Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024718.1 Corchorus olitorius cultivar O-4 contig24751, 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: 10917
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:6706 original size:48 final size:48

Alignment explanation


    Indices: 6570--6709  Score: 133
    Period size: 48  Copynumber: 2.9  Consensus size: 48

       6560 AAAGGCACCA

                                      *      *            *   
       6570 GGTTATGAAGCACAGAGGGGGACC-ACTTATGAAGTGTC-AAGAGGGCCT
          1 GGTTATGAAGCACAGA-GGGGACCTAGTTATGATG-GTCAAAGAGGACCT

                     *    *     *   *    *                *  
       6618 GGTTATGAATCACAAAGGGGTCCTGGTTACGAT-GTGCAAAGAGGATCT
          1 GGTTATGAAGCACAGAGGGGACCTAGTTATGATGGT-CAAAGAGGACCT

                       *     *                          
       6666 GGTTATGAAGCGCAGAGAGGACCTAGTTATGATGGTCAAAGAGG
          1 GGTTATGAAGCACAGAGGGGACCTAGTTATGATGGTCAAAGAGG

       6710 CCTTAACTAT


Statistics
Matches: 72,  Mismatches: 16, Indels: 8
        0.75            0.17        0.08

Matches are distributed among these distances:
  46    2  0.03
  47    7  0.10
  48   61  0.85
  49    2  0.03

ACGTcount: A:0.30, C:0.14, G:0.34, T:0.21


Consensus pattern (48 bp):   
GGTTATGAAGCACAGAGGGGACCTAGTTATGATGGTCAAAGAGGACCT

Found at i:6709 original size:24 final size:24

Alignment explanation


    Indices: 6608--6697  Score: 63
    Period size: 24  Copynumber: 3.8  Consensus size: 24

       6598 ATGAAGTGTC

                  *   *        * *  
       6608 AAGAGGGCCTGGTTATGAATCACA
          1 AAGAGGACCTAGTTATGAAGCGCA

               *  *   *    *  * *   
       6632 AAGGGGTCCTGGTTACGATGTGCA
          1 AAGAGGACCTAGTTATGAAGCGCA

                   *  *             
       6656 AAGAGGATCTGGTTATGAAGCGCA
          1 AAGAGGACCTAGTTATGAAGCGCA

            *                 
       6680 GAGAGGACCTAGTTATGA
          1 AAGAGGACCTAGTTATGA

       6698 TGGTCAAAGA


Statistics
Matches: 50,  Mismatches: 16, Indels: 0
        0.76            0.24        0.00

Matches are distributed among these distances:
  24   50  1.00

ACGTcount: A:0.30, C:0.14, G:0.33, T:0.22


Consensus pattern (24 bp):   
AAGAGGACCTAGTTATGAAGCGCA

Found at i:10462 original size:16 final size:16

Alignment explanation


    Indices: 10443--10473  Score: 62
    Period size: 16  Copynumber: 1.9  Consensus size: 16

      10433 ATTAACATGC

                            
      10443 AAAGTCTAAAACAAAG
          1 AAAGTCTAAAACAAAG

                           
      10459 AAAGTCTAAAACAAA
          1 AAAGTCTAAAACAAA

      10474 CACATCTAAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.65, C:0.13, G:0.10, T:0.13


Consensus pattern (16 bp):   
AAAGTCTAAAACAAAG
Done.