Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013865.1 Kokia drynarioides strain JFW-HI SEQ_128893, 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: 4423
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.41


Found at i:398 original size:29 final size:29

Alignment explanation


    Indices: 335--479  Score: 172
    Period size: 29  Copynumber: 5.0  Consensus size: 29

        325 ACCCCAGAGG

                 *                        
        335 ACCCTAAACCTTCCAAAAATCCCATTTTTA
          1 ACCCTGAACCTTCCAAAAATCCCA-TTTTA

                                          
        365 ACCCTGAACCTTCCAAAAATCACCATTTT-
          1 ACCCTGAACCTTCCAAAAATC-CCATTTTA

                      *                   
        394 ACCCTCGAA-TTTCCAAAAATCCCATTTTA
          1 ACCCT-GAACCTTCCAAAAATCCCATTTTA

                     *           *        
        423 ACCCTGAACATTCCAAAAATTACCATTTT-
          1 ACCCTGAACCTTCCAAAAA-TCCCATTTTA

               *                         
        452 ACCTTCGAA-CTTCCAAAAATCCCATTTT
          1 ACCCT-GAACCTTCCAAAAATCCCATTTT

        480 CGACCTCGAA


Statistics
Matches: 102,  Mismatches: 7, Indels: 14
        0.83            0.06        0.11

Matches are distributed among these distances:
  28   18  0.18
  29   43  0.42
  30   38  0.37
  31    3  0.03

ACGTcount: A:0.35, C:0.32, G:0.03, T:0.30


Consensus pattern (29 bp):   
ACCCTGAACCTTCCAAAAATCCCATTTTA

Found at i:441 original size:58 final size:58

Alignment explanation


    Indices: 344--479  Score: 227
    Period size: 58  Copynumber: 2.3  Consensus size: 58

        334 GACCCTAAAC

                                          *                            
        344 CTTCCAAAAATCCCATTTTTAACCCTGAACCTTCCAAAAATCACCATTTTACCCTCGAA
          1 CTTCCAAAAATCCCA-TTTTAACCCTGAACATTCCAAAAATCACCATTTTACCCTCGAA

            *                                       *           *     
        403 TTTCCAAAAATCCCATTTTAACCCTGAACATTCCAAAAATTACCATTTTACCTTCGAA
          1 CTTCCAAAAATCCCATTTTAACCCTGAACATTCCAAAAATCACCATTTTACCCTCGAA

                               
        461 CTTCCAAAAATCCCATTTT
          1 CTTCCAAAAATCCCATTTT

        480 CGACCTCGAA


Statistics
Matches: 72,  Mismatches: 5, Indels: 1
        0.92            0.06        0.01

Matches are distributed among these distances:
  58   58  0.81
  59   14  0.19

ACGTcount: A:0.35, C:0.31, G:0.03, T:0.32


Consensus pattern (58 bp):   
CTTCCAAAAATCCCATTTTAACCCTGAACATTCCAAAAATCACCATTTTACCCTCGAA

Found at i:500 original size:58 final size:58

Alignment explanation


    Indices: 344--519  Score: 207
    Period size: 58  Copynumber: 3.0  Consensus size: 58

        334 GACCCTAAAC

                                         *            *                 
        344 CTTCCAAAAATCCCATTTTTAACCCTGAACCT-TCCAAAAATCACCATTTTACCCTCGAA
          1 CTTCCAAAAATCCCA-TTTTAACCCTGAAACTCT-CAAAAATTACCATTTTACCCTCGAA

            *                             *                      *     
        403 TTTCCAAAAATCCCATTTTAACCCTGAACATTC-CAAAAATTACCATTTTACCTTCGAA
          1 CTTCCAAAAATCCCATTTTAACCCTGAA-ACTCTCAAAAATTACCATTTTACCCTCGAA

                                *                      *                 
        461 CTTCCAAAAATCCCATTTTCGA-CCTCGAAACTCTC-AAAATTGCCATTTTTACCCTCGAA
          1 CTTCCAAAAATCCCATTTT-AACCCT-GAAACTCTCAAAAATTACCA-TTTTACCCTCGAA

        520 TGTTTTAAAT


Statistics
Matches: 101,  Mismatches: 10, Indels: 12
        0.82            0.08        0.10

Matches are distributed among these distances:
  58   69  0.68
  59   32  0.32

ACGTcount: A:0.34, C:0.31, G:0.05, T:0.31


Consensus pattern (58 bp):   
CTTCCAAAAATCCCATTTTAACCCTGAAACTCTCAAAAATTACCATTTTACCCTCGAA

Found at i:517 original size:30 final size:29

Alignment explanation


    Indices: 346--519  Score: 144
    Period size: 29  Copynumber: 5.9  Consensus size: 29

        336 CCCTAAACCT

                                        * 
        346 TCCAAAAATCCCATTTTTAACCCT-GAACC
          1 TCCAAAAATCCCATTTTT-ACCCTCGAAAC

                                         **
        375 TTCCAAAAATCACCA-TTTTACCCTCGAATT
          1 -TCCAAAAATC-CCATTTTTACCCTCGAAAC

                             *           *
        405 TCCAAAAATCCCATTTTAACCCT-GAACAT
          1 TCCAAAAATCCCATTTTTACCCTCGAA-AC

                      *           *       
        434 TCCAAAAATTACCA-TTTTACCTTCG-AAC
          1 TCCAAAAA-TCCCATTTTTACCCTCGAAAC

                               *           
        462 TTCCAAAAATCCCATTTTCGA-CCTCGAAAC
          1 -TCCAAAAATCCCATTTT-TACCCTCGAAAC

                    * *                 
        492 TCTCAAAATTGCCATTTTTACCCTCGAA
          1 TC-CAAAAATCCCATTTTTACCCTCGAA

        520 TGTTTTAAAT


Statistics
Matches: 118,  Mismatches: 14, Indels: 24
        0.76            0.09        0.15

Matches are distributed among these distances:
  28   11  0.09
  29   58  0.49
  30   46  0.39
  31    3  0.03

ACGTcount: A:0.34, C:0.31, G:0.05, T:0.30


Consensus pattern (29 bp):   
TCCAAAAATCCCATTTTTACCCTCGAAAC
Done.