Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009761.1 Kokia drynarioides strain JFW-HI SEQ_124480, 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: 2608
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.38


Found at i:744 original size:94 final size:92

Alignment explanation


    Indices: 570--755  Score: 227
    Period size: 95  Copynumber: 2.0  Consensus size: 92

        560 GTGTTTAAAT

                                                     *      *               *
        570 TTTCAAAATTATAAAAAAAACTCTCAAATTTTTTTAAAAAATAATTAAGATCTTACTTTTTTTTT
          1 TTTCAAAATTATAAAAAAAACTCTCAAATTTTTTTAAAAAACAATTAAAATCTTACTTTTTTTTA

                *               *      
        635 TTTTTCAAATCAATTAGATATTTGAAC
         66 TTTTGCAAATCAATTAGATACTTGAAC

                                                                             
        662 TTTCAAAATGTATAAAAAAAA-TCTTCAAAACTTTTTTTAAAAAAGCAATTAAAA-CTCTA-TTT
          1 TTTCAAAAT-TATAAAAAAAACTC-TC-AAA-TTTTTTTAAAAAA-CAATTAAAATCT-TACTTT

                          * *                
        724 TTTTTATTTTGC-ATTTAATTAGATACTTGAAC
         60 TTTTTATTTTGCAAATCAATTAGATACTTGAAC

        756 CGTCATTAAC


Statistics
Matches: 81,  Mismatches: 7, Indels: 10
        0.83            0.07        0.10

Matches are distributed among these distances:
  92   11  0.14
  93   13  0.16
  94   20  0.25
  95   28  0.35
  96    9  0.11

ACGTcount: A:0.41, C:0.10, G:0.04, T:0.44


Consensus pattern (92 bp):   
TTTCAAAATTATAAAAAAAACTCTCAAATTTTTTTAAAAAACAATTAAAATCTTACTTTTTTTTA
TTTTGCAAATCAATTAGATACTTGAAC

Found at i:1942 original size:19 final size:19

Alignment explanation


    Indices: 1918--1964  Score: 76
    Period size: 19  Copynumber: 2.5  Consensus size: 19

       1908 GAACTAGAAA

                         *     
       1918 CGGTGGATAAAATGTTTGG
          1 CGGTGGATAAAATATTTGG

                               
       1937 CGGTGGATAAAATATTTGG
          1 CGGTGGATAAAATATTTGG

                *    
       1956 CGGTAGATA
          1 CGGTGGATA

       1965 GCTATCATTG


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  19   26  1.00

ACGTcount: A:0.30, C:0.06, G:0.34, T:0.30


Consensus pattern (19 bp):   
CGGTGGATAAAATATTTGG

Found at i:2200 original size:22 final size:22

Alignment explanation


    Indices: 2173--2214  Score: 57
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       2163 TATTTCAACT

                                  
       2173 TTCAAAATGTATAAAAAAAATC
          1 TTCAAAATGTATAAAAAAAATC

                  * * *         
       2195 TTCAAACTTTTTAAAAAAAA
          1 TTCAAAATGTATAAAAAAAA

       2215 GCAATTAAAA


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  22   17  1.00

ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31


Consensus pattern (22 bp):   
TTCAAAATGTATAAAAAAAATC
Done.