Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018964.1 Corchorus olitorius cultivar O-4 contig18997, 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, 934

Length: 1558
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35


Found at i:337 original size:51 final size:50

Alignment explanation


    Indices: 194--568  Score: 615
    Period size: 50  Copynumber: 7.5  Consensus size: 50

        184 CGAATGCTTT

                      *   *                                   
        194 GGCTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCAATTATCAACATA
          1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA

                          * *                               * 
        244 GGCTTTTCCACAAGTCGAACTCGTTTCCATACGAGTCAATTATCAACACA
          1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA

              *       *                                      * 
        294 GGTTTTTCCATAAGCCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
          1 GGCTTTTCCACAAG-CCAAACTCGTTTCCATACGAGTCAATTATCAACATA

                      *                                        
        345 GGCTTTTCCATAAGCCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
          1 GGCTTTTCCACAAG-CCAAACTCGTTTCCATACGAGTCAATTATCAACATA

                                                          * * 
        396 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAAAACA
          1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA

                                                             *
        446 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATG
          1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA

                              *                               
        496 GGCTTTTCCACAAGCCAAGCTCGTTTCCATACGAGTCAATTATCAACATA
          1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA

                                   
        546 GGCTTTTCCACAAGCCAAACTCG
          1 GGCTTTTCCACAAGCCAAACTCG

        569 AGGATCTCTC


Statistics
Matches: 306,  Mismatches: 18, Indels: 2
        0.94            0.06        0.01

Matches are distributed among these distances:
  50  210  0.69
  51   96  0.31

ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28


Consensus pattern (50 bp):   
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA

Found at i:1151 original size:25 final size:25

Alignment explanation


    Indices: 1122--1169  Score: 87
    Period size: 25  Copynumber: 1.9  Consensus size: 25

       1112 GTATTTTGCG

                                     
       1122 TTCATGTAGCTCAAAGCTAATTTCA
          1 TTCATGTAGCTCAAAGCTAATTTCA

                           *       
       1147 TTCATGTAGCTCAAATCTAATTT
          1 TTCATGTAGCTCAAAGCTAATTT

       1170 GACATTGCAT


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  25   22  1.00

ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40


Consensus pattern (25 bp):   
TTCATGTAGCTCAAAGCTAATTTCA
Done.