Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013833.1 Corchorus olitorius cultivar O-4 contig13866, 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: 9398
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30


Found at i:2152 original size:19 final size:18

Alignment explanation


    Indices: 2119--2154  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       2109 TCGAGATAAT

                              
       2119 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       2137 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       2155 TAAGTCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:3519 original size:27 final size:27

Alignment explanation


    Indices: 3489--3545  Score: 114
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       3479 ATGTTGGTCA

                                       
       3489 AAGTTAGCAGGAGGTAGCACAGTGAAG
          1 AAGTTAGCAGGAGGTAGCACAGTGAAG

                                       
       3516 AAGTTAGCAGGAGGTAGCACAGTGAAG
          1 AAGTTAGCAGGAGGTAGCACAGTGAAG

               
       3543 AAG
          1 AAG

       3546 GGTGTGATGA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   30  1.00

ACGTcount: A:0.39, C:0.11, G:0.37, T:0.14


Consensus pattern (27 bp):   
AAGTTAGCAGGAGGTAGCACAGTGAAG

Found at i:8534 original size:76 final size:76

Alignment explanation


    Indices: 8384--8527  Score: 186
    Period size: 76  Copynumber: 1.9  Consensus size: 76

       8374 ACAAGGACCC

                                                               *           * 
       8384 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT

                       
       8449 GGGCAGTGTCA
         66 GGGCAGTGTCA

                    *                    *                            **     
       8460 CGACTCCAGCTGGGCGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
          1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA

                  
       8522 GATGGG
         63 GATGGG

       8528 TTGTGTCTTA


Statistics
Matches: 59,  Mismatches: 6, Indels: 6
        0.83            0.08        0.08

Matches are distributed among these distances:
  75    4  0.07
  76   49  0.83
  77    6  0.10

ACGTcount: A:0.17, C:0.31, G:0.29, T:0.23


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Done.