Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024710.1 Corchorus olitorius cultivar O-4 contig24743, 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: 7214
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30


Found at i:4050 original size:76 final size:76

Alignment explanation


    Indices: 3900--4043  Score: 175
    Period size: 76  Copynumber: 1.9  Consensus size: 76

       3890 ACAAGGACCC

                                             *                 *           * 
       3900 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGCACACCCATGTGGTTTGCTTGAGAACCCAGGT
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAACACCCATGTGGTTTGCCTGAGAACCCAGAT

                       
       3965 GGGCAGTGTCA
         66 GGGCAGTGTCA

                    *     *              *      *                    **      
       3976 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAGACCCATGT-GTTTCGCCTGATCACCCAG
          1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTGAACACCCATGTGGTTT-GCCTGAGAACCCAG

                 
       4039 ATGGG
         64 ATGGG

       4044 TTGTGTCTTA


Statistics
Matches: 57,  Mismatches: 9, Indels: 4
        0.81            0.13        0.06

Matches are distributed among these distances:
  75    4  0.07
  76   49  0.86
  77    4  0.07

ACGTcount: A:0.17, C:0.31, G:0.28, T:0.24


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAACACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA

Found at i:5010 original size:26 final size:26

Alignment explanation


    Indices: 4968--5017  Score: 73
    Period size: 26  Copynumber: 1.9  Consensus size: 26

       4958 ATGATTTAGG

                      *               
       4968 GGTTACTAACTCCCTTTTTCTTTTGA
          1 GGTTACTAACACCCTTTTTCTTTTGA

                        *      *    
       4994 GGTTACTAACACTCTTTTTTTTTT
          1 GGTTACTAACACCCTTTTTCTTTT

       5018 TCAAAGGGAC


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  26   21  1.00

ACGTcount: A:0.16, C:0.20, G:0.10, T:0.54


Consensus pattern (26 bp):   
GGTTACTAACACCCTTTTTCTTTTGA

Found at i:6777 original size:16 final size:15

Alignment explanation


    Indices: 6739--6780  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       6729 ACAGAGGTTG

                   *       
       6739 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
       6754 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       6769 ACTAGAAAACAA
          1 AC-AGAAAACAA

       6781 AGCAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.