Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012870.1 Kokia drynarioides strain JFW-HI SEQ_127884, 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: 6386
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31

Warning! 117 characters in sequence are not A, C, G, or T


Found at i:3306 original size:28 final size:28

Alignment explanation


    Indices: 3253--3311  Score: 75
    Period size: 28  Copynumber: 2.1  Consensus size: 28

       3243 CATTTTTCAC

                                *       
       3253 TTGGAATTAATTAAGTTTATGATTGAAT
          1 TTGGAATTAATTAAGTTTATAATTGAAT

                        **               
       3281 TTGGAATTAATTCTGTTTA-AATTTGAAT
          1 TTGGAATTAATTAAGTTTATAA-TTGAAT

               
       3309 TTG
          1 TTG

       3312 TTTAATAATT


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  27    1  0.04
  28   26  0.96

ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49


Consensus pattern (28 bp):   
TTGGAATTAATTAAGTTTATAATTGAAT

Found at i:4850 original size:23 final size:23

Alignment explanation


    Indices: 4819--4945  Score: 141
    Period size: 23  Copynumber: 5.4  Consensus size: 23

       4809 AGTGTTGGGC

                *                  
       4819 AACATAGAGCACACACAGTGCTA
          1 AACAGAGAGCACACACAGTGCTA

                     *     *   *   
       4842 AACAGAGAGTACACAAAGTACTA
          1 AACAGAGAGCACACACAGTGCTA

                            *       
       4865 ATA-AGAGAGCACACAAAGTGCTA
          1 A-ACAGAGAGCACACACAGTGCTA

             *                      
       4888 ATCAGAGAGCACACACAGTGCTAA
          1 AACAGAGAGCACACACAGTGCT-A

                           *         
       4912 TAACAGAGAGCACGAGAC-GTGCTA
          1 -AACAGAGAGCAC-ACACAGTGCTA

                      
       4936 AACAGAGAGC
          1 AACAGAGAGC

       4946 GCGCTAGTGT


Statistics
Matches: 89,  Mismatches: 10, Indels: 10
        0.82            0.09        0.09

Matches are distributed among these distances:
  23   67  0.75
  24    3  0.03
  25   16  0.18
  26    3  0.03

ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12


Consensus pattern (23 bp):   
AACAGAGAGCACACACAGTGCTA

Found at i:4878 original size:46 final size:48

Alignment explanation


    Indices: 4819--4945  Score: 161
    Period size: 46  Copynumber: 2.7  Consensus size: 48

       4809 AGTGTTGGGC

                *                           *               
       4819 AACATAGAGCACACACAGTGCTAAACAGAGAGTACACAAAGTACTAAT
          1 AACAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT

                           *        *             *   *     
       4867 -A-AGAGAGCACACAAAGTGCTAATCAGAGAGCACACACAGTGCTAAT
          1 AACAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT

                          *                   
       4913 AACAGAGAGCACGAGAC-GTGCTAAACAGAGAGC
          1 AACAGAGAGCAC-ACACAGTGCTAAACAGAGAGC

       4946 GCGCTAGTGT


Statistics
Matches: 67,  Mismatches: 9, Indels: 6
        0.82            0.11        0.07

Matches are distributed among these distances:
  46   39  0.58
  47    2  0.03
  48   24  0.36
  49    2  0.03

ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12


Consensus pattern (48 bp):   
AACAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT

Done.