Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000762.1 Corchorus capsularis cultivar CVL-1 contig00762, 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: 9877
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:7078 original size:30 final size:30

Alignment explanation


    Indices: 7044--7112  Score: 129
    Period size: 30  Copynumber: 2.3  Consensus size: 30

       7034 CTGTATCTCT

                                 *        
       7044 AAGCCTTCTGAGATTCCTGAAGAGGATAAG
          1 AAGCCTTCTGAGATTCCTGAAAAGGATAAG

                                          
       7074 AAGCCTTCTGAGATTCCTGAAAAGGATAAG
          1 AAGCCTTCTGAGATTCCTGAAAAGGATAAG

                     
       7104 AAGCCTTCT
          1 AAGCCTTCT

       7113 CAAGTTGTGC


Statistics
Matches: 38,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   38  1.00

ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25


Consensus pattern (30 bp):   
AAGCCTTCTGAGATTCCTGAAAAGGATAAG

Found at i:7919 original size:66 final size:65

Alignment explanation


    Indices: 7806--7929  Score: 194
    Period size: 66  Copynumber: 1.9  Consensus size: 65

       7796 GGAGGCGCAG

                         *     *  *                   *                      
       7806 ACCCCAAGTTCAAGCAAGAGTTTGCCTAAAAAGGAAACTTCAGCAGGCAAAGAAGAAACTGCGAA
          1 ACCCCAAGTTCAAACAAGAATTCGCCTAAAAAGGAAACTTCAACAGGCAAAGAAGAAACTGCGAA

                                                               *       
       7871 ACCCACAAGTTCAAACAAGAATTCGCCTAAAAAGGAAACTTCAACAGGCAAGGAAGAAA
          1 ACCC-CAAGTTCAAACAAGAATTCGCCTAAAAAGGAAACTTCAACAGGCAAAGAAGAAA

       7930 GTGCAGACAA


Statistics
Matches: 53,  Mismatches: 5, Indels: 1
        0.90            0.08        0.02

Matches are distributed among these distances:
  65    4  0.08
  66   49  0.92

ACGTcount: A:0.46, C:0.22, G:0.19, T:0.13


Consensus pattern (65 bp):   
ACCCCAAGTTCAAACAAGAATTCGCCTAAAAAGGAAACTTCAACAGGCAAAGAAGAAACTGCGAA

Found at i:8031 original size:14 final size:15

Alignment explanation


    Indices: 8012--8040  Score: 51
    Period size: 14  Copynumber: 2.0  Consensus size: 15

       8002 AGGAAGCTTC

                           
       8012 AAGTGCAGG-CAAGG
          1 AAGTGCAGGCCAAGG

                           
       8026 AAGTGCAGGCCAAGG
          1 AAGTGCAGGCCAAGG

       8041 CTTTAACAAG


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14    9  0.64
  15    5  0.36

ACGTcount: A:0.34, C:0.17, G:0.41, T:0.07


Consensus pattern (15 bp):   
AAGTGCAGGCCAAGG
Done.