Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008681.1 Kokia drynarioides strain JFW-HI SEQ_123363, 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: 14638
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35


Found at i:5954 original size:41 final size:42

Alignment explanation


    Indices: 5862--5960  Score: 155
    Period size: 42  Copynumber: 2.4  Consensus size: 42

       5852 AGTGGGTCTA

                  *                                   
       5862 CTCACATGAGCTGTGGGTTGGGATGGTAGCTAAACGATTATG
          1 CTCACACGAGCTGTGGGTTGGGATGGTAGCTAAACGATTATG

                                            * *       
       5904 CTCACACGAGCTGTGGGTTGGGATGGTA-CTACATGATTATG
          1 CTCACACGAGCTGTGGGTTGGGATGGTAGCTAAACGATTATG

                *           
       5945 CTCATACGAGCTGTGG
          1 CTCACACGAGCTGTGG

       5961 AGAATCCGTA


Statistics
Matches: 53,  Mismatches: 4, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  41   26  0.49
  42   27  0.51

ACGTcount: A:0.22, C:0.17, G:0.32, T:0.28


Consensus pattern (42 bp):   
CTCACACGAGCTGTGGGTTGGGATGGTAGCTAAACGATTATG

Found at i:8801 original size:31 final size:31

Alignment explanation


    Indices: 8766--8871  Score: 110
    Period size: 31  Copynumber: 3.5  Consensus size: 31

       8756 AATTAATCAC

                      *                    
       8766 ATAAATATTATATTAATAAAATACTATCTAG
          1 ATAAATATTAAATTAATAAAATACTATCTAG

                              **           *
       8797 ATAAATATTAAATTAAATTTAATA-TATC-AT
          1 ATAAATATTAAATT-AATAAAATACTATCTAG

              *                  *        * 
       8827 ATTAATATTAAATTAATAAAAAACTAT-TGTG
          1 ATAAATATTAAATTAATAAAATACTATCT-AG

                          
       8858 ATAAATATTAAATT
          1 ATAAATATTAAATT

       8872 CATTAAAACA


Statistics
Matches: 60,  Mismatches: 11, Indels: 8
        0.76            0.14        0.10

Matches are distributed among these distances:
  29    6  0.10
  30   17  0.28
  31   30  0.50
  32    7  0.12

ACGTcount: A:0.53, C:0.04, G:0.03, T:0.41


Consensus pattern (31 bp):   
ATAAATATTAAATTAATAAAATACTATCTAG

Found at i:11030 original size:20 final size:20

Alignment explanation


    Indices: 11007--11055  Score: 89
    Period size: 20  Copynumber: 2.5  Consensus size: 20

      10997 TATTTTCTAG

                                
      11007 TTTTTGCTCATTTTTCACTC
          1 TTTTTGCTCATTTTTCACTC

                     *          
      11027 TTTTTGCTCGTTTTTCACTC
          1 TTTTTGCTCATTTTTCACTC

                     
      11047 TTTTTGCTC
          1 TTTTTGCTC

      11056 CGAAATACTT


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  20   28  1.00

ACGTcount: A:0.06, C:0.24, G:0.08, T:0.61


Consensus pattern (20 bp):   
TTTTTGCTCATTTTTCACTC

Found at i:13067 original size:16 final size:18

Alignment explanation


    Indices: 13046--13091  Score: 51
    Period size: 16  Copynumber: 2.6  Consensus size: 18

      13036 TTAATTATAA

                              
      13046 TATATTTTTTAAA-T-TT
          1 TATATTTTTTAAATTATT

                  *  *        
      13062 TATATTATTAAAATTATT
          1 TATATTTTTTAAATTATT

                        
      13080 TATAATTTTTTA
          1 TAT-ATTTTTTA

      13092 CAAATATAAT


Statistics
Matches: 23,  Mismatches: 4, Indels: 3
        0.77            0.13        0.10

Matches are distributed among these distances:
  16   11  0.48
  17    1  0.04
  18    5  0.22
  19    6  0.26

ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63


Consensus pattern (18 bp):   
TATATTTTTTAAATTATT
Done.