Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008550.1 Kokia drynarioides strain JFW-HI SEQ_123227, 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: 7373
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.36


Found at i:2828 original size:18 final size:18

Alignment explanation


    Indices: 2805--2867  Score: 65
    Period size: 19  Copynumber: 3.3  Consensus size: 18

       2795 TCTTGACATG

                              
       2805 AATTTTATTTATTTTTAT
          1 AATTTTATTTATTTTTAT

                    *        *  
       2823 AATTTTATATAGTTTTAAAT
          1 AATTTTATTTA-TTTT-TAT

                                
       2843 AATTTTAAGTTT-TTTTTAT
          1 AATTTT-A-TTTATTTTTAT

                  
       2862 AATTTT
          1 AATTTT

       2868 TATATAAAAT


Statistics
Matches: 37,  Mismatches: 4, Indels: 7
        0.77            0.08        0.15

Matches are distributed among these distances:
  18   10  0.27
  19   12  0.32
  20   12  0.32
  21    1  0.03
  22    2  0.05

ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65


Consensus pattern (18 bp):   
AATTTTATTTATTTTTAT

Found at i:5331 original size:18 final size:19

Alignment explanation


    Indices: 5286--5365  Score: 67
    Period size: 18  Copynumber: 4.3  Consensus size: 19

       5276 GTCATGATTT

                                 
       5286 TAAAAATTAAGAAAATATAAA
          1 TAAAAATTAAGAAAATAT--A

              *          *     
       5307 TATAAATTAA-AAGATATA
          1 TAAAAATTAAGAAAATATA

                    *          
       5325 TAAAAATTCA-AAAAT-TA
          1 TAAAAATTAAGAAAATATA

             *        *    *   
       5342 TTAAAATTAATAAAACATA
          1 TAAAAATTAAGAAAATATA

                 
       5361 TAAAA
          1 TAAAA

       5366 TACTCAAAAA


Statistics
Matches: 48,  Mismatches: 9, Indels: 6
        0.76            0.14        0.10

Matches are distributed among these distances:
  17   10  0.21
  18   17  0.35
  19    6  0.12
  20    6  0.12
  21    9  0.19

ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29


Consensus pattern (19 bp):   
TAAAAATTAAGAAAATATA

Found at i:5608 original size:18 final size:18

Alignment explanation


    Indices: 5585--5634  Score: 57
    Period size: 19  Copynumber: 2.7  Consensus size: 18

       5575 CCTTTTTTTA

                            *  
       5585 TTTATAATTTTT-TAGTAT
          1 TTTATAATTTTTATA-AAT

                               
       5603 TTTATATATTTTTATAAAT
          1 TTTATA-ATTTTTATAAAT

                         
       5622 TTTAATAATTTTT
          1 TTT-ATAATTTTT

       5635 GAATTTTATG


Statistics
Matches: 28,  Mismatches: 1, Indels: 5
        0.82            0.03        0.15

Matches are distributed among these distances:
  18    6  0.21
  19   17  0.61
  20    5  0.18

ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66


Consensus pattern (18 bp):   
TTTATAATTTTTATAAAT

Found at i:5673 original size:20 final size:20

Alignment explanation


    Indices: 5589--5686  Score: 71
    Period size: 20  Copynumber: 5.0  Consensus size: 20

       5579 TTTTTATTTA

                       *      *  
       5589 TAATTTTTTAGTATTTTATA-
          1 TAATTTTTTA-AATTTTAAAT

                                 
       5609 T-ATTTTTATAAATTTT-AA-
          1 TAATTTTT-TAAATTTTAAAT

                     *       ** 
       5627 TAA-TTTTTGAATTTTATGT
          1 TAATTTTTTAAATTTTAAAT

                                
       5646 TAATTTTTTAAATTTTAAAT
          1 TAATTTTTTAAATTTTAAAT

                         *       
       5666 TATATTTTCTTAATTTTTAAA
          1 TA-ATTTT-TTAAATTTTAAA

       5687 ATCATGATAA


Statistics
Matches: 62,  Mismatches: 9, Indels: 12
        0.75            0.11        0.14

Matches are distributed among these distances:
  17    7  0.11
  18    6  0.10
  19   15  0.24
  20   18  0.29
  21    5  0.08
  22   11  0.18

ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62


Consensus pattern (20 bp):   
TAATTTTTTAAATTTTAAAT
Done.