Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018223.1 Corchorus olitorius cultivar O-4 contig18256, 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: 11661
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31


Found at i:6333 original size:21 final size:21

Alignment explanation


    Indices: 6305--6373  Score: 113
    Period size: 21  Copynumber: 3.3  Consensus size: 21

       6295 TACCGTGTCA

                                 
       6305 CAATGAGCTTGGAACCTTCTC
          1 CAATGAGCTTGGAACCTTCTC

             *                   
       6326 CGATGAGCTTGGAACCTTCTC
          1 CAATGAGCTTGGAACCTTCTC

                                  
       6347 CAATGAGCTTGGAA-CTTGCTC
          1 CAATGAGCTTGGAACCTT-CTC

                  
       6368 CAATGA
          1 CAATGA

       6374 TCTCCTAGCA


Statistics
Matches: 45,  Mismatches: 2, Indels: 2
        0.92            0.04        0.04

Matches are distributed among these distances:
  20    3  0.07
  21   42  0.93

ACGTcount: A:0.25, C:0.26, G:0.22, T:0.28


Consensus pattern (21 bp):   
CAATGAGCTTGGAACCTTCTC

Found at i:6432 original size:40 final size:40

Alignment explanation


    Indices: 6377--6456  Score: 160
    Period size: 40  Copynumber: 2.0  Consensus size: 40

       6367 CCAATGATCT

                                                    
       6377 CCTAGCATCTTCAAGACCATGATGAGTCCGTGGCGCATCA
          1 CCTAGCATCTTCAAGACCATGATGAGTCCGTGGCGCATCA

                                                    
       6417 CCTAGCATCTTCAAGACCATGATGAGTCCGTGGCGCATCA
          1 CCTAGCATCTTCAAGACCATGATGAGTCCGTGGCGCATCA

       6457 GTTAGGTTAT


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  40   40  1.00

ACGTcount: A:0.25, C:0.30, G:0.23, T:0.23


Consensus pattern (40 bp):   
CCTAGCATCTTCAAGACCATGATGAGTCCGTGGCGCATCA

Found at i:8681 original size:25 final size:24

Alignment explanation


    Indices: 8645--8691  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

       8635 TCCTTCTATT

                                    
       8645 CATCTATCATC-AAGTTTTTCATC
          1 CATCTATCATCAAAGTTTTTCATC

                                    
       8668 CATCTCATCCATCAAAGTTTTTCA
          1 CATCT-AT-CATCAAAGTTTTTCA

       8692 AATTTTCAAG


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    2  0.10
  25    4  0.19
  26   10  0.48

ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40


Consensus pattern (24 bp):   
CATCTATCATCAAAGTTTTTCATC

Done.