Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011989.1 Corchorus olitorius cultivar O-4 contig12022, 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: 14794
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33


Found at i:1904 original size:9 final size:8

Alignment explanation


    Indices: 1856--1905  Score: 73
    Period size: 8  Copynumber: 6.1  Consensus size: 8

       1846 CAACTTCTCC

                *   
       1856 AAAACTTG
          1 AAAATTTG

                *   
       1864 AAAACTTG
          1 AAAATTTG

                    
       1872 AAAATTTG
          1 AAAATTTG

                    
       1880 AAAATTTG
          1 AAAATTTG

                    
       1888 AAAATTTG
          1 AAAATTTG

                     
       1896 AAGAATTTG
          1 AA-AATTTG

             
       1905 A
          1 A

       1906 TGGAAAAGGT


Statistics
Matches: 40,  Mismatches: 1, Indels: 1
        0.95            0.02        0.02

Matches are distributed among these distances:
   8   33  0.82
   9    7  0.17

ACGTcount: A:0.50, C:0.04, G:0.14, T:0.32


Consensus pattern (8 bp):   
AAAATTTG

Found at i:6925 original size:21 final size:21

Alignment explanation


    Indices: 6899--6939  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       6889 AAGAGTTTTC

                  *              
       6899 GGTTTTGCGATAAAAAAAAAG
          1 GGTTTTACGATAAAAAAAAAG

                     * *        
       6920 GGTTTTACGTTTAAAAAAAA
          1 GGTTTTACGATAAAAAAAAA

       6940 TATTTGTCTA


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.46, C:0.05, G:0.20, T:0.29


Consensus pattern (21 bp):   
GGTTTTACGATAAAAAAAAAG

Found at i:6973 original size:2 final size:2

Alignment explanation


    Indices: 6966--6990  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       6956 TCTAAAAATC

                                                 
       6966 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

       6991 TTTCTTTATT


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

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:13818 original size:21 final size:22

Alignment explanation


    Indices: 13779--13871  Score: 124
    Period size: 21  Copynumber: 4.4  Consensus size: 22

      13769 TGACGACCGA

                                   
      13779 TCAATTGGAGCAA-GTTCCAAGC
          1 TCAATTGGAG-AAGGTTCCAAGC

                                  
      13801 TCAATT-GAGAAGGTTCCAAGC
          1 TCAATTGGAGAAGGTTCCAAGC

                                  
      13822 TC-ATTGGAGAAGGTTCCAAGC
          1 TCAATTGGAGAAGGTTCCAAGC

                     *      *     
      13843 TC-ATTGGAAAAGGTTTCAAGC
          1 TCAATTGGAGAAGGTTCCAAGC

                     
      13864 TC-ATTGGA
          1 TCAATTGGA

      13872 ATTGCCTTAG


Statistics
Matches: 67,  Mismatches: 2, Indels: 5
        0.91            0.03        0.07

Matches are distributed among these distances:
  20    5  0.07
  21   56  0.84
  22    6  0.09

ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26


Consensus pattern (22 bp):   
TCAATTGGAGAAGGTTCCAAGC

Done.