Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007058.1 Corchorus olitorius cultivar O-4 contig07083, 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: 2931
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:25 original size:2 final size:2

Alignment explanation


    Indices: 18--52  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

          8 GTAAAACTAG

                                                                
         18 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         53 GAAAATATCT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:1202 original size:29 final size:30

Alignment explanation


    Indices: 1164--1238  Score: 89
    Period size: 29  Copynumber: 2.5  Consensus size: 30

       1154 TACACAAAAC

                                 *     ** 
       1164 GGCCAAATAAGCCCTTGAACTTTAATTGTA
          1 GGCCAAATAAGCCCTTGAACTCTAATTAAA

              *           **              
       1194 -GTCAAATAAGCCCCCGAACTCTAATTAAA
          1 GGCCAAATAAGCCCTTGAACTCTAATTAAA

                            
       1223 GGCCAAATAAGCCCTT
          1 GGCCAAATAAGCCCTT

       1239 TTTAGACGGC


Statistics
Matches: 35,  Mismatches: 9, Indels: 2
        0.76            0.20        0.04

Matches are distributed among these distances:
  29   23  0.66
  30   12  0.34

ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24


Consensus pattern (30 bp):   
GGCCAAATAAGCCCTTGAACTCTAATTAAA

Found at i:1728 original size:29 final size:30

Alignment explanation


    Indices: 1674--1743  Score: 97
    Period size: 29  Copynumber: 2.4  Consensus size: 30

       1664 CGTCCAAAAA

                          ***             
       1674 GGGCTTATTTGGCTTTTATTAAGAGTTCAG
          1 GGGCTTATTTGGCTGCAATTAAGAGTTCAG

                                       *  
       1704 GGGCTTATTTGGCTGCAATT-AGAGTTTAG
          1 GGGCTTATTTGGCTGCAATTAAGAGTTCAG

                       
       1733 GGGCTTATTTG
          1 GGGCTTATTTG

       1744 TAAGTTTAGG


Statistics
Matches: 36,  Mismatches: 4, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  29   19  0.53
  30   17  0.47

ACGTcount: A:0.19, C:0.10, G:0.30, T:0.41


Consensus pattern (30 bp):   
GGGCTTATTTGGCTGCAATTAAGAGTTCAG

Found at i:2832 original size:21 final size:21

Alignment explanation


    Indices: 2808--2856  Score: 89
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       2798 AGATAATGTC

                                 
       2808 CGTAGCAAATGTAAATAAGCT
          1 CGTAGCAAATGTAAATAAGCT

                    *            
       2829 CGTAGCAACTGTAAATAAGCT
          1 CGTAGCAAATGTAAATAAGCT

                   
       2850 CGTAGCA
          1 CGTAGCA

       2857 TATAAGAATA


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  21   27  1.00

ACGTcount: A:0.39, C:0.18, G:0.20, T:0.22


Consensus pattern (21 bp):   
CGTAGCAAATGTAAATAAGCT

Done.