Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01004299.1 Corchorus olitorius cultivar O-4 contig04312, 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: 2145
ACGTcount: A:0.26, C:0.26, G:0.32, T:0.16


Found at i:298 original size:39 final size:40

Alignment explanation


    Indices: 255--333  Score: 106
    Period size: 42  Copynumber: 1.9  Consensus size: 40

        245 CAGGCTAAAC

                             *                      
        255 AGCAGGCT-GAGCAGCAGAAAGCGGCCGAAGCAGCTGCAA
          1 AGCAGGCTAGAGCAGCAAAAAGCGGCCGAAGCAGCTGCAA

                                        *     *     
        294 AGCAGGCTCAGGAGCAGCAAAAAGCGGCTGAAGCGGCTGC
          1 AGCAGGCT-A-GAGCAGCAAAAAGCGGCCGAAGCAGCTGC

        334 CGCACAGGCG


Statistics
Matches: 34,  Mismatches: 3, Indels: 3
        0.85            0.08        0.08

Matches are distributed among these distances:
  39    8  0.24
  42   26  0.76

ACGTcount: A:0.32, C:0.25, G:0.37, T:0.06


Consensus pattern (40 bp):   
AGCAGGCTAGAGCAGCAAAAAGCGGCCGAAGCAGCTGCAA

Found at i:593 original size:24 final size:24

Alignment explanation


    Indices: 566--642  Score: 66
    Period size: 24  Copynumber: 3.2  Consensus size: 24

        556 GAAAGCGCAG

                    *  *        *   
        566 GCAGCGGCCGATGCCAAAGCTAAA
          1 GCAGCGGCAGAGGCCAAAGCCAAA

                          *         
        590 GCAGCGGCAGAGGCGAAAGCCAAA
          1 GCAGCGGCAGAGGCCAAAGCCAAA

              *         *       **   
        614 GCTGC-GCAGGAAGCCAAAGAGAAA
          1 GCAGCGGCA-GAGGCCAAAGCCAAA

                 
        638 GCAGC
          1 GCAGC

        643 AGAGGCGGCA


Statistics
Matches: 42,  Mismatches: 10, Indels: 2
        0.78            0.19        0.04

Matches are distributed among these distances:
  23    3  0.07
  24   39  0.93

ACGTcount: A:0.36, C:0.26, G:0.34, T:0.04


Consensus pattern (24 bp):   
GCAGCGGCAGAGGCCAAAGCCAAA

Found at i:663 original size:48 final size:50

Alignment explanation


    Indices: 611--709  Score: 121
    Period size: 48  Copynumber: 2.0  Consensus size: 50

        601 GGCGAAAGCC

                       *                       *              
        611 AAAGCTGCGCAGGAAGCCAAAGAGAAAGCAGCAGAGGCGGC-AAAG-GAA
          1 AAAGCTGCGCAAGAAGCCAAAGAGAAAGCAGCAGAAGCGGCTAAAGAGAA

                     *   **  *              *                 
        659 AAAGCTGCGGAAGCCGCTAAAGAGAAAGCAGCTGAAGCGGCTAAAGAGAA
          1 AAAGCTGCGCAAGAAGCCAAAGAGAAAGCAGCAGAAGCGGCTAAAGAGAA

             
        709 A
          1 A

        710 GCGGCCGCTG


Statistics
Matches: 42,  Mismatches: 7, Indels: 2
        0.82            0.14        0.04

Matches are distributed among these distances:
  48   34  0.81
  49    4  0.10
  50    4  0.10

ACGTcount: A:0.43, C:0.18, G:0.33, T:0.05


Consensus pattern (50 bp):   
AAAGCTGCGCAAGAAGCCAAAGAGAAAGCAGCAGAAGCGGCTAAAGAGAA

Found at i:686 original size:24 final size:24

Alignment explanation


    Indices: 629--711  Score: 87
    Period size: 24  Copynumber: 3.5  Consensus size: 24

        619 GCAGGAAGCC

                          *  *  *   
        629 AAAGAGAAAGCAGCAGAGGCGGC-
          1 AAAGAGAAAGCAGCGGAAGCCGCT

                  *     *            
        652 AAAGGAAAAAGCTGCGGAAGCCGCT
          1 AAA-GAGAAAGCAGCGGAAGCCGCT

                          *     *   
        677 AAAGAGAAAGCAGCTGAAGCGGCT
          1 AAAGAGAAAGCAGCGGAAGCCGCT

                       
        701 AAAGAGAAAGC
          1 AAAGAGAAAGC

        712 GGCCGCTGAG


Statistics
Matches: 49,  Mismatches: 9, Indels: 3
        0.80            0.15        0.05

Matches are distributed among these distances:
  23    3  0.06
  24   43  0.88
  25    3  0.06

ACGTcount: A:0.45, C:0.17, G:0.34, T:0.05


Consensus pattern (24 bp):   
AAAGAGAAAGCAGCGGAAGCCGCT

Found at i:752 original size:24 final size:24

Alignment explanation


    Indices: 725--809  Score: 89
    Period size: 24  Copynumber: 3.5  Consensus size: 24

        715 CGCTGAGGCG

                          *  *  *   
        725 AAAGCGAAAGCAGACGCCGCTGCC
          1 AAAGCGAAAGCAGATGCAGCCGCC

                       *           *
        749 AAAGCGAAAGCGGATGCAGCCGCT
          1 AAAGCGAAAGCAGATGCAGCCGCC

                 *              *  *
        773 AAAGCAAAAGCAGATGCAGCGGCG
          1 AAAGCGAAAGCAGATGCAGCCGCC

                 *       
        797 AAAGCCAAAGCAG
          1 AAAGCGAAAGCAG

        810 CCGCGGACGC


Statistics
Matches: 51,  Mismatches: 10, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  24   51  1.00

ACGTcount: A:0.39, C:0.26, G:0.31, T:0.05


Consensus pattern (24 bp):   
AAAGCGAAAGCAGATGCAGCCGCC

Found at i:801 original size:48 final size:48

Alignment explanation


    Indices: 670--807  Score: 116
    Period size: 48  Copynumber: 2.9  Consensus size: 48

        660 AAGCTGCGGA

                                 *  *      *    *        *   
        670 AGCCGCTAAAG-AGAAAGCAGCTGAAGCGGCTAAAGAGAAAGCGGCCGC
          1 AGCCGCTAAAGCA-AAAGCAGATGCAGCGGCCAAAGCGAAAGCGGACGC

            * **  *     *        *  *  *                 *  
        718 TGAGGCGAAAGCGAAAGCAGACGCCGCTGCCAAAGCGAAAGCGGATGC
          1 AGCCGCTAAAGCAAAAGCAGATGCAGCGGCCAAAGCGAAAGCGGACGC

                                          *     *     
        766 AGCCGCTAAAGCAAAAGCAGATGCAGCGGCGAAAGCCAAAGC
          1 AGCCGCTAAAGCAAAAGCAGATGCAGCGGCCAAAGCGAAAGC

        808 AGCCGCGGAC


Statistics
Matches: 65,  Mismatches: 24, Indels: 2
        0.71            0.26        0.02

Matches are distributed among these distances:
  48   65  1.00

ACGTcount: A:0.37, C:0.25, G:0.33, T:0.06


Consensus pattern (48 bp):   
AGCCGCTAAAGCAAAAGCAGATGCAGCGGCCAAAGCGAAAGCGGACGC
Done.