Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014408.1 Corchorus olitorius cultivar O-4 contig14441, 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: 7509
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32


Found at i:806 original size:2 final size:2

Alignment explanation


    Indices: 801--830  Score: 53
    Period size: 2  Copynumber: 15.5  Consensus size: 2

        791 TATAACTCAT

                                                          
        801 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

        831 GTGAACCAAC


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   26  0.96

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Found at i:3553 original size:20 final size:20

Alignment explanation


    Indices: 3528--3575  Score: 78
    Period size: 20  Copynumber: 2.4  Consensus size: 20

       3518 ATGGTAATCT

                        *       
       3528 GAAAATTGTATCCTCTCAAA
          1 GAAAATTGTATCATCTCAAA

                            *   
       3548 GAAAATTGTATCATCTTAAA
          1 GAAAATTGTATCATCTCAAA

                    
       3568 GAAAATTG
          1 GAAAATTG

       3576 GGAAAAGTTA


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  20   26  1.00

ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31


Consensus pattern (20 bp):   
GAAAATTGTATCATCTCAAA

Found at i:4861 original size:13 final size:13

Alignment explanation


    Indices: 4843--4869  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       4833 TAGTCAGTGG

                         
       4843 ATACTTTATTGAA
          1 ATACTTTATTGAA

                         
       4856 ATACTTTATTGAA
          1 ATACTTTATTGAA

             
       4869 A
          1 A

       4870 AATAGCACGG


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44


Consensus pattern (13 bp):   
ATACTTTATTGAA

Found at i:5678 original size:22 final size:21

Alignment explanation


    Indices: 5652--5699  Score: 69
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       5642 AGGTTACTAA

                                 
       5652 TAAAAAGGCTTATAAGCTTAC
          1 TAAAAAGGCTTATAAGCTTAC

                  *      *     * 
       5673 TAAAAATGCTTATGAGCTTCC
          1 TAAAAAGGCTTATAAGCTTAC

                  
       5694 TAAAAA
          1 TAAAAA

       5700 AGTTTTTACA


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29


Consensus pattern (21 bp):   
TAAAAAGGCTTATAAGCTTAC

Found at i:6285 original size:10 final size:10

Alignment explanation


    Indices: 6270--6302  Score: 66
    Period size: 10  Copynumber: 3.3  Consensus size: 10

       6260 CAACGGAATT

                      
       6270 AAAAAAAAAC
          1 AAAAAAAAAC

                      
       6280 AAAAAAAAAC
          1 AAAAAAAAAC

                      
       6290 AAAAAAAAAC
          1 AAAAAAAAAC

               
       6300 AAA
          1 AAA

       6303 CGTTGATATG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   23  1.00

ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00


Consensus pattern (10 bp):   
AAAAAAAAAC

Found at i:6652 original size:31 final size:31

Alignment explanation


    Indices: 6563--6661  Score: 114
    Period size: 31  Copynumber: 3.3  Consensus size: 31

       6553 TTACAATTAT

                               *           
       6563 TTTGAGCATTTTGGCAAACGTTAGGCCCTTA
          1 TTTGAGCATTTTGGCAAACATTAGGCCCTTA

                     **    *   *  *         
       6594 TTTG-GCCAAATT--AAAAGATCAGGCCCTTA
          1 TTTGAG-CATTTTGGCAAACATTAGGCCCTTA

                                           
       6623 TTTGAGCATTTTGGCAAACATTAGGCCCTTA
          1 TTTGAGCATTTTGGCAAACATTAGGCCCTTA

                    
       6654 TTTGAGCA
          1 TTTGAGCA

       6662 ATTAGAATTA


Statistics
Matches: 53,  Mismatches: 11, Indels: 8
        0.74            0.15        0.11

Matches are distributed among these distances:
  29   21  0.40
  30    2  0.04
  31   30  0.57

ACGTcount: A:0.27, C:0.19, G:0.20, T:0.33


Consensus pattern (31 bp):   
TTTGAGCATTTTGGCAAACATTAGGCCCTTA
Done.