Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022830.1 Corchorus olitorius cultivar O-4 contig22863, 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: 5656
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31


Found at i:230 original size:57 final size:58

Alignment explanation


    Indices: 166--287  Score: 192
    Period size: 57  Copynumber: 2.1  Consensus size: 58

        156 TACAATGTTT

                                                  *       *         * 
        166 TCCACTGATTGCTCCCAATTGTTGATTGAACGCGATCCTTCCTCCTTTGTCGGA-CTG
          1 TCCACTGATTGCTCCCAATTGTTGATTGAACGCGATCCATCCTCCTCTGTCGGATCAG

                          *                                    *      
        223 TCCACTGATTGCTCGCAATTGTTGATTGAACGCGATCCATCCTCCTCTGTCTGATCAG
          1 TCCACTGATTGCTCCCAATTGTTGATTGAACGCGATCCATCCTCCTCTGTCGGATCAG

                   
        281 TCCACTG
          1 TCCACTG

        288 TGATTCTGAT


Statistics
Matches: 59,  Mismatches: 5, Indels: 1
        0.91            0.08        0.02

Matches are distributed among these distances:
  57   50  0.85
  58    9  0.15

ACGTcount: A:0.17, C:0.30, G:0.19, T:0.34


Consensus pattern (58 bp):   
TCCACTGATTGCTCCCAATTGTTGATTGAACGCGATCCATCCTCCTCTGTCGGATCAG

Found at i:694 original size:19 final size:19

Alignment explanation


    Indices: 670--711  Score: 75
    Period size: 19  Copynumber: 2.2  Consensus size: 19

        660 ATTTCAAATT

                  *            
        670 TTAGATGTATTTATATATC
          1 TTAGATATATTTATATATC

                               
        689 TTAGATATATTTATATATC
          1 TTAGATATATTTATATATC

                
        708 TTAG
          1 TTAG

        712 TAGCGGCATA


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  19   22  1.00

ACGTcount: A:0.33, C:0.05, G:0.10, T:0.52


Consensus pattern (19 bp):   
TTAGATATATTTATATATC

Found at i:3256 original size:12 final size:12

Alignment explanation


    Indices: 3227--3257  Score: 53
    Period size: 13  Copynumber: 2.5  Consensus size: 12

       3217 CTCCCTTCTC

                        
       3227 TGTTTTCTTTTT
          1 TGTTTTCTTTTT

                         
       3239 TGGTTTTCTTTTT
          1 T-GTTTTCTTTTT

                  
       3252 TGTTTT
          1 TGTTTT

       3258 GTTTCTGTAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  12    6  0.33
  13   12  0.67

ACGTcount: A:0.00, C:0.06, G:0.13, T:0.81


Consensus pattern (12 bp):   
TGTTTTCTTTTT
Done.