Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01003149.1 Corchorus olitorius cultivar O-4 contig03154, 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, 754

Length: 1257
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.26


Found at i:243 original size:21 final size:22

Alignment explanation


    Indices: 227--339  Score: 146
    Period size: 21  Copynumber: 5.4  Consensus size: 22

        217 AGCTTCCTTG

                                  
        227 ATGAACTTGGAACCTT-CTCCA
          1 ATGAACTTGGAACCTTCCTCCA

                                  
        248 ATGAACTTGGAACCTT-CTCCA
          1 ATGAACTTGGAACCTTCCTCCA

                *           *     
        269 ATGAGCTTGGAA-CTTGCTCCA
          1 ATGAACTTGGAACCTTCCTCCA

                *           *     
        290 ATGAGCTTGGAA-CTTGCTCCA
          1 ATGAACTTGGAACCTTCCTCCA

                            *     
        311 ATGAACTTGGAA-CTTGCTCCA
          1 ATGAACTTGGAACCTTCCTCCA

                    
        332 ATGAACTT
          1 ATGAACTT

        340 CTAGCATCTT


Statistics
Matches: 89,  Mismatches: 2, Indels: 2
        0.96            0.02        0.02

Matches are distributed among these distances:
  20    3  0.03
  21   86  0.97

ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29


Consensus pattern (22 bp):   
ATGAACTTGGAACCTTCCTCCA

Found at i:279 original size:42 final size:42

Alignment explanation


    Indices: 227--339  Score: 176
    Period size: 42  Copynumber: 2.7  Consensus size: 42

        217 AGCTTCCTTG

                                                        
        227 ATGAACTTGGAACCTT-CTCCAATGAACTTGGAACCTT-CTCCA
          1 ATGAACTTGGAA-CTTGCTCCAATGAACTTGGAA-CTTGCTCCA

                *                    *                
        269 ATGAGCTTGGAACTTGCTCCAATGAGCTTGGAACTTGCTCCA
          1 ATGAACTTGGAACTTGCTCCAATGAACTTGGAACTTGCTCCA

                                         
        311 ATGAACTTGGAACTTGCTCCAATGAACTT
          1 ATGAACTTGGAACTTGCTCCAATGAACTT

        340 CTAGCATCTT


Statistics
Matches: 65,  Mismatches: 4, Indels: 4
        0.89            0.05        0.05

Matches are distributed among these distances:
  41    6  0.09
  42   59  0.91

ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29


Consensus pattern (42 bp):   
ATGAACTTGGAACTTGCTCCAATGAACTTGGAACTTGCTCCA
Done.