Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009117.1 Kokia drynarioides strain JFW-HI SEQ_123819, 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: 21257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34


Found at i:5019 original size:14 final size:15

Alignment explanation


    Indices: 4986--5020  Score: 54
    Period size: 16  Copynumber: 2.3  Consensus size: 15

       4976 CAAGGTAAAA

                            
       4986 GTCAAAGTCAACTTTG
          1 GTCAAAGTCAAC-TTG

                           
       5002 GTCAAAGTCAAC-TG
          1 GTCAAAGTCAACTTG

                 
       5016 GTCAA
          1 GTCAA

       5021 GTTTGGTCAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  14    7  0.37
  16   12  0.63

ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26


Consensus pattern (15 bp):   
GTCAAAGTCAACTTG

Found at i:6199 original size:16 final size:16

Alignment explanation


    Indices: 6178--6208  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       6168 AATTTTAATT

                  *         
       6178 AATTAACTAATTTTTC
          1 AATTAAATAATTTTTC

                           
       6194 AATTAAATAATTTTT
          1 AATTAAATAATTTTT

       6209 TAACCTGATT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52


Consensus pattern (16 bp):   
AATTAAATAATTTTTC

Found at i:11938 original size:43 final size:43

Alignment explanation


    Indices: 11890--11999  Score: 105
    Period size: 43  Copynumber: 2.6  Consensus size: 43

      11880 ATATTCGATC

                          **                            
      11890 TAGTAAAAAAATTTTGAGTT-AATTGAGTTGACGAATCTTATTT
          1 TAGTAAAAAAA-TTAAAGTTGAATTGAGTTGACGAATCTTATTT

                  ***       *    *                     
      11933 TAGTAATTGAATTAAATTTGAGTTGAGTTGACGAATCTTATTT
          1 TAGTAAAAAAATTAAAGTTGAATTGAGTTGACGAATCTTATTT

                  ***       *       
      11976 TAGTAATTGAATTAAATTTGAATT
          1 TAGTAAAAAAATTAAAGTTGAATT

      12000 TTTTTTTCTA


Statistics
Matches: 58,  Mismatches: 8, Indels: 2
        0.85            0.12        0.03

Matches are distributed among these distances:
  42    5  0.09
  43   53  0.91

ACGTcount: A:0.36, C:0.04, G:0.16, T:0.44


Consensus pattern (43 bp):   
TAGTAAAAAAATTAAAGTTGAATTGAGTTGACGAATCTTATTT

Found at i:13165 original size:5 final size:5

Alignment explanation


    Indices: 13155--13184  Score: 51
    Period size: 5  Copynumber: 6.0  Consensus size: 5

      13145 CTTTACCAAT

                                        *      
      13155 ATATA ATATA ATATA ATATA ATATT ATATA
          1 ATATA ATATA ATATA ATATA ATATA ATATA

      13185 GTGTTTTCGT


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   5   23  1.00

ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43


Consensus pattern (5 bp):   
ATATA

Found at i:13858 original size:16 final size:15

Alignment explanation


    Indices: 13827--13856  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

      13817 GTAATATATC

                           
      13827 ATTTTAATAATTTTT
          1 ATTTTAATAATTTTT

                 *         
      13842 ATTTTTATAATTTTT
          1 ATTTTAATAATTTTT

      13857 TAAGGATTAA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70


Consensus pattern (15 bp):   
ATTTTAATAATTTTT

Found at i:13885 original size:29 final size:31

Alignment explanation


    Indices: 13842--13904  Score: 85
    Period size: 30  Copynumber: 2.1  Consensus size: 31

      13832 AATAATTTTT

                                   *       
      13842 ATTTTTATAATTTTTTAA-GGATTAAATCAA
          1 ATTTTTATAATTTTTTAAGGGATCAAATCAA

                    *                   *  
      13872 ATTTTTATCA-TTTTTAAGGGATCAAATTAA
          1 ATTTTTATAATTTTTTAAGGGATCAAATCAA

               
      13902 ATT
          1 ATT

      13905 ATTAACTTAA


Statistics
Matches: 29,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  29    7  0.24
  30   22  0.76

ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49


Consensus pattern (31 bp):   
ATTTTTATAATTTTTTAAGGGATCAAATCAA
Done.