Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000173.1 Corchorus olitorius cultivar O-4 contig00173, 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, 760

Length: 1267
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33


Found at i:570 original size:18 final size:18

Alignment explanation


    Indices: 549--607  Score: 50
    Period size: 18  Copynumber: 3.2  Consensus size: 18

        539 GGGCCATACG

                              
        549 CTGGCCCGTGCGCCAGGC
          1 CTGGCCCGTGCGCCAGGC

                 *      *        
        567 CTGG-GCGTTTGGGCC-GCGC
          1 CTGGCCCG--TGCGCCAG-GC

                    *         
        586 CTGGCCCGCGCGCCAGGC
          1 CTGGCCCGTGCGCCAGGC

                
        604 CTGG
          1 CTGG

        608 GCGCTTGGGC


Statistics
Matches: 31,  Mismatches: 5, Indels: 10
        0.67            0.11        0.22

Matches are distributed among these distances:
  17    2  0.06
  18   15  0.48
  19   12  0.39
  20    2  0.06

ACGTcount: A:0.03, C:0.41, G:0.42, T:0.14


Consensus pattern (18 bp):   
CTGGCCCGTGCGCCAGGC

Found at i:591 original size:37 final size:37

Alignment explanation


    Indices: 549--628  Score: 133
    Period size: 37  Copynumber: 2.2  Consensus size: 37

        539 GGGCCATACG

                    *                *           
        549 CTGGCCCGTGCGCCAGGCCTGGGCGTTTGGGCCGCGC
          1 CTGGCCCGCGCGCCAGGCCTGGGCGCTTGGGCCGCGC

                                                 
        586 CTGGCCCGCGCGCCAGGCCTGGGCGCTTGGGCCGCGC
          1 CTGGCCCGCGCGCCAGGCCTGGGCGCTTGGGCCGCGC

             *    
        623 CAGGCC
          1 CTGGCC

        629 TGGGCGCTTG


Statistics
Matches: 40,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  37   40  1.00

ACGTcount: A:0.04, C:0.41, G:0.42, T:0.12


Consensus pattern (37 bp):   
CTGGCCCGCGCGCCAGGCCTGGGCGCTTGGGCCGCGC

Found at i:626 original size:24 final size:24

Alignment explanation


    Indices: 594--647  Score: 108
    Period size: 24  Copynumber: 2.2  Consensus size: 24

        584 GCCTGGCCCG

                                    
        594 CGCGCCAGGCCTGGGCGCTTGGGC
          1 CGCGCCAGGCCTGGGCGCTTGGGC

                                    
        618 CGCGCCAGGCCTGGGCGCTTGGGC
          1 CGCGCCAGGCCTGGGCGCTTGGGC

                  
        642 CGCGCC
          1 CGCGCC

        648 TGGCTGGCCC


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   30  1.00

ACGTcount: A:0.04, C:0.41, G:0.44, T:0.11


Consensus pattern (24 bp):   
CGCGCCAGGCCTGGGCGCTTGGGC

Found at i:695 original size:3 final size:3

Alignment explanation


    Indices: 689--718  Score: 51
    Period size: 3  Copynumber: 9.7  Consensus size: 3

        679 CTCTTTTTTT

                                                   
        689 TTC TTC TTC TTC TTC TTC TTC TTC TCTC TT
          1 TTC TTC TTC TTC TTC TTC TTC TTC T-TC TT

        719 TGTTGATTTG


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   3   23  0.88
   4    3  0.12

ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67


Consensus pattern (3 bp):   
TTC

Done.