Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015880.1 Corchorus olitorius cultivar O-4 contig15913, 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: 11059
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31


Found at i:259 original size:21 final size:21

Alignment explanation


    Indices: 235--347  Score: 158
    Period size: 21  Copynumber: 5.4  Consensus size: 21

        225 CTTAGGCATT

                         *       
        235 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
        256 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *          * 
        277 TCCAATGAACTTGGAACCTGC
          1 TCCAATGAGCTTGGAACCTTC

                                  
        298 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                                  
        319 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
        340 TCCAATGA
          1 TCCAATGA

        348 ACTTCTAGCA


Statistics
Matches: 85,  Mismatches: 6, Indels: 2
        0.91            0.06        0.02

Matches are distributed among these distances:
  20    2  0.02
  21   83  0.98

ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Found at i:10203 original size:14 final size:15

Alignment explanation


    Indices: 10175--10203  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

      10165 GTGTGAATTC

                           
      10175 AAATTGATCTTTTGA
          1 AAATTGATCTTTTGA

                           
      10190 AAATTGAT-TTTTGA
          1 AAATTGATCTTTTGA

      10204 TAAACTTACA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14    6  0.43
  15    8  0.57

ACGTcount: A:0.34, C:0.03, G:0.14, T:0.48


Consensus pattern (15 bp):   
AAATTGATCTTTTGA
Done.