Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023304.1 Corchorus olitorius cultivar O-4 contig23337, 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: 3590
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.30


Found at i:43 original size:11 final size:11

Alignment explanation


    Indices: 27--57  Score: 53
    Period size: 11  Copynumber: 2.8  Consensus size: 11

         17 TTTATTTTTT

                       
         27 GTTTTTGTTTC
          1 GTTTTTGTTTC

                      *
         38 GTTTTTGTTTT
          1 GTTTTTGTTTC

                     
         49 GTTTTTGTT
          1 GTTTTTGTT

         58 AAGCTGTCAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  11   19  1.00

ACGTcount: A:0.00, C:0.03, G:0.19, T:0.77


Consensus pattern (11 bp):   
GTTTTTGTTTC

Found at i:2677 original size:260 final size:260

Alignment explanation


    Indices: 2184--2706  Score: 856
    Period size: 260  Copynumber: 2.0  Consensus size: 260

       2174 TGTGAGAGAT

                         *                      *            *               
       2184 TAAATAGCATAAAGCATAAAAGTATAGGGATCATTTGCTAAATATCCCAGCAAAAAAAAGATTAG
          1 TAAATAGCATAAAACATAAAAGTATAGGGATCATTTACTAAATATCCCACCAAAAAAAAGATTAG

                                    *                                    *   
       2249 TTTATTCAGAGTGGGACCCACTAATAGTAACTTTTAATCCAAAGTTCCCAAAACGCCCTTGGCTA
         66 TTTATTCAGAGTGGGACCCACTAAAAGTAACTTTTAATCCAAAGTTCCCAAAACGCCCTTGACTA

                                                                             
       2314 TCAACCTAAATAGCGAAAAAAACCGAGTATGAAAAGTACCAAAATACCCCTGACAATTTGTTCTT
        131 TCAACCTAAATAGCG-AAAAAACCGAGTATGAAAAGTACCAAAATACCCCTGACAATTTGTTCTT

                                   *     *                *                  
       2379 GGGTGAATGGTGTGCATCTTATAGCTGGATAAAAGGGTAATTTCATTTTCAACTTTAATATATGT
        195 GGGTGAATGGTGTGCATCTTATAACTGGACAAAAGGGTAA-TTCATATTCAACTTTAATATATGT

              
       2444 TA
        259 TA

                                                         *                   
       2446 TAAATAGCATAAAACATAAAAGTATAGGGATCATTTACTAAATATTCCACCAAAAAAAAAAGATT
          1 TAAATAGCATAAAACATAAAAGTATAGGGATCATTTACTAAATATCCCACC--AAAAAAAAGATT

                    *                                              *         
       2511 AGTTTATTGAGAGTGGGACCCACTAAAAGTAACTTTTAAT-CAAAGTTCCCAAAATGCCCTTGAC
         64 AGTTTATTCAGAGTGGGACCCACTAAAAGTAACTTTTAATCCAAAGTTCCCAAAACGCCCTTGAC

                                                                             
       2575 TATCAACCTAAATAGCG-AAAAACCGAGTATG-AAAGTACCAAAATACCCCTGACAATTTGTTCT
        129 TATCAACCTAAATAGCGAAAAAACCGAGTATGAAAAGTACCAAAATACCCCTGACAATTTGTTCT

                            *                *                               
       2638 TGGGTGAAT-GTGGTGTATCTTATAACTGGACAGAAGGGTAATTCATATTCAACTTTAATATATG
        194 TGGGTGAATGGT-GTGCATCTTATAACTGGACAAAAGGGTAATTCATATTCAACTTTAATATATG

               
       2702 TTA
        258 TTA

              
       2705 TA
          1 TA

       2707 TTTGATAATA


Statistics
Matches: 245,  Mismatches: 13, Indels: 9
        0.92            0.05        0.03

Matches are distributed among these distances:
 259   29  0.12
 260   66  0.27
 261   14  0.06
 262   47  0.19
 263   39  0.16
 264   50  0.20

ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29


Consensus pattern (260 bp):   
TAAATAGCATAAAACATAAAAGTATAGGGATCATTTACTAAATATCCCACCAAAAAAAAGATTAG
TTTATTCAGAGTGGGACCCACTAAAAGTAACTTTTAATCCAAAGTTCCCAAAACGCCCTTGACTA
TCAACCTAAATAGCGAAAAAACCGAGTATGAAAAGTACCAAAATACCCCTGACAATTTGTTCTTG
GGTGAATGGTGTGCATCTTATAACTGGACAAAAGGGTAATTCATATTCAACTTTAATATATGTTA

Found at i:2924 original size:2 final size:2

Alignment explanation


    Indices: 2911--2946  Score: 56
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       2901 ACAACCTTGG

                   *                                               
       2911 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       2947 TACTCCCTCC


Statistics
Matches: 31,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   30  0.97

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Done.