Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021854.1 Corchorus olitorius cultivar O-4 contig21887, 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: 3053
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30


Found at i:193 original size:16 final size:16

Alignment explanation


    Indices: 172--226  Score: 51
    Period size: 16  Copynumber: 3.4  Consensus size: 16

        162 GCGGGCTGGC

                            
        172 CTGGCGATGCCGCGTG
          1 CTGGCGATGCCGCGTG

                   *    *     
        188 CTGGCG-CG-CGGGCTAG
          1 CTGGCGATGCCGCG-T-G

                             
        204 CCTGGCGATGCCGCGTG
          1 -CTGGCGATGCCGCGTG

                  
        221 CTGGCG
          1 CTGGCG

        227 CGCGGGCTAG


Statistics
Matches: 30,  Mismatches: 4, Indels: 10
        0.68            0.09        0.23

Matches are distributed among these distances:
  14    3  0.10
  15    2  0.07
  16   13  0.43
  17    7  0.23
  18    2  0.07
  19    3  0.10

ACGTcount: A:0.05, C:0.33, G:0.45, T:0.16


Consensus pattern (16 bp):   
CTGGCGATGCCGCGTG

Found at i:198 original size:33 final size:33

Alignment explanation


    Indices: 152--282  Score: 219
    Period size: 33  Copynumber: 3.9  Consensus size: 33

        142 AGTGGCCTGC

                             *                
        152 TGCTCGGCGCGCGGGCTGGCCTGGCGATGCCGCG
          1 TGCT-GGCGCGCGGGCTAGCCTGGCGATGCCGCG

                                             
        186 TGCTGGCGCGCGGGCTAGCCTGGCGATGCCGCG
          1 TGCTGGCGCGCGGGCTAGCCTGGCGATGCCGCG

                                        *    
        219 TGCTGGCGCGCGGGCTAGCCTGGCGATGTCGCG
          1 TGCTGGCGCGCGGGCTAGCCTGGCGATGCCGCG

                                            
        252 TGCTGGCGCGCGGGCTAGCCT-GCTGATGCCG
          1 TGCTGGCGCGCGGGCTAGCCTGGC-GATGCCG

        283 ATGCTTGTCC


Statistics
Matches: 93,  Mismatches: 3, Indels: 3
        0.94            0.03        0.03

Matches are distributed among these distances:
  32    2  0.02
  33   87  0.94
  34    4  0.04

ACGTcount: A:0.05, C:0.33, G:0.45, T:0.17


Consensus pattern (33 bp):   
TGCTGGCGCGCGGGCTAGCCTGGCGATGCCGCG

Done.