Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019873.1 Corchorus olitorius cultivar O-4 contig19906, 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: 5895
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35


Found at i:909 original size:19 final size:18

Alignment explanation


    Indices: 885--920  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

        875 TGAAGAATTA

                               
        885 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
        904 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

        921 ATAATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT

Found at i:3084 original size:26 final size:26

Alignment explanation


    Indices: 3055--3106  Score: 77
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       3045 GTGCTAGCAA

                 *         *     *    
       3055 TGAATTAAAAATGACTAAAATGCCCC
          1 TGAATAAAAAATGACCAAAATACCCC

                                      
       3081 TGAATAAAAAATGACCAAAATACCCC
          1 TGAATAAAAAATGACCAAAATACCCC

       3107 CTGGGTGATT


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  26   23  1.00

ACGTcount: A:0.50, C:0.21, G:0.10, T:0.19


Consensus pattern (26 bp):   
TGAATAAAAAATGACCAAAATACCCC

Found at i:4123 original size:21 final size:21

Alignment explanation


    Indices: 4099--4190  Score: 150
    Period size: 21  Copynumber: 4.4  Consensus size: 21

       4089 CTTAGGCAAT

                         *       
       4099 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                            *    
       4120 TCCAATGAGCTTGGAATCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
       4141 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                  
       4162 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
       4183 TCCAATGA
          1 TCCAATGA

       4191 TCTCCTAGCA


Statistics
Matches: 67,  Mismatches: 3, Indels: 2
        0.93            0.04        0.03

Matches are distributed among these distances:
  20    3  0.04
  21   64  0.96

ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Done.