Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023622.1 Corchorus olitorius cultivar O-4 contig23655, 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: 6952
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33

Warning! 2 characters in sequence are not A, C, G, or T


Found at i:663 original size:24 final size:24

Alignment explanation


    Indices: 610--678  Score: 88
    Period size: 24  Copynumber: 2.9  Consensus size: 24

        600 AAAAAAAGTT

                                      
        610 TTGTGTTTTGCGTCA-AGAAAAAAAA
          1 TTGT-TTTTGCGTCATA-AAAAAAAA

             *                      
        635 -AGTTTTTGCGTCATAAAAAAAAA
          1 TTGTTTTTGCGTCATAAAAAAAAA

                  *              
        658 TTGTTTCTGCGTCATAAAAAA
          1 TTGTTTTTGCGTCATAAAAAA

        679 TATTTTTTCT


Statistics
Matches: 39,  Mismatches: 3, Indels: 5
        0.83            0.06        0.11

Matches are distributed among these distances:
  23   18  0.46
  24   21  0.54

ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33


Consensus pattern (24 bp):   
TTGTTTTTGCGTCATAAAAAAAAA

Found at i:687 original size:23 final size:24

Alignment explanation


    Indices: 618--688  Score: 76
    Period size: 23  Copynumber: 3.0  Consensus size: 24

        608 TTTTGTGTTT

                              **     
        618 TGCGTCA-AGAAAAAAAAAGTTTT-
          1 TGCGTCATA-AAAAAAAATTTTTTC

                               *    
        641 TGCGTCATAAAAAAAAATTGTTTC
          1 TGCGTCATAAAAAAAAATTTTTTC

                           *        
        665 TGCGTCAT-AAAAAATATTTTTTC
          1 TGCGTCATAAAAAAAAATTTTTTC

             
        688 T
          1 T

        689 TTTATTTTCT


Statistics
Matches: 41,  Mismatches: 5, Indels: 4
        0.82            0.10        0.08

Matches are distributed among these distances:
  23   32  0.78
  24    9  0.22

ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35


Consensus pattern (24 bp):   
TGCGTCATAAAAAAAAATTTTTTC

Found at i:767 original size:12 final size:14

Alignment explanation


    Indices: 736--765  Score: 53
    Period size: 14  Copynumber: 2.2  Consensus size: 14

        726 CTACTAACAA

                          
        736 TTTTCTTTTGAGTT
          1 TTTTCTTTTGAGTT

                          
        750 TTTTCTTTT-AGTT
          1 TTTTCTTTTGAGTT

               
        763 TTT
          1 TTT

        766 CTAGGAAGCT


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13    7  0.44
  14    9  0.56

ACGTcount: A:0.07, C:0.07, G:0.10, T:0.77


Consensus pattern (14 bp):   
TTTTCTTTTGAGTT

Found at i:3066 original size:2 final size:2

Alignment explanation


    Indices: 3059--3090  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       3049 TGGTGTGCTG

                                                           
       3059 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       3091 GTGTAAAAGA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:5673 original size:16 final size:15

Alignment explanation


    Indices: 5637--5676  Score: 53
    Period size: 15  Copynumber: 2.6  Consensus size: 15

       5627 AGAATTTGAA

                 *         
       5637 AGAAAGCAATTAAAC
          1 AGAAAACAATTAAAC

                        *  
       5652 AGAAAACAATTATAC
          1 AGAAAACAATTAAAC

                      
       5667 TAGAAAACAA
          1 -AGAAAACAA

       5677 AGCAAAGTAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15


Consensus pattern (15 bp):   
AGAAAACAATTAAAC
Done.