Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017926.1 Corchorus olitorius cultivar O-4 contig17959, 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: 3023
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.26


Found at i:1779 original size:11 final size:12

Alignment explanation


    Indices: 1765--1806  Score: 54
    Period size: 11  Copynumber: 3.8  Consensus size: 12

       1755 CCAAGCCACA

                        
       1765 ACCG-GCCATTC
          1 ACCGTGCCATTC

                      * 
       1776 ACCGTGCCA-CC
          1 ACCGTGCCATTC

                        
       1787 ACCG-GCCATTC
          1 ACCGTGCCATTC

                     
       1798 ACCGTGCCA
          1 ACCGTGCCA

       1807 CCACCGGTTA


Statistics
Matches: 26,  Mismatches: 2, Indels: 5
        0.79            0.06        0.15

Matches are distributed among these distances:
  10    4  0.15
  11   14  0.54
  12    8  0.31

ACGTcount: A:0.19, C:0.48, G:0.19, T:0.14


Consensus pattern (12 bp):   
ACCGTGCCATTC

Found at i:1784 original size:22 final size:22

Alignment explanation


    Indices: 1759--1848  Score: 107
    Period size: 22  Copynumber: 4.2  Consensus size: 22

       1749 CCACTACCAA

                 *                
       1759 GCCACAACCGGCCATTCACCGT
          1 GCCACCACCGGCCATTCACCGT

                                  
       1781 GCCACCACCGGCCATTCACCGT
          1 GCCACCACCGGCCATTCACCGT

                            *       
       1803 GCCACCACCGG---TTAAGCCTGT
          1 GCCACCACCGGCCATTCA-CC-GT

                           *      
       1824 GCCACCACCGGCCATGC-CCGT
          1 GCCACCACCGGCCATTCACCGT

                
       1845 GCCA
          1 GCCA

       1849 TCATCATTCA


Statistics
Matches: 59,  Mismatches: 4, Indels: 11
        0.80            0.05        0.15

Matches are distributed among these distances:
  19    3  0.05
  20    2  0.03
  21   19  0.32
  22   34  0.58
  24    1  0.02

ACGTcount: A:0.19, C:0.47, G:0.21, T:0.13


Consensus pattern (22 bp):   
GCCACCACCGGCCATTCACCGT

Found at i:1811 original size:11 final size:11

Alignment explanation


    Indices: 1775--1812  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

       1765 ACCGGCCATT

                       
       1775 CACCGTGCCAC
          1 CACCGTGCCAC

                       *
       1786 CACCG-GCCATT
          1 CACCGTGCCA-C

                       
       1797 CACCGTGCCAC
          1 CACCGTGCCAC

                 
       1808 CACCG
          1 CACCG

       1813 GTTAAGCCTG


Statistics
Matches: 23,  Mismatches: 2, Indels: 4
        0.79            0.07        0.14

Matches are distributed among these distances:
  10    4  0.17
  11   15  0.65
  12    4  0.17

ACGTcount: A:0.18, C:0.53, G:0.18, T:0.11


Consensus pattern (11 bp):   
CACCGTGCCAC

Done.