Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023985.1 Corchorus olitorius cultivar O-4 contig24018, 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: 6270
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.32


Found at i:5879 original size:38 final size:37

Alignment explanation


    Indices: 5828--5939  Score: 149
    Period size: 38  Copynumber: 3.0  Consensus size: 37

       5818 AATTGAAAAC

                                                  
       5828 TAAAACTTGATGGGAACTTTCCCAATTTAAAAACTTTG
          1 TAAAAC-TGATGGGAACTTTCCCAATTTAAAAACTTTG

                                                   
       5866 TAAAACTGAATGGGAACTTTCCCAATTTGAAAAAC--T-
          1 TAAAACTG-ATGGGAACTTTCCCAATTT-AAAAACTTTG

                    *                  *          
       5902 TAAAACTGGTGGGAACTTTCCCAATTAAAAAAACTTTG
          1 TAAAACTGATGGGAACTTTCCCAATT-TAAAAACTTTG

       5940 AACATGATGA


Statistics
Matches: 66,  Mismatches: 2, Indels: 12
        0.82            0.03        0.15

Matches are distributed among these distances:
  35   23  0.35
  36    8  0.12
  37    4  0.06
  38   25  0.38
  39    6  0.09

ACGTcount: A:0.39, C:0.16, G:0.14, T:0.30


Consensus pattern (37 bp):   
TAAAACTGATGGGAACTTTCCCAATTTAAAAACTTTG

Found at i:5924 original size:35 final size:35

Alignment explanation


    Indices: 5761--5937  Score: 166
    Period size: 35  Copynumber: 4.9  Consensus size: 35

       5751 AAAACGCTTT

                             *                 
       5761 TGATGGGAACTTTCCCACTTTG-AAAAC-TAAAAC
          1 TGATGGGAACTTTCCCAATTTGAAAAACTTAAAAC

                                     *                
       5794 TGAAAATGACGGGAACTTTCCCTAAATTG-AAAAC-TAAAAC
          1 TG---AT---GGGAACTTTCCC-AATTTGAAAAACTTAAAAC

                                                   
       5834 TTGATGGGAACTTTCCCAATTT-AAAAACTTTGTAAAAC
          1 -TGATGGGAACTTTCCCAATTTGAAAAAC--T-TAAAAC

                                                
       5872 TGAATGGGAACTTTCCCAATTTGAAAAACTTAAAAC
          1 TG-ATGGGAACTTTCCCAATTTGAAAAACTTAAAAC

              *                 **        
       5908 TGGTGGGAACTTTCCCAATTAAAAAAACTT
          1 TGATGGGAACTTTCCCAATTTGAAAAACTT

       5938 TGAACATGAT


Statistics
Matches: 123,  Mismatches: 6, Indels: 28
        0.78            0.04        0.18

Matches are distributed among these distances:
  33    2  0.02
  34    9  0.07
  35   37  0.30
  36   10  0.08
  37    3  0.02
  38   27  0.22
  39   18  0.15
  40   15  0.12
  41    2  0.02

ACGTcount: A:0.40, C:0.18, G:0.15, T:0.28


Consensus pattern (35 bp):   
TGATGGGAACTTTCCCAATTTGAAAAACTTAAAAC
Done.