Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007729.1 Corchorus olitorius cultivar O-4 contig07755, 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, 932

Length: 1554
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35


Found at i:400 original size:27 final size:27

Alignment explanation


    Indices: 330--393  Score: 128
    Period size: 27  Copynumber: 2.4  Consensus size: 27

        320 AAATTACGTA

                                       
        330 TTTGCCCCTATCAGCTAAAGTTACAGT
          1 TTTGCCCCTATCAGCTAAAGTTACAGT

                                       
        357 TTTGCCCCTATCAGCTAAAGTTACAGT
          1 TTTGCCCCTATCAGCTAAAGTTACAGT

                      
        384 TTTGCCCCTA
          1 TTTGCCCCTA

        394 AAGGCTAGAA


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   37  1.00

ACGTcount: A:0.23, C:0.28, G:0.14, T:0.34


Consensus pattern (27 bp):   
TTTGCCCCTATCAGCTAAAGTTACAGT

Found at i:797 original size:13 final size:12

Alignment explanation


    Indices: 767--822  Score: 57
    Period size: 12  Copynumber: 4.8  Consensus size: 12

        757 CCCGTTGAGG

                        
        767 AAATG-TTTTAT
          1 AAATGCTTTTAT

              *          
        778 AACTGCTTTATAT
          1 AAATGCTTT-TAT

                        
        791 AAATGC-TTTAT
          1 AAATGCTTTTAT

                         
        802 AAATG-TTTTAAT
          1 AAATGCTTTT-AT

                      
        814 AAATG-TTTT
          1 AAATGCTTTT

        823 GGGTGCATAA


Statistics
Matches: 39,  Mismatches: 2, Indels: 7
        0.81            0.04        0.15

Matches are distributed among these distances:
  11   15  0.38
  12   16  0.41
  13    8  0.21

ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50


Consensus pattern (12 bp):   
AAATGCTTTTAT

Found at i:800 original size:24 final size:23

Alignment explanation


    Indices: 767--818  Score: 68
    Period size: 24  Copynumber: 2.2  Consensus size: 23

        757 CCCGTTGAGG

                 *       *          
        767 AAATGTTTTATAACTGCTTTATAT
          1 AAATGCTTTATAAATGCTTTA-AT

                            *      
        791 AAATGCTTTATAAATGTTTTAAT
          1 AAATGCTTTATAAATGCTTTAAT

                 
        814 AAATG
          1 AAATG

        819 TTTTGGGTGC


Statistics
Matches: 25,  Mismatches: 3, Indels: 1
        0.86            0.10        0.03

Matches are distributed among these distances:
  23    7  0.28
  24   18  0.72

ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46


Consensus pattern (23 bp):   
AAATGCTTTATAAATGCTTTAAT
Done.