Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015949.1 Corchorus olitorius cultivar O-4 contig15982, 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: 2842
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.28


Found at i:2228 original size:21 final size:20

Alignment explanation


    Indices: 2204--2297  Score: 125
    Period size: 21  Copynumber: 4.5  Consensus size: 20

       2194 ATCTTAGGCA

                      *          
       2204 TCTCCAATGATCTTGGAACCT
          1 TCTCCAATGAGCTTGGAA-CT

                      *          
       2225 TCTCCAATGAACTTGGAACCT
          1 TCTCCAATGAGCTTGGAA-CT

            *                   
       2246 GCTCCAATGAGCTTGGAACT
          1 TCTCCAATGAGCTTGGAACT

                                 
       2266 TGCTCCAATGAGCTTGGAACT
          1 T-CTCCAATGAGCTTGGAACT

                       
       2287 TGCTCCAATGA
          1 T-CTCCAATGA

       2298 ACTTCTAGCA


Statistics
Matches: 68,  Mismatches: 4, Indels: 2
        0.92            0.05        0.03

Matches are distributed among these distances:
  20    2  0.03
  21   66  0.97

ACGTcount: A:0.26, C:0.27, G:0.19, T:0.29


Consensus pattern (20 bp):   
TCTCCAATGAGCTTGGAACT

Found at i:2252 original size:42 final size:42

Alignment explanation


    Indices: 2205--2297  Score: 143
    Period size: 42  Copynumber: 2.2  Consensus size: 42

       2195 TCTTAGGCAT

                     *                                 
       2205 CTCCAATGATCTTGGAACCTT-CTCCAATGAACTTGGAACCTG
          1 CTCCAATGAGCTTGGAA-CTTGCTCCAATGAACTTGGAACCTG

                                          *        *  
       2247 CTCCAATGAGCTTGGAACTTGCTCCAATGAGCTTGGAACTTG
          1 CTCCAATGAGCTTGGAACTTGCTCCAATGAACTTGGAACCTG

                     
       2289 CTCCAATGA
          1 CTCCAATGA

       2298 ACTTCTAGCA


Statistics
Matches: 47,  Mismatches: 3, Indels: 2
        0.90            0.06        0.04

Matches are distributed among these distances:
  41    3  0.06
  42   44  0.94

ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28


Consensus pattern (42 bp):   
CTCCAATGAGCTTGGAACTTGCTCCAATGAACTTGGAACCTG
Done.