Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005064.1 Kokia drynarioides strain JFW-HI SEQ_118862, 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: 5429
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32


Found at i:2562 original size:15 final size:15

Alignment explanation


    Indices: 2544--2575  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       2534 GGTTTAATGG

                      *    
       2544 TTTAGAGTTTTAAAT
          1 TTTAGAGTTTCAAAT

                           
       2559 TTTAGAGTTTCAAAT
          1 TTTAGAGTTTCAAAT

              
       2574 TT
          1 TT

       2576 AAGGTATTTG


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.31, C:0.03, G:0.12, T:0.53


Consensus pattern (15 bp):   
TTTAGAGTTTCAAAT

Found at i:2645 original size:7 final size:7

Alignment explanation


    Indices: 2630--2675  Score: 65
    Period size: 7  Copynumber: 6.6  Consensus size: 7

       2620 TGGTTTTTAA

                   
       2630 TTTAAGG
          1 TTTAAGG

                *  
       2637 TTTAGGG
          1 TTTAAGG

                * *
       2644 TTTATGA
          1 TTTAAGG

                   
       2651 TTTAAGG
          1 TTTAAGG

                   
       2658 TTTAAGG
          1 TTTAAGG

                   
       2665 TTTAAGG
          1 TTTAAGG

                
       2672 TTTA
          1 TTTA

       2676 TAAGTATGAA


Statistics
Matches: 34,  Mismatches: 5, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
   7   34  1.00

ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48


Consensus pattern (7 bp):   
TTTAAGG

Found at i:2645 original size:21 final size:21

Alignment explanation


    Indices: 2616--2668  Score: 70
    Period size: 21  Copynumber: 2.5  Consensus size: 21

       2606 GAAATTGAGA

                      *           
       2616 TTAATGGTTTTTAATTTAAGGT
          1 TTAA-GGTTTATAATTTAAGGT

               *       *         
       2638 TTAGGGTTTATGATTTAAGGT
          1 TTAAGGTTTATAATTTAAGGT

                      
       2659 TTAAGGTTTA
          1 TTAAGGTTTA

       2669 AGGTTTATAA


Statistics
Matches: 27,  Mismatches: 4, Indels: 1
        0.84            0.12        0.03

Matches are distributed among these distances:
  21   24  0.89
  22    3  0.11

ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51


Consensus pattern (21 bp):   
TTAAGGTTTATAATTTAAGGT

Found at i:3662 original size:43 final size:43

Alignment explanation


    Indices: 3595--3688  Score: 120
    Period size: 43  Copynumber: 2.2  Consensus size: 43

       3585 GATGAACTGC

                                *       *              
       3595 ATAA-TTAATAACATGTCAAGATATTAATAAGAGTAAAGTAAT
          1 ATAATTTAATAACATGTCAACATATTAACAAGAGTAAAGTAAT

                                           *    **      
       3637 ATAATTTAATAACATG-CAACCATATTAACACGAGTCGAGTAAT
          1 ATAATTTAATAACATGTCAA-CATATTAACAAGAGTAAAGTAAT

                     
       3680 ATAATTTAA
          1 ATAATTTAA

       3689 CATGTTAATG


Statistics
Matches: 45,  Mismatches: 5, Indels: 3
        0.85            0.09        0.06

Matches are distributed among these distances:
  42    7  0.16
  43   38  0.84

ACGTcount: A:0.49, C:0.10, G:0.11, T:0.31


Consensus pattern (43 bp):   
ATAATTTAATAACATGTCAACATATTAACAAGAGTAAAGTAAT

Found at i:4961 original size:29 final size:30

Alignment explanation


    Indices: 4872--4966  Score: 104
    Period size: 30  Copynumber: 3.2  Consensus size: 30

       4862 TCAAAATAGG

                        *                 
       4872 TTATTTACTAAACTGGTACAAAATAAATAT
          1 TTATTTACTAAAATGGTACAAAATAAATAT

                *   *           * *  * *   
       4902 TTATATACCAAAATGGTATCCACA-CACTA-
          1 TTATTTACTAAAATGGTA-CAAAATAAATAT

                                          
       4931 TTATTTACTAAAATGGTACAAAATAAATAT
          1 TTATTTACTAAAATGGTACAAAATAAATAT

                  
       4961 TTATTT
          1 TTATTT

       4967 TGTACCATTT


Statistics
Matches: 49,  Mismatches: 13, Indels: 6
        0.72            0.19        0.09

Matches are distributed among these distances:
  28    3  0.06
  29   19  0.39
  30   24  0.49
  31    3  0.06

ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37


Consensus pattern (30 bp):   
TTATTTACTAAAATGGTACAAAATAAATAT
Done.