Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015231.1 Corchorus olitorius cultivar O-4 contig15264, 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: 15704
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31


Found at i:2880 original size:21 final size:21

Alignment explanation


    Indices: 2856--2928  Score: 74
    Period size: 21  Copynumber: 3.4  Consensus size: 21

       2846 GGCTTGGAAT

                                 
       2856 GGTGATGGCACGGGCATGGCC
          1 GGTGATGGCACGGGCATGGCC

                *          * **  
       2877 GGTGGTGGCACGGGCTTAACC
          1 GGTGATGGCACGGGCATGGCC

                *          *      
       2898 GGTGGTGGCACGGTGAATGGCC
          1 GGTGATGGCACGG-GCATGGCC

               *     
       2920 GGTAATGGC
          1 GGTGATGGC

       2929 TTGGTAGTGG


Statistics
Matches: 41,  Mismatches: 10, Indels: 1
        0.79            0.19        0.02

Matches are distributed among these distances:
  21   30  0.73
  22   11  0.27

ACGTcount: A:0.15, C:0.21, G:0.47, T:0.18


Consensus pattern (21 bp):   
GGTGATGGCACGGGCATGGCC

Found at i:3097 original size:42 final size:42

Alignment explanation


    Indices: 3046--3140  Score: 113
    Period size: 42  Copynumber: 2.3  Consensus size: 42

       3036 ACAGAGGATA

                                                        
       3046 GCGCAGATGGCGCGG-AGTAAGGCACGGAT-AACCGGGCAGGCG
          1 GCGCAGATGGCGCGGAAG-AAGGCA-GGATCAACCGGGCAGGCG

                *     *               *  *            
       3088 GCGCGGATGGTGCGGAAGAAGGCAGGCTCGACCGGGCAGGCG
          1 GCGCAGATGGCGCGGAAGAAGGCAGGATCAACCGGGCAGGCG

                  *    
       3130 GCGCAGTTGGC
          1 GCGCAGATGGC

       3141 CGGTTGTGGC


Statistics
Matches: 44,  Mismatches: 7, Indels: 4
        0.80            0.13        0.07

Matches are distributed among these distances:
  41    3  0.07
  42   39  0.89
  43    2  0.05

ACGTcount: A:0.20, C:0.24, G:0.47, T:0.08


Consensus pattern (42 bp):   
GCGCAGATGGCGCGGAAGAAGGCAGGATCAACCGGGCAGGCG

Found at i:6664 original size:15 final size:16

Alignment explanation


    Indices: 6640--6680  Score: 57
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       6630 AGAGGTTGAT

                 *          
       6640 AGAAAGCAATTAAAC-
          1 AGAAAACAATTAAACA

                             
       6655 AGAAAACAATTAAACTA
          1 AGAAAACAATTAAAC-A

                     
       6672 AGAAAACAA
          1 AGAAAACAA

       6681 AGCAAAGTAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  15   14  0.61
  17    9  0.39

ACGTcount: A:0.66, C:0.12, G:0.10, T:0.12


Consensus pattern (16 bp):   
AGAAAACAATTAAACA

Found at i:9573 original size:30 final size:30

Alignment explanation


    Indices: 9539--9603  Score: 80
    Period size: 30  Copynumber: 2.2  Consensus size: 30

       9529 TTGTTATTTA

                       *                    
       9539 GTTCATATAAAGACATTA-ATTTGTTTTCTG-
          1 GTTCATATAAACAC-TTAGATTTGTTTT-TGT

                  *                       
       9569 GTTCATTTAAACACTTAGATTTGTTTTTGT
          1 GTTCATATAAACACTTAGATTTGTTTTTGT

                 
       9599 GTTCA
          1 GTTCA

       9604 ATTAGGTGCC


Statistics
Matches: 31,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
  29    5  0.16
  30   26  0.84

ACGTcount: A:0.26, C:0.11, G:0.14, T:0.49


Consensus pattern (30 bp):   
GTTCATATAAACACTTAGATTTGTTTTTGT
Done.