Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000817.1 Kokia drynarioides strain JFW-HI SEQ_111904, 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, 641

Length: 1069
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27


Found at i:604 original size:29 final size:29

Alignment explanation


    Indices: 535--636  Score: 109
    Period size: 29  Copynumber: 3.6  Consensus size: 29

        525 GCTTACGAAA

                 *           *           
        535 AGTTCGCATAT-AACAATTTGCATACAAT
          1 AGTTCACATATAAACAAGTTGCATACAAT

                **  *                    
        563 AGTTTGCACATAAACAAGTTGCATACAAT
          1 AGTTCACATATAAACAAGTTGCATACAAT

              *                 *         
        592 AGCTCACATATAAAC-AGCTCGCATACAAT
          1 AGTTCACATATAAACAAG-TTGCATACAAT

                     *      
        621 AGTTCACATGTAAACA
          1 AGTTCACATATAAACA

        637 GTTCACGTAC


Statistics
Matches: 61,  Mismatches: 10, Indels: 4
        0.81            0.13        0.05

Matches are distributed among these distances:
  28   11  0.18
  29   50  0.82

ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26


Consensus pattern (29 bp):   
AGTTCACATATAAACAAGTTGCATACAAT

Found at i:647 original size:29 final size:29

Alignment explanation


    Indices: 584--655  Score: 90
    Period size: 29  Copynumber: 2.4  Consensus size: 29

        574 AAACAAGTTG

                                        *
        584 CATACAATAGCTCACATATAAACAGCTCG
          1 CATACAATAGCTCACATATAAACAGCTCA

                      *      *       *   
        613 CATACAATAGTTCACATGTAAACAGTTCA
          1 CATACAATAGCTCACATATAAACAGCTCA

             *            
        642 CGTACAATAAGCTC
          1 CATACAAT-AGCTC

        656 GCACATGAGA


Statistics
Matches: 36,  Mismatches: 6, Indels: 1
        0.84            0.14        0.02

Matches are distributed among these distances:
  29   32  0.89
  30    4  0.11

ACGTcount: A:0.40, C:0.25, G:0.11, T:0.24


Consensus pattern (29 bp):   
CATACAATAGCTCACATATAAACAGCTCA

Found at i:979 original size:31 final size:31

Alignment explanation


    Indices: 921--980  Score: 77
    Period size: 31  Copynumber: 1.9  Consensus size: 31

        911 ACAACGACGA

                      **        *          
        921 CCTACCACCTTGGATTGCCTGGAAATGATAG
          1 CCTACCACCTCAGATTGCCTCGAAATGATAG

                                          
        952 CCTACCACCTCAGATTGCC-CGACAATGAT
          1 CCTACCACCTCAGATTGCCTCGA-AATGAT

        981 GTCCTACTGG


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  30    2  0.08
  31   23  0.92

ACGTcount: A:0.27, C:0.32, G:0.18, T:0.23


Consensus pattern (31 bp):   
CCTACCACCTCAGATTGCCTCGAAATGATAG

Found at i:987 original size:31 final size:30

Alignment explanation


    Indices: 902--987  Score: 75
    Period size: 31  Copynumber: 2.8  Consensus size: 30

        892 TACCACCCTG

                  *      *  *            **
        902 GATTGCTCGACAACGACGACCTACCACCTTG
          1 GATTGCCCGACAATGATG-CCTACCACCTCA

                    *                       
        933 GATTGCCTGGA-AATGATAGCCTACCACCTCA
          1 GATTGCC-CGACAATGAT-GCCTACCACCTCA

                                    
        964 GATTGCCCGACAATGATGTCCTAC
          1 GATTGCCCGACAATGATG-CCTAC

        988 TGGAACGATG


Statistics
Matches: 44,  Mismatches: 7, Indels: 8
        0.75            0.12        0.14

Matches are distributed among these distances:
  30    3  0.07
  31   38  0.86
  32    3  0.07

ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22


Consensus pattern (30 bp):   
GATTGCCCGACAATGATGCCTACCACCTCA
Done.