Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007448.1 Kokia drynarioides strain JFW-HI SEQ_122069, 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: 36148
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37


Found at i:30716 original size:15 final size:15

Alignment explanation


    Indices: 30669--30718  Score: 50
    Period size: 15  Copynumber: 3.5  Consensus size: 15

      30659 TTGCCTCAGA

                *          
      30669 TTACATTTTAGTCAC
          1 TTACGTTTTAGTCAC

               *    * *    
      30684 TTATGTTTAAAT--C
          1 TTACGTTTTAGTCAC

                           
      30697 TTACGTTTTAGTCAC
          1 TTACGTTTTAGTCAC

                   
      30712 TTACGTT
          1 TTACGTT

      30719 ATTGTGTTGT


Statistics
Matches: 26,  Mismatches: 7, Indels: 4
        0.70            0.19        0.11

Matches are distributed among these distances:
  13   10  0.38
  15   16  0.62

ACGTcount: A:0.24, C:0.16, G:0.10, T:0.50


Consensus pattern (15 bp):   
TTACGTTTTAGTCAC

Found at i:34204 original size:15 final size:15

Alignment explanation


    Indices: 34186--34235  Score: 50
    Period size: 14  Copynumber: 3.3  Consensus size: 15

      34176 AAGTTGTAGA

                           
      34186 TTTAATTTTTGTATT
          1 TTTAATTTTTGTATT

                     *    * 
      34201 TTT-ATTTAAT-TAAT
          1 TTTAATTT-TTGTATT

                            
      34215 TTTAATTTTTGTACTT
          1 TTTAATTTTTGTA-TT

                 
      34231 TTTAA
          1 TTTAA

      34236 ATTGATTATT


Statistics
Matches: 27,  Mismatches: 4, Indels: 7
        0.71            0.11        0.18

Matches are distributed among these distances:
  14   11  0.41
  15   10  0.37
  16    6  0.22

ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68


Consensus pattern (15 bp):   
TTTAATTTTTGTATT

Found at i:34517 original size:18 final size:18

Alignment explanation


    Indices: 34494--34533  Score: 71
    Period size: 18  Copynumber: 2.2  Consensus size: 18

      34484 TTCAGGAATA

                              
      34494 TTTTTATCTCAAAAGTAT
          1 TTTTTATCTCAAAAGTAT

                   *          
      34512 TTTTTATTTCAAAAGTAT
          1 TTTTTATCTCAAAAGTAT

                
      34530 TTTT
          1 TTTT

      34534 GAGAAGCAAT


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.30, C:0.07, G:0.05, T:0.57


Consensus pattern (18 bp):   
TTTTTATCTCAAAAGTAT

Found at i:35057 original size:32 final size:32

Alignment explanation


    Indices: 35016--35079  Score: 110
    Period size: 32  Copynumber: 2.0  Consensus size: 32

      35006 TAGCTTAAAT

                                            
      35016 GACTTATTTAAACAATATTTTAATCTAATTCA
          1 GACTTATTTAAACAATATTTTAATCTAATTCA

                        *   *               
      35048 GACTTATTTAAATAATTTTTTAATCTAATTCA
          1 GACTTATTTAAACAATATTTTAATCTAATTCA

      35080 ATTAATTTGT


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  32   30  1.00

ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47


Consensus pattern (32 bp):   
GACTTATTTAAACAATATTTTAATCTAATTCA

Found at i:35322 original size:29 final size:29

Alignment explanation


    Indices: 35276--35356  Score: 98
    Period size: 29  Copynumber: 2.9  Consensus size: 29

      35266 TTAATTGTAC

                                           
      35276 AATTATTTTATATGTTTAATTATA-ATATGT
          1 AATT-TTTTATATGTTTAATTATATAT-TGT

                        *              * 
      35306 AATTTTTTATATTTTTAATTATATATTTT
          1 AATTTTTTATATGTTTAATTATATATTGT

                                     
      35335 AATTTTTTA-A-GTTTAATT-TATA
          1 AATTTTTTATATGTTTAATTATATA

      35357 AAAATTAACA


Statistics
Matches: 47,  Mismatches: 3, Indels: 6
        0.84            0.05        0.11

Matches are distributed among these distances:
  26    4  0.09
  27    7  0.15
  28    1  0.02
  29   29  0.62
  30    6  0.13

ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62


Consensus pattern (29 bp):   
AATTTTTTATATGTTTAATTATATATTGT

Done.