Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009101.1 Corchorus olitorius cultivar O-4 contig09129, 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, 639

Length: 1066
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26


Found at i:463 original size:21 final size:21

Alignment explanation


    Indices: 439--576  Score: 199
    Period size: 21  Copynumber: 6.6  Consensus size: 21

        429 CTTAGGCAAT

                        **       
        439 TCCAATGAGCTTCAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
        460 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
        481 TCCAATGAACTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
        502 TCCAATGAACTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                  
        523 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                                  
        544 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                        
        565 TCCAATGAGCTT
          1 TCCAATGAGCTT

        577 CTAGCATCTT


Statistics
Matches: 111,  Mismatches: 5, Indels: 2
        0.94            0.04        0.02

Matches are distributed among these distances:
  20    3  0.03
  21  108  0.97

ACGTcount: A:0.26, C:0.28, G:0.17, T:0.30


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Found at i:968 original size:154 final size:154

Alignment explanation


    Indices: 678--1066  Score: 643
    Period size: 154  Copynumber: 2.5  Consensus size: 154

        668 TTGGCGCATC

                   *                                   *                     
        678 AACAAGTTTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATTTCACAAAAATGATTATAGTTA
          1 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACAAAAATGATTATAGTTA

                                                                     *       
        743 GTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAATCGAAACT
         66 GTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGAAACT

                                    
        808 AATGGGCCCCGATAGGCCCAAAAT
        131 AATGGGCCCCGATAGGCCCAAAAT

                                    *          *            *            *   
        832 AACAAGTGTTCCAAATGAGCTAAATACTTCACAGTAGACTAATCTCACCAAAATGATTATACTTA
          1 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACAAAAATGATTATAGTTA

             *                       *                                  **   
        897 GGCCATAAACAATGGAAAGAAAAGCCTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACT
         66 GTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGAAACT

             *      *               
        962 ATTGGGCCGCGATAGGCCCAAAAT
        131 AATGGGCCCCGATAGGCCCAAAAT

                                                            *                
        986 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACGAAAATGATTATAGTTA
          1 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACAAAAATGATTATAGTTA

                     *      
       1051 GTCCATAAATAATGGA
         66 GTCCATAAACAATGGA


Statistics
Matches: 216,  Mismatches: 19, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
 154  216  1.00

ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23


Consensus pattern (154 bp):   
AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACAAAAATGATTATAGTTA
GTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGAAACT
AATGGGCCCCGATAGGCCCAAAAT
Done.