Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002819.1 Kokia drynarioides strain JFW-HI SEQ_115174, 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: 2167
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34


Found at i:1929 original size:29 final size:29

Alignment explanation


    Indices: 1897--1988  Score: 80
    Period size: 29  Copynumber: 3.1  Consensus size: 29

       1887 TTTTGGTAAA

                                         
       1897 TAATATGATGGGGATATTATTTTCATAAT
          1 TAATATGATGGGGATATTATTTTCATAAT

                      ****           *     *
       1926 TAAT-T-ATTTTTTATATTATATTTTAGTAAA
          1 TAATATGA-TGGGGATATTAT-TTTCA-TAAT

                                   *     
       1956 TAATATGATGGGGATATTATTTTGATAAT
          1 TAATATGATGGGGATATTATTTTCATAAT

                
       1985 TAAT
          1 TAAT

       1989 TTTTTTTATA


Statistics
Matches: 46,  Mismatches: 12, Indels: 10
        0.68            0.18        0.15

Matches are distributed among these distances:
  27    1  0.02
  28    9  0.20
  29   15  0.33
  30   11  0.24
  31    9  0.20
  32    1  0.02

ACGTcount: A:0.36, C:0.01, G:0.13, T:0.50


Consensus pattern (29 bp):   
TAATATGATGGGGATATTATTTTCATAAT

Found at i:1959 original size:59 final size:58

Alignment explanation


    Indices: 1886--2017  Score: 228
    Period size: 59  Copynumber: 2.3  Consensus size: 58

       1876 ATTTTGTACC

                                                                       
       1886 ATTTTGGTAAATAATATGATGGGGATATTATTTTCATAATTAATTATTTTTTATATTAT
          1 ATTTTGGTAAATAATATGATGGGGATATTATTTTCATAATTAATT-TTTTTTATATTAT

                 *                            *                       
       1945 ATTTTAGTAAATAATATGATGGGGATATTATTTTGATAATTAATTTTTTTTATATTAT
          1 ATTTTGGTAAATAATATGATGGGGATATTATTTTCATAATTAATTTTTTTTATATTAT

                      *    
       2003 ATTTTGGTAATTAAT
          1 ATTTTGGTAAATAAT

       2018 TAGCTAGGTT


Statistics
Matches: 69,  Mismatches: 4, Indels: 1
        0.93            0.05        0.01

Matches are distributed among these distances:
  58   26  0.38
  59   43  0.62

ACGTcount: A:0.34, C:0.01, G:0.12, T:0.53


Consensus pattern (58 bp):   
ATTTTGGTAAATAATATGATGGGGATATTATTTTCATAATTAATTTTTTTTATATTAT
Done.