Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021013.1 Corchorus olitorius cultivar O-4 contig21046, 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: 13924
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32


Found at i:682 original size:27 final size:27

Alignment explanation


    Indices: 652--733  Score: 96
    Period size: 27  Copynumber: 3.0  Consensus size: 27

        642 AACCCAGGGA

                                       
        652 ACTAACTTTGAATGGGAAACTGACTTG
          1 ACTAACTTTGAATGGGAAACTGACTTG

                *                       
        679 ACTAGCTTTGAAT-GGAGAACTGACTTG
          1 ACTAACTTTGAATGGGA-AACTGACTTG

               *           *  *         
        706 ACTGAC-TTGTAATGAGAGACTGACTTG
          1 ACTAACTTTG-AATGGGAAACTGACTTG

             
        733 A
          1 A

        734 ATGATCCTTA


Statistics
Matches: 47,  Mismatches: 5, Indels: 6
        0.81            0.09        0.10

Matches are distributed among these distances:
  26    6  0.13
  27   39  0.83
  28    2  0.04

ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29


Consensus pattern (27 bp):   
ACTAACTTTGAATGGGAAACTGACTTG

Found at i:13737 original size:109 final size:109

Alignment explanation


    Indices: 13546--13754  Score: 382
    Period size: 109  Copynumber: 1.9  Consensus size: 109

      13536 AAGAGGGAAT

                            *                                                
      13546 TTAATAAACTACTCCGTTGTTTTTGGGAAGTGGAGCACACGGGGTTCGGTATCACAAATATCAAC
          1 TTAATAAACTACTCCGCTGTTTTTGGGAAGTGGAGCACACGGGGTTCGGTATCACAAATATCAAC

                 *                                      
      13611 CTTCGCGTCAGTCATGAACCAAAATTATGAGTATGTAAAGCATC
         66 CTTCGAGTCAGTCATGAACCAAAATTATGAGTATGTAAAGCATC

                  * *                                                        
      13655 TTAATATATTACTCCGCTGTTTTTGGGAAGTGGAGCACACGGGGTTCGGTATCACAAATATCAAC
          1 TTAATAAACTACTCCGCTGTTTTTGGGAAGTGGAGCACACGGGGTTCGGTATCACAAATATCAAC

                                               
      13720 CTTCGAGTCAGTCATGAACCAAAATTATGAGTATG
         66 CTTCGAGTCAGTCATGAACCAAAATTATGAGTATG

      13755 CAAGGCACCT


Statistics
Matches: 96,  Mismatches: 4, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
 109   96  1.00

ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29


Consensus pattern (109 bp):   
TTAATAAACTACTCCGCTGTTTTTGGGAAGTGGAGCACACGGGGTTCGGTATCACAAATATCAAC
CTTCGAGTCAGTCATGAACCAAAATTATGAGTATGTAAAGCATC

Done.