Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009986.1 Kokia drynarioides strain JFW-HI SEQ_124739, 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: 11470
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34


Found at i:5667 original size:7 final size:7

Alignment explanation


    Indices: 5649--5716  Score: 50
    Period size: 7  Copynumber: 9.9  Consensus size: 7

       5639 TTGGATTTTG

                *  
       5649 GGTTGAA
          1 GGTTTAA

                   
       5656 GGTTTAA
          1 GGTTTAA

                   
       5663 GGTTT-A
          1 GGTTTAA

                  *
       5669 GGTTTAG
          1 GGTTTAA

                *   
       5676 GGTTCATA
          1 GGTTTA-A

             *   * 
       5684 GTTTTGA
          1 GGTTTAA

                   
       5691 GGTTTAA
          1 GGTTTAA

                ** 
       5698 GGTTCGA
          1 GGTTTAA

                   
       5705 -GTTTAA
          1 GGTTTAA

                  
       5711 GGTTTA
          1 GGTTTA

       5717 GGGGTTTTGG


Statistics
Matches: 45,  Mismatches: 13, Indels: 6
        0.70            0.20        0.09

Matches are distributed among these distances:
   6   10  0.22
   7   32  0.71
   8    3  0.07

ACGTcount: A:0.22, C:0.03, G:0.32, T:0.43


Consensus pattern (7 bp):   
GGTTTAA

Found at i:5696 original size:22 final size:20

Alignment explanation


    Indices: 5664--5719  Score: 60
    Period size: 20  Copynumber: 2.8  Consensus size: 20

       5654 AAGGTTTAAG

                               * 
       5664 GTTT-AGGTTTAGGGTTCATA
          1 GTTTAAGGTTTAGGGTTC-GA

                 *       *       
       5684 GTTTTGAGGTTTAAGGTTCGA
          1 G-TTTAAGGTTTAGGGTTCGA

                           
       5705 GTTTAAGGTTTAGGG
          1 GTTTAAGGTTTAGGG

       5720 GTTTTGGGTT


Statistics
Matches: 30,  Mismatches: 4, Indels: 4
        0.79            0.11        0.11

Matches are distributed among these distances:
  20   13  0.43
  21    5  0.17
  22   12  0.40

ACGTcount: A:0.20, C:0.04, G:0.34, T:0.43


Consensus pattern (20 bp):   
GTTTAAGGTTTAGGGTTCGA

Found at i:6040 original size:18 final size:19

Alignment explanation


    Indices: 6000--6040  Score: 50
    Period size: 18  Copynumber: 2.3  Consensus size: 19

       5990 ATTTTGTCTT

                             * 
       6000 TAAAATTTGATTATGTGGC
          1 TAAAATTTGATTATGTGCC

                    *          
       6019 -AAAATTTTATTA-GTGCC
          1 TAAAATTTGATTATGTGCC

                 
       6036 TAAAA
          1 TAAAA

       6041 ACCTTAATTT


Statistics
Matches: 19,  Mismatches: 2, Indels: 3
        0.79            0.08        0.12

Matches are distributed among these distances:
  17    4  0.21
  18   15  0.79

ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39


Consensus pattern (19 bp):   
TAAAATTTGATTATGTGCC

Found at i:8358 original size:20 final size:18

Alignment explanation


    Indices: 8316--8370  Score: 56
    Period size: 20  Copynumber: 2.9  Consensus size: 18

       8306 AAGTCAATTT

                      *        
       8316 GTATTGATACCTTTATAAA
          1 GTATTGATA-TTTTATAAA

                                
       8335 GTATTGATATTTTATGATAA
          1 GTATTGATATTTTAT-A-AA

                *      *    
       8355 GTATCGATATTGTATA
          1 GTATTGATATTTTATA

       8371 TTGGTATCGA


Statistics
Matches: 31,  Mismatches: 3, Indels: 4
        0.82            0.08        0.11

Matches are distributed among these distances:
  18    5  0.16
  19   11  0.35
  20   15  0.48

ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45


Consensus pattern (18 bp):   
GTATTGATATTTTATAAA
Done.