Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010976.1 Corchorus olitorius cultivar O-4 contig11008, 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: 1886
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.27


Found at i:565 original size:21 final size:21

Alignment explanation


    Indices: 541--653  Score: 158
    Period size: 21  Copynumber: 5.4  Consensus size: 21

        531 CTTAGGCATT

                         *       
        541 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
        562 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *          * 
        583 TCCAATGAACTTGGAACCTGC
          1 TCCAATGAGCTTGGAACCTTC

                                  
        604 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                                  
        625 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
        646 TCCAATGA
          1 TCCAATGA

        654 ACTTCTAGTA


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:1040 original size:154 final size:154

Alignment explanation


    Indices: 760--1147  Score: 643
    Period size: 154  Copynumber: 2.5  Consensus size: 154

        750 TGGCGCATCA

                                                                             
        760 GCCATAAACAATGGAAAGAAAAGACTTTAGAGTTGCCAAATCGGAGATGATTCAAAACGGAACTA
          1 GCCATAAACAATGGAAAGAAAAGACTTTAGAGTTGCCAAATCGGAGATGATTCAAAACGGAACTA

                                        *          **                        
        825 ATGGGCCCCGGTAGGCCCAAAATAACAAGTGTTCCAAATTTGCTAAAAACTTCACAGTGGACTAA
         66 ATGGGCCCCGGTAGGCCCAAAATAACAAATGTTCCAAATGGGCTAAAAACTTCACAGTGGACTAA

             *                      
        890 TTTCACCAAAATGATTATAGTTAG
        131 TCTCACCAAAATGATTATAGTTAG

                                        *   *           *   *           **   
        914 GCCATAAACAATGGAAAGAAAAG-CATTGAGATTTGCCAAATCGAAGACGATTCAAAACGTCACT
          1 GCCATAAACAATGGAAAGAAAAGAC-TTTAGAGTTGCCAAATCGGAGATGATTCAAAACGGAACT

                  *    *                                          *          
        978 AATGGGTCCCGATAGGCCCAAAATAACAAATGTTCCAAATGGGCTAAAAACTTCTCAGTGGACTA
         65 AATGGGCCCCGGTAGGCCCAAAATAACAAATGTTCCAAATGGGCTAAAAACTTCACAGTGGACTA

                                     
       1043 ATCTCACCAAAATGATTATAGTTAG
        130 ATCTCACCAAAATGATTATAGTTAG

                                                                             
       1068 GCCATAAACAATGGAAAGAAAAGACTTTAGAGTTGCCAAATCGGAGATGATTCAAAACGGAACTA
          1 GCCATAAACAATGGAAAGAAAAGACTTTAGAGTTGCCAAATCGGAGATGATTCAAAACGGAACTA

                           
       1133 ATGGGCCCCGGTAGG
         66 ATGGGCCCCGGTAGG

       1148 TGATACGAAT


Statistics
Matches: 211,  Mismatches: 21, Indels: 4
        0.89            0.09        0.02

Matches are distributed among these distances:
 153    1  0.00
 154  209  0.99
 155    1  0.00

ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21


Consensus pattern (154 bp):   
GCCATAAACAATGGAAAGAAAAGACTTTAGAGTTGCCAAATCGGAGATGATTCAAAACGGAACTA
ATGGGCCCCGGTAGGCCCAAAATAACAAATGTTCCAAATGGGCTAAAAACTTCACAGTGGACTAA
TCTCACCAAAATGATTATAGTTAG
Done.