Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021988.1 Corchorus olitorius cultivar O-4 contig22021, 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: 5133
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:1618 original size:27 final size:27

Alignment explanation


    Indices: 1555--1651  Score: 124
    Period size: 27  Copynumber: 3.6  Consensus size: 27

       1545 TAAATCAACT

                               *         
       1555 AGGGGCATTTTGGTCATTTTC-CAATTCC
          1 AGGGGCATTTTGGTCATTTGCAC-A-TCC

                       *               
       1583 AGGGGCATTTTAGTCATTTGCACATCC
          1 AGGGGCATTTTGGTCATTTGCACATCC

             *                     *   
       1610 AAGGGCATTTTGGTCATTTGCACGTCC
          1 AGGGGCATTTTGGTCATTTGCACATCC

                     *     
       1637 AGGGGCATTCTGGTC
          1 AGGGGCATTTTGGTC

       1652 CTTTTAAGTT


Statistics
Matches: 61,  Mismatches: 7, Indels: 3
        0.86            0.10        0.04

Matches are distributed among these distances:
  27   40  0.66
  28   20  0.33
  29    1  0.02

ACGTcount: A:0.19, C:0.22, G:0.26, T:0.34


Consensus pattern (27 bp):   
AGGGGCATTTTGGTCATTTGCACATCC

Found at i:4338 original size:21 final size:21

Alignment explanation


    Indices: 4314--4384  Score: 117
    Period size: 21  Copynumber: 3.4  Consensus size: 21

       4304 CTTAGGCAAT

                         *       
       4314 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
       4335 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                  
       4356 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
       4377 TCCAATGA
          1 TCCAATGA

       4385 TCTCCTAGCA


Statistics
Matches: 48,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  20    3  0.06
  21   45  0.94

ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC
Done.