Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016032.1 Corchorus olitorius cultivar O-4 contig16065, 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: 1960
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37


Found at i:295 original size:21 final size:22

Alignment explanation


    Indices: 269--381  Score: 155
    Period size: 21  Copynumber: 5.4  Consensus size: 22

        259 CTTAGGCATT

                         *      * 
        269 TCCAATGAGCTTGAAACCTTCC
          1 TCCAATGAGCTTGGAACCTTGC

                    *             
        291 T-CAATGATCTTGGAACCTT-C
          1 TCCAATGAGCTTGGAACCTTGC

                    *             
        311 TCCAATGAACTTGGAACC-TGC
          1 TCCAATGAGCTTGGAACCTTGC

                                  
        332 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTTGC

                                  
        353 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTTGC

                    
        374 TCCAATGA
          1 TCCAATGA

        382 ACTTCTAGCA


Statistics
Matches: 84,  Mismatches: 4, Indels: 7
        0.88            0.04        0.07

Matches are distributed among these distances:
  20    4  0.05
  21   79  0.94
  22    1  0.01

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


Consensus pattern (22 bp):   
TCCAATGAGCTTGGAACCTTGC

Found at i:580 original size:120 final size:120

Alignment explanation


    Indices: 367--607  Score: 446
    Period size: 120  Copynumber: 2.0  Consensus size: 120

        357 ATGAGCTTGG

                                                                             
        367 AACTTGCTCCAATGAACTTCTAGCATCTTCAAGCTTCTTCAAGCCTCCTTGCCGCATATGCACAT
          1 AACTTGCTCCAATGAACTTCTAGCATCTTCAAGCTTCTTCAAGCCTCCTTGCCGCATATGCACAT

                          *                                        
        432 TCCCTCCATGATCTGCATTGTGCTCTTCTAGACCATGATGAGTCCTTGGCGCATC
         66 TCCCTCCATGATCTCCATTGTGCTCTTCTAGACCATGATGAGTCCTTGGCGCATC

                           *                    *                            
        487 AACTTGCTCCAATGAGCTTCTAGCATCTTCAAGCTTTTTCAAGCCTCCTTGCCGCATATGCACAT
          1 AACTTGCTCCAATGAACTTCTAGCATCTTCAAGCTTCTTCAAGCCTCCTTGCCGCATATGCACAT

                                                               *   
        552 TCCCTCCATGATCTCCATTGTGCTCTTCTAGACCATGATGAGTCCTTGGCGTATC
         66 TCCCTCCATGATCTCCATTGTGCTCTTCTAGACCATGATGAGTCCTTGGCGCATC

             
        607 A
          1 A

        608 CAACTAATAT


Statistics
Matches: 117,  Mismatches: 4, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
 120  117  1.00

ACGTcount: A:0.21, C:0.31, G:0.16, T:0.32


Consensus pattern (120 bp):   
AACTTGCTCCAATGAACTTCTAGCATCTTCAAGCTTCTTCAAGCCTCCTTGCCGCATATGCACAT
TCCCTCCATGATCTCCATTGTGCTCTTCTAGACCATGATGAGTCCTTGGCGCATC
Done.