Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015481.1 Corchorus olitorius cultivar O-4 contig15514, 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: 8215
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24


Found at i:70 original size:47 final size:47

Alignment explanation


    Indices: 1--274  Score: 404
    Period size: 47  Copynumber: 5.7  Consensus size: 47

                  *   *               *            *       
          1 AGTTTAGTTCTAGGTAATTAAACTAAATAGTAAAAGAAGGAGAAATT
          1 AGTTTAATTCCAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAAATT

                     **                      *           *    
         48 AGTTTAATTATAGGTAATTAAACTAAATAGTAGAAAAAGAAGAAGTAATT
          1 AGTTTAATTCCAGGTAATTAAACT--A-AGTAGTAAAAGAAGAAGAAATT

                                                           
         98 AGTTTAATTCCAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAAATT
          1 AGTTTAATTCCAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAAATT

                      *                            *         
        145 AGTTTAATTCTAGGTAATTAAACTAAGTAGTAGAAAGAAAAAGAAATTT
          1 AGTTTAATTCCAGGTAATTAAACTAAGTAGTA-AAAGAAGAAGAAA-TT

                                                           
        194 AGTTTAATTCCAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAAATT
          1 AGTTTAATTCCAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAAATT

                                       *      
        241 AGTTTAATTCCAGGTAATTAAACTAAGCAGTAAA
          1 AGTTTAATTCCAGGTAATTAAACTAAGTAGTAAA

        275 GAGTAGTCAA


Statistics
Matches: 207,  Mismatches: 15, Indels: 10
        0.89            0.06        0.04

Matches are distributed among these distances:
  47  108  0.52
  48   25  0.12
  49   34  0.16
  50   40  0.19

ACGTcount: A:0.49, C:0.05, G:0.17, T:0.29


Consensus pattern (47 bp):   
AGTTTAATTCCAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAAATT

Found at i:167 original size:97 final size:96

Alignment explanation


    Indices: 1--266  Score: 426
    Period size: 97  Copynumber: 2.8  Consensus size: 96

                  *   *               *            *                *        
          1 AGTTTAGTTCTAGGTAATTAAACTAAATAGTAAAAGAAGGAGAAATTAGTTTAATTATAGGTAAT
          1 AGTTTAATTCCAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAAT

                                 *           
         66 TAAACTAAATAGTAGAAA-AAGAAGAAGTAATT
         66 TAAACTAAATAGTAGAAAGAAAAAGAA--AATT

                                                                             
         98 AGTTTAATTCCAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAAT
          1 AGTTTAATTCCAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAAT

                    *                   *  
        163 TAAACTAAGTAGTAGAAAGAAAAAGAAATTT
         66 TAAACTAAATAGTAGAAAGAAAAAGAAAATT

                                                                     *       
        194 AGTTTAATTCCAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAAATTAGTTTAATTCCAGGTAAT
          1 AGTTTAATTCCAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAAT

                    
        259 TAAACTAA
         66 TAAACTAA

        267 GCAGTAAAGA


Statistics
Matches: 159,  Mismatches: 9, Indels: 3
        0.93            0.05        0.02

Matches are distributed among these distances:
  96   75  0.47
  97   77  0.48
  98    7  0.04

ACGTcount: A:0.48, C:0.05, G:0.17, T:0.30


Consensus pattern (96 bp):   
AGTTTAATTCCAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAAT
TAAACTAAATAGTAGAAAGAAAAAGAAAATT

Found at i:233 original size:96 final size:96

Alignment explanation


    Indices: 1--272  Score: 429
    Period size: 96  Copynumber: 2.8  Consensus size: 96

                  *   *               *            *                *        
          1 AGTTTAGTTCTAGGTAATTAAACTAAATAGTAAAAGAAGGAGAAATTAGTTTAATTATAGGTAAT
          1 AGTTTAATTCCAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAAT

                    *           *           
         66 TAAACTAAATAGTAGAAAAAGAAGAAGTAATT
         66 TAAACTAAGTAGTAGAAAAAAAAGAAG-AATT

                                                                             
         98 AGTTTAATTCCAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAAT
          1 AGTTTAATTCCAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAAT

                                         *  
        163 TAAACTAAGTAGTAGAAAGAAAAAGAA-ATTT
         66 TAAACTAAGTAGTAGAAA-AAAAAGAAGAATT

                                                                     *       
        194 AGTTTAATTCCAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAAATTAGTTTAATTCCAGGTAAT
          1 AGTTTAATTCCAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAAT

                     *    
        259 TAAACTAAGCAGTA
         66 TAAACTAAGTAGTA

        273 AAGAGTAGTC


Statistics
Matches: 164,  Mismatches: 10, Indels: 3
        0.93            0.06        0.02

Matches are distributed among these distances:
  96   80  0.49
  97   77  0.47
  98    7  0.04

ACGTcount: A:0.48, C:0.06, G:0.17, T:0.29


Consensus pattern (96 bp):   
AGTTTAATTCCAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAAT
TAAACTAAGTAGTAGAAAAAAAAGAAGAATT
Done.