Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015097.1 Corchorus olitorius cultivar O-4 contig15130, 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: 3196
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26


Found at i:2276 original size:47 final size:47

Alignment explanation


    Indices: 2214--2451  Score: 333
    Period size: 47  Copynumber: 5.1  Consensus size: 47

       2204 AGTAAGTAGA

                   **                                      
       2214 AAACTAAACAGTAAAAGGAGAAGAGATTAGTTTAATTCTAGGTAATT
          1 AAACTAAGTAGTAAAAGGAGAAGAGATTAGTTTAATTCTAGGTAATT

                      *      *                             
       2261 AAACTAAGTAATAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATT
          1 AAACTAAGTAGTAAAAGGAGAAGAGATTAGTTTAATTCTAGGTAATT

             *              **                             
       2308 AGACTAAGTAGTAAAATAAGAAGAGATTAGTTTAATTCTAGGTAATT
          1 AAACTAAGTAGTAAAAGGAGAAGAGATTAGTTTAATTCTAGGTAATT

                                                           
       2355 AAACT-A--AGTAAAAGGAGAAGAGATTAGTTTAATTCTAGGTAATT
          1 AAACTAAGTAGTAAAAGGAGAAGAGATTAGTTTAATTCTAGGTAATT

                         *       *          *               
       2399 AAACTAAGTAGTAGAA-GA-AGGAGATTAGTTCAATTCTAGGTAAATT
          1 AAACTAAGTAGTAAAAGGAGAAGAGATTAGTTTAATTCTAGGT-AATT

            *      
       2445 GAACTAA
          1 AAACTAA

       2452 AGAAGAGGTT


Statistics
Matches: 173,  Mismatches: 14, Indels: 9
        0.88            0.07        0.05

Matches are distributed among these distances:
  44   41  0.24
  45   22  0.13
  46   13  0.08
  47   97  0.56

ACGTcount: A:0.46, C:0.05, G:0.19, T:0.29


Consensus pattern (47 bp):   
AAACTAAGTAGTAAAAGGAGAAGAGATTAGTTTAATTCTAGGTAATT

Found at i:2412 original size:94 final size:92

Alignment explanation


    Indices: 2214--2451  Score: 347
    Period size: 91  Copynumber: 2.6  Consensus size: 92

       2204 AGTAAGTAGA

                   **        *                                               
       2214 AAACTAAACAGTAAAAGGAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAATAAAAGA
          1 AAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAG--ATAAAAGA

                                         
       2279 AGAAGAGATTAGTTTAATTCTAGGTAATT
         64 AGAAGAGATTAGTTTAATTCTAGGTAATT

             *              *                                             *  
       2308 AGACTAAGTAGTAAAATAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAG-TAAAAGGAG
          1 AAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGATAAAAGAAG

                                       
       2372 AAGAGATTAGTTTAATTCTAGGTAATT
         66 AAGAGATTAGTTTAATTCTAGGTAATT

                         *                  *               *      
       2399 AAACTAAGTAGTAGAAGAAG--GAGATTAGTTCAATTCTAGGTAAATTGAACTAA
          1 AAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGT-AATTAAACTAA

       2452 AGAAGAGGTT


Statistics
Matches: 132,  Mismatches: 11, Indels: 6
        0.89            0.07        0.04

Matches are distributed among these distances:
  89   20  0.15
  90   10  0.08
  91   52  0.39
  94   50  0.38

ACGTcount: A:0.46, C:0.05, G:0.19, T:0.29


Consensus pattern (92 bp):   
AAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGATAAAAGAAG
AAGAGATTAGTTTAATTCTAGGTAATT
Done.