Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022012.1 Corchorus olitorius cultivar O-4 contig22045, 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: 39813
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30


Found at i:5791 original size:178 final size:178

Alignment explanation


    Indices: 5522--5859  Score: 466
    Period size: 178  Copynumber: 1.9  Consensus size: 178

       5512 CCGATTAAGG

                 *                                             *     *       
       5522 TGATTTAAGTGTCTATTAAAAGATTGTTCCATGATCTAAAACTTTCATGAAGGACTCGAAAACAA
          1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTAAAACTTTCATGAAAGACTCAAAAACAA

                     *         *                     *                **     
       5587 AATTTAATATTTCAAGTATCAAAAATGCTTCCGAAA-AATTTGTTGTTTCGGCTAACGGGAATAG
         66 AATTTAATAGTTCAAGTATAAAAAATGCTTCC-AAAGAATTAGTTGTTTCGGCTAACGAAAATAG

                    *         *                               
       5651 ACGGTCCACTTAATATTATATAACTT-TTGCTCCAGATGTCTGATTGAGA
        130 ACGGTCCAATTAATATTACATAA-TTCTTGCTCCAGATGTCTGATTGAGA

                          *  *    *               *                        * 
       5700 TGATTCAAGTGTCTCTTCAAAGGTTGTTCCATGATCTACAACTTTCATGAAAGACTCAAAAACTA
          1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTAAAACTTTCATGAAAGACTCAAAAACAA

            *                                                   *            
       5765 TATTTAAT-GTTCAAGATATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGGTTAACGAAAATAG
         66 AATTTAATAGTTCAAG-TATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGGCTAACGAAAATAG

                  *                        
       5829 ACGGTCTAATTAATATTACATAATTCTTGCT
        130 ACGGTCCAATTAATATTACATAATTCTTGCT

       5860 TATGGTGAAA


Statistics
Matches: 139,  Mismatches: 18, Indels: 6
        0.85            0.11        0.04

Matches are distributed among these distances:
 177   11  0.08
 178  128  0.92

ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35


Consensus pattern (178 bp):   
TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTAAAACTTTCATGAAAGACTCAAAAACAA
AATTTAATAGTTCAAGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGGCTAACGAAAATAGA
CGGTCCAATTAATATTACATAATTCTTGCTCCAGATGTCTGATTGAGA

Found at i:7674 original size:38 final size:38

Alignment explanation


    Indices: 7623--7695  Score: 146
    Period size: 38  Copynumber: 1.9  Consensus size: 38

       7613 TTTTAAGTCA

                                                  
       7623 TGCATGTTCATGATAAATGATTGAACATATATTGTTGC
          1 TGCATGTTCATGATAAATGATTGAACATATATTGTTGC

                                               
       7661 TGCATGTTCATGATAAATGATTGAACATATATTGT
          1 TGCATGTTCATGATAAATGATTGAACATATATTGT

       7696 CCATTGCAAC


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  38   35  1.00

ACGTcount: A:0.33, C:0.10, G:0.18, T:0.40


Consensus pattern (38 bp):   
TGCATGTTCATGATAAATGATTGAACATATATTGTTGC

Found at i:15983 original size:44 final size:41

Alignment explanation


    Indices: 15910--15998  Score: 142
    Period size: 44  Copynumber: 2.1  Consensus size: 41

      15900 ACTAGACTGT

                                                     
      15910 GGATAGTCCTGCACAATATGTGCAAGGCAATCCCAAATGTA
          1 GGATAGTCCTGCACAATATGTGCAAGGCAATCCCAAATGTA

                       *                                
      15951 GGATAGTCCTGTACCAATTATAGTGCAAGGCAATCCCAAATGTA
          1 GGATAGTCCTGCA-CAA-TAT-GTGCAAGGCAATCCCAAATGTA

                
      15995 GGAT
          1 GGAT

      15999 GGCTACCTTC


Statistics
Matches: 44,  Mismatches: 1, Indels: 3
        0.92            0.02        0.06

Matches are distributed among these distances:
  41   12  0.27
  42    3  0.07
  43    3  0.07
  44   26  0.59

ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24


Consensus pattern (41 bp):   
GGATAGTCCTGCACAATATGTGCAAGGCAATCCCAAATGTA

Found at i:21178 original size:36 final size:36

Alignment explanation


    Indices: 21109--21178  Score: 95
    Period size: 36  Copynumber: 1.9  Consensus size: 36

      21099 TTAAATTTTT

                           *         ****       
      21109 TATTAGTTAATGAGCTTGATTCGAGTTTTTTTTTCC
          1 TATTAGTTAATGAGCGTGATTCGAGGGGGTTTTTCC

                                              
      21145 TATTAGTTAATGAGCGTGATTCGAGGGGGTTTTT
          1 TATTAGTTAATGAGCGTGATTCGAGGGGGTTTTT

      21179 TTTAATTTTA


Statistics
Matches: 29,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  36   29  1.00

ACGTcount: A:0.20, C:0.09, G:0.24, T:0.47


Consensus pattern (36 bp):   
TATTAGTTAATGAGCGTGATTCGAGGGGGTTTTTCC
Done.