Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011456.1 Corchorus olitorius cultivar O-4 contig11489, 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: 2949
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27


Found at i:675 original size:19 final size:19

Alignment explanation


    Indices: 647--692  Score: 65
    Period size: 19  Copynumber: 2.4  Consensus size: 19

        637 ACGGAAAAGC

                 *             
        647 AAAAGCATCAATCCATGTA
          1 AAAAGAATCAATCCATGTA

                      * *      
        666 AAAAGAATCAGTTCATGTA
          1 AAAAGAATCAATCCATGTA

                    
        685 AAAAGAAT
          1 AAAAGAAT

        693 TGATATAAAC


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  19   24  1.00

ACGTcount: A:0.52, C:0.13, G:0.13, T:0.22


Consensus pattern (19 bp):   
AAAAGAATCAATCCATGTA

Found at i:1563 original size:178 final size:176

Alignment explanation


    Indices: 1238--1581  Score: 530
    Period size: 178  Copynumber: 1.9  Consensus size: 176

       1228 ATTATGGTGA

                 *                                                           
       1238 GAACATCACTTATCAGAACTCAATGGCCAAATTACACACAAAAACAATGGATCTGAAGAAAACAT
          1 GAACAGCACTTATCAGAACTCAATGGCCAAATTACACACAAAAACAATGGATCTGAAGAAAACAT

                                              *                        *     
       1303 ATTAGGCTTAAGGGATATTTCAGTAATCAACCACGTGAGAAAAGACCAAAACGGGGCGATAAGGT
         66 ATTAGGCTTAAGGGATATTTCAGTAATCAACCACATGAGAAAAGACCAAAACGGGGCGAAAAGGT

               *                       *                    
       1368 CATTCCACATCAAAAGTTGATGGGGGATCCTTTAGTAAAAGTATGTGG
        131 CATCCCACATCAAAAGTTGAT--GGGAGCCTTTAGTAAAAGTATGTGG

                    *    *                            *                      
       1416 GAACAGCATTTATTAGAACTCAATGGCCAAATTACACACAAAGACAATGGATCT-AACGAAAACA
          1 GAACAGCACTTATCAGAACTCAATGGCCAAATTACACACAAAAACAATGGATCTGAA-GAAAACA

             *         *                                             *       
       1480 TGTTAGGCTTAGGGGATATTTCAGTAATCAACCACATGAGAAAAGACCAAAACGGGGTGAAAAGG
         65 TATTAGGCTTAAGGGATATTTCAGTAATCAACCACATGAGAAAAGACCAAAACGGGGCGAAAAGG

                        *                         
       1545 TTC-TCCCACATTAAAAGTTGATGGGAGCCTTTAGTAA
        130 -TCATCCCACATCAAAAGTTGATGGGAGCCTTTAGTAA

       1582 TTTCTAGAGG


Statistics
Matches: 152,  Mismatches: 12, Indels: 6
        0.89            0.07        0.04

Matches are distributed among these distances:
 176   14  0.09
 177    2  0.01
 178  134  0.88
 179    2  0.01

ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22


Consensus pattern (176 bp):   
GAACAGCACTTATCAGAACTCAATGGCCAAATTACACACAAAAACAATGGATCTGAAGAAAACAT
ATTAGGCTTAAGGGATATTTCAGTAATCAACCACATGAGAAAAGACCAAAACGGGGCGAAAAGGT
CATCCCACATCAAAAGTTGATGGGAGCCTTTAGTAAAAGTATGTGG

Found at i:2469 original size:23 final size:23

Alignment explanation


    Indices: 2424--2472  Score: 62
    Period size: 23  Copynumber: 2.1  Consensus size: 23

       2414 CTAAATTTCT

                     * *   *       
       2424 AAGTTTAAATAGTCATCTCTATA
          1 AAGTTTAAACAATCAACTCTATA

                              *    
       2447 AAGTTTAAACAATCAACTTTATA
          1 AAGTTTAAACAATCAACTCTATA

               
       2470 AAG
          1 AAG

       2473 CTAAATTTCT


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  23   22  1.00

ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35


Consensus pattern (23 bp):   
AAGTTTAAACAATCAACTCTATA
Done.