Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024906.1 Corchorus olitorius cultivar O-4 contig24939, 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: 15987
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33


Found at i:2837 original size:12 final size:12

Alignment explanation


    Indices: 2820--2845  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       2810 GCATCGCATA

                        
       2820 GGAGGCCTATAG
          1 GGAGGCCTATAG

                        
       2832 GGAGGCCTATAG
          1 GGAGGCCTATAG

              
       2844 GG
          1 GG

       2846 CTTGGTGCGA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.23, C:0.15, G:0.46, T:0.15


Consensus pattern (12 bp):   
GGAGGCCTATAG

Found at i:3422 original size:33 final size:32

Alignment explanation


    Indices: 3358--3433  Score: 100
    Period size: 33  Copynumber: 2.3  Consensus size: 32

       3348 TTCCTTCAAC

                      *                     
       3358 AATTGCTTCTAATCGAAATTTCTCCTCCAAAG
          1 AATTGCTTCTTATCGAAATTTCTCCTCCAAAG

                                     *        
       3390 AATTGCTTCTTATCGAAAATTTGCTTCT-CAAAG
          1 AATTGCTTCTTATCG-AAATTT-CTCCTCCAAAG

            *          
       3423 TATTGCTTCTT
          1 AATTGCTTCTT

       3434 GCGTTTTGAT


Statistics
Matches: 39,  Mismatches: 3, Indels: 3
        0.87            0.07        0.07

Matches are distributed among these distances:
  32   14  0.36
  33   21  0.54
  34    4  0.10

ACGTcount: A:0.28, C:0.21, G:0.11, T:0.41


Consensus pattern (32 bp):   
AATTGCTTCTTATCGAAATTTCTCCTCCAAAG

Found at i:3892 original size:22 final size:22

Alignment explanation


    Indices: 3859--3908  Score: 68
    Period size: 22  Copynumber: 2.3  Consensus size: 22

       3849 GGCATGGTCT

                    *              
       3859 GGTCATG-CCCGAGCCATGATGC
          1 GGTCATGTGCCGAGCCATGAT-C

                                  
       3881 GG-CATGTGCCGAGCCATGATC
          1 GGTCATGTGCCGAGCCATGATC

                   
       3902 GGTCATG
          1 GGTCATG

       3909 GTTCCTTGCT


Statistics
Matches: 25,  Mismatches: 1, Indels: 4
        0.83            0.03        0.13

Matches are distributed among these distances:
  21    7  0.28
  22   18  0.72

ACGTcount: A:0.18, C:0.28, G:0.34, T:0.20


Consensus pattern (22 bp):   
GGTCATGTGCCGAGCCATGATC

Found at i:9670 original size:1 final size:1

Alignment explanation


    Indices: 9664--9689  Score: 52
    Period size: 1  Copynumber: 26.0  Consensus size: 1

       9654 GAAGAAGAGT

                                      
       9664 GGGGGGGGGGGGGGGGGGGGGGGGGG
          1 GGGGGGGGGGGGGGGGGGGGGGGGGG

       9690 CTCTAAGCTT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   25  1.00

ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00


Consensus pattern (1 bp):   
G

Done.