Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020347.1 Corchorus olitorius cultivar O-4 contig20380, 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: 16158
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:267 original size:33 final size:34

Alignment explanation


    Indices: 219--284  Score: 98
    Period size: 33  Copynumber: 2.0  Consensus size: 34

        209 AAAAGAAAAT

                            *    *   *        
        219 TATATATTTTTTATGTTATATGCTATAAATTAAA
          1 TATATATTTTTTATGTCATATACTACAAATTAAA

                                             
        253 TATAT-TTTTTTATGTCATATACTACAAATTAA
          1 TATATATTTTTTATGTCATATACTACAAATTAA

        285 TGTAATTTAT


Statistics
Matches: 29,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  33   24  0.83
  34    5  0.17

ACGTcount: A:0.38, C:0.06, G:0.05, T:0.52


Consensus pattern (34 bp):   
TATATATTTTTTATGTCATATACTACAAATTAAA

Found at i:5819 original size:255 final size:255

Alignment explanation


    Indices: 5368--5874  Score: 978
    Period size: 255  Copynumber: 2.0  Consensus size: 255

       5358 TGTTCAAATT

                                                                             
       5368 TATTCGGATGTTGCTTGCAATAGCTGCATTTTATGGCTAAATATCCAATTTGGGCCTAAACCTTT
          1 TATTCGGATGTTGCTTGCAATAGCTGCATTTTATGGCTAAATATCCAATTTGGGCCTAAACCTTT

                                                                             
       5433 TGAGGATTGCTCAATTCCAGCCCAAACCTTTAAAGCGCTCCAATTTGAGCCTAAAGGTTTTCAAA
         66 TGAGGATTGCTCAATTCCAGCCCAAACCTTTAAAGCGCTCCAATTTGAGCCTAAAGGTTTTCAAA

                           *      *                                          
       5498 ACCCTCCAAATTGGGTCTAAGTTAGACGAAAATTAGAGAGTATAGCACACGCTCTAGTTAAACGC
        131 ACCCTCCAAATTGGGCCTAAGTCAGACGAAAATTAGAGAGTATAGCACACGCTCTAGTTAAACGC

                                                        *               
       5563 GTAAGTAGACAAATGCTCATGCTTACATGGAATTTTTGGGCCACGTTAGTGTCCACGCTC
        196 GTAAGTAGACAAATGCTCATGCTTACATGGAATTTTTGGGCCACATTAGTGTCCACGCTC

                                                                             
       5623 TATTCGGATGTTGCTTGCAATAGCTGCATTTTATGGCTAAATATCCAATTTGGGCCTAAACCTTT
          1 TATTCGGATGTTGCTTGCAATAGCTGCATTTTATGGCTAAATATCCAATTTGGGCCTAAACCTTT

                                                    *                        
       5688 TGAGGATTGCTCAATTCCAGCCCAAACCTTTAAAGCGCTCTAATTTGAGCCTAAAGGTTTTCAAA
         66 TGAGGATTGCTCAATTCCAGCCCAAACCTTTAAAGCGCTCCAATTTGAGCCTAAAGGTTTTCAAA

                                                                             
       5753 ACCCTCCAAATTGGGCCTAAGTCAGACGAAAATTAGAGAGTATAGCACACGCTCTAGTTAAACGC
        131 ACCCTCCAAATTGGGCCTAAGTCAGACGAAAATTAGAGAGTATAGCACACGCTCTAGTTAAACGC

                                                                     
       5818 GTAAGTAGACAAATGCTCATGCTTACATGGAATTTTTGGGCCACATTAGTGTCCACG
        196 GTAAGTAGACAAATGCTCATGCTTACATGGAATTTTTGGGCCACATTAGTGTCCACG

       5875 TGGAATTATC


Statistics
Matches: 248,  Mismatches: 4, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 255  248  1.00

ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30


Consensus pattern (255 bp):   
TATTCGGATGTTGCTTGCAATAGCTGCATTTTATGGCTAAATATCCAATTTGGGCCTAAACCTTT
TGAGGATTGCTCAATTCCAGCCCAAACCTTTAAAGCGCTCCAATTTGAGCCTAAAGGTTTTCAAA
ACCCTCCAAATTGGGCCTAAGTCAGACGAAAATTAGAGAGTATAGCACACGCTCTAGTTAAACGC
GTAAGTAGACAAATGCTCATGCTTACATGGAATTTTTGGGCCACATTAGTGTCCACGCTC

Found at i:12260 original size:29 final size:29

Alignment explanation


    Indices: 12196--12299  Score: 158
    Period size: 29  Copynumber: 3.7  Consensus size: 29

      12186 AAGGTCATCT

                       *            *    
      12196 AGGGGCATTTTGGTCATTTTT--ATATTC
          1 AGGGGCATTTTAGTCATTTTTGCACATTC

                                         
      12223 AGGGGCATTTTAGTCATTTTTGCACATTC
          1 AGGGGCATTTTAGTCATTTTTGCACATTC

                                         
      12252 AGGGGCATTTTAGTCATTTTTGCACATTC
          1 AGGGGCATTTTAGTCATTTTTGCACATTC

                 *     *       
      12281 AGGGGTATTTTGGTCATTT
          1 AGGGGCATTTTAGTCATTT

      12300 GTACTCCAGG


Statistics
Matches: 71,  Mismatches: 4, Indels: 2
        0.92            0.05        0.03

Matches are distributed among these distances:
  27   20  0.28
  29   51  0.72

ACGTcount: A:0.19, C:0.13, G:0.23, T:0.44


Consensus pattern (29 bp):   
AGGGGCATTTTAGTCATTTTTGCACATTC
Done.