Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006947.1 Kokia drynarioides strain JFW-HI SEQ_121552, 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: 1829
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30


Found at i:443 original size:32 final size:32

Alignment explanation


    Indices: 407--552  Score: 130
    Period size: 30  Copynumber: 4.8  Consensus size: 32

        397 AAAAAATGGG

                  *                          
        407 ATTTTTGGAA-GTCTCGGGGTAAAATGGTGGTA
          1 ATTTTTAGAAGGT-TCGGGGTAAAATGGTGGTA

                                             
        439 ATTTTTAGAAGGTTCGGGGGTAAAA---TGGTA
          1 ATTTTTAGAAGGTTC-GGGGTAAAATGGTGGTA

                            *       ***    *
        469 ATTTTTAGAAGGTTCGAGGTAAAAAAATGG-G
          1 ATTTTTAGAAGGTTCGGGGTAAAATGGTGGTA

                  *                          
        500 ATTTTTGGAA-GTTCGAGGGTAAAA---TGGTA
          1 ATTTTTAGAAGGTTCG-GGGTAAAATGGTGGTA

              *                     
        529 ATATTTAGAAGGTTCGGGGTAAAA
          1 ATTTTTAGAAGGTTCGGGGTAAAA

        553 AATGAGATTT


Statistics
Matches: 98,  Mismatches: 8, Indels: 19
        0.78            0.06        0.15

Matches are distributed among these distances:
  28    3  0.03
  29   24  0.24
  30   30  0.31
  31   16  0.16
  32   14  0.14
  33   11  0.11

ACGTcount: A:0.32, C:0.04, G:0.32, T:0.32


Consensus pattern (32 bp):   
ATTTTTAGAAGGTTCGGGGTAAAATGGTGGTA

Found at i:470 original size:30 final size:30

Alignment explanation


    Indices: 434--597  Score: 171
    Period size: 30  Copynumber: 5.5  Consensus size: 30

        424 GGTAAAATGG

                                          
        434 TGGTAATTTTTAGAAGGTTCGGGGGTAAAA
          1 TGGTAATTTTTAGAAGGTTCGGGGGTAAAA

                                  *          
        464 TGGTAATTTTTAGAAGGTTC-GAGGTAAAAAAA
          1 TGGTAATTTTTAGAAGGTTCGGGGGT---AAAA

                *      *         *        
        496 TGG-GATTTTTGGAA-GTTCGAGGGTAAAA
          1 TGGTAATTTTTAGAAGGTTCGGGGGTAAAA

                   *                        
        524 TGGTAATATTTAGAAGGTTC-GGGGTAAAAAA
          1 TGGTAATTTTTAGAAGGTTCGGGGGT--AAAA

                        *                  
        555 T-G-AGATTTTTGGAA-GTTCGGGGGTAAAA
          1 TGGTA-ATTTTTAGAAGGTTCGGGGGTAAAA

                           
        583 TGGTAATTTTTAGAA
          1 TGGTAATTTTTAGAA

        598 ATTTAGGGAC


Statistics
Matches: 110,  Mismatches: 12, Indels: 25
        0.75            0.08        0.17

Matches are distributed among these distances:
  28   12  0.11
  29   31  0.28
  30   43  0.39
  31   17  0.15
  32    7  0.06

ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33


Consensus pattern (30 bp):   
TGGTAATTTTTAGAAGGTTCGGGGGTAAAA

Found at i:582 original size:59 final size:60

Alignment explanation


    Indices: 439--597  Score: 257
    Period size: 59  Copynumber: 2.6  Consensus size: 60

        429 AATGGTGGTA

                  *                                                    * 
        439 ATTTTTAGAAGGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTAAAAAAATGGG
          1 ATTTTTGGAA-GTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTAAAAAAATGAG

                           *               *             *              
        500 ATTTTTGGAAGTTCGAGGGTAAAATGGTAATATTTAGAAGGTTCGGGGT-AAAAAATGAG
          1 ATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTAAAAAAATGAG

                                                   
        559 ATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAA
          1 ATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAA

        598 ATTTAGGGAC


Statistics
Matches: 91,  Mismatches: 7, Indels: 2
        0.91            0.07        0.02

Matches are distributed among these distances:
  59   46  0.51
  60   36  0.40
  61    9  0.10

ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33


Consensus pattern (60 bp):   
ATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTAAAAAAATGAG
Done.