Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001427.1 Kokia drynarioides strain JFW-HI SEQ_112932, 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: 15952
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34


Found at i:1968 original size:59 final size:58

Alignment explanation


    Indices: 1829--1969  Score: 158
    Period size: 59  Copynumber: 2.4  Consensus size: 58

       1819 ATAAATTTAT

                *       *                 *                             
       1829 GTACTAAATTGAATCTAAAATAAAGCTTAAGTACCAAAATAAGAAAAATGTCAAATTCAA
          1 GTACCAAATTGAGTC-AAAA-AAAGCTTAAATACCAAAATAAGAAAAATGTCAAATTCAA

                           *       *         *  *                *     
       1889 GTACCAAATTGAGTCCAAAAAAGTTTAAATACCGAATTAAGAAAAAATGTCAAGTTCAA
          1 GTACCAAATTGAGTCAAAAAAAGCTTAAATACCAAAATAAG-AAAAATGTCAAATTCAA

               *                   
       1948 GTATCAAATT-AGGTCAAAAAAA
          1 GTACCAAATTGA-GTCAAAAAAA

       1970 AAAAGTTAAA


Statistics
Matches: 69,  Mismatches: 10, Indels: 5
        0.82            0.12        0.06

Matches are distributed among these distances:
  58   19  0.28
  59   37  0.54
  60   13  0.19

ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24


Consensus pattern (58 bp):   
GTACCAAATTGAGTCAAAAAAAGCTTAAATACCAAAATAAGAAAAATGTCAAATTCAA

Found at i:12728 original size:23 final size:23

Alignment explanation


    Indices: 12702--12745  Score: 79
    Period size: 23  Copynumber: 1.9  Consensus size: 23

      12692 CATAGAAATG

                  *                
      12702 CAAAAAGAAAAACATAAAATTTC
          1 CAAAAAAAAAAACATAAAATTTC

                                 
      12725 CAAAAAAAAAAACATAAAATT
          1 CAAAAAAAAAAACATAAAATT

      12746 CTTAAGAAGT


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  23   20  1.00

ACGTcount: A:0.70, C:0.11, G:0.02, T:0.16


Consensus pattern (23 bp):   
CAAAAAAAAAAACATAAAATTTC

Found at i:15509 original size:13 final size:14

Alignment explanation


    Indices: 15491--15519  Score: 51
    Period size: 13  Copynumber: 2.1  Consensus size: 14

      15481 ATCTAATCGA

                          
      15491 TTCAAAGTTAT-TT
          1 TTCAAAGTTATATT

                          
      15504 TTCAAAGTTATATT
          1 TTCAAAGTTATATT

              
      15518 TT
          1 TT

      15520 AATCAATTTC


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13   11  0.73
  14    4  0.27

ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55


Consensus pattern (14 bp):   
TTCAAAGTTATATT
Done.