Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022160.1 Corchorus olitorius cultivar O-4 contig22193, 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: 6707
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34


Found at i:3595 original size:52 final size:52

Alignment explanation


    Indices: 3512--3611  Score: 148
    Period size: 52  Copynumber: 1.9  Consensus size: 52

       3502 AGGTAATCAA

                *                *    *                         
       3512 ATCTGACTTATTTATTGCTTTTATTTTAAATTATATATTCTGAAATTGGATT
          1 ATCTAACTTATTTATTGCTTTCATTTCAAATTATATATTCTGAAATTGGATT

                                               *             
       3564 ATCTAACTTATTTATT-CATTTCATTTCAAATTATTTATTCTGAAATTG
          1 ATCTAACTTATTTATTGC-TTTCATTTCAAATTATATATTCTGAAATTG

       3612 ATCCCTACAT


Statistics
Matches: 43,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  51    1  0.02
  52   42  0.98

ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53


Consensus pattern (52 bp):   
ATCTAACTTATTTATTGCTTTCATTTCAAATTATATATTCTGAAATTGGATT

Found at i:4704 original size:15 final size:15

Alignment explanation


    Indices: 4686--4715  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       4676 TATATATAGA

                     *     
       4686 ACAAACCCATAAAAC
          1 ACAAACCCAGAAAAC

                           
       4701 ACAAACCCAGAAAAC
          1 ACAAACCCAGAAAAC

       4716 CCATAAAAAA


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

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.60, C:0.33, G:0.03, T:0.03


Consensus pattern (15 bp):   
ACAAACCCAGAAAAC

Found at i:5065 original size:11 final size:11

Alignment explanation


    Indices: 5045--5078  Score: 59
    Period size: 11  Copynumber: 3.1  Consensus size: 11

       5035 AACGAAATCG

                       
       5045 AAAGAGAGAGA
          1 AAAGAGAGAGA

                 *     
       5056 AAAGATAGAGA
          1 AAAGAGAGAGA

                       
       5067 AAAGAGAGAGA
          1 AAAGAGAGAGA

             
       5078 A
          1 A

       5079 TTATCGTTTT


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  11   21  1.00

ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03


Consensus pattern (11 bp):   
AAAGAGAGAGA
Done.