Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009690.1 Corchorus olitorius cultivar O-4 contig09722, 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: 13198
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29


Found at i:573 original size:42 final size:42

Alignment explanation


    Indices: 526--609  Score: 168
    Period size: 42  Copynumber: 2.0  Consensus size: 42

        516 CAAGCCACAG

                                                      
        526 AAATTCAACCCTCCAAATATAACACATGGTCTAATATGCCTT
          1 AAATTCAACCCTCCAAATATAACACATGGTCTAATATGCCTT

                                                      
        568 AAATTCAACCCTCCAAATATAACACATGGTCTAATATGCCTT
          1 AAATTCAACCCTCCAAATATAACACATGGTCTAATATGCCTT

        610 TTTCAAGCTA


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  42   42  1.00

ACGTcount: A:0.38, C:0.26, G:0.07, T:0.29


Consensus pattern (42 bp):   
AAATTCAACCCTCCAAATATAACACATGGTCTAATATGCCTT

Found at i:5102 original size:225 final size:225

Alignment explanation


    Indices: 4706--5151  Score: 732
    Period size: 225  Copynumber: 2.0  Consensus size: 225

       4696 TTGCCCAGCT

                *          *        *                *                   *   
       4706 TTCAGAGAATTAAATTATAAGAATTGAGCAGCCCACTCTGTTTTAGGGATAAAGAAAATGTTGGT
          1 TTCAAAGAATTAAATCATAAGAATCGAGCAGCCCACTCTGTGTTAGGGATAAAGAAAATGTCGGT

                         *                              * *                  
       4771 CCACCTAGACAGTTGGCATTAAACCAATAGCAGATTAATCACCCTAGAGCAGCCTAGCATGACCA
         66 CCACCTAGACAGTGGGCATTAAACCAATAGCAGATTAATCACCCAAAAGCAGCCTAGCATGACCA

                                                                             
       4836 AACATAATATTGGCAACAGGGAAAAGAGGAGATAGACAAGAATTTATCACCTCGGCAAAGTTGCC
        131 AACATAATATTGGCAACAGGGAAAAGAGGAGATAGACAAGAATTTATCACCTCGGCAAAGTTGCC

                                          
       4901 TAGCCTTCAAATTTCTATTCAACATCCTAA
        196 TAGCCTTCAAATTTCTATTCAACATCCTAA

                               *                 *       *      *            
       4931 TTCAAAGAATTAAATCATAGGAATCGAGCAGCCCACTTTGTGTTATGGATAAGGAAAATGTCGGT
          1 TTCAAAGAATTAAATCATAAGAATCGAGCAGCCCACTCTGTGTTAGGGATAAAGAAAATGTCGGT

                            *                   *                            
       4996 CCACCTAGACAGTGGGTATTAAACCAATAGCAGATTCATCACCCAAAAGCAGCCTAGCATGACCA
         66 CCACCTAGACAGTGGGCATTAAACCAATAGCAGATTAATCACCCAAAAGCAGCCTAGCATGACCA

                                                                             
       5061 AAGC-TAATATTGGCAACAGGGAAAAGAGGAGATAGACAAGAATTTATCACCTCGGCAAAGTTGC
        131 AA-CATAATATTGGCAACAGGGAAAAGAGGAGATAGACAAGAATTTATCACCTCGGCAAAGTTGC

               *                 *     
       5125 CTATCCTTCAAATTTCTATTCCACATC
        195 CTAGCCTTCAAATTTCTATTCAACATC

       5152 TTACAATTAC


Statistics
Matches: 204,  Mismatches: 16, Indels: 2
        0.92            0.07        0.01

Matches are distributed among these distances:
 225  203  1.00
 226    1  0.00

ACGTcount: A:0.37, C:0.21, G:0.19, T:0.24


Consensus pattern (225 bp):   
TTCAAAGAATTAAATCATAAGAATCGAGCAGCCCACTCTGTGTTAGGGATAAAGAAAATGTCGGT
CCACCTAGACAGTGGGCATTAAACCAATAGCAGATTAATCACCCAAAAGCAGCCTAGCATGACCA
AACATAATATTGGCAACAGGGAAAAGAGGAGATAGACAAGAATTTATCACCTCGGCAAAGTTGCC
TAGCCTTCAAATTTCTATTCAACATCCTAA
Done.