Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023189.1 Corchorus olitorius cultivar O-4 contig23222, 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: 18259
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:12269 original size:213 final size:213

Alignment explanation


    Indices: 11902--12323  Score: 677
    Period size: 213  Copynumber: 2.0  Consensus size: 213

      11892 AAAACTGCTA

                                                                             
      11902 AGTTTGGAGCAACCACTGAGATTCAGAGTCTCAAGAGATGTTAAGTTGCAAATGCTATCTGGAAG
          1 AGTTTGGAGCAACCACTGAGATTCAGAGTCTCAAGAGATGTTAAGTTGCAAATGCTATCTGGAAG

                    * *                          *                           
      11967 TTCCCTCAGGTTCTTGCACTCTGCCAAATTCAAGAATTCAAGTCTTTCCACATCCCCAATGGATT
         66 TTCCCTCAAGCTCTTGCACTCTGCCAAATTCAAGAATGCAAGTCTTTCCACATCCCCAATGGATT

                                                                *            
      12032 GGTGAACCTTAGTTAAACTTGTACAACCCTCGAGTTCAAGCCTTGTCAAACTTTTGCATCTACAA
        131 GGTGAACCTTAGTTAAACTTGTACAACCCTCGAGTTCAAGCCTTGTCAAACTATTGCATCTACAA

                              
      12097 AAGTTTGGGATCTCCAAT
        196 AAGTTTGGGATCTCCAAT

                                                                  * *        
      12115 AGTTTGGAGCAACCACTGAGATTCAGAGTCTCAAGAGATGTTAAGTTGCAAATGTTGTCTGGAAG
          1 AGTTTGGAGCAACCACTGAGATTCAGAGTCTCAAGAGATGTTAAGTTGCAAATGCTATCTGGAAG

                         *                                     *  **         
      12180 TTCCC-CTAAGCTGTTGCACTCTGCCAAATTCAAGAATGCAAGTCTTTCCAGATTTCCAATGGAT
         66 TTCCCTC-AAGCTCTTGCACTCTGCCAAATTCAAGAATGCAAGTCTTTCCACATCCCCAATGGAT

                                                  *   *   *   *              
      12244 TGGTGAACCTT-GCTTAAACTTGTACAACCCTCGAGTTGAAGTCTTTTCAGACTATTGCATCTAC
        130 TGGTGAACCTTAG-TTAAACTTGTACAACCCTCGAGTTCAAGCCTTGTCAAACTATTGCATCTAC

                       *    
      12308 AAAAGTTTGGGGTCTC
        194 AAAAGTTTGGGATCTC

      12324 AACAAGACGT


Statistics
Matches: 192,  Mismatches: 15, Indels: 4
        0.91            0.07        0.02

Matches are distributed among these distances:
 212    2  0.01
 213  190  0.99

ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31


Consensus pattern (213 bp):   
AGTTTGGAGCAACCACTGAGATTCAGAGTCTCAAGAGATGTTAAGTTGCAAATGCTATCTGGAAG
TTCCCTCAAGCTCTTGCACTCTGCCAAATTCAAGAATGCAAGTCTTTCCACATCCCCAATGGATT
GGTGAACCTTAGTTAAACTTGTACAACCCTCGAGTTCAAGCCTTGTCAAACTATTGCATCTACAA
AAGTTTGGGATCTCCAAT

Found at i:17796 original size:36 final size:36

Alignment explanation


    Indices: 17749--17818  Score: 104
    Period size: 36  Copynumber: 1.9  Consensus size: 36

      17739 TTCAATAACC

                         *  *   *               
      17749 TTACATCTTTTGTGATTTTGGTTATCATATTTCTAA
          1 TTACATCTTTTGTAATCTTGATTATCATATTTCTAA

                  *                           
      17785 TTACATTTTTTGTAATCTTGATTATCATATTTCT
          1 TTACATCTTTTGTAATCTTGATTATCATATTTCT

      17819 CCAAAATCTC


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  36   30  1.00

ACGTcount: A:0.23, C:0.11, G:0.09, T:0.57


Consensus pattern (36 bp):   
TTACATCTTTTGTAATCTTGATTATCATATTTCTAA
Done.