Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021949.1 Corchorus olitorius cultivar O-4 contig21982, 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: 22036
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32


Found at i:905 original size:49 final size:48

Alignment explanation


    Indices: 840--969  Score: 156
    Period size: 49  Copynumber: 2.7  Consensus size: 48

        830 TACTTTTCAC

                                 **                 *       
        840 TGCACTTTTTCTCAATTTTTACTACAAAATTGAACTTTTATTTTTACT
          1 TGCACTTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAATTTTACT

                                              *               
        888 TGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCTTTTAATTTT-CAT
          1 TGCA-CTTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAATTTTAC-T

            *          *          *           
        937 CGCACTTTTTTATCAATTTTT-TGACAAAATTGA
          1 TGCAC-TTTTTCTCAATTTTTAAGACAAAATTGA

        970 TTGGCACGCT


Statistics
Matches: 72,  Mismatches: 7, Indels: 6
        0.85            0.08        0.07

Matches are distributed among these distances:
  48   17  0.24
  49   55  0.76

ACGTcount: A:0.28, C:0.15, G:0.06, T:0.50


Consensus pattern (48 bp):   
TGCACTTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAATTTTACT

Found at i:4162 original size:17 final size:18

Alignment explanation


    Indices: 4140--4180  Score: 66
    Period size: 17  Copynumber: 2.3  Consensus size: 18

       4130 AAGAAATCAA

                              
       4140 AAATATTCAATTAA-AAT
          1 AAATATTCAATTAATAAT

                              
       4157 AAATATTCAATTAATAAT
          1 AAATATTCAATTAATAAT

            *     
       4175 GAATAT
          1 AAATAT

       4181 ATTAATTAGA


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  17   14  0.64
  18    8  0.36

ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37


Consensus pattern (18 bp):   
AAATATTCAATTAATAAT

Found at i:5058 original size:48 final size:48

Alignment explanation


    Indices: 4984--5129  Score: 172
    Period size: 49  Copynumber: 3.0  Consensus size: 48

       4974 AGCGTGCCAA

                                 *                       *  
       4984 TCAATTTTGTCAAAAAATTGATAAAAA-GTGCAATGAAAAGTAAATAT
          1 TCAATTTTGTCAAAAAATTGAGAAAAAGGTGCAATGAAAAGTAAAGAT

                                           *   *     *     * 
       5031 TCAATTTTGTCATAAAAATTGAGAAAAAGGTTCAAGGAAAATTAAAGGT
          1 TCAATTTTGTCA-AAAAATTGAGAAAAAGGTGCAATGAAAAGTAAAGAT

                                                     *         
       5080 TCAATTTTGTTGC-AAAAATTGAGAAAAAGGTGC-ATGAAATGTAAAAGAT
          1 TCAATTTTG-T-CAAAAAATTGAGAAAAAGGTGCAATGAAAAGT-AAAGAT

             
       5129 T
          1 T

       5130 GCTTTGAATG


Statistics
Matches: 83,  Mismatches: 11, Indels: 8
        0.81            0.11        0.08

Matches are distributed among these distances:
  47   12  0.14
  48   20  0.24
  49   49  0.59
  50    1  0.01
  51    1  0.01

ACGTcount: A:0.47, C:0.06, G:0.17, T:0.29


Consensus pattern (48 bp):   
TCAATTTTGTCAAAAAATTGAGAAAAAGGTGCAATGAAAAGTAAAGAT

Done.