Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022178.1 Corchorus olitorius cultivar O-4 contig22211, 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: 17673
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30


Found at i:15434 original size:27 final size:27

Alignment explanation


    Indices: 15404--15524  Score: 224
    Period size: 27  Copynumber: 4.5  Consensus size: 27

      15394 TCCAAAATTG

                 *                     
      15404 GATCCTGATGGTCGGGATGCCAAGGTT
          1 GATCCCGATGGTCGGGATGCCAAGGTT

                                       
      15431 GATCCCGATGGTCGGGATGCCAAGGTT
          1 GATCCCGATGGTCGGGATGCCAAGGTT

                                       
      15458 GATCCCGATGGTCGGGATGCCAAGGTT
          1 GATCCCGATGGTCGGGATGCCAAGGTT

                               *       
      15485 GATCCCGATGGTCGGGATGACAAGGTT
          1 GATCCCGATGGTCGGGATGCCAAGGTT

                         
      15512 GATCCCGATGGTC
          1 GATCCCGATGGTC

      15525 ATGAGATGAT


Statistics
Matches: 92,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  27   92  1.00

ACGTcount: A:0.19, C:0.21, G:0.36, T:0.23


Consensus pattern (27 bp):   
GATCCCGATGGTCGGGATGCCAAGGTT

Found at i:15729 original size:16 final size:15

Alignment explanation


    Indices: 15698--15741  Score: 61
    Period size: 16  Copynumber: 2.9  Consensus size: 15

      15688 ATCGACTCAC

                 *         
      15698 CATCAAGACGCTTAT
          1 CATCAGGACGCTTAT

                            
      15713 CATCAGGACGACTTAT
          1 CATCAGGACG-CTTAT

               *         
      15729 CATTAGGACGCTT
          1 CATCAGGACGCTT

      15742 TCCATCGGGA


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
  15   12  0.46
  16   14  0.54

ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27


Consensus pattern (15 bp):   
CATCAGGACGCTTAT

Found at i:17275 original size:15 final size:15

Alignment explanation


    Indices: 17255--17284  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

      17245 TCGTGTTGGG

                           
      17255 AATGGAAACAGGCAT
          1 AATGGAAACAGGCAT

                     *     
      17270 AATGGAAACGGGCAT
          1 AATGGAAACAGGCAT

      17285 TGGAACGGCA


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:0.43, C:0.13, G:0.30, T:0.13


Consensus pattern (15 bp):   
AATGGAAACAGGCAT
Done.