Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009137.1 Kokia drynarioides strain JFW-HI SEQ_123841, 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: 19386
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:3782 original size:20 final size:20

Alignment explanation


    Indices: 3754--3801  Score: 62
    Period size: 20  Copynumber: 2.4  Consensus size: 20

       3744 AAGTGCATTA

                                 
       3754 TTACATTTAT-TGTTTTCTTT
          1 TTACATTTATCTG-TTTCTTT

                *               
       3774 TTACTTTTATCTGTTTCTTT
          1 TTACATTTATCTGTTTCTTT

               *    
       3794 TTAGATTT
          1 TTACATTT

       3802 TATGCAAGAA


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  20   22  0.92
  21    2  0.08

ACGTcount: A:0.15, C:0.10, G:0.06, T:0.69


Consensus pattern (20 bp):   
TTACATTTATCTGTTTCTTT

Found at i:6033 original size:17 final size:17

Alignment explanation


    Indices: 6011--6047  Score: 56
    Period size: 17  Copynumber: 2.2  Consensus size: 17

       6001 GTCATTGTAT

                             
       6011 TTTTATTTGTCACTGCA
          1 TTTTATTTGTCACTGCA

                      * *    
       6028 TTTTATTTGTTAGTGCA
          1 TTTTATTTGTCACTGCA

               
       6045 TTT
          1 TTT

       6048 GCATTGTAGT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.16, C:0.11, G:0.14, T:0.59


Consensus pattern (17 bp):   
TTTTATTTGTCACTGCA

Found at i:10503 original size:53 final size:53

Alignment explanation


    Indices: 10438--10846  Score: 518
    Period size: 53  Copynumber: 7.8  Consensus size: 53

      10428 GCCTTGTGCC

                          *         *                *     *     
      10438 ATGGATTAAAGGTCCGATGACTTTATGTCATCGTGAGTTATTTGAATTCTATT
          1 ATGGATTAAAGGTCTGATGACTTTGTGTCATCGTGAGTTATATGAATCCTATT

             *             *                                     
      10491 ACGGATTAAAGGTCTAATGACTTTGTGTCATCGTGAGTTATATGAATCCTATT
          1 ATGGATTAAAGGTCTGATGACTTTGTGTCATCGTGAGTTATATGAATCCTATT

             *             *      *                    *        *
      10544 ACGGATTAAAGGTCTAATGACTCTGTGTCATCGTGAGTTATATAAATCCTATC
          1 ATGGATTAAAGGTCTGATGACTTTGTGTCATCGTGAGTTATATGAATCCTATT

                   *  *   *       *                         *    
      10597 ATGGATTGAATGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCTTATT
          1 ATGGATTAAAGGTCTGATGACTTTGTGTCATCGTGAGTTATATGAATCCTATT

                *     *  *      *           *                    
      10650 ATGGTTTAAATGTTTGATGATTTTGTGTCATCATGAGTTATATGAATCCTATT
          1 ATGGATTAAAGGTCTGATGACTTTGTGTCATCGTGAGTTATATGAATCCTATT

                          *       *         *             *      
      10703 ATGGATTAAAGGTCCGATGACTATGTGTCATCATGAGTTATATGAACCCTATT
          1 ATGGATTAAAGGTCTGATGACTTTGTGTCATCGTGAGTTATATGAATCCTATT

                     *                  *        *  *           *
      10756 ATGGATTAAGGGTCTGATGACTTTGTGTTATCGTGAGATACATGAATCC-ATC
          1 ATGGATTAAAGGTCTGATGACTTTGTGTCATCGTGAGTTATATGAATCCTATT

                                            *        
      10808 ATGGATTAAAGGTCTGATGAC--TGTGTCATCATGAGTTAT
          1 ATGGATTAAAGGTCTGATGACTTTGTGTCATCGTGAGTTAT

      10847 CAAATGCGAA


Statistics
Matches: 310,  Mismatches: 46, Indels: 3
        0.86            0.13        0.01

Matches are distributed among these distances:
  50   14  0.05
  52   22  0.07
  53  274  0.88

ACGTcount: A:0.28, C:0.13, G:0.22, T:0.38


Consensus pattern (53 bp):   
ATGGATTAAAGGTCTGATGACTTTGTGTCATCGTGAGTTATATGAATCCTATT

Found at i:11561 original size:21 final size:21

Alignment explanation


    Indices: 11507--11563  Score: 69
    Period size: 21  Copynumber: 2.7  Consensus size: 21

      11497 TAGAAATAAG

                  *   *     *   *
      11507 ACTTGTTTCGATAGAATTGTT
          1 ACTTGTATCGGTAGAACTGTC

                                 
      11528 ACTTGTATCGGTAGAACTGTC
          1 ACTTGTATCGGTAGAACTGTC

                    *      
      11549 ACTTGTATTGGTAGA
          1 ACTTGTATCGGTAGA

      11564 GGCCTGCACT


Statistics
Matches: 31,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   31  1.00

ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40


Consensus pattern (21 bp):   
ACTTGTATCGGTAGAACTGTC

Found at i:14544 original size:19 final size:20

Alignment explanation


    Indices: 14520--14557  Score: 60
    Period size: 19  Copynumber: 1.9  Consensus size: 20

      14510 TATTATTGTA

                                
      14520 TATATATATTT-TTTCTTTT
          1 TATATATATTTCTTTCTTTT

                   *           
      14539 TATATATTTTTCTTTCTTT
          1 TATATATATTTCTTTCTTT

      14558 CTTTTCTTTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  19   10  0.59
  20    7  0.41

ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74


Consensus pattern (20 bp):   
TATATATATTTCTTTCTTTT

Found at i:14548 original size:15 final size:16

Alignment explanation


    Indices: 14522--14553  Score: 55
    Period size: 16  Copynumber: 1.9  Consensus size: 16

      14512 TTATTGTATA

                             
      14522 TATATATTTTTTCTTTT
          1 TATATA-TTTTTCTTTT

                           
      14539 TATATATTTTTCTTT
          1 TATATATTTTTCTTT

      14554 CTTTCTTTTC


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

Matches are distributed among these distances:
  16    9  0.60
  17    6  0.40

ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75


Consensus pattern (16 bp):   
TATATATTTTTCTTTT
Done.