Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007447.1 Kokia drynarioides strain JFW-HI SEQ_122068, 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: 36172
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37


Found at i:30740 original size:15 final size:15

Alignment explanation


    Indices: 30693--30742  Score: 50
    Period size: 15  Copynumber: 3.5  Consensus size: 15

      30683 TTGCCTCAGA

                *          
      30693 TTACATTTTAGTCAC
          1 TTACGTTTTAGTCAC

               *    * *    
      30708 TTATGTTTAAAT--C
          1 TTACGTTTTAGTCAC

                           
      30721 TTACGTTTTAGTCAC
          1 TTACGTTTTAGTCAC

                   
      30736 TTACGTT
          1 TTACGTT

      30743 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:34228 original size:15 final size:15

Alignment explanation


    Indices: 34210--34259  Score: 50
    Period size: 14  Copynumber: 3.3  Consensus size: 15

      34200 AAGTTGTAGA

                           
      34210 TTTAATTTTTGTATT
          1 TTTAATTTTTGTATT

                     *    * 
      34225 TTT-ATTTAAT-TAAT
          1 TTTAATTT-TTGTATT

                            
      34239 TTTAATTTTTGTACTT
          1 TTTAATTTTTGTA-TT

                 
      34255 TTTAA
          1 TTTAA

      34260 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:34541 original size:18 final size:18

Alignment explanation


    Indices: 34518--34557  Score: 71
    Period size: 18  Copynumber: 2.2  Consensus size: 18

      34508 TTCAGGAATA

                              
      34518 TTTTTATCTCAAAAGTAT
          1 TTTTTATCTCAAAAGTAT

                   *          
      34536 TTTTTATTTCAAAAGTAT
          1 TTTTTATCTCAAAAGTAT

                
      34554 TTTT
          1 TTTT

      34558 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:35081 original size:32 final size:32

Alignment explanation


    Indices: 35040--35103  Score: 110
    Period size: 32  Copynumber: 2.0  Consensus size: 32

      35030 TAGCTTAAAT

                                            
      35040 GACTTATTTAAACAATATTTTAATCTAATTCA
          1 GACTTATTTAAACAATATTTTAATCTAATTCA

                        *   *               
      35072 GACTTATTTAAATAATTTTTTAATCTAATTCA
          1 GACTTATTTAAACAATATTTTAATCTAATTCA

      35104 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:35346 original size:29 final size:29

Alignment explanation


    Indices: 35300--35380  Score: 98
    Period size: 29  Copynumber: 2.9  Consensus size: 29

      35290 TTAATTGTAC

                                           
      35300 AATTATTTTATATGTTTAATTATA-ATATGT
          1 AATT-TTTTATATGTTTAATTATATAT-TGT

                        *              * 
      35330 AATTTTTTATATTTTTAATTATATATTTT
          1 AATTTTTTATATGTTTAATTATATATTGT

                                     
      35359 AATTTTTTA-A-GTTTAATT-TATA
          1 AATTTTTTATATGTTTAATTATATA

      35381 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.