Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021253.1 Corchorus olitorius cultivar O-4 contig21286, 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: 4344
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29


Found at i:846 original size:21 final size:21

Alignment explanation


    Indices: 776--848  Score: 112
    Period size: 21  Copynumber: 3.5  Consensus size: 21

        766 CTTAGGCAAT

                         *       
        776 TCCAATG-ACTTGAAACCTTC
          1 TCCAATGAACTTGGAACCTTC

                    *            
        796 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAACTTGGAACCTTC

                           *     
        817 TCCAATGAACTTGGAGCCTTC
          1 TCCAATGAACTTGGAACCTTC

                       
        838 TCCAATGAACT
          1 TCCAATGAACT

        849 GCTAGCATCT


Statistics
Matches: 48,  Mismatches: 4, Indels: 1
        0.91            0.08        0.02

Matches are distributed among these distances:
  20    7  0.15
  21   41  0.85

ACGTcount: A:0.27, C:0.29, G:0.14, T:0.30


Consensus pattern (21 bp):   
TCCAATGAACTTGGAACCTTC

Found at i:2723 original size:33 final size:33

Alignment explanation


    Indices: 2653--2797  Score: 127
    Period size: 33  Copynumber: 4.4  Consensus size: 33

       2643 ATGATCAACC

                                     ** *      
       2653 AAAACAGATTT-GTTTTCATCACAATTAGCATCC-
          1 AAAACAGATTTAG-TTTCATCACAAACAACA-CCT

                                              
       2686 AAAACAGAATTT-GTTTCATCACAAACAACACCT
          1 AAAACAG-ATTTAGTTTCATCACAAACAACACCT

                          *        *         
       2719 AAAACAGATTTAGTGTCATCACATACAACA-CT
          1 AAAACAGATTTAGTTTCATCACAAACAACACCT

                **  *      *     *         *  
       2751 CAAATTAGGTTTAGTATCATCGCAAACAACATCT
          1 -AAAACAGATTTAGTTTCATCACAAACAACACCT

                         
       2785 AAAACAGATTTAG
          1 AAAACAGATTTAG

       2798 AATTACTCTT


Statistics
Matches: 93,  Mismatches: 14, Indels: 10
        0.79            0.12        0.09

Matches are distributed among these distances:
  32    8  0.09
  33   78  0.84
  34    7  0.08

ACGTcount: A:0.42, C:0.21, G:0.10, T:0.28


Consensus pattern (33 bp):   
AAAACAGATTTAGTTTCATCACAAACAACACCT
Done.