Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024207.1 Corchorus olitorius cultivar O-4 contig24240, 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: 8705
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33


Found at i:4086 original size:21 final size:21

Alignment explanation


    Indices: 4037--4076  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       4027 TTTCCAACAA

                  *      *       
       4037 TCAAGAACCCTAATTTGAAAC
          1 TCAAGAGCCCTAAATTGAAAC

                               
       4058 TCAAGAGCCCTAAATTGAA
          1 TCAAGAGCCCTAAATTGAA

       4077 TTCAATGAGC


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

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23


Consensus pattern (21 bp):   
TCAAGAGCCCTAAATTGAAAC

Found at i:5980 original size:2 final size:2

Alignment explanation


    Indices: 5973--6005  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       5963 ACATTTAGTG

                                                             
       5973 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       6006 TAATAAAAAG


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:6243 original size:22 final size:22

Alignment explanation


    Indices: 6215--6432  Score: 247
    Period size: 22  Copynumber: 9.5  Consensus size: 22

       6205 TGGAAACATT

                             *    
       6215 TTTGCAGAGCATTATTTACCAC
          1 TTTGCAGAGCATTATTTTCCAC

                               *  
       6237 TTTGCAGAGCATTATTTTCTAC
          1 TTTGCAGAGCATTATTTTCCAC

                                  
       6259 TTTGCAGAGCATTATTTTCCAC
          1 TTTGCAGAGCATTATTTTCCAC

                            **    
       6281 TTTGCAGAGCATTATTCACCAC
          1 TTTGCAGAGCATTATTTTCCAC

                                  
       6303 TTTGCAGAGCATTATTTTCCAC
          1 TTTGCAGAGCATTATTTTCCAC

                                  
       6325 TTTGCAGAGCATTATTTTCCAC
          1 TTTGCAGAGCATTATTTTCCAC

               *                       
       6347 TTTACAGAGTGCATTATTTTCTTCAAC
          1 TTTGCAGA--GCATTATTTTC--C-AC

               *  ***          ***    
       6374 TTCAGCTTTGCATTATTGGAAACATC
          1 TT-TGCAGAGCATTATT--TTCCA-C

                                  
       6400 TTTGCAGAGCATTATTTTCCAC
          1 TTTGCAGAGCATTATTTTCCAC

                       
       6422 TTTGCAGAGCA
          1 TTTGCAGAGCA

       6433 CTTCTTGTTG


Statistics
Matches: 164,  Mismatches: 23, Indels: 18
        0.80            0.11        0.09

Matches are distributed among these distances:
  22  122  0.74
  23    2  0.01
  24   11  0.07
  25   11  0.07
  26   13  0.08
  27    4  0.02
  28    1  0.01

ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39


Consensus pattern (22 bp):   
TTTGCAGAGCATTATTTTCCAC

Done.