Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021594.1 Corchorus olitorius cultivar O-4 contig21627, 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: 4316
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.32


Found at i:2810 original size:14 final size:13

Alignment explanation


    Indices: 2791--2829  Score: 51
    Period size: 14  Copynumber: 2.9  Consensus size: 13

       2781 AAATTGTAAA

                         
       2791 ATTTAAAAAATTT
          1 ATTTAAAAAATTT

                   *    * 
       2804 CATTTAAGAAATAT
          1 -ATTTAAAAAATTT

                        
       2818 ATTTAAAAAATT
          1 ATTTAAAAAATT

       2830 CTAATATATA


Statistics
Matches: 21,  Mismatches: 4, Indels: 1
        0.81            0.15        0.04

Matches are distributed among these distances:
  13   10  0.48
  14   11  0.52

ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41


Consensus pattern (13 bp):   
ATTTAAAAAATTT

Found at i:3059 original size:122 final size:128

Alignment explanation


    Indices: 2815--3068  Score: 403
    Period size: 122  Copynumber: 2.0  Consensus size: 128

       2805 ATTTAAGAAA

                                                                             
       2815 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATAAAA
          1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGT---AATAAAA

              *                                                        *     
       2880 TAGATATAAGAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
         63 TACATATAAGAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA

             
       2945 G
        128 G

                                                 *                           
       2946 TATATTT-AAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGT-A-AAAAT-C
          1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAATAAAATAC

                                           *                               
       3007 ATA-AAG-ATATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAAACTATAAAAG
         66 ATATAAGAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG

             
       3068 T
          1 T

       3069 TTAAACAATG


Statistics
Matches: 119,  Mismatches: 4, Indels: 9
        0.90            0.03        0.07

Matches are distributed among these distances:
 122   54  0.45
 123    3  0.03
 124    3  0.03
 125    5  0.04
 126    1  0.01
 130   46  0.39
 131    7  0.06

ACGTcount: A:0.50, C:0.02, G:0.10, T:0.37


Consensus pattern (128 bp):   
TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAATAAAATAC
ATATAAGAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
Done.