Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000430.1 Kokia drynarioides strain JFW-HI SEQ_111262, 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: 9404
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:3911 original size:4 final size:4

Alignment explanation


    Indices: 3902--3927  Score: 52
    Period size: 4  Copynumber: 6.5  Consensus size: 4

       3892 TGGAAAAATG

                                            
       3902 TACA TACA TACA TACA TACA TACA TA
          1 TACA TACA TACA TACA TACA TACA TA

       3928 TGTATGTGTA


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   22  1.00

ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27


Consensus pattern (4 bp):   
TACA

Found at i:7697 original size:18 final size:18

Alignment explanation


    Indices: 7674--7718  Score: 81
    Period size: 18  Copynumber: 2.5  Consensus size: 18

       7664 ATTAGAGAGT

                      *       
       7674 ACATGCATCAGGTGCAAG
          1 ACATGCATCAAGTGCAAG

                              
       7692 ACATGCATCAAGTGCAAG
          1 ACATGCATCAAGTGCAAG

                     
       7710 ACATGCATC
          1 ACATGCATC

       7719 GTGAACCCCT


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  18   26  1.00

ACGTcount: A:0.36, C:0.24, G:0.22, T:0.18


Consensus pattern (18 bp):   
ACATGCATCAAGTGCAAG

Found at i:8821 original size:23 final size:23

Alignment explanation


    Indices: 8791--8936  Score: 152
    Period size: 23  Copynumber: 6.3  Consensus size: 23

       8781 GCTGGGCAAC

                                   
       8791 AGAG-ACACACAGTGCTAAACAG
          1 AGAGCACACACAGTGCTAAACAG

                      *   *    *   
       8813 AGAGCACACAAAGTACTAATCAG
          1 AGAGCACACACAGTGCTAAACAG

             *        *   *    *   
       8836 ATAGCACACAAAGTACTAATCAG
          1 AGAGCACACACAGTGCTAAACAG

             *                       
       8859 ATAGCACACACAGTGCTAATAACAG
          1 AGAGCACACACAGTGCT-A-AACAG

                     *      *       
       8884 AGAGCACGAGAC-GTGATAAACAG
          1 AGAGCAC-ACACAGTGCTAAACAG

                               *   
       8907 AGAGCACACACAGTGCTAATCAG
          1 AGAGCACACACAGTGCTAAACAG

                   
       8930 AGAGCAC
          1 AGAGCAC

       8937 GCTAGTGTTT


Statistics
Matches: 106,  Mismatches: 13, Indels: 9
        0.83            0.10        0.07

Matches are distributed among these distances:
  22    7  0.07
  23   80  0.75
  24    2  0.02
  25   14  0.13
  26    3  0.03

ACGTcount: A:0.45, C:0.23, G:0.21, T:0.12


Consensus pattern (23 bp):   
AGAGCACACACAGTGCTAAACAG

Found at i:8913 original size:48 final size:47

Alignment explanation


    Indices: 8805--8937  Score: 155
    Period size: 48  Copynumber: 2.8  Consensus size: 47

       8795 ACACACAGTG

                              *   *         *              
       8805 CTAAACAGAGAGCACACAAAGTACTAATCAGATAGCAC-ACAAAGTA
          1 CTAAACAGAGAGCACACACAGTGCTAATCAGAGAGCACGACAAAGTA

                *    *                                 * *    
       8851 CTAATCAGATAGCACACACAGTGCTAATAACAGAGAGCACGA-GACGTGA
          1 CTAAACAGAGAGCACACACAGTGCTAAT--CAGAGAGCACGACAAAGT-A

                                                   
       8900 -TAAACAGAGAGCACACACAGTGCTAATCAGAGAGCACG
          1 CTAAACAGAGAGCACACACAGTGCTAATCAGAGAGCACG

       8938 CTAGTGTTTC


Statistics
Matches: 74,  Mismatches: 9, Indels: 8
        0.81            0.10        0.09

Matches are distributed among these distances:
  46   35  0.47
  48   37  0.50
  49    2  0.03

ACGTcount: A:0.44, C:0.23, G:0.20, T:0.13


Consensus pattern (47 bp):   
CTAAACAGAGAGCACACACAGTGCTAATCAGAGAGCACGACAAAGTA

Found at i:8913 original size:71 final size:69

Alignment explanation


    Indices: 8791--8936  Score: 172
    Period size: 71  Copynumber: 2.1  Consensus size: 69

       8781 GCTGGGCAAC

                                                      *    *                 
       8791 AGAG-ACACACAGTGCTAAACAGAGAGCACACAAAGTACTAATCAGATAGCACACAAAGTACTAA
          1 AGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAACAGAGAGCACACAAAGTACTAA

                
       8855 TCAG
         66 TCAG

             *                                 * *                      *   *
       8859 ATAGCACACACAGTGCTAATAACAGAGAGCACGA-GACGTGA-TAAACAGAGAGCACACACAGTG
          1 AGAGCACACACAGTGCT-A-AACAGAGAGCAC-ACAAAGT-ACTAAACAGAGAGCACACAAAGTA

                    
       8922 CTAATCAG
         62 CTAATCAG

                   
       8930 AGAGCAC
          1 AGAGCAC

       8937 GCTAGTGTTT


Statistics
Matches: 65,  Mismatches: 8, Indels: 7
        0.81            0.10        0.09

Matches are distributed among these distances:
  68    3  0.05
  69   12  0.18
  70    1  0.02
  71   47  0.72
  72    2  0.03

ACGTcount: A:0.45, C:0.23, G:0.21, T:0.12


Consensus pattern (69 bp):   
AGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAACAGAGAGCACACAAAGTACTAA
TCAG
Done.