Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000549.1 Corchorus olitorius cultivar O-4 contig00549, 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, 956

Length: 1594
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37


Found at i:133 original size:50 final size:50

Alignment explanation


    Indices: 1--138  Score: 215
    Period size: 50  Copynumber: 2.7  Consensus size: 50

                          *                  *                 
          1 AAAAGCGAAGTTTTTATCTTGAACTCTCAAATGAAAAGCAATTTTATTTTG
          1 AAAAGCGAA-TTTTGATCTTGAACTCTCAAATGGAAAGCAATTTTATTTTG

                 *                                            
         52 AAAAGAGAATTTTGATCTTGAACTCTCAAATGGAAAGCAATTTTATTTTG
          1 AAAAGCGAATTTTGATCTTGAACTCTCAAATGGAAAGCAATTTTATTTTG

                              *                   
        102 AAAAGCGAATTTTGATCTAGAACTCAT-AAATGGAAAG
          1 AAAAGCGAATTTTGATCTTGAACTC-TCAAATGGAAAG

        139 AAATCTTGTT


Statistics
Matches: 81,  Mismatches: 5, Indels: 3
        0.91            0.06        0.03

Matches are distributed among these distances:
  50   72  0.89
  51    9  0.11

ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33


Consensus pattern (50 bp):   
AAAAGCGAATTTTGATCTTGAACTCTCAAATGGAAAGCAATTTTATTTTG

Found at i:754 original size:6 final size:6

Alignment explanation


    Indices: 743--792  Score: 61
    Period size: 6  Copynumber: 8.7  Consensus size: 6

        733 ATCAATTCTC

                                                    *               
        743 TTTTGA TTTTGA TTTTGA -TTTGA -TTTGA TTTTTTA TTTTGA -TTTGA
          1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA -TTTTGA TTTTGA TTTTGA

                
        789 TTTT
          1 TTTT

        793 TTTTGGTTGA


Statistics
Matches: 39,  Mismatches: 2, Indels: 6
        0.83            0.04        0.13

Matches are distributed among these distances:
   5   15  0.38
   6   20  0.51
   7    4  0.10

ACGTcount: A:0.16, C:0.00, G:0.14, T:0.70


Consensus pattern (6 bp):   
TTTTGA

Found at i:766 original size:5 final size:5

Alignment explanation


    Indices: 744--816  Score: 55
    Period size: 5  Copynumber: 14.6  Consensus size: 5

        734 TCAATTCTCT

                                                                    
        744 TTTGA TTTTGA TTTTGA TTTGA TTTGA TTT-- TTT-A TTTTGA TTTGA
          1 TTTGA -TTTGA -TTTGA TTTGA TTTGA TTTGA TTTGA -TTTGA TTTGA

               **       *                     
        789 TTTTT TTTG- GTTGA CTTTGA TTTGA TTT
          1 TTTGA TTTGA TTTGA -TTTGA TTTGA TTT

        817 TTTTATTTTT


Statistics
Matches: 57,  Mismatches: 5, Indels: 11
        0.78            0.07        0.15

Matches are distributed among these distances:
   3    3  0.05
   4    3  0.05
   5   35  0.61
   6   16  0.28

ACGTcount: A:0.15, C:0.01, G:0.16, T:0.67


Consensus pattern (5 bp):   
TTTGA

Found at i:811 original size:20 final size:18

Alignment explanation


    Indices: 743--794  Score: 72
    Period size: 18  Copynumber: 2.9  Consensus size: 18

        733 ATCAATTCTC

                             * 
        743 TTTTGATTTTGA-TTTTGA
          1 TTTTGA-TTTGATTTTTTA

                              
        761 -TTTGATTTGATTTTTTA
          1 TTTTGATTTGATTTTTTA

                             
        778 TTTTGATTTGATTTTTT
          1 TTTTGATTTGATTTTTT

        795 TTGGTTGACT


Statistics
Matches: 31,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
  16    5  0.16
  17   10  0.32
  18   16  0.52

ACGTcount: A:0.15, C:0.00, G:0.13, T:0.71


Consensus pattern (18 bp):   
TTTTGATTTGATTTTTTA
Done.