Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013252.1 Kokia drynarioides strain JFW-HI SEQ_128272, 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: 6793
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33


Found at i:4880 original size:96 final size:95

Alignment explanation


    Indices: 4696--4887  Score: 228
    Period size: 96  Copynumber: 2.0  Consensus size: 95

       4686 TCTTTGAGAA

                     *                     **                     *          
       4696 AAGGATATTTGATTATCTTGATTTGAAGAAAGGTTGCACCTAGAAAGTTAAGGCGCAATATTTCA
          1 AAGGATATTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGAAAGTTAAGGCACAATATTTCA

            *                              
       4761 GAATCGAAGATAAGGAAACATTGCCTCGATT
         66 AAATCGAAGATAAGG-AACATTGCCTCGATT

                *           *         *                *                     
       4792 AAGGGTATTCGATTATTTTGATTTGAGGAAAAATTGCACCTAGTAAGTTAAGGCACAA-ATTTTC
          1 AAGGATATTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGAAAGTTAAGGCACAATA-TTTC

                                 *            
       4856 AAAACTCGAA-ATAAAAGG-ATATTGCCTCGATT
         65 AAAA-TCGAAGAT--AAGGAACATTGCCTCGATT

       4888 TTAAAGTTTT


Statistics
Matches: 82,  Mismatches: 10, Indels: 8
        0.82            0.10        0.08

Matches are distributed among these distances:
  95    1  0.01
  96   72  0.88
  97    5  0.06
  98    4  0.05

ACGTcount: A:0.37, C:0.12, G:0.20, T:0.30


Consensus pattern (95 bp):   
AAGGATATTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGAAAGTTAAGGCACAATATTTCA
AAATCGAAGATAAGGAACATTGCCTCGATT

Found at i:5322 original size:29 final size:29

Alignment explanation


    Indices: 5290--5618  Score: 235
    Period size: 29  Copynumber: 11.2  Consensus size: 29

       5280 AGACTTTCGA

                                       * 
       5290 AAGTTCGGGGGTAAAATGGTAATTTTTTG
          1 AAGTTCGGGGGTAAAATGGTAATTTTTGG

                                   *  *     *
       5319 AAGTTTC-GGGGTCAAAAATGG-GA-CTTTGAA
          1 AAG-TTCGGGGGT--AAAATGGTAATTTTTG-G

                   *                  *  
       5349 AAGTTCGAGGGTAAAATGGTAATTTTAGG
          1 AAGTTCGGGGGTAAAATGGTAATTTTTGG

                     *                     
       5378 AAGTTTC-GAGGTCAAAATGG-AATTTTTGG
          1 AAG-TTCGGGGGT-AAAATGGTAATTTTTGG

              *  *                    *  
       5407 AATTTTGGGGGTAAAATGGTAATTTTAGG
          1 AAGTTCGGGGGTAAAATGGTAATTTTTGG

                     *             *        
       5436 AAGGTTC-GAGGTCAAAAATGG-GATTTTTGG
          1 AA-GTTCGGGGGT--AAAATGGTAATTTTTGG

                  **                  *  
       5466 AAGTTCAAGGGTAAAATGGTAATTTTAGG
          1 AAGTTCGGGGGTAAAATGGTAATTTTTGG

                  *    *          *        
       5495 AAGTTTTGGGGTTAAAAATGG-GATTTTTGG
          1 AAG-TTCGGGGGT-AAAATGGTAATTTTTGG

                 * *                  *  
       5525 AAGTTTGAGGGTAAAATGGTAATTTTAGG
          1 AAGTTCGGGGGTAAAATGGTAATTTTTGG

                 **   *                    
       5554 AAGTTTTGGGATCAAAAATGG-AATTTTTGG
          1 AAGTTCGGGGGT--AAAATGGTAATTTTTGG

                   *              *      
       5584 AAGTTCGAGGGTAAAATGGTAAATTTTGG
          1 AAGTTCGGGGGTAAAATGGTAATTTTTGG

                  
       5613 ATAGTT
          1 A-AGTT

       5619 TAGGGACCTC


Statistics
Matches: 233,  Mismatches: 44, Indels: 45
        0.72            0.14        0.14

Matches are distributed among these distances:
  28   37  0.16
  29   95  0.41
  30   73  0.31
  31   28  0.12

ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34


Consensus pattern (29 bp):   
AAGTTCGGGGGTAAAATGGTAATTTTTGG

Found at i:5344 original size:59 final size:59

Alignment explanation


    Indices: 5235--5619  Score: 445
    Period size: 59  Copynumber: 6.5  Consensus size: 59

       5225 TTCGGACATC

                *                 *      *    *  *      **  *   * *     
       5235 CGAGAGTAAAATGGTAATTTTTTGGAAGTGTCGATGTTAAAAATAAGACTTTCGAAAGTT
          1 CGAGGGTAAAATGGTAA-TTTTAGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTT

              *                  **         *               *     *     
       5295 CGGGGGTAAAATGGTAATTTTTTGAAGTTTCGGGGTCAAAAATGGGA-CTTTGAAAAGTT
          1 CGAGGGTAAAATGGTAATTTTAGGAAGTTTCGAGGTCAAAAATGGGATTTTTG-GAAGTT

                                                         *          *  
       5354 CGAGGGTAAAATGGTAATTTTAGGAAGTTTCGAGGTC-AAAATGGAATTTTTGGAATTT
          1 CGAGGGTAAAATGGTAATTTTAGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTT

            * *                        *                               
       5412 TGGGGGTAAAATGGTAATTTTAGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTT
          1 CGAGGGTAAAATGGTAATTTTAGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTT

             *                            * *   *                      
       5471 CAAGGGTAAAATGGTAATTTTAGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTT
          1 CGAGGGTAAAATGGTAATTTTAGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTT

            *                             *               *             
       5530 TGAGGGTAAAATGGTAATTTTAGGAAGTTTTG-GGATCAAAAATGGAATTTTTGGAAGTT
          1 CGAGGGTAAAATGGTAATTTTAGGAAGTTTCGAGG-TCAAAAATGGGATTTTTGGAAGTT

                                            
       5589 CGAGGGTAAAATGGTAAATTTT-GGATAGTTT
          1 CGAGGGTAAAATGGT-AATTTTAGGA-AGTTT

       5620 AGGGACCTCC


Statistics
Matches: 283,  Mismatches: 36, Indels: 12
        0.85            0.11        0.04

Matches are distributed among these distances:
  58   51  0.18
  59  206  0.73
  60   26  0.09

ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34


Consensus pattern (59 bp):   
CGAGGGTAAAATGGTAATTTTAGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTT

Found at i:6632 original size:13 final size:13

Alignment explanation


    Indices: 6609--6647  Score: 51
    Period size: 13  Copynumber: 3.0  Consensus size: 13

       6599 TTTTTATTCT

                *        
       6609 TAATAATTAATAC
          1 TAATTATTAATAC

             *          *
       6622 TGATTATTAATAA
          1 TAATTATTAATAC

                         
       6635 TAATTATTAATAC
          1 TAATTATTAATAC

       6648 AGTTATCAAT


Statistics
Matches: 21,  Mismatches: 5, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  13   21  1.00

ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44


Consensus pattern (13 bp):   
TAATTATTAATAC
Done.