Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023112.1 Corchorus olitorius cultivar O-4 contig23145, 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: 6504
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:119 original size:29 final size:28

Alignment explanation


    Indices: 55--111  Score: 80
    Period size: 28  Copynumber: 2.0  Consensus size: 28

         45 AACAAAGGGG

                         *     *         
         55 ACCTTTGTTCTTTGATTCATATATCCCTT
          1 ACCTTTGTTC-TTCATTCACATATCCCTT

                                        
         84 ACCTTTGTTCTTCATTCACATA-CCCTT
          1 ACCTTTGTTCTTCATTCACATATCCCTT

             
        111 A
          1 A

        112 TTCCTTTGAA


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

Matches are distributed among these distances:
  27    6  0.23
  28   10  0.38
  29   10  0.38

ACGTcount: A:0.19, C:0.28, G:0.05, T:0.47


Consensus pattern (28 bp):   
ACCTTTGTTCTTCATTCACATATCCCTT

Found at i:5201 original size:37 final size:37

Alignment explanation


    Indices: 5157--5238  Score: 155
    Period size: 37  Copynumber: 2.2  Consensus size: 37

       5147 GACAATTTCG

                                                 
       5157 AGAATTGAAGAGCATTGAAGAATTATTTCAAGAAGCA
          1 AGAATTGAAGAGCATTGAAGAATTATTTCAAGAAGCA

                                                 
       5194 AGAATTGAAGAGCATTGAAGAATTATTTCAAGAAGCA
          1 AGAATTGAAGAGCATTGAAGAATTATTTCAAGAAGCA

             *      
       5231 ATAATTGA
          1 AGAATTGA

       5239 GGATTGAGCT


Statistics
Matches: 44,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  37   44  1.00

ACGTcount: A:0.46, C:0.07, G:0.21, T:0.26


Consensus pattern (37 bp):   
AGAATTGAAGAGCATTGAAGAATTATTTCAAGAAGCA

Found at i:5826 original size:10 final size:11

Alignment explanation


    Indices: 5801--5826  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

       5791 TTGTCTCTTA

                       
       5801 TTTTTCTCTAG
          1 TTTTTCTCTAG

                       
       5812 TTTTTCTCTAG
          1 TTTTTCTCTAG

                
       5823 TTTT
          1 TTTT

       5827 AGAAGAGGGT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69


Consensus pattern (11 bp):   
TTTTTCTCTAG
Done.