Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004809.1 Kokia drynarioides strain JFW-HI SEQ_118439, 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, 883

Length: 1472
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34


Found at i:664 original size:11 final size:11

Alignment explanation


    Indices: 648--722  Score: 59
    Period size: 11  Copynumber: 6.9  Consensus size: 11

        638 CCGAACTCCC

                       
        648 TTTAAATTTAT
          1 TTTAAATTTAT

                      *
        659 TTTAAA---AA
          1 TTTAAATTTAT

                       
        667 TTTAAATTTAT
          1 TTTAAATTTAT

               *       *
        678 TTTGAATTTAAA
          1 TTTAAATTT-AT

                       *
        690 TTT-AATTTAAG
          1 TTTAAATTT-AT

                        
        701 TTTAAATTTATT
          1 TTTAAATTTA-T

                      
        713 TTTAAATTTA
          1 TTTAAATTTA

        723 AAATTACTAT


Statistics
Matches: 52,  Mismatches: 6, Indels: 11
        0.75            0.09        0.16

Matches are distributed among these distances:
   8    7  0.13
  11   26  0.50
  12   19  0.37

ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57


Consensus pattern (11 bp):   
TTTAAATTTAT

Found at i:673 original size:6 final size:6

Alignment explanation


    Indices: 664--742  Score: 65
    Period size: 6  Copynumber: 13.7  Consensus size: 6

        654 TTTATTTTAA

                            *    *                      *          
        664 AAATTT AAATTT -ATTTT GAATTT AAATTT -AATTT AAGTTT AAATTT
          1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT

             **              *     * *             
        710 ATTTTT AAATTT AAAATT -ACTAT AAATTT AAAT
          1 AAATTT AAATTT AAATTT AAATTT AAATTT AAAT

        743 AAAGCTAAAA


Statistics
Matches: 55,  Mismatches: 15, Indels: 6
        0.72            0.20        0.08

Matches are distributed among these distances:
   5   11  0.20
   6   44  0.80

ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52


Consensus pattern (6 bp):   
AAATTT

Found at i:687 original size:17 final size:17

Alignment explanation


    Indices: 648--742  Score: 109
    Period size: 17  Copynumber: 5.4  Consensus size: 17

        638 CCGAACTCCC

                               
        648 TTTAAATTTATTTTAAAAA
          1 TTTAAATTTATTTT--AAA

                          *  
        667 TTTAAATTTATTTTGAA
          1 TTTAAATTTATTTTAAA

                      *     *
        684 TTTAAATTTAATTTAAG
          1 TTTAAATTTATTTTAAA

                              
        701 TTTAAATTTATTTTTAAA
          1 TTTAAATTTA-TTTTAAA

                  *   * *    
        719 TTTAAAATTACTATAAA
          1 TTTAAATTTATTTTAAA

                   
        736 TTTAAAT
          1 TTTAAAT

        743 AAAGCTAAAA


Statistics
Matches: 65,  Mismatches: 10, Indels: 4
        0.82            0.13        0.05

Matches are distributed among these distances:
  17   37  0.57
  18   14  0.22
  19   14  0.22

ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54


Consensus pattern (17 bp):   
TTTAAATTTATTTTAAA

Found at i:794 original size:18 final size:17

Alignment explanation


    Indices: 755--794  Score: 55
    Period size: 18  Copynumber: 2.3  Consensus size: 17

        745 AGCTAAAATA

                             
        755 CAAA-AATTAAAAAGTC
          1 CAAATAATTAAAAAGTC

                               
        771 CAAAATAATTACAAAAGTC
          1 C-AAATAATTA-AAAAGTC

                 
        790 CAAAT
          1 CAAAT

        795 TACATTCTTA


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  16    1  0.05
  17    3  0.14
  18    9  0.43
  19    8  0.38

ACGTcount: A:0.60, C:0.15, G:0.05, T:0.20


Consensus pattern (17 bp):   
CAAATAATTAAAAAGTC
Done.