Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016335.1 Corchorus olitorius cultivar O-4 contig16368, 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: 5720
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34


Found at i:4985 original size:213 final size:213

Alignment explanation


    Indices: 4618--5035  Score: 581
    Period size: 213  Copynumber: 2.0  Consensus size: 213

       4608 GTTTGGTTGA

                                                      *         *    *  *    
       4618 GCTTTATTTAGATGGGACGGGCATTCGACATCTTCCCTCTCTGATTGGACATCTGAGTGGTCTTG
          1 GCTTTATTTAGATGGGACGGGCATTCGACATCTTCCCTCTCTAATTGGACATATGAGGGGCCTTG

                              *                         *            *       
       4683 TTCGATTGAATCTGAAAGGTTGCAGAAACTTGGCGAGCCTCCCAGGCAACATTAATGGGTTGAAA
         66 TTCGATTGAATCTGAAAGATTGCAGAAACTTGGCGAGCCTCCCAAGCAACATTAATGAGTTGAAA

                  *   *                                                      
       4748 TGCCTAGAAATTCTTAATCTCTCAGGCTGCTC-AAAATTGGAAAATTTGCCAGAGAATTTGCAGC
        131 TGCCTAAAAACTCTTAATCTCTCAGGCTGCTCTAAAATT-GAAAATTTGCCAGAGAATTTGCAGC

                               
       4812 AAGTAGAATCTTTGAAGGT
        195 AAGTAGAATCTTTGAAGGT

                                        *           *                        
       4831 GCTTTATTTAGATGGGACGGGCATTCGAGATCTTCCCTCTTTAATTGGACATATGAGGGGCCTTG
          1 GCTTTATTTAGATGGGACGGGCATTCGACATCTTCCCTCTCTAATTGGACATATGAGGGGCCTTG

              ***                      **          *          *    *         
       4896 TTTTCTT-AAGTCTGAAAGATTGCAGAGGCATT-GCGAGTCTCCCAAGCAGCATTCATGAGTTGA
         66 TTCGATTGAA-TCTGAAAGATTGCAGAAAC-TTGGCGAGCCTCCCAAGCAACATTAATGAGTTGA

                *            *                    *                  *       
       4959 AATGTCTAAAAACTCTTGATCTCTCAGGCTGCTCTAAACTTGAAAATTTGCCAGAGAGTTTGCAG
        129 AATGCCTAAAAACTCTTAATCTCTCAGGCTGCTCTAAAATTGAAAATTTGCCAGAGAATTTGCAG

                        
       5024 CAAGTAGAATCT
        194 CAAGTAGAATCT

       5036 CTCGAGGAGC


Statistics
Matches: 179,  Mismatches: 23, Indels: 6
        0.86            0.11        0.03

Matches are distributed among these distances:
 212    2  0.01
 213  170  0.95
 214    7  0.04

ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31


Consensus pattern (213 bp):   
GCTTTATTTAGATGGGACGGGCATTCGACATCTTCCCTCTCTAATTGGACATATGAGGGGCCTTG
TTCGATTGAATCTGAAAGATTGCAGAAACTTGGCGAGCCTCCCAAGCAACATTAATGAGTTGAAA
TGCCTAAAAACTCTTAATCTCTCAGGCTGCTCTAAAATTGAAAATTTGCCAGAGAATTTGCAGCA
AGTAGAATCTTTGAAGGT

Found at i:5676 original size:1 final size:1

Alignment explanation


    Indices: 5670--5695  Score: 52
    Period size: 1  Copynumber: 26.0  Consensus size: 1

       5660 ATCAAAGAGG

                                      
       5670 TTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTT

       5696 AACGGGGGGG


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   25  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Done.