Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007086.1 Corchorus olitorius cultivar O-4 contig07111, 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: 8526
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32


Found at i:7794 original size:22 final size:22

Alignment explanation


    Indices: 7766--7820  Score: 76
    Period size: 22  Copynumber: 2.5  Consensus size: 22

       7756 TAGATTATTG

                                   
       7766 AAATTTCATAGTATGGCTATC-A
          1 AAATTTCATAGTATGGCTA-CAA

                      *     *     
       7788 AAATTTCATAATATGGTTACAA
          1 AAATTTCATAGTATGGCTACAA

                       
       7810 AAATTTCATAG
          1 AAATTTCATAG

       7821 AAGGTAATCA


Statistics
Matches: 29,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  21    1  0.03
  22   28  0.97

ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36


Consensus pattern (22 bp):   
AAATTTCATAGTATGGCTACAA

Found at i:7917 original size:20 final size:20

Alignment explanation


    Indices: 7892--7929  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       7882 CTATAGGGAA

                    *           
       7892 GTTATCAACATTCCATAGAG
          1 GTTATCAAAATTCCATAGAG

                        *     
       7912 GTTATCAAAATTTCATAG
          1 GTTATCAAAATTCCATAG

       7930 TTTGATTATC


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34


Consensus pattern (20 bp):   
GTTATCAAAATTCCATAGAG

Found at i:7939 original size:22 final size:22

Alignment explanation


    Indices: 7913--7954  Score: 75
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       7903 TCCATAGAGG

                                  
       7913 TTATCAAAATTTCATAGTTTGA
          1 TTATCAAAATTTCATAGTTTGA

                 *              
       7935 TTATCCAAATTTCATAGTTT
          1 TTATCAAAATTTCATAGTTT

       7955 ACCAAATAAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.33, C:0.12, G:0.07, T:0.48


Consensus pattern (22 bp):   
TTATCAAAATTTCATAGTTTGA

Found at i:8078 original size:22 final size:22

Alignment explanation


    Indices: 8034--8207  Score: 104
    Period size: 22  Copynumber: 7.9  Consensus size: 22

       8024 TTAGTATGGA

                               *   
       8034 GGTTATCACAAATTT-ATATTGT
          1 GGTTATCA-AAATTTCATAGTGT

                            *     
       8056 GGTTATCAAAATTTCAGAGTGT
          1 GGTTATCAAAATTTCATAGTGT

               * *                *
       8078 GGTGACCAAAATTTCATAG-GAC
          1 GGTTATCAAAATTTCATAGTG-T

                    *             
       8100 GGTTATCAGAATTTCATAGTGT
          1 GGTTATCAAAATTTCATAGTGT

            *     *   ** *  *  * *
       8122 AGTTATTAAAGCTCCACAGGGA
          1 GGTTATCAAAATTTCATAGTGT

                    *      *      *
       8144 GGTTATCACAATTTCTTAAG-GA
          1 GGTTATCAAAATTTCAT-AGTGT

                         *        *
       8166 GGTTATCAAAATAAT-ATAGTGA
          1 GGTTATCAAAAT-TTCATAGTGT

             *                  
       8188 GATTATCAAAATTTCATAGT
          1 GGTTATCAAAATTTCATAGT

       8208 AAAACTATGT


Statistics
Matches: 113,  Mismatches: 32, Indels: 14
        0.71            0.20        0.09

Matches are distributed among these distances:
  21   10  0.09
  22   99  0.88
  23    4  0.04

ACGTcount: A:0.35, C:0.11, G:0.19, T:0.34


Consensus pattern (22 bp):   
GGTTATCAAAATTTCATAGTGT
Done.