCTTAAAATCTTAAGGGCTCTAACCAAAGGAACCGAATAAGT-AAAACATCAACTCATGGAA

                                                  
       9949 TAAAAGAATTTGACATTTGAGACACTTGTATGATCTTG
         65 TAAAAGAATTTGACATTTGAGACACTTGTATGATCTTG

                                                * *                          
       9987 TTTGCTTAAAATCTTAAGGGCTCTAACCAAAGGAACTGGATAAGT-AAACATCAACTCATGGAAT
          1 TTTGCTTAAAATCTTAAGGGCTCTAACCAAAGGAACCGAATAAGTAAAACATCAACTCATGGAAT

               *                              
      10051 AAAGGAATTTGACATTTGAGACACTTGTATGATC
         66 AAAAGAATTTGACATTTGAGACACTTGTATGATC

      10085 AACACACATA


Statistics
Matches: 94,  Mismatches: 4, Indels: 2
        0.94            0.04        0.02

Matches are distributed among these distances:
 101   52  0.55
 103   42  0.45

ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28


Consensus pattern (102 bp):   
TTTGCTTAAAATCTTAAGGGCTCTAACCAAAGGAACCGAATAAGTAAAACATCAACTCATGGAAT
AAAAGAATTTGACATTTGAGACACTTGTATGATCTTG
Done.