Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018570.1 Corchorus olitorius cultivar O-4 contig18603, 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: 23431
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31


Found at i:15995 original size:22 final size:22

Alignment explanation


    Indices: 15953--15995  Score: 52
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      15943 AAAACTCGAG

                          *       
      15953 GTGGCTCGGTGGATGGCCGGTT
          1 GTGGCTCGGTGGATAGCCGGTT

                  *               
      15975 GTGGCTTGGT-GATAGCGCGGT
          1 GTGGCTCGGTGGATAGC-CGGT

      15996 ACTAGGCAGA


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  21    5  0.28
  22   13  0.72

ACGTcount: A:0.07, C:0.16, G:0.49, T:0.28


Consensus pattern (22 bp):   
GTGGCTCGGTGGATAGCCGGTT

Found at i:19103 original size:29 final size:29

Alignment explanation


    Indices: 19043--19101  Score: 86
    Period size: 29  Copynumber: 2.1  Consensus size: 29

      19033 TATATATATA

                            *            
      19043 TTTAAAAAAAAACGCAGAAACAACTTTTT
          1 TTTAAAAAAAAACGCAAAAACAACTTTTT

                          *              
      19072 TTTAAAAAAAAACGTAAAAAC--CTTTTT
          1 TTTAAAAAAAAACGCAAAAACAACTTTTT

               
      19099 TTT
          1 TTT

      19102 TTCAAAAACG


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  27    9  0.32
  29   19  0.68

ACGTcount: A:0.49, C:0.12, G:0.05, T:0.34


Consensus pattern (29 bp):   
TTTAAAAAAAAACGCAAAAACAACTTTTT

Found at i:22253 original size:33 final size:33

Alignment explanation


    Indices: 22155--22285  Score: 145
    Period size: 33  Copynumber: 3.8  Consensus size: 33

      22145 AAAAACTGAA

                              *            ****
      22155 TGGGAACTTTCCCAATTTGAAAACTTAAAAGTTAA
          1 TGGGAACTTTCCCAA-TTAAAAACTTAAAA-CCGG

                                                
      22190 TGGGAACTTTCCCAATTTTTAAAAACTTAAAACCGG
          1 TGGGAACTTTCCCAA---TTAAAAACTTAAAACCGG

                         *        *       *  
      22226 TGGGAACTTTCCCGATTAAAAATTTAAAACTGG
          1 TGGGAACTTTCCCAATTAAAAACTTAAAACCGG

                                       
      22259 TGGGAACTTTCCCAATTAAAAACTTAA
          1 TGGGAACTTTCCCAATTAAAAACTTAA

      22286 TGAAATTCTT


Statistics
Matches: 84,  Mismatches: 10, Indels: 6
        0.84            0.10        0.06

Matches are distributed among these distances:
  33   41  0.49
  35   15  0.18
  36   14  0.17
  37   14  0.17

ACGTcount: A:0.38, C:0.17, G:0.15, T:0.31


Consensus pattern (33 bp):   
TGGGAACTTTCCCAATTAAAAACTTAAAACCGG

Found at i:23013 original size:23 final size:23

Alignment explanation


    Indices: 22967--23029  Score: 63
    Period size: 23  Copynumber: 2.7  Consensus size: 23

      22957 GGAACTAAAT

                  *        *        
      22967 CCAAAGTATAAACTAGAATCTAAG
          1 CCAAAGCAT-AACTAAAATCTAAG

              *    *          *    
      22991 CCCAAGCCTAACTAAAATTTAAG
          1 CCAAAGCATAACTAAAATCTAAG

                  *         
      23014 CCAAAGTATAACTAAA
          1 CCAAAGCATAACTAAA

      23030 GTTCAAAGGC


Statistics
Matches: 31,  Mismatches: 8, Indels: 1
        0.77            0.20        0.03

Matches are distributed among these distances:
  23   25  0.81
  24    6  0.19

ACGTcount: A:0.49, C:0.21, G:0.10, T:0.21


Consensus pattern (23 bp):   
CCAAAGCATAACTAAAATCTAAG
Done.