Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009769.1 Kokia drynarioides strain JFW-HI SEQ_124490, 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: 10201
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31


Found at i:689 original size:18 final size:18

Alignment explanation


    Indices: 647--689  Score: 52
    Period size: 18  Copynumber: 2.4  Consensus size: 18

        637 TCACAACAAC

                           *  
        647 AAAT-AATTTAAAAATTA
          1 AAATAAATTTAAAAAATA

            *  *              
        664 TAAGAAATTTAAAAAATA
          1 AAATAAATTTAAAAAATA

                    
        682 AAATAAAT
          1 AAATAAAT

        690 ATTGATGAAA


Statistics
Matches: 20,  Mismatches: 5, Indels: 1
        0.77            0.19        0.04

Matches are distributed among these distances:
  17    2  0.10
  18   18  0.90

ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30


Consensus pattern (18 bp):   
AAATAAATTTAAAAAATA

Found at i:1001 original size:36 final size:36

Alignment explanation


    Indices: 954--1035  Score: 119
    Period size: 36  Copynumber: 2.3  Consensus size: 36

        944 GAAAATAGAT

                                           * *  
        954 TCTTGTCTTGCCAATCCACTACTTGCAAAAGTATAA
          1 TCTTGTCTTGCCAATCCACTACTTGCAAAAGCAGAA

                                *     *        *
        990 TCTTGTCTTGCCAATCCACTGCTTGCGAAAGCAGAT
          1 TCTTGTCTTGCCAATCCACTACTTGCAAAAGCAGAA

                      
       1026 TCTTGTCTTG
          1 TCTTGTCTTG

       1036 GCGATTGATA


Statistics
Matches: 41,  Mismatches: 5, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  36   41  1.00

ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35


Consensus pattern (36 bp):   
TCTTGTCTTGCCAATCCACTACTTGCAAAAGCAGAA

Found at i:2514 original size:20 final size:20

Alignment explanation


    Indices: 2486--2523  Score: 67
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       2476 GATATGATCC

                *               
       2486 TTGTGATCTTAGAGATTTGA
          1 TTGTAATCTTAGAGATTTGA

                              
       2506 TTGTAATCTTAGAGATTT
          1 TTGTAATCTTAGAGATTT

       2524 TTTTTGTAGA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.26, C:0.05, G:0.21, T:0.47


Consensus pattern (20 bp):   
TTGTAATCTTAGAGATTTGA
Done.