Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008422.1 Kokia drynarioides strain JFW-HI SEQ_123093, 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: 9026
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39


Found at i:4989 original size:3 final size:3

Alignment explanation


    Indices: 4981--5021  Score: 82
    Period size: 3  Copynumber: 13.7  Consensus size: 3

       4971 TCTTAAATAA

                                                                  
       4981 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT

       5022 AAAAAGGTGA


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   38  1.00

ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66


Consensus pattern (3 bp):   
ATT

Found at i:5138 original size:17 final size:18

Alignment explanation


    Indices: 5105--5138  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       5095 AATTAATAGA

                *             
       5105 TAAATAAAAATAGTTAGG
          1 TAAACAAAAATAGTTAGG

                             
       5123 TAAACAAAAATA-TTAG
          1 TAAACAAAAATAGTTAG

       5139 AGTTGGTGAT


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    4  0.27
  18   11  0.73

ACGTcount: A:0.59, C:0.03, G:0.12, T:0.26


Consensus pattern (18 bp):   
TAAACAAAAATAGTTAGG

Found at i:5878 original size:13 final size:13

Alignment explanation


    Indices: 5860--5885  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       5850 TAACAGAAAA

                         
       5860 CCAAGGTGTAAAT
          1 CCAAGGTGTAAAT

                         
       5873 CCAAGGTGTAAAT
          1 CCAAGGTGTAAAT

       5886 TTATCATTAT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23


Consensus pattern (13 bp):   
CCAAGGTGTAAAT

Found at i:8858 original size:23 final size:23

Alignment explanation


    Indices: 8825--8876  Score: 72
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       8815 AACCCTTTTT

                             *      
       8825 AATTT-ATTTTAAATTTGAT-TTA
          1 AATTTAATTTTAAA-TTAATCTTA

                                   
       8847 AATTTAATTTTAAATTAATCTTA
          1 AATTTAATTTTAAATTAATCTTA

                   
       8870 AATTTAA
          1 AATTTAA

       8877 ATTAAGTTTA


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  22    9  0.33
  23   18  0.67

ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54


Consensus pattern (23 bp):   
AATTTAATTTTAAATTAATCTTA

Found at i:8864 original size:17 final size:17

Alignment explanation


    Indices: 8844--8900  Score: 62
    Period size: 17  Copynumber: 3.3  Consensus size: 17

       8834 TAAATTTGAT

                             
       8844 TTAAATTTAATTTTAAA
          1 TTAAATTTAATTTTAAA

                       *      
       8861 TT-AATCTTAAATTTAAA
          1 TTAAAT-TTAATTTTAAA

                *         *   
       8878 TTAAGTTTAATTTCAAAA
          1 TTAAATTTAATTT-TAAA

                 
       8896 TTAAA
          1 TTAAA

       8901 AAGTCCAAAA


Statistics
Matches: 32,  Mismatches: 5, Indels: 5
        0.76            0.12        0.12

Matches are distributed among these distances:
  16    3  0.09
  17   20  0.62
  18    9  0.28

ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47


Consensus pattern (17 bp):   
TTAAATTTAATTTTAAA

Found at i:8881 original size:11 final size:12

Alignment explanation


    Indices: 8820--8890  Score: 69
    Period size: 11  Copynumber: 6.2  Consensus size: 12

       8810 GATTGAACCC

                *       
       8820 TTTTTAATTT-A
          1 TTTTAAATTTAA

                      * 
       8831 TTTTAAATTTGA
          1 TTTTAAATTTAA

                        
       8843 -TTTAAATTTAA
          1 TTTTAAATTTAA

                        
       8854 TTTTAAA-TTAA
          1 TTTTAAATTTAA

             *          
       8865 TCTTAAATTTAA
          1 TTTTAAATTTAA

             *    *     
       8877 -ATTAAGTTTAA
          1 TTTTAAATTTAA

               
       8888 TTT
          1 TTT

       8891 CAAAATTAAA


Statistics
Matches: 50,  Mismatches: 6, Indels: 7
        0.79            0.10        0.11

Matches are distributed among these distances:
  11   38  0.76
  12   12  0.24

ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58


Consensus pattern (12 bp):   
TTTTAAATTTAA
Done.