Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014036.1 Corchorus olitorius cultivar O-4 contig14069, 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: 23484
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32


Found at i:3858 original size:25 final size:24

Alignment explanation


    Indices: 3822--3868  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

       3812 TCCTTCTATT

                                    
       3822 CATCTATCATC-AAGTTTTTCATC
          1 CATCTATCATCAAAGTTTTTCATC

                                    
       3845 CATCTTATCCATCAAAGTTTTTCA
          1 CATC-TAT-CATCAAAGTTTTTCA

       3869 AATTTTCAAG


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    4  0.19
  24    3  0.14
  25    4  0.19
  26   10  0.48

ACGTcount: A:0.28, C:0.26, G:0.04, T:0.43


Consensus pattern (24 bp):   
CATCTATCATCAAAGTTTTTCATC

Found at i:9776 original size:76 final size:76

Alignment explanation


    Indices: 9639--9790  Score: 177
    Period size: 76  Copynumber: 2.0  Consensus size: 76

       9629 ACAAGGGCCC

                                                               *             
       9639 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCA-AG
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGA-

                        
       9703 TGGGCAGTGTCA
         65 TGGGCAGTGTCA

                    *     *              *                            **     
       9715 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGATG-ACCCATGT-GTTTCGCCTGATCACCCA
          1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTGA-GCACCCATGTGGTTT-GCCTGAGAACCCA

                   *      
       9777 GATGGGCTGTGTCA
         63 GATGGGCAGTGTCA

       9791 TGGCTCGGTA


Statistics
Matches: 65,  Mismatches: 7, Indels: 8
        0.81            0.09        0.10

Matches are distributed among these distances:
  75    4  0.06
  76   55  0.85
  77    6  0.09

ACGTcount: A:0.17, C:0.30, G:0.28, T:0.25


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA

Found at i:16987 original size:34 final size:34

Alignment explanation


    Indices: 16943--17018  Score: 143
    Period size: 34  Copynumber: 2.2  Consensus size: 34

      16933 ACGTTGGCTG

                 *                            
      16943 CTGGGGGCGCGGGGGACAAGGGCCCCGACTCCAC
          1 CTGGGCGCGCGGGGGACAAGGGCCCCGACTCCAC

                                              
      16977 CTGGGCGCGCGGGGGACAAGGGCCCCGACTCCAC
          1 CTGGGCGCGCGGGGGACAAGGGCCCCGACTCCAC

                    
      17011 CTGGGCGC
          1 CTGGGCGC

      17019 CCACATGGTT


Statistics
Matches: 41,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  34   41  1.00

ACGTcount: A:0.13, C:0.37, G:0.43, T:0.07


Consensus pattern (34 bp):   
CTGGGCGCGCGGGGGACAAGGGCCCCGACTCCAC

Found at i:17153 original size:76 final size:76

Alignment explanation


    Indices: 17002--17145  Score: 168
    Period size: 76  Copynumber: 1.9  Consensus size: 76

      16992 ACAAGGGCCC

                                                               *           * 
      17002 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT

                       
      17067 GGGCAGTGTCA
         66 GGGCAGTGTCA

                    *     *  *           *                            **     
      17078 CGACTCCAGCTGGGTGCTCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
          1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA

                  
      17140 GATGGG
         63 GATGGG

      17146 TTGTGTCATG


Statistics
Matches: 57,  Mismatches: 8, Indels: 6
        0.80            0.11        0.08

Matches are distributed among these distances:
  75    4  0.07
  76   47  0.82
  77    6  0.11

ACGTcount: A:0.17, C:0.29, G:0.29, T:0.24


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA

Found at i:19557 original size:25 final size:24

Alignment explanation


    Indices: 19521--19567  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

      19511 TCCTTCTATT

                                    
      19521 CATCTATCATC-AAGTTTTTCATC
          1 CATCTATCATCAAAGTTTTTCATC

                                    
      19544 CATCTCATCCATCAAAGTTTTTCA
          1 CATCT-AT-CATCAAAGTTTTTCA

      19568 AATTTTCAAG


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    2  0.10
  25    4  0.19
  26   10  0.48

ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40


Consensus pattern (24 bp):   
CATCTATCATCAAAGTTTTTCATC

Done.