Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011381.1 Corchorus olitorius cultivar O-4 contig11414, 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: 7353
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36


Found at i:767 original size:161 final size:161

Alignment explanation


    Indices: 494--793  Score: 566
    Period size: 161  Copynumber: 1.9  Consensus size: 161

        484 GGGAGAAAAC

                               *                                             
        494 CCAATAATTTTAATTTCCTTTTTATCTTCCATTTTAAGTTTTTAATTTTCTTATTTTTAATTTCT
          1 CCAATAATTTTAATTTCCTATTTATCTTCCATTTTAAGTTTTTAATTTTCTTATTTTTAATTTCT

                                                                             
        559 AAATTCTAACTTGAATTTATTTTGTCTTGATAGGTTTCAAGAATTTTTCTTCATTAAATTGGAAG
         66 AAATTCTAACTTGAATTTATTTTGTCTTGATAGGTTTCAAGAATTTTTCTTCATTAAATTGGAAG

                                           
        624 AAAAAGAAGCAAAAAAATTGAAATAAGAAGG
        131 AAAAAGAAGCAAAAAAATTGAAATAAGAAGG

                                                                             
        655 CCAATAATTTTAATTTCCTATTTATCTTCCATTTTAAGTTTTTAATTTTCTTATTTTTAATTTCT
          1 CCAATAATTTTAATTTCCTATTTATCTTCCATTTTAAGTTTTTAATTTTCTTATTTTTAATTTCT

              *                                                              
        720 AACTTCTAACTTGAATTTATTTTGTCTTGATAGGTTTCATA-AATTTTTCTTCATTAAATTGGAA
         66 AAATTCTAACTTGAATTTATTTTGTCTTGATAGGTTTCA-AGAATTTTTCTTCATTAAATTGGAA

                      
        784 GAAAAAGAAG
        130 GAAAAAGAAG

        794 GCCAAAAATG


Statistics
Matches: 136,  Mismatches: 2, Indels: 2
        0.97            0.01        0.01

Matches are distributed among these distances:
 161  135  0.99
 162    1  0.01

ACGTcount: A:0.33, C:0.11, G:0.09, T:0.48


Consensus pattern (161 bp):   
CCAATAATTTTAATTTCCTATTTATCTTCCATTTTAAGTTTTTAATTTTCTTATTTTTAATTTCT
AAATTCTAACTTGAATTTATTTTGTCTTGATAGGTTTCAAGAATTTTTCTTCATTAAATTGGAAG
AAAAAGAAGCAAAAAAATTGAAATAAGAAGG

Found at i:7123 original size:37 final size:37

Alignment explanation


    Indices: 7073--7156  Score: 150
    Period size: 37  Copynumber: 2.3  Consensus size: 37

       7063 AACTCAATCC

                             *            *      
       7073 TCAATTCTTGCTTCTTGTAATAATTCTTCAGTGCTCT
          1 TCAATTCTTGCTTCTTGAAATAATTCTTCAATGCTCT

                                                 
       7110 TCAATTCTTGCTTCTTGAAATAATTCTTCAATGCTCT
          1 TCAATTCTTGCTTCTTGAAATAATTCTTCAATGCTCT

                      
       7147 TCAATTCTTG
          1 TCAATTCTTG

       7157 AAATTGTCTT


Statistics
Matches: 45,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  37   45  1.00

ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48


Consensus pattern (37 bp):   
TCAATTCTTGCTTCTTGAAATAATTCTTCAATGCTCT
Done.