Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024315.1 Corchorus olitorius cultivar O-4 contig24348, 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: 8878
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27


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

Alignment explanation


    Indices: 1--178  Score: 196
    Period size: 47  Copynumber: 3.8  Consensus size: 47

                                      *               *    
          1 GTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGACAACA
          1 GTTTAATTCTAGGTAATTAAACTAAAAAGTAAAAGAAGAAGAAAACA

                                        *   *            * 
         48 GTTTAATTCTAGGTAATTAAACTAAAAATTAAGAGAAGAAGAAAAGA
          1 GTTTAATTCTAGGTAATTAAACTAAAAAGTAAAAGAAGAAGAAAACA

                     **               *  *  *              
         95 GTTTAATTCCGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACA
          1 GTTTAATTCTAGGTAATTAAACTAAAAAGTAAAAGAAGAAGAAAACA

            *   *             *  *    **          
        142 ATTTGATTCT-GGATAATCAAGCTAAGCAGTAAAAGAA
          1 GTTTAATTCTAGG-TAATTAAACTAAAAAGTAAAAGAA

        179 AGAGTAATCA


Statistics
Matches: 110,  Mismatches: 20, Indels: 2
        0.83            0.15        0.02

Matches are distributed among these distances:
  46    2  0.02
  47  108  0.98

ACGTcount: A:0.49, C:0.08, G:0.18, T:0.24


Consensus pattern (47 bp):   
GTTTAATTCTAGGTAATTAAACTAAAAAGTAAAAGAAGAAGAAAACA

Found at i:197 original size:22 final size:22

Alignment explanation


    Indices: 169--258  Score: 126
    Period size: 22  Copynumber: 4.1  Consensus size: 22

        159 CAAGCTAAGC

                                  
        169 AGTAAAAGAAAGAGTAATCAGA
          1 AGTAAAAGAAAGAGTAATCAGA

                              *   
        191 AGTAAAAGAAAGAGTAATAAGA
          1 AGTAAAAGAAAGAGTAATCAGA

              * *               * 
        213 AGCAGAAGAAAGAGTAATCATA
          1 AGTAAAAGAAAGAGTAATCAGA

               *              *   
        235 AGTGAAAGAAAGAGTAATTAGA
          1 AGTAAAAGAAAGAGTAATCAGA

              
        257 AG
          1 AG

        259 ATTAGAGTAA


Statistics
Matches: 58,  Mismatches: 10, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  22   58  1.00

ACGTcount: A:0.58, C:0.03, G:0.24, T:0.14


Consensus pattern (22 bp):   
AGTAAAAGAAAGAGTAATCAGA

Found at i:231 original size:44 final size:44

Alignment explanation


    Indices: 174--258  Score: 143
    Period size: 44  Copynumber: 1.9  Consensus size: 44

        164 TAAGCAGTAA

                                                        
        174 AAGAAAGAGTAATCAGAAGTAAAAGAAAGAGTAATAAGAAGCAG
          1 AAGAAAGAGTAATCAGAAGTAAAAGAAAGAGTAATAAGAAGCAG

                           *    *              *     
        218 AAGAAAGAGTAATCATAAGTGAAAGAAAGAGTAATTAGAAG
          1 AAGAAAGAGTAATCAGAAGTAAAAGAAAGAGTAATAAGAAG

        259 ATTAGAGTAA


Statistics
Matches: 38,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  44   38  1.00

ACGTcount: A:0.58, C:0.04, G:0.25, T:0.14


Consensus pattern (44 bp):   
AAGAAAGAGTAATCAGAAGTAAAAGAAAGAGTAATAAGAAGCAG

Found at i:298 original size:47 final size:44

Alignment explanation


    Indices: 234--332  Score: 110
    Period size: 47  Copynumber: 2.2  Consensus size: 44

        224 GAGTAATCAT

                *              *         *                
        234 AAGTGAAAGAAAGAGTAATTAGAAGATTAGAG-TAATTAAGCTAAA
          1 AAGTAAAAGAAAGAGTAATCAGAAG--TAAAGTTAATTAAGCTAAA

                       *            *                     
        279 AGATGTAAAAGCAAGAGTAATCAGTAGTAAAGTTAATTAAGCTAAA
          1 A-A-GTAAAAGAAAGAGTAATCAGAAGTAAAGTTAATTAAGCTAAA

                    
        325 AAGTAAAA
          1 AAGTAAAA

        333 AGTAATAATA


Statistics
Matches: 46,  Mismatches: 5, Indels: 7
        0.79            0.09        0.12

Matches are distributed among these distances:
  44    6  0.13
  45    6  0.13
  46   15  0.33
  47   19  0.41

ACGTcount: A:0.54, C:0.04, G:0.20, T:0.22


Consensus pattern (44 bp):   
AAGTAAAAGAAAGAGTAATCAGAAGTAAAGTTAATTAAGCTAAA

Found at i:5281 original size:38 final size:38

Alignment explanation


    Indices: 5219--5337  Score: 125
    Period size: 38  Copynumber: 3.1  Consensus size: 38

       5209 GCCGACCTCA

                 *    *                           
       5219 AAACAAGTCACCTTTCAGCAGTTATCAAGATCGACTGG
          1 AAACAGGTCATCTTTCAGCAGTTATCAAGATCGACTGG

              *               *          *    *   
       5257 AAGCAGGTCATCTTTCAGTAGTTATCAAGTTCGATTGG
          1 AAACAGGTCATCTTTCAGCAGTTATCAAGATCGACTGG

                *            *               *      
       5295 AAACGGGTCATCTTTCAACA-TATATCAA-AGTTGACTGG
          1 AAACAGGTCATCTTTCAGCAGT-TATCAAGA-TCGACTGG

                 
       5333 AAACA
          1 AAACA

       5338 TGAAGGAAAC


Statistics
Matches: 65,  Mismatches: 14, Indels: 4
        0.78            0.17        0.05

Matches are distributed among these distances:
  37    1  0.02
  38   64  0.98

ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28


Consensus pattern (38 bp):   
AAACAGGTCATCTTTCAGCAGTTATCAAGATCGACTGG
Done.