Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010542.1 Kokia drynarioides strain JFW-HI SEQ_125461, 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: 17462
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:2602 original size:18 final size:19

Alignment explanation


    Indices: 2579--2624  Score: 58
    Period size: 20  Copynumber: 2.4  Consensus size: 19

       2569 AAATTTTCAA

                               
       2579 AAAATTTT-GAGCATAATT
          1 AAAATTTTAGAGCATAATT

                       * *      
       2597 AAAATTTTAAGGGTATAATT
          1 AAAATTTT-AGAGCATAATT

                    
       2617 AAAATTTT
          1 AAAATTTT

       2625 TAAAAACTAT


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  18    8  0.33
  20   16  0.67

ACGTcount: A:0.46, C:0.02, G:0.11, T:0.41


Consensus pattern (19 bp):   
AAAATTTTAGAGCATAATT

Found at i:5734 original size:23 final size:22

Alignment explanation


    Indices: 5683--5735  Score: 63
    Period size: 23  Copynumber: 2.4  Consensus size: 22

       5673 ATATTTATCA

                   *              
       5683 TATATTATAAATATATTTAAAT
          1 TATATTAAAAATATATTTAAAT

              *                     
       5705 TAAATTAAAATATATATTTTAAAT
          1 TATATTAAAA-ATATA-TTTAAAT

                    
       5729 T-TATTAA
          1 TATATTAA

       5736 GTCAATCAAT


Statistics
Matches: 26,  Mismatches: 3, Indels: 3
        0.81            0.09        0.09

Matches are distributed among these distances:
  22    8  0.31
  23   10  0.38
  24    8  0.31

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (22 bp):   
TATATTAAAAATATATTTAAAT

Found at i:11304 original size:38 final size:38

Alignment explanation


    Indices: 11262--11337  Score: 134
    Period size: 38  Copynumber: 2.0  Consensus size: 38

      11252 ATTGGTAAAG

                                                  
      11262 ATAAAATTATATTTTGACCTCGTAAAAATATAAAAATC
          1 ATAAAATTATATTTTGACCTCGTAAAAATATAAAAATC

                    *           *                 
      11300 ATAAAATTGTATTTTGACCTTGTAAAAATATAAAAATC
          1 ATAAAATTATATTTTGACCTCGTAAAAATATAAAAATC

      11338 TGATTTAATC


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  38   36  1.00

ACGTcount: A:0.49, C:0.09, G:0.07, T:0.36


Consensus pattern (38 bp):   
ATAAAATTATATTTTGACCTCGTAAAAATATAAAAATC

Found at i:13076 original size:7 final size:7

Alignment explanation


    Indices: 13061--13105  Score: 54
    Period size: 7  Copynumber: 6.4  Consensus size: 7

      13051 GCGGTTGTAC

                *  
      13061 GTTGTAT
          1 GTTGAAT

                   
      13068 GTTGAAT
          1 GTTGAAT

                   
      13075 GTTGAAT
          1 GTTGAAT

                   
      13082 GTTGAAT
          1 GTTGAAT

            *  *   
      13089 ATTAAAT
          1 GTTGAAT

                 * 
      13096 GTTGATT
          1 GTTGAAT

               
      13103 GTT
          1 GTT

      13106 AAGGTTCACT


Statistics
Matches: 32,  Mismatches: 6, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
   7   32  1.00

ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49


Consensus pattern (7 bp):   
GTTGAAT

Found at i:13267 original size:2 final size:2

Alignment explanation


    Indices: 13262--13286  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      13252 TCTCTCTCTT

                                                 
      13262 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

      13287 CAAATTTTTA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:15427 original size:24 final size:24

Alignment explanation


    Indices: 15400--15464  Score: 130
    Period size: 24  Copynumber: 2.7  Consensus size: 24

      15390 TTGTATGTAT

                                    
      15400 TATTTGATATTATTGTCACGTCAC
          1 TATTTGATATTATTGTCACGTCAC

                                    
      15424 TATTTGATATTATTGTCACGTCAC
          1 TATTTGATATTATTGTCACGTCAC

                             
      15448 TATTTGATATTATTGTC
          1 TATTTGATATTATTGTC

      15465 GCGTGACCCC


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   41  1.00

ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49


Consensus pattern (24 bp):   
TATTTGATATTATTGTCACGTCAC

Found at i:16142 original size:28 final size:28

Alignment explanation


    Indices: 16104--16170  Score: 82
    Period size: 28  Copynumber: 2.4  Consensus size: 28

      16094 ATGTGAGGAA

                  *                  *   
      16104 CACGTCGTCACGTCGTAAT-GTTCCTATT
          1 CACGTCATCACGTCGT-ATCGTTCCCATT

            * *                         
      16132 TATGTCATCACGTCGTATCGTTCCCATT
          1 CACGTCATCACGTCGTATCGTTCCCATT

                       
      16160 CACGTCATCAC
          1 CACGTCATCAC

      16171 AATGTCAAAA


Statistics
Matches: 32,  Mismatches: 6, Indels: 2
        0.80            0.15        0.05

Matches are distributed among these distances:
  27    2  0.06
  28   30  0.94

ACGTcount: A:0.19, C:0.31, G:0.15, T:0.34


Consensus pattern (28 bp):   
CACGTCATCACGTCGTATCGTTCCCATT
Done.