Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021823.1 Corchorus olitorius cultivar O-4 contig21856, 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: 8298
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31


Found at i:51 original size:35 final size:35

Alignment explanation


    Indices: 4--173  Score: 161
    Period size: 35  Copynumber: 5.0  Consensus size: 35

          1 AAT

                                               
          4 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAAC
          1 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAAC

                   *           * *             
         39 TGAAGAACGACCGCCCTGGATTAACTGAAATAAAC
          1 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAAC

              *                              * 
         74 TGGAGAAAGACCGCCCTGGGTCAA--G---TAAGC
          1 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAAC

                       *        *  * * *    *  *
        104 TGAAGAAAAGATCGCCCTGGATCCATTAAAATGAAT
          1 TGAAG-AAAGACCGCCCTGGGTCAACTGAAATAAAC

                   *             *  *         
        140 TGAAGAAGGACCGCCCTGGGTAAAATGAAATAAA
          1 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAA

        174 GATCGCCCTG


Statistics
Matches: 105,  Mismatches: 24, Indels: 12
        0.74            0.17        0.09

Matches are distributed among these distances:
  30    8  0.08
  31   16  0.15
  33    1  0.01
  35   73  0.70
  36    7  0.07

ACGTcount: A:0.39, C:0.20, G:0.24, T:0.16


Consensus pattern (35 bp):   
TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAAC

Found at i:159 original size:66 final size:65

Alignment explanation


    Indices: 1--294  Score: 181
    Period size: 66  Copynumber: 4.4  Consensus size: 65

                                                          *  *          *    
          1 AATTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAG-AACGACCGCCCTGGATTAACT
          1 AATTGAAGAAAGACCGCCCTGGGTCAA--G---T-AACTGAAGAAAAGATCGCCCTGGATCAACT

            *     
         65 GAAATA
         60 AAAATA

              *  *                                                  * *      
         71 AACTGGAGAAAGACCGCCCTGGGTCAAGTAAGCTGAAGAAAAGATCGCCCTGGATCCATTAAAAT
          1 AATTGAAGAAAGACCGCCCTGGGTCAAGTAA-CTGAAGAAAAGATCGCCCTGGATCAACTAAAAT

            *
        136 G
         65 A

                      *                                                 *  * 
        137 AATTGAAGAAGGACCGCCCTGGGT-AA--AA-TGAA-ATAAAGATCGCCCTGGATCAACTGAAGT
          1 AATTGAAGAAAGACCGCCCTGGGTCAAGTAACTGAAGA-AAAGATCGCCCTGGATCAACTAAAAT

             
        197 -
         65 A

                  *      * *             *  *                    *        *  
        197 AATTGAGGAAAGATCACCCTGGATGACTTAAAATGAACTGAAGAAAA-ATCGCTCTGGATCAGCT
          1 AATTGAAGAAAGACCGCCCTGG--G---TCAAGT-AACTGAAGAAAAGATCGCCCTGGATCAACT

            *     
        261 GAAATA
         60 AAAATA

               *          *    *   *    
        267 AATGGAAGGAAAGATCGCCTTGGATCAA
          1 AATTGAA-GAAAGACCGCCCTGGGTCAA

        295 CTAAAATAAA


Statistics
Matches: 179,  Mismatches: 29, Indels: 36
        0.73            0.12        0.15

Matches are distributed among these distances:
  60   19  0.11
  61   26  0.15
  62    1  0.01
  63    2  0.01
  64    2  0.01
  65   10  0.06
  66   46  0.26
  68    1  0.01
  69   21  0.12
  70   37  0.21
  71   14  0.08

ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18


Consensus pattern (65 bp):   
AATTGAAGAAAGACCGCCCTGGGTCAAGTAACTGAAGAAAAGATCGCCCTGGATCAACTAAAATA

Found at i:291 original size:36 final size:35

Alignment explanation


    Indices: 162--305  Score: 123
    Period size: 35  Copynumber: 4.1  Consensus size: 35

        152 GCCCTGGGTA

                   **                     *  * 
        162 AAATGAAATAAAGATCGCCCTGGATCAACTGAAGT
          1 AAATGAAGGAAAGATCGCCCTGGATCAACTAAAAT

              *             *         *         
        197 AATTG-AGGAAAGATCACCCTGGAT-GACTTAAAAT
          1 AAATGAAGGAAAGATCGCCCTGGATCAAC-TAAAAT

               *         *     *        *  *    
        231 GAACTGAA-GAAAAATCGCTCTGGATCAGCTGAAAT
          1 -AAATGAAGGAAAGATCGCCCTGGATCAACTAAAAT

                                *               
        266 AAATGGAAGGAAAGATCGCCTTGGATCAACTAAAAT
          1 AAAT-GAAGGAAAGATCGCCCTGGATCAACTAAAAT

                
        302 AAAT
          1 AAAT

        306 CTTCAGCAAT


Statistics
Matches: 83,  Mismatches: 20, Indels: 11
        0.73            0.18        0.10

Matches are distributed among these distances:
  33    2  0.02
  34   23  0.28
  35   30  0.36
  36   28  0.34

ACGTcount: A:0.43, C:0.15, G:0.21, T:0.21


Consensus pattern (35 bp):   
AAATGAAGGAAAGATCGCCCTGGATCAACTAAAAT
Done.