Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023724.1 Corchorus olitorius cultivar O-4 contig23757, 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: 29662
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:6772 original size:21 final size:21

Alignment explanation


    Indices: 6725--6773  Score: 53
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       6715 GGGTTGCTGG

                   **       *    
       6725 GCACCCACATGGTTTGTCTGA
          1 GCACCCATGTGGTTTGCCTGA

             *                   
       6746 GGACCCATGTGGTTTGCCTGA
          1 GCACCCATGTGGTTTGCCTGA

            *      
       6767 TCACCCA
          1 GCACCCA

       6774 GGTAGGCAGT


Statistics
Matches: 22,  Mismatches: 6, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.18, C:0.31, G:0.24, T:0.27


Consensus pattern (21 bp):   
GCACCCATGTGGTTTGCCTGA

Found at i:15005 original size:29 final size:29

Alignment explanation


    Indices: 14963--15059  Score: 178
    Period size: 29  Copynumber: 3.3  Consensus size: 29

      14953 TTAGGGGATG

                                         
      14963 AAATTGAAAAATTGAAAAATGTAAGGACC
          1 AAATTGAAAAATTGAAAAATGTAAGGACC

                                         
      14992 AAATTGAAAAATTGAAAAATGTAAGGACC
          1 AAATTGAAAAATTGAAAAATGTAAGGACC

                                          
      15021 AAATTGAAAAATTGAAAAATGTAATGG-CC
          1 AAATTGAAAAATTGAAAAATGTAA-GGACC

                      
      15050 AAATTGAAAA
          1 AAATTGAAAA

      15060 GATTATTTGC


Statistics
Matches: 67,  Mismatches: 0, Indels: 2
        0.97            0.00        0.03

Matches are distributed among these distances:
  29   65  0.97
  30    2  0.03

ACGTcount: A:0.56, C:0.06, G:0.16, T:0.22


Consensus pattern (29 bp):   
AAATTGAAAAATTGAAAAATGTAAGGACC

Found at i:20180 original size:14 final size:14

Alignment explanation


    Indices: 20153--20199  Score: 67
    Period size: 14  Copynumber: 3.4  Consensus size: 14

      20143 CCCCTCTTTT

                  *  *    
      20153 CACTCAGCGCTCAC
          1 CACTCACCGTTCAC

            *             
      20167 AACTCACCGTTCAC
          1 CACTCACCGTTCAC

                          
      20181 CACTCACCGTTCAC
          1 CACTCACCGTTCAC

                 
      20195 CACTC
          1 CACTC

      20200 CCACCGATGC


Statistics
Matches: 29,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  14   29  1.00

ACGTcount: A:0.23, C:0.49, G:0.09, T:0.19


Consensus pattern (14 bp):   
CACTCACCGTTCAC

Found at i:27110 original size:32 final size:32

Alignment explanation


    Indices: 27074--27134  Score: 79
    Period size: 32  Copynumber: 1.9  Consensus size: 32

      27064 TGAAGATAAC

                          *          *       
      27074 GGCGTTT-TACTTTTGAAACGCCGCTAATTAGT
          1 GGCGTTTCTAC-TTAGAAACGCCGCCAATTAGT

                     *                   
      27106 GGCGTTTCTGCTTAGAAACGCCGCCAATT
          1 GGCGTTTCTACTTAGAAACGCCGCCAATT

      27135 GAATAATTCC


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  32   23  0.92
  33    2  0.08

ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33


Consensus pattern (32 bp):   
GGCGTTTCTACTTAGAAACGCCGCCAATTAGT
Done.