Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012806.1 Corchorus olitorius cultivar O-4 contig12839, 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: 7358
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35


Found at i:1885 original size:3 final size:3

Alignment explanation


    Indices: 1879--1904  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

       1869 TAAAAAAAAA

                                              
       1879 AAG AAG AAG AAG AAG AAG AAG AAG AA
          1 AAG AAG AAG AAG AAG AAG AAG AAG AA

       1905 TGGGTGAGTT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00


Consensus pattern (3 bp):   
AAG

Found at i:1957 original size:35 final size:36

Alignment explanation


    Indices: 1907--1974  Score: 111
    Period size: 35  Copynumber: 1.9  Consensus size: 36

       1897 AAGAAGAATG

                                        *       
       1907 GGTGAGTTAGGAAGGAAGAAAGAGAGTCGTGGACAT
          1 GGTGAGTTAGGAAGGAAGAAAGAGAGTCATGGACAT

                              *              
       1943 GGTGAG-TAGGAAGGAAGTAAGAGAGTCATGGA
          1 GGTGAGTTAGGAAGGAAGAAAGAGAGTCATGGA

       1975 AGGGAGAGTT


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  35   24  0.80
  36    6  0.20

ACGTcount: A:0.37, C:0.04, G:0.43, T:0.16


Consensus pattern (36 bp):   
GGTGAGTTAGGAAGGAAGAAAGAGAGTCATGGACAT

Found at i:2245 original size:10 final size:9

Alignment explanation


    Indices: 2226--2250  Score: 50
    Period size: 9  Copynumber: 2.8  Consensus size: 9

       2216 GAATGTACTG

                     
       2226 AAAAAGAAA
          1 AAAAAGAAA

                     
       2235 AAAAAGAAA
          1 AAAAAGAAA

                   
       2244 AAAAAGA
          1 AAAAAGA

       2251 CAATCAGTGT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   16  1.00

ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00


Consensus pattern (9 bp):   
AAAAAGAAA

Found at i:3003 original size:10 final size:10

Alignment explanation


    Indices: 2988--3016  Score: 58
    Period size: 10  Copynumber: 2.9  Consensus size: 10

       2978 CTTTTATTAT

                      
       2988 TATCTATACC
          1 TATCTATACC

                      
       2998 TATCTATACC
          1 TATCTATACC

                     
       3008 TATCTATAC
          1 TATCTATAC

       3017 TATATTAAAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   19  1.00

ACGTcount: A:0.31, C:0.28, G:0.00, T:0.41


Consensus pattern (10 bp):   
TATCTATACC

Found at i:4735 original size:31 final size:31

Alignment explanation


    Indices: 4684--4855  Score: 211
    Period size: 31  Copynumber: 5.5  Consensus size: 31

       4674 CCCTTTTGTG

                *   *                      
       4684 CACGAGGCATGCCACGTGTCACTTTTTGGTA
          1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA

               *       *                    
       4715 CACATGGCGTGACA-GATGTCACTTTTTGGTA
          1 CACGTGGCGTGCCACG-TGTCACTTTTTGGTA

              *   *                        
       4746 CATGTGACGTGCCACGTGTCACTTTTTGGTA
          1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA

              *    *      *     *          
       4777 CATGTGGTGTGCCATGTGTCGCTTTTTGGTA
          1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA

                           *    *          
       4808 CACGTGGCGTGCCACATGTCGCTTTTTGGTA
          1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA

                    *        
       4839 CACGTGGCATGCCACGT
          1 CACGTGGCGTGCCACGT

       4856 CGGACACCGT


Statistics
Matches: 121,  Mismatches: 18, Indels: 4
        0.85            0.13        0.03

Matches are distributed among these distances:
  30    1  0.01
  31  119  0.98
  32    1  0.01

ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33


Consensus pattern (31 bp):   
CACGTGGCGTGCCACGTGTCACTTTTTGGTA

Done.