Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005181.1 Kokia drynarioides strain JFW-HI SEQ_119038, 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: 7057
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:2978 original size:20 final size:20

Alignment explanation


    Indices: 2937--2978  Score: 59
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       2927 GTTTTCTCTA

                             *  
       2937 AATCTCGAACTCCGAACTTG
          1 AATCTCGAACTCCGAACATG

                                 
       2957 AATCTCGAACT-CGAACCATG
          1 AATCTCGAACTCCGAA-CATG

              
       2977 AA
          1 AA

       2979 CCTTAAACTT


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  19    4  0.20
  20   16  0.80

ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21


Consensus pattern (20 bp):   
AATCTCGAACTCCGAACATG

Found at i:4850 original size:25 final size:24

Alignment explanation


    Indices: 4765--4861  Score: 90
    Period size: 25  Copynumber: 4.0  Consensus size: 24

       4755 TGCGTCACAA

                                     
       4765 TAAATTAGATATGTTAATTCATACG
          1 TAAA-TAGATATGTTAATTCATACG

                *                  ***
       4790 TAAACAGAT-TGATTGAATT-ATTTT
          1 TAAATAGATATG-TT-AATTCATACG

                  *       *         
       4814 TAAATATATATGTTCATTCATACG
          1 TAAATAGATATGTTAATTCATACG

                                    
       4838 TAAATTAGATATGTTAATTCATAC
          1 TAAA-TAGATATGTTAATTCATAC

       4862 AAAAATTAAA


Statistics
Matches: 55,  Mismatches: 12, Indels: 10
        0.71            0.16        0.13

Matches are distributed among these distances:
  23    5  0.09
  24   23  0.42
  25   27  0.49

ACGTcount: A:0.39, C:0.08, G:0.10, T:0.42


Consensus pattern (24 bp):   
TAAATAGATATGTTAATTCATACG

Found at i:4867 original size:25 final size:25

Alignment explanation


    Indices: 4821--4869  Score: 71
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       4811 TTTTAAATAT

                   *        **       
       4821 ATATGTTCATTCATACGTAAATTAG
          1 ATATGTTAATTCATACAAAAATTAG

                                    
       4846 ATATGTTAATTCATACAAAAATTA
          1 ATATGTTAATTCATACAAAAATTA

       4870 AAATATAAAC


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  25   21  1.00

ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39


Consensus pattern (25 bp):   
ATATGTTAATTCATACAAAAATTAG
Done.