Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023858.1 Corchorus olitorius cultivar O-4 contig23891, 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: 25211
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:3031 original size:2 final size:2

Alignment explanation


    Indices: 3024--3050  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       3014 TCTTTACTAG

                                                    
       3024 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

       3051 GATTCAGTTT


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

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:14162 original size:7 final size:6

Alignment explanation


    Indices: 14133--14172  Score: 55
    Period size: 6  Copynumber: 6.7  Consensus size: 6

      14123 CCACCTCTTA

                      *                                    
      14133 AAAAAG AAATAG AAAAA- AAAAAGG AAAAAG AAAAAG AAAA
          1 AAAAAG AAAAAG AAAAAG AAAAA-G AAAAAG AAAAAG AAAA

      14173 CTTAGCACAC


Statistics
Matches: 30,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
   5    5  0.17
   6   20  0.67
   7    5  0.17

ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03


Consensus pattern (6 bp):   
AAAAAG

Found at i:17180 original size:24 final size:25

Alignment explanation


    Indices: 17139--17185  Score: 62
    Period size: 24  Copynumber: 1.9  Consensus size: 25

      17129 AAAGACGAGG

                         *           
      17139 AGGAAAAAAAAACCATA-TACTAAA
          1 AGGAAAAAAAAACAATATTACTAAA

                                    
      17163 AGGAAAACAAAAA-AATATTACTA
          1 AGGAAAA-AAAAACAATATTACTA

      17186 CTTGTACGTG


Statistics
Matches: 20,  Mismatches: 1, Indels: 3
        0.83            0.04        0.12

Matches are distributed among these distances:
  24   10  0.50
  25   10  0.50

ACGTcount: A:0.66, C:0.11, G:0.09, T:0.15


Consensus pattern (25 bp):   
AGGAAAAAAAAACAATATTACTAAA

Found at i:22108 original size:31 final size:32

Alignment explanation


    Indices: 22039--22116  Score: 97
    Period size: 31  Copynumber: 2.5  Consensus size: 32

      22029 CTCAAAAGGC

                          *       *    *     
      22039 GATCAATTTAGTCAAATGTACTTATAAGATTAG
          1 GATCAATTTAGTC-CATGTACTCATAAAATTAG

                                            
      22072 G-TCAATTTAGTCCATGTACTCATAAAATT-G
          1 GATCAATTTAGTCCATGTACTCATAAAATTAG

                    *      
      22102 GATCAATTGAGTCCA
          1 GATCAATTTAGTCCA

      22117 ATCGACAAAG


Statistics
Matches: 40,  Mismatches: 4, Indels: 4
        0.83            0.08        0.08

Matches are distributed among these distances:
  30    2  0.05
  31   26  0.65
  32   11  0.28
  33    1  0.03

ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35


Consensus pattern (32 bp):   
GATCAATTTAGTCCATGTACTCATAAAATTAG

Found at i:22291 original size:62 final size:63

Alignment explanation


    Indices: 22199--22320  Score: 219
    Period size: 62  Copynumber: 2.0  Consensus size: 63

      22189 CAACCTTATG

                                                 *                         
      22199 ATGAGTACATAAACCCAAATAGATCGCTTTTTGAGTATATGGGCAAAATTGAACATTTTTGTA
          1 ATGAGTACATAAACCCAAATAGATCGCTTTTTGAGTACATGGGCAAAATTGAACATTTTTGTA

                                                       *                
      22262 ATGAGTACATAAA-CCAAATAGATCGCTTTTTGAGTACATGGGTAAAATTGAACATTTTT
          1 ATGAGTACATAAACCCAAATAGATCGCTTTTTGAGTACATGGGCAAAATTGAACATTTTT

      22321 TTACAGTACA


Statistics
Matches: 57,  Mismatches: 2, Indels: 1
        0.95            0.03        0.02

Matches are distributed among these distances:
  62   44  0.77
  63   13  0.23

ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34


Consensus pattern (63 bp):   
ATGAGTACATAAACCCAAATAGATCGCTTTTTGAGTACATGGGCAAAATTGAACATTTTTGTA

Found at i:25203 original size:7 final size:8

Alignment explanation


    Indices: 25187--25211  Score: 50
    Period size: 8  Copynumber: 3.1  Consensus size: 8

      25177 TGATTTCATC

                    
      25187 AAAAGAAA
          1 AAAAGAAA

                    
      25195 AAAAGAAA
          1 AAAAGAAA

                    
      25203 AAAAGAAA
          1 AAAAGAAA

             
      25211 A
          1 A


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   17  1.00

ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00


Consensus pattern (8 bp):   
AAAAGAAA
Done.