Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023889.1 Corchorus olitorius cultivar O-4 contig23922, 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: 17176
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32


Found at i:6715 original size:112 final size:112

Alignment explanation


    Indices: 6539--6740  Score: 341
    Period size: 112  Copynumber: 1.8  Consensus size: 112

       6529 GGTGTCATCA

                      **                               *                     
       6539 AATCTTTGCTTGTCAATCTTGTTCCTCCTTATCAATTATGAGAGGACATAACCCAATGACACAAG
          1 AATCTTTGCTCATCAATCTTGTTCCTCCTTATCAATTATGAGAAGACATAACCCAATGACACAAG

             *                                             
       6604 TGTCACAATGTTCCAACAACATAACAATGTGTTTACCAGTGTAGTCG
         66 TCTCACAATGTTCCAACAACATAACAATGTGTTTACCAGTGTAGTCG

                                                               *             
       6651 AATCTTTGCTCATCAATCTTGTTCCTCCTTATCAATTATGAGAAGACATAATCCAATGACACAAG
          1 AATCTTTGCTCATCAATCTTGTTCCTCCTTATCAATTATGAGAAGACATAACCCAATGACACAAG

                        *  *         
       6716 TCTCACAATGTTGCAGCAACATAAC
         66 TCTCACAATGTTCCAACAACATAAC

       6741 GATAAGGTTT


Statistics
Matches: 83,  Mismatches: 7, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
 112   83  1.00

ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31


Consensus pattern (112 bp):   
AATCTTTGCTCATCAATCTTGTTCCTCCTTATCAATTATGAGAAGACATAACCCAATGACACAAG
TCTCACAATGTTCCAACAACATAACAATGTGTTTACCAGTGTAGTCG

Found at i:8862 original size:76 final size:76

Alignment explanation


    Indices: 8725--8875  Score: 182
    Period size: 76  Copynumber: 2.0  Consensus size: 76

       8715 ACAAGGACCC

                                                               *           * 
       8725 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT

                       
       8790 GGGCAGTGTCA
         66 GGGCAGTGTCA

                    *     *              *                            **     
       8801 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
          1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA

                   *     
       8863 GATGGGCTGTGTC
         63 GATGGGCAGTGTC

       8876 TTAGCTCATC


Statistics
Matches: 64,  Mismatches: 8, Indels: 6
        0.82            0.10        0.08

Matches are distributed among these distances:
  75    4  0.06
  76   54  0.84
  77    6  0.09

ACGTcount: A:0.17, C:0.30, G:0.29, T:0.25


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA

Found at i:12192 original size:9 final size:8

Alignment explanation


    Indices: 12161--12194  Score: 50
    Period size: 8  Copynumber: 4.1  Consensus size: 8

      12151 CAAATTCTCC

                *   
      12161 AAAACTTG
          1 AAAATTTG

                    
      12169 AAAATTTG
          1 AAAATTTG

                    
      12177 AAAATTTG
          1 AAAATTTG

                     
      12185 AGAAATTTG
          1 A-AAATTTG

             
      12194 A
          1 A

      12195 TGGAAAAGGT


Statistics
Matches: 24,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
   8   16  0.67
   9    8  0.33

ACGTcount: A:0.50, C:0.03, G:0.15, T:0.32


Consensus pattern (8 bp):   
AAAATTTG

Found at i:14854 original size:21 final size:21

Alignment explanation


    Indices: 14821--14869  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

      14811 AAGAATTGTA

                          **     
      14821 GCTT-CTTGGAAATGGCTCTT
          1 GCTTCCTTGGAAATCCCTCTT

                    *            
      14841 GCTTCCTTTGAAATCCCTCTT
          1 GCTTCCTTGGAAATCCCTCTT

                    
      14862 GCATTCCT
          1 GC-TTCCT

      14870 AAAGCATTGA


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  20    4  0.17
  21   15  0.62
  22    5  0.21

ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41


Consensus pattern (21 bp):   
GCTTCCTTGGAAATCCCTCTT
Done.