Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023676.1 Corchorus olitorius cultivar O-4 contig23709, 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: 3457
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32


Found at i:2735 original size:27 final size:28

Alignment explanation


    Indices: 2705--2763  Score: 70
    Period size: 27  Copynumber: 2.2  Consensus size: 28

       2695 GAAAAACGCA

                            *            
       2705 AAAACTTTT-TTTTTATGACGCAAAA-AC
          1 AAAACTTTTCTTTTT-CGACGCAAAACAC

                              *         
       2732 AAAA-TTTTCTTTTTCGATGCAAAACAC
          1 AAAACTTTTCTTTTTCGACGCAAAACAC

                 
       2759 AAAAC
          1 AAAAC

       2764 AAATTTTTTT


Statistics
Matches: 27,  Mismatches: 2, Indels: 5
        0.79            0.06        0.15

Matches are distributed among these distances:
  26   12  0.44
  27   15  0.56

ACGTcount: A:0.42, C:0.17, G:0.07, T:0.34


Consensus pattern (28 bp):   
AAAACTTTTCTTTTTCGACGCAAAACAC

Found at i:3129 original size:15 final size:15

Alignment explanation


    Indices: 3109--3150  Score: 57
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       3099 ACAGAGATTG

                   *       
       3109 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
       3124 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                 *      
       3139 ACTAGGAAACAA
          1 AC-AGAAAACAA

       3151 AGCATAGTAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  15   16  0.67
  16    8  0.33

ACGTcount: A:0.62, C:0.14, G:0.12, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:3150 original size:16 final size:15

Alignment explanation


    Indices: 3112--3150  Score: 51
    Period size: 16  Copynumber: 2.5  Consensus size: 15

       3102 GAGATTGACA

                            
       3112 GAAAGCAATTAAACAG
          1 GAAA-CAATTAAACAG

            *               
       3128 AAAACAATTAAACTAG
          1 GAAACAATTAAAC-AG

                   
       3144 GAAACAA
          1 GAAACAA

       3151 AGCATAGTAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  15    9  0.45
  16   11  0.55

ACGTcount: A:0.62, C:0.13, G:0.13, T:0.13


Consensus pattern (15 bp):   
GAAACAATTAAACAG
Done.