Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016149.1 Corchorus olitorius cultivar O-4 contig16182, 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: 3216
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31


Found at i:260 original size:25 final size:25

Alignment explanation


    Indices: 218--265  Score: 69
    Period size: 25  Copynumber: 1.9  Consensus size: 25

        208 ATGCAATATT

                      *  *           
        218 AAATTAGATTTGAGCTACATGAATG
          1 AAATTAGATTGGAACTACATGAATG

                   *               
        243 AAATTAGCTTGGAACTACATGAA
          1 AAATTAGATTGGAACTACATGAA

        266 CGCAAAATAC


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  25   20  1.00

ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29


Consensus pattern (25 bp):   
AAATTAGATTGGAACTACATGAATG

Found at i:468 original size:25 final size:27

Alignment explanation


    Indices: 402--499  Score: 85
    Period size: 27  Copynumber: 3.7  Consensus size: 27

        392 AAGTGGACTC

                *      *            *   
        402 AAAATGACCAACATGCCCCTGAATATG-
          1 AAAAAGACCAAAATG-CCCTGAATGTGA

            *   *                *     
        429 CAAATGACCAAAATGCCCT-AGTGT-A
          1 AAAAAGACCAAAATGCCCTGAATGTGA

                      *                 
        454 AAAAAGACCATAATGCCACTGAATGTGA
          1 AAAAAGACCAAAATGCC-CTGAATGTGA

                *             
        482 AAAATGACCAAAATGCCC
          1 AAAAAGACCAAAATGCCC

        500 CTTGATTTCT


Statistics
Matches: 57,  Mismatches: 10, Indels: 8
        0.76            0.13        0.11

Matches are distributed among these distances:
  25   17  0.30
  26    6  0.11
  27   18  0.32
  28   16  0.28

ACGTcount: A:0.44, C:0.23, G:0.15, T:0.17


Consensus pattern (27 bp):   
AAAAAGACCAAAATGCCCTGAATGTGA

Found at i:868 original size:50 final size:50

Alignment explanation


    Indices: 804--1028  Score: 396
    Period size: 50  Copynumber: 4.5  Consensus size: 50

        794 GAGAGATCCT

                                        *                     
        804 CGAGTTTGGCTTGTGGAAAAGCCTATGTCGATAATTGACTCGTATGGAAA
          1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA

                *                  *                          
        854 CGAGCTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAA
          1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA

                                                 **           
        904 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGTTTCGTATGGAAA
          1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA

                  *                                           
        954 CGAGTTGGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
          1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA

                                     
       1004 CGAGTTTGGCTTGTGGAAAAGCCTA
          1 CGAGTTTGGCTTGTGGAAAAGCCTA

       1029 AAGCATTCGG


Statistics
Matches: 164,  Mismatches: 11, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  50  164  1.00

ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31


Consensus pattern (50 bp):   
CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA

Found at i:1758 original size:50 final size:50

Alignment explanation


    Indices: 1699--1832  Score: 198
    Period size: 50  Copynumber: 2.7  Consensus size: 50

       1689 TTGAAAAAAT

                                         *                *   
       1699 GAATTTTGATCTTGGACTCACAAATGGAATGCAATCCTACTTTGAAGAGC
          1 GAATTTTGATCTTGGACTCACAAATGGAAAGCAATCCTACTTTGAAAAGC

                              *                **             
       1749 GAATTTTGATCTTGGACTTACAAATGGAAAGCAATTTTACTTTGAAAAGC
          1 GAATTTTGATCTTGGACTCACAAATGGAAAGCAATCCTACTTTGAAAAGC

                          *     *              
       1799 GAATTTTGATCTTGAACTCATAAA-GGAAAGCAAT
          1 GAATTTTGATCTTGGACTCACAAATGGAAAGCAAT

       1833 TTTATTGTAA


Statistics
Matches: 76,  Mismatches: 8, Indels: 1
        0.89            0.09        0.01

Matches are distributed among these distances:
  49   10  0.13
  50   66  0.87

ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31


Consensus pattern (50 bp):   
GAATTTTGATCTTGGACTCACAAATGGAAAGCAATCCTACTTTGAAAAGC
Done.