Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014060.1 Kokia drynarioides strain JFW-HI SEQ_129091, 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: 2349
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.26

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


Found at i:633 original size:45 final size:45

Alignment explanation


    Indices: 465--597  Score: 248
    Period size: 45  Copynumber: 3.0  Consensus size: 45

        455 GCATAGCTCA

                                   *                     
        465 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATGC
          1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATGC

                                                  *      
        510 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCACAATGC
          1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATGC

                                                       
        555 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAAT
          1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAAT

        598 ACTTTAGGAA


Statistics
Matches: 85,  Mismatches: 3, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  45   85  1.00

ACGTcount: A:0.32, C:0.31, G:0.20, T:0.18


Consensus pattern (45 bp):   
TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATGC

Found at i:667 original size:21 final size:21

Alignment explanation


    Indices: 641--683  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        631 AGCTATCGCG

                    *            
        641 ATACTCTATTCCTCCCGGGCA
          1 ATACTCTACTCCTCCCGGGCA

                         * *     
        662 ATACTCTACTCCTTCGGGGCA
          1 ATACTCTACTCCTCCCGGGCA

             
        683 A
          1 A

        684 ATGGACCCTA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.21, C:0.35, G:0.16, T:0.28


Consensus pattern (21 bp):   
ATACTCTACTCCTCCCGGGCA

Found at i:1098 original size:45 final size:45

Alignment explanation


    Indices: 1036--1203  Score: 257
    Period size: 45  Copynumber: 3.7  Consensus size: 45

       1026 GCATAGCTCA

                                   *                     
       1036 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATGC
          1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATGC

                                                         
       1081 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATGC
          1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATGC

                                                       * 
       1126 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
          1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATGC

                  **           *  * *         
       1171 T-ATAGGGAAGGATATCAGGCTGAGTTTGACGAG
          1 TCA-AGCCAAGGATATCAGCCTCAATTTGACGAG

       1204 GCATCGCGAT


Statistics
Matches: 115,  Mismatches: 7, Indels: 2
        0.93            0.06        0.02

Matches are distributed among these distances:
  44    1  0.01
  45  114  0.99

ACGTcount: A:0.31, C:0.27, G:0.23, T:0.19


Consensus pattern (45 bp):   
TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATGC

Found at i:1245 original size:21 final size:20

Alignment explanation


    Indices: 1212--1253  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 20

       1202 AGGCATCGCG

                    *            
       1212 ATACACTATTCCTCCCGGGCA
          1 ATACACTACTCCT-CCGGGCA

                *               
       1233 ATACTCTACTCCTCCGGGCA
          1 ATACACTACTCCTCCGGGCA

             
       1253 A
          1 A

       1254 CCTCGACGTA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  20    8  0.42
  21   11  0.58

ACGTcount: A:0.24, C:0.38, G:0.14, T:0.24


Consensus pattern (20 bp):   
ATACACTACTCCTCCGGGCA
Done.