Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009943.1 Corchorus olitorius cultivar O-4 contig09975, 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: 1862
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:814 original size:18 final size:17

Alignment explanation


    Indices: 788--873  Score: 82
    Period size: 18  Copynumber: 4.8  Consensus size: 17

        778 GTGTGGCAAC

                             
        788 TTGGTGCGGTGCGACCA
          1 TTGGTGCGGTGCGACCA

                        *     
        805 TTGAGTGCGGTGTGACCA
          1 TTG-GTGCGGTGCGACCA

                   *          
        823 CTTGGTGTGGTGCGACCA
          1 -TTGGTGCGGTGCGACCA

                   *     * ** 
        841 TTTGGTGTGGTGCAAATA
          1 -TTGGTGCGGTGCGACCA

                           
        859 CTTGGTGCGGTGCGA
          1 -TTGGTGCGGTGCGA

        874 TTTGTTGTTG


Statistics
Matches: 57,  Mismatches: 10, Indels: 3
        0.81            0.14        0.04

Matches are distributed among these distances:
  17    3  0.05
  18   51  0.89
  19    3  0.05

ACGTcount: A:0.14, C:0.17, G:0.40, T:0.29


Consensus pattern (17 bp):   
TTGGTGCGGTGCGACCA

Found at i:826 original size:36 final size:36

Alignment explanation


    Indices: 786--873  Score: 106
    Period size: 36  Copynumber: 2.4  Consensus size: 36

        776 AAGTGTGGCA

                                            ** * 
        786 ACTTGGTGCGGTGCGACCA-TTGAGTGCGGTGTGACC
          1 ACTTGGTGCGGTGCGACCATTTG-GTGCGGTGCAAAC

                    *                 *        *
        822 ACTTGGTGTGGTGCGACCATTTGGTGTGGTGCAAAT
          1 ACTTGGTGCGGTGCGACCATTTGGTGCGGTGCAAAC

                            
        858 ACTTGGTGCGGTGCGA
          1 ACTTGGTGCGGTGCGA

        874 TTTGTTGTTG


Statistics
Matches: 44,  Mismatches: 7, Indels: 2
        0.83            0.13        0.04

Matches are distributed among these distances:
  36   41  0.93
  37    3  0.07

ACGTcount: A:0.15, C:0.18, G:0.39, T:0.28


Consensus pattern (36 bp):   
ACTTGGTGCGGTGCGACCATTTGGTGCGGTGCAAAC

Found at i:1469 original size:48 final size:50

Alignment explanation


    Indices: 1393--1520  Score: 138
    Period size: 49  Copynumber: 2.6  Consensus size: 50

       1383 GAGCGTGCCA

                         *         *            *  *   *      
       1393 ATCAATTTTGTCAAAAAAATTGATAAAAAGTACG-ATG-GAAATTAAAAG
          1 ATCAATTTTGTCATAAAAATTGAGAAAAAGTACGCAAGTAAAAATAAAAG

                        *                   *                 
       1441 ATCAATTTTGTCTTAAAAATTGAGAAAAAG-ATGCAAGTAAAAATAAAAG
          1 ATCAATTTTGTCATAAAAATTGAGAAAAAGTACGCAAGTAAAAATAAAAG

            * *                             
       1490 TTTAATTTTGT-AGTAAAAATTGAGAAAAAGT
          1 ATCAATTTTGTCA-TAAAAATTGAGAAAAAGT

       1521 GCAGTGAAAA


Statistics
Matches: 66,  Mismatches: 10, Indels: 6
        0.80            0.12        0.07

Matches are distributed among these distances:
  47    2  0.03
  48   29  0.44
  49   35  0.53

ACGTcount: A:0.51, C:0.05, G:0.15, T:0.30


Consensus pattern (50 bp):   
ATCAATTTTGTCATAAAAATTGAGAAAAAGTACGCAAGTAAAAATAAAAG
Done.