Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013375.1 Corchorus olitorius cultivar O-4 contig13408, 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: 11999
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:1386 original size:30 final size:31

Alignment explanation


    Indices: 1350--1414  Score: 89
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       1340 AAATGGGTCT

                                            
       1350 CTGAAGTGAACG-T-AGTGAGCAATTGAGTCC
          1 CTGAAGTGAA-GTTAAGTGAGCAATTGAGTCC

                           *          *    
       1380 CTGAAGTGAAGTTAATTGAGCAATTGGGTCC
          1 CTGAAGTGAAGTTAAGTGAGCAATTGAGTCC

                
       1411 CTGA
          1 CTGA

       1415 TTATTTTTTT


Statistics
Matches: 31,  Mismatches: 2, Indels: 3
        0.86            0.06        0.08

Matches are distributed among these distances:
  29    1  0.03
  30   11  0.35
  31   19  0.61

ACGTcount: A:0.29, C:0.15, G:0.29, T:0.26


Consensus pattern (31 bp):   
CTGAAGTGAAGTTAAGTGAGCAATTGAGTCC

Found at i:2915 original size:65 final size:65

Alignment explanation


    Indices: 2811--2932  Score: 217
    Period size: 65  Copynumber: 1.9  Consensus size: 65

       2801 TAGTCTTACC

                             *                                 *             
       2811 CATGCATGGGGTACCCTTGGCCTACCAACGCCTGGGCTAGTGCAGAAAGTTTGAATCTTCCAACT
          1 CATGCATGGGGTACCCTCGGCCTACCAACGCCTGGGCTAGTGCAGAAAGTTGGAATCTTCCAACT

                                      *                              
       2876 CATGCATGGGGTACCCTCGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTGGAATC
          1 CATGCATGGGGTACCCTCGGCCTACCAACGCCTGGGCTAGTGCAGAAAGTTGGAATC

       2933 AATAGCAAGC


Statistics
Matches: 54,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  65   54  1.00

ACGTcount: A:0.22, C:0.29, G:0.27, T:0.22


Consensus pattern (65 bp):   
CATGCATGGGGTACCCTCGGCCTACCAACGCCTGGGCTAGTGCAGAAAGTTGGAATCTTCCAACT

Found at i:3148 original size:21 final size:21

Alignment explanation


    Indices: 3124--3215  Score: 159
    Period size: 21  Copynumber: 4.4  Consensus size: 21

       3114 CTTAGGCAAT

                         *       
       3124 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
       3145 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
       3166 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                  
       3187 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
       3208 TCCAATGA
          1 TCCAATGA

       3216 ACTCCTAGCA


Statistics
Matches: 69,  Mismatches: 1, Indels: 2
        0.96            0.01        0.03

Matches are distributed among these distances:
  20    3  0.04
  21   66  0.96

ACGTcount: A:0.26, C:0.27, G:0.18, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Found at i:7706 original size:15 final size:16

Alignment explanation


    Indices: 7676--7715  Score: 64
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       7666 TTACTTTGCT

                            
       7676 TTGTTTTCTAGTTTAA
          1 TTGTTTTCTAGTTTAA

                            
       7692 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTTTAA

               *     
       7707 TTGCTTTCT
          1 TTGTTTTCT

       7716 TTCAACCTCT


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  15   14  0.61
  16    9  0.39

ACGTcount: A:0.12, C:0.10, G:0.12, T:0.65


Consensus pattern (16 bp):   
TTGTTTTCTAGTTTAA
Done.