Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000201.1 Corchorus olitorius cultivar O-4 contig00201, 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, 804

Length: 1340
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33


Found at i:417 original size:15 final size:15

Alignment explanation


    Indices: 399--429  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

        389 CAAGGGCTGA

                  *        
        399 AATTAATTAATTATT
          1 AATTAAATAATTATT

                           
        414 AATTAAATAATTATT
          1 AATTAAATAATTATT

             
        429 A
          1 A

        430 TTTTATTGAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (15 bp):   
AATTAAATAATTATT

Found at i:1159 original size:131 final size:133

Alignment explanation


    Indices: 980--1234  Score: 372
    Period size: 132  Copynumber: 1.9  Consensus size: 133

        970 TCATTTATTC

                 *        *                 **                               
        980 AAATTTTAATATATCTAAGTTTTTTAATTAAATTAGTAAAATGATAAAAA-TAAAT-TAGGTATA
          1 AAATTCTAATATATATAAGTTTTTTAATTAAAAAAGTAAAATGATAAAAATTAAATATAGGTATA

             *              *                         *     *                
       1043 AGGATATAAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAGTAACACTATAAAAGTATATT
         66 AAGATATAAGATTTAAGTAAAT-AAAAATAGAGTTTTTAGTTCAGTAAAACTATAAAAGTATATT

                
       1108 TAAA
        130 TAAA

                                                       *                *    
       1112 AAATTCTAATATATATAAG-TTTTTAATTAAAAAAGTAAAATGGTAAAAATTAAATATAGTTATA
          1 AAATTCTAATATATATAAGTTTTTTAATTAAAAAAGTAAAATGATAAAAATTAAATATAGGTATA

                   *                                         *         
       1176 AAGATATTAGATTTAAGTAAATAAAAATAGAGTTTTTAGTTCAGTAAAATTATAAAAGT
         66 AAGATATAAGATTTAAGTAAATAAAAATAGAGTTTTTAGTTCAGTAAAACTATAAAAGT

       1235 TTAAACAATG


Statistics
Matches: 109,  Mismatches: 12, Indels: 4
        0.87            0.10        0.03

Matches are distributed among these distances:
 131   27  0.25
 132   56  0.51
 133   26  0.24

ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37


Consensus pattern (133 bp):   
AAATTCTAATATATATAAGTTTTTTAATTAAAAAAGTAAAATGATAAAAATTAAATATAGGTATA
AAGATATAAGATTTAAGTAAATAAAAATAGAGTTTTTAGTTCAGTAAAACTATAAAAGTATATTT
AAA

Done.