Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002066.1 Kokia drynarioides strain JFW-HI SEQ_113975, 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: 15823
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:7011 original size:18 final size:17

Alignment explanation


    Indices: 6979--7018  Score: 55
    Period size: 17  Copynumber: 2.3  Consensus size: 17

       6969 TAAAATTTAT

                             
       6979 AAAAATAAAAATTCA-A
          1 AAAAATAAAAATTCACA

                               
       6995 AAAATATAAAAAGTTCACA
          1 AAAA-ATAAAAA-TTCACA

                 
       7014 AAAAA
          1 AAAAA

       7019 AATTAGCATG


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  16    4  0.19
  17    7  0.33
  18    5  0.24
  19    5  0.24

ACGTcount: A:0.72, C:0.07, G:0.03, T:0.17


Consensus pattern (17 bp):   
AAAAATAAAAATTCACA

Found at i:8709 original size:22 final size:22

Alignment explanation


    Indices: 8684--8728  Score: 72
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       8674 TGTTTAATAA

                                  
       8684 TGTTTAATCGATGTTGATGTTT
          1 TGTTTAATCGATGTTGATGTTT

                    *       *     
       8706 TGTTTAATTGATGTTGTTGTTT
          1 TGTTTAATCGATGTTGATGTTT

             
       8728 T
          1 T

       8729 ACTGAGAGTA


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  22   21  1.00

ACGTcount: A:0.16, C:0.02, G:0.22, T:0.60


Consensus pattern (22 bp):   
TGTTTAATCGATGTTGATGTTT

Found at i:11043 original size:22 final size:22

Alignment explanation


    Indices: 11015--11060  Score: 92
    Period size: 22  Copynumber: 2.1  Consensus size: 22

      11005 CTGACACCGA

                                  
      11015 GTGAAACCCTTGGAAGGACTCG
          1 GTGAAACCCTTGGAAGGACTCG

                                  
      11037 GTGAAACCCTTGGAAGGACTCG
          1 GTGAAACCCTTGGAAGGACTCG

              
      11059 GT
          1 GT

      11061 CCAAGCTTTC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   24  1.00

ACGTcount: A:0.26, C:0.22, G:0.33, T:0.20


Consensus pattern (22 bp):   
GTGAAACCCTTGGAAGGACTCG

Found at i:12652 original size:18 final size:18

Alignment explanation


    Indices: 12631--12677  Score: 67
    Period size: 18  Copynumber: 2.6  Consensus size: 18

      12621 CCTTACCTGA

                     *     *  
      12631 ACCCTCACCTCCTCCTTC
          1 ACCCTCACCACCTCCATC

                       *      
      12649 ACCCTCACCACTTCCATC
          1 ACCCTCACCACCTCCATC

                       
      12667 ACCCTCACCAC
          1 ACCCTCACCAC

      12678 GCTTACTGTT


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  18   26  1.00

ACGTcount: A:0.19, C:0.60, G:0.00, T:0.21


Consensus pattern (18 bp):   
ACCCTCACCACCTCCATC

Found at i:12701 original size:30 final size:29

Alignment explanation


    Indices: 12667--12751  Score: 98
    Period size: 30  Copynumber: 2.8  Consensus size: 29

      12657 CACTTCCATC

                               *          
      12667 ACCCTCACCACGCTTACTGTTAACATCTAA
          1 ACCCTCACCAC-CTTACTGCTAACATCTAA

                              *   *       
      12697 ACCCTCACCACCCTTACTACTAGCATCTAA
          1 ACCCTCACCA-CCTTACTGCTAACATCTAA

             *                  *    
      12727 ATCCTCACCACCTTTACTGCCAACA
          1 ACCCTCACCACC-TTACTGCTAACA

      12752 ACCTCACCAC


Statistics
Matches: 46,  Mismatches: 7, Indels: 4
        0.81            0.12        0.07

Matches are distributed among these distances:
  29    2  0.04
  30   43  0.93
  31    1  0.02

ACGTcount: A:0.29, C:0.41, G:0.05, T:0.25


Consensus pattern (29 bp):   
ACCCTCACCACCTTACTGCTAACATCTAA

Found at i:12795 original size:30 final size:30

Alignment explanation


    Indices: 12759--12817  Score: 82
    Period size: 30  Copynumber: 2.0  Consensus size: 30

      12749 ACAACCTCAC

                      *          *        
      12759 CACCCTCACCCTCACAATCACTACCTTTAA
          1 CACCCTCACCATCACAATCACCACCTTTAA

                           **            
      12789 CACCCTCACCATCACCCTCACCACCTTTA
          1 CACCCTCACCATCACAATCACCACCTTTA

      12818 TTCCCATCAA


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  30   25  1.00

ACGTcount: A:0.27, C:0.51, G:0.00, T:0.22


Consensus pattern (30 bp):   
CACCCTCACCATCACAATCACCACCTTTAA

Found at i:14122 original size:9 final size:9

Alignment explanation


    Indices: 14110--14140  Score: 53
    Period size: 9  Copynumber: 3.4  Consensus size: 9

      14100 TATGTTAAAG

                     
      14110 TTGTTTTAA
          1 TTGTTTTAA

                     
      14119 TTGTTTTAA
          1 TTGTTTTAA

              *      
      14128 TTATTTTAA
          1 TTGTTTTAA

                
      14137 TTGT
          1 TTGT

      14141 GGGGTAAACC


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   9   20  1.00

ACGTcount: A:0.23, C:0.00, G:0.10, T:0.68


Consensus pattern (9 bp):   
TTGTTTTAA
Done.