Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012879.1 Corchorus olitorius cultivar O-4 contig12912, 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: 28355
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30


Found at i:3661 original size:34 final size:34

Alignment explanation


    Indices: 3618--3687  Score: 131
    Period size: 34  Copynumber: 2.1  Consensus size: 34

       3608 TATTAGTTTA

                                              
       3618 AAACCATGAGTGCCAAGGAGCTAGAGACATTCGC
          1 AAACCATGAGTGCCAAGGAGCTAGAGACATTCGC

                          *                   
       3652 AAACCATGAGTGCCTAGGAGCTAGAGACATTCGC
          1 AAACCATGAGTGCCAAGGAGCTAGAGACATTCGC

              
       3686 AA
          1 AA

       3688 CAGATTACAG


Statistics
Matches: 35,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  34   35  1.00

ACGTcount: A:0.36, C:0.23, G:0.26, T:0.16


Consensus pattern (34 bp):   
AAACCATGAGTGCCAAGGAGCTAGAGACATTCGC

Found at i:23404 original size:21 final size:21

Alignment explanation


    Indices: 23369--23410  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      23359 TATGGGTGTG

                    *             
      23369 TGTGATTGTTTGGTTTGGTAGA
          1 TGTGATTGATTGGTTT-GTAGA

                                 
      23391 TGTGA-TGATTGGTTTGTAGA
          1 TGTGATTGATTGGTTTGTAGA

      23411 GACCGAGCGA


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  20    5  0.26
  21    9  0.47
  22    5  0.26

ACGTcount: A:0.17, C:0.00, G:0.36, T:0.48


Consensus pattern (21 bp):   
TGTGATTGATTGGTTTGTAGA

Found at i:25450 original size:13 final size:13

Alignment explanation


    Indices: 25428--25471  Score: 79
    Period size: 13  Copynumber: 3.4  Consensus size: 13

      25418 ACGTGAGTAG

                         
      25428 TTTTTGACAGTTT
          1 TTTTTGACAGTTT

                 *       
      25441 TTTTTTACAGTTT
          1 TTTTTGACAGTTT

                         
      25454 TTTTTGACAGTTT
          1 TTTTTGACAGTTT

                 
      25467 TTTTT
          1 TTTTT

      25472 TAAAATAATA


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  13   29  1.00

ACGTcount: A:0.14, C:0.07, G:0.11, T:0.68


Consensus pattern (13 bp):   
TTTTTGACAGTTT

Found at i:25847 original size:16 final size:16

Alignment explanation


    Indices: 25828--25862  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

      25818 GAGCCGAAAA

                     *      
      25828 ACCCAAAACTCGAATG
          1 ACCCAAAACCCGAATG

                         *  
      25844 ACCCAAAACCCGAGTG
          1 ACCCAAAACCCGAATG

               
      25860 ACC
          1 ACC

      25863 TGAGGCCAAA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.40, C:0.37, G:0.14, T:0.09


Consensus pattern (16 bp):   
ACCCAAAACCCGAATG
Done.