Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012447.1 Kokia drynarioides strain JFW-HI SEQ_127451, 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: 9561
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34


Found at i:4120 original size:40 final size:39

Alignment explanation


    Indices: 4028--4143  Score: 119
    Period size: 40  Copynumber: 2.9  Consensus size: 39

       4018 ACCCTGGAAA

                      *                *         *   
       4028 ATTATTATTATTGAACTGGCAGTGACATTGTAAACACTGCG
          1 ATTATT-TTACTGAACTGGC-GTGACACTGTAAACACCGCG

                                                     
       4069 A-TATTTCTACTGAACTGGCGGTGACACTGTAAACACCGC-
          1 ATTATTT-TACTGAACTGGC-GTGACACTGTAAACACCGCG

                               *     *          
       4108 ATTATTGTTACTGAACTAGACGTGATACTGTAAACA
          1 ATTATT-TTACTGAACT-GGCGTGACACTGTAAACA

       4144 TTGCTAGACT


Statistics
Matches: 65,  Mismatches: 6, Indels: 9
        0.81            0.08        0.11

Matches are distributed among these distances:
  39    2  0.03
  40   59  0.91
  41    4  0.06

ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Consensus pattern (39 bp):   
ATTATTTTACTGAACTGGCGTGACACTGTAAACACCGCG

Found at i:5142 original size:25 final size:25

Alignment explanation


    Indices: 5091--5144  Score: 65
    Period size: 25  Copynumber: 2.2  Consensus size: 25

       5081 CTACCAATAC

                                 **  
       5091 AAGTACACAAACTACCGATACTTCT
          1 AAGTACACAAACTACCGATACACCT

                           *          
       5116 AAGTACA-AAACTACTGATACAACCT
          1 AAGTACACAAACTACCGATAC-ACCT

                
       5141 AAGT
          1 AAGT

       5145 CAGTGAACAA


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  24   12  0.48
  25   13  0.52

ACGTcount: A:0.44, C:0.24, G:0.09, T:0.22


Consensus pattern (25 bp):   
AAGTACACAAACTACCGATACACCT

Found at i:6883 original size:20 final size:20

Alignment explanation


    Indices: 6847--6896  Score: 50
    Period size: 20  Copynumber: 2.5  Consensus size: 20

       6837 TCATTAAGCT

                    *            
       6847 TTAATTAACCACTTTTA-ATC
          1 TTAATTAAACACTTTTATA-C

                                 
       6867 TTAATTAAAC-CTATTTATAC
          1 TTAATTAAACACT-TTTATAC

                      
       6887 TTAATATAAA
          1 TTAAT-TAAA

       6897 TCAAGCTAAT


Statistics
Matches: 26,  Mismatches: 1, Indels: 5
        0.81            0.03        0.16

Matches are distributed among these distances:
  19    2  0.08
  20   19  0.73
  21    5  0.19

ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44


Consensus pattern (20 bp):   
TTAATTAAACACTTTTATAC
Done.