Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024309.1 Corchorus olitorius cultivar O-4 contig24342, 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: 5103
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:2006 original size:24 final size:24

Alignment explanation


    Indices: 1974--2030  Score: 80
    Period size: 24  Copynumber: 2.4  Consensus size: 24

       1964 CCCGTTGAGG

                                     
       1974 AAATGTTTTAT-AACTGCTTTATAT
          1 AAATGTTTTATAAACTGCTTTA-AT

                          *  *      
       1998 AAATGTTTTATAAATTGTTTTAAT
          1 AAATGTTTTATAAACTGCTTTAAT

                     
       2022 AAATGTTTT
          1 AAATGTTTT

       2031 GGGTGCATAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  24   22  0.73
  25    8  0.27

ACGTcount: A:0.35, C:0.04, G:0.09, T:0.53


Consensus pattern (24 bp):   
AAATGTTTTATAAACTGCTTTAAT

Found at i:2018 original size:12 final size:11

Alignment explanation


    Indices: 1974--2030  Score: 69
    Period size: 12  Copynumber: 4.8  Consensus size: 11

       1964 CCCGTTGAGG

                       
       1974 AAATGTTTTAT
          1 AAATGTTTTAT

              *          
       1985 AACTGCTTTATAT
          1 AAATG-TTT-TAT

                       
       1998 AAATGTTTTAT
          1 AAATGTTTTAT

                         
       2009 AAATTGTTTTAAT
          1 AAA-TGTTTT-AT

                     
       2022 AAATGTTTT
          1 AAATGTTTT

       2031 GGGTGCATAA


Statistics
Matches: 40,  Mismatches: 2, Indels: 7
        0.82            0.04        0.14

Matches are distributed among these distances:
  11   10  0.25
  12   18  0.45
  13   12  0.30

ACGTcount: A:0.35, C:0.04, G:0.09, T:0.53


Consensus pattern (11 bp):   
AAATGTTTTAT

Found at i:4877 original size:36 final size:36

Alignment explanation


    Indices: 4830--4898  Score: 129
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       4820 TCAATAACCA

                               *                
       4830 TACATTTTTTGTAATTTTGGTTATCATATTTCTTAT
          1 TACATTTTTTGTAATTTTGATTATCATATTTCTTAT

                                             
       4866 TACATTTTTTGTAATTTTGATTATCATATTTCT
          1 TACATTTTTTGTAATTTTGATTATCATATTTCT

       4899 CCAAAATCTC


Statistics
Matches: 32,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  36   32  1.00

ACGTcount: A:0.23, C:0.09, G:0.07, T:0.61


Consensus pattern (36 bp):   
TACATTTTTTGTAATTTTGATTATCATATTTCTTAT
Done.