Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010215.1 Kokia drynarioides strain JFW-HI SEQ_125037, 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: 2957
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30

Warning! 5 characters in sequence are not A, C, G, or T


Found at i:352 original size:28 final size:28

Alignment explanation


    Indices: 351--407  Score: 89
    Period size: 28  Copynumber: 2.0  Consensus size: 28

        341 ACTAAACTTA

                                         
        351 AAACTTAAAAC-CTTAAACCGTAAACACT
          1 AAACTTAAAACTC-TAAACCGTAAACACT

                  *                     
        379 AAACTTGAAACTCTAAACCGTAAACACT
          1 AAACTTAAAACTCTAAACCGTAAACACT

             
        407 A
          1 A

        408 GATTGATTAA


Statistics
Matches: 27,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  28   26  0.96
  29    1  0.04

ACGTcount: A:0.49, C:0.25, G:0.05, T:0.21


Consensus pattern (28 bp):   
AAACTTAAAACTCTAAACCGTAAACACT

Found at i:360 original size:35 final size:36

Alignment explanation


    Indices: 315--403  Score: 128
    Period size: 35  Copynumber: 2.5  Consensus size: 36

        305 TCATAACATT

                *                               
        315 AAACCCTAAAACCTTAAACCATAAACACTAAACTTA
          1 AAACTCTAAAACCTTAAACCATAAACACTAAACTTA

                                *              *
        351 AAACT-TAAAACCTTAAACCGTAAACACTAAACTTG
          1 AAACTCTAAAACCTTAAACCATAAACACTAAACTTA

                         *     
        386 AAACTCT-AAACCGTAAAC
          1 AAACTCTAAAACCTTAAAC

        404 ACTAGATTGA


Statistics
Matches: 48,  Mismatches: 4, Indels: 3
        0.87            0.07        0.05

Matches are distributed among these distances:
  35   43  0.90
  36    5  0.10

ACGTcount: A:0.51, C:0.26, G:0.03, T:0.20


Consensus pattern (36 bp):   
AAACTCTAAAACCTTAAACCATAAACACTAAACTTA

Found at i:381 original size:14 final size:14

Alignment explanation


    Indices: 364--407  Score: 54
    Period size: 14  Copynumber: 3.1  Consensus size: 14

        354 CTTAAAACCT

                          
        364 TAAACCGTAAACAC
          1 TAAACCGTAAACAC

                  *      * 
        378 TAAA-CTTGAAACTC
          1 TAAACCGT-AAACAC

                          
        392 TAAACCGTAAACAC
          1 TAAACCGTAAACAC

              
        406 TA
          1 TA

        408 GATTGATTAA


Statistics
Matches: 24,  Mismatches: 4, Indels: 4
        0.75            0.12        0.12

Matches are distributed among these distances:
  13    2  0.08
  14   20  0.83
  15    2  0.08

ACGTcount: A:0.48, C:0.25, G:0.07, T:0.20


Consensus pattern (14 bp):   
TAAACCGTAAACAC
Done.