Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000459.1 Kokia drynarioides strain JFW-HI SEQ_111321, 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: 8188
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32


Found at i:1144 original size:23 final size:23

Alignment explanation


    Indices: 1115--1167  Score: 79
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       1105 GTGGCATCAT

                          *        
       1115 GTCAGCAGCTTCTAGAAGGTCCA
          1 GTCAGCAGCTTCTAAAAGGTCCA

                                ** 
       1138 GTCAGCAGCTTCTAAAAGGTTTA
          1 GTCAGCAGCTTCTAAAAGGTCCA

                   
       1161 GTCAGCA
          1 GTCAGCA

       1168 ATGATGGACG


Statistics
Matches: 27,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  23   27  1.00

ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25


Consensus pattern (23 bp):   
GTCAGCAGCTTCTAAAAGGTCCA

Found at i:3000 original size:65 final size:65

Alignment explanation


    Indices: 2891--3022  Score: 221
    Period size: 65  Copynumber: 2.0  Consensus size: 65

       2881 AACTACGGCG

                                                   *                         
       2891 AAGCATACTTGGAATCCACCAAAAAGATGAAGAGTCACTTTACGACTAAT-GAGAGCGATTTAAG
          1 AAGCATACTTGGAATCCACCAAAAAGATGAAGAGTCACTCTACGACTAATAG-GAGCGATTTAAG

             
       2955 A
         65 A

                                         *                  *                
       2956 AAGCATACTTGGAATCCACCAAAAAGATGGAGAGTCACTCTACGACTACTAGGAGCGATTTAAGA
          1 AAGCATACTTGGAATCCACCAAAAAGATGAAGAGTCACTCTACGACTAATAGGAGCGATTTAAGA

              
       3021 AA
          1 AA

       3023 CTCTACGCTA


Statistics
Matches: 63,  Mismatches: 3, Indels: 2
        0.93            0.04        0.03

Matches are distributed among these distances:
  65   62  0.98
  66    1  0.02

ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20


Consensus pattern (65 bp):   
AAGCATACTTGGAATCCACCAAAAAGATGAAGAGTCACTCTACGACTAATAGGAGCGATTTAAGA

Found at i:7740 original size:6 final size:6

Alignment explanation


    Indices: 7729--7765  Score: 51
    Period size: 6  Copynumber: 6.3  Consensus size: 6

       7719 ATTATTTCGG

                                                         
       7729 TTATTT TTA-TT TTATTT TTATTT ATT-TTT TTATTT TT
          1 TTATTT TTATTT TTATTT TTATTT -TTATTT TTATTT TT

       7766 GGTAATTTAA


Statistics
Matches: 28,  Mismatches: 0, Indels: 6
        0.82            0.00        0.18

Matches are distributed among these distances:
   5    7  0.25
   6   19  0.68
   7    2  0.07

ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84


Consensus pattern (6 bp):   
TTATTT

Found at i:7758 original size:12 final size:11

Alignment explanation


    Indices: 7729--7764  Score: 54
    Period size: 11  Copynumber: 3.2  Consensus size: 11

       7719 ATTATTTCGG

                       
       7729 TTATTTTTATT
          1 TTATTTTTATT

                       
       7740 TTATTTTTATT
          1 TTATTTTTATT

               *        
       7751 TATTTTTTTATT
          1 T-TATTTTTATT

              
       7763 TT
          1 TT

       7765 TGGTAATTTA


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  11   13  0.57
  12   10  0.43

ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83


Consensus pattern (11 bp):   
TTATTTTTATT
Done.