Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024188.1 Corchorus olitorius cultivar O-4 contig24221, 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: 9549
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:5416 original size:21 final size:21

Alignment explanation


    Indices: 5392--5434  Score: 77
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       5382 AATGCAAGTA

                           *     
       5392 ATGAAATGAAACAAGTAACTC
          1 ATGAAATGAAACAAGCAACTC

                                 
       5413 ATGAAATGAAACAAGCAACTC
          1 ATGAAATGAAACAAGCAACTC

             
       5434 A
          1 A

       5435 AACATATAAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.53, C:0.16, G:0.14, T:0.16


Consensus pattern (21 bp):   
ATGAAATGAAACAAGCAACTC

Found at i:5830 original size:36 final size:35

Alignment explanation


    Indices: 5790--5883  Score: 100
    Period size: 36  Copynumber: 2.6  Consensus size: 35

       5780 AAACGGAACT

                     *   *                      
       5790 CTAAACATGCTTCCAAACGAAATTCTAAATAAAGAC
          1 CTAAACATGATTCTAAACGAAA-TCTAAATAAAGAC

                            *               *    
       5826 CTAAACAAAT-ATTCTGAACGAAATCTAAATAGAGAC
          1 CTAAAC--ATGATTCTAAACGAAATCTAAATAAAGAC

                   * *            
       5862 CTAAACAGGTTTCTAAACGAAA
          1 CTAAACATGATTCTAAACGAAA

       5884 CATTGAACAG


Statistics
Matches: 48,  Mismatches: 7, Indels: 7
        0.77            0.11        0.11

Matches are distributed among these distances:
  34    1  0.02
  35   11  0.23
  36   24  0.50
  37   10  0.21
  38    2  0.04

ACGTcount: A:0.48, C:0.19, G:0.11, T:0.22


Consensus pattern (35 bp):   
CTAAACATGATTCTAAACGAAATCTAAATAAAGAC
Done.