Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012804.1 Corchorus olitorius cultivar O-4 contig12837, 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: 5372
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:76 original size:50 final size:50

Alignment explanation


    Indices: 1--290  Score: 490
    Period size: 50  Copynumber: 5.8  Consensus size: 50

                                *                      *      
          1 TAATTGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCTGTGTTGA
          1 TAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGA

                                                       *      
         51 TAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGA
          1 TAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGA

                                                      *       
        101 TAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGA
          1 TAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGA

                                           *          *       
        151 TAATTGACTCGTATGGAAACGAGTTTGGCTTATGGAAAAGCCCATGTTGA
          1 TAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGA

                        *              *                      
        201 TAATTGACTCGTGTGGAAACGAGTTTGCCTTGTGGAAAAGCCTATGTTGA
          1 TAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGA

                             *             *        
        251 TAATTGACTCGTATGGAGACGAGTTTGGCTTATGGAAAAG
          1 TAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG

        291 TCCACACATC


Statistics
Matches: 228,  Mismatches: 12, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  50  228  1.00

ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31


Consensus pattern (50 bp):   
TAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGA

Found at i:934 original size:50 final size:50

Alignment explanation


    Indices: 815--937  Score: 167
    Period size: 50  Copynumber: 2.5  Consensus size: 50

        805 TGGTTTTGGT

                 *      **     *   *                          
        815 CTCACAAATGGAGTGCAATCTTATTTTGAAAAGCAAATTTTGATCTTGAA
          1 CTCACCAATGGAAAGCAATTTTACTTTGAAAAGCAAATTTTGATCTTGAA

                                              *               
        865 CTCACCAATGGAAAGCAATTTTACTTTGAAAAGCGAATTTTGATCTTGAA
          1 CTCACCAATGGAAAGCAATTTTACTTTGAAAAGCAAATTTTGATCTTGAA

                 *                  
        915 CTCA-TAAGTGGAAAGCAATTTTA
          1 CTCACCAA-TGGAAAGCAATTTTA

        938 TTCTAAAACT


Statistics
Matches: 65,  Mismatches: 7, Indels: 2
        0.88            0.09        0.03

Matches are distributed among these distances:
  49    2  0.03
  50   63  0.97

ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33


Consensus pattern (50 bp):   
CTCACCAATGGAAAGCAATTTTACTTTGAAAAGCAAATTTTGATCTTGAA

Found at i:1960 original size:15 final size:15

Alignment explanation


    Indices: 1942--1989  Score: 62
    Period size: 15  Copynumber: 3.2  Consensus size: 15

       1932 TCCAAGTGCC

                           
       1942 TTTATTTTCATTTTT
          1 TTTATTTTCATTTTT

                         *  
       1957 TTTATTTTC-TTCATT
          1 TTTATTTTCATT-TTT

              *            
       1972 TTCATTTTCATTTTT
          1 TTTATTTTCATTTTT

               
       1987 TTT
          1 TTT

       1990 TGGGAAATCA


Statistics
Matches: 27,  Mismatches: 4, Indels: 4
        0.77            0.11        0.11

Matches are distributed among these distances:
  14    2  0.07
  15   23  0.85
  16    2  0.07

ACGTcount: A:0.12, C:0.10, G:0.00, T:0.77


Consensus pattern (15 bp):   
TTTATTTTCATTTTT

Found at i:3088 original size:42 final size:42

Alignment explanation


    Indices: 3041--3124  Score: 114
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       3031 ATGTAGTAAT

                          *    *                      
       3041 GAATGGATAATGCATGACCTATGCATGAACATATATACAAAG
          1 GAATGGATAATGCACGACCGATGCATGAACATATATACAAAG

                    *        **    *                  
       3083 GAATGGATGATGCACGATGGATGTATGAACATATATACAAAG
          1 GAATGGATAATGCACGACCGATGCATGAACATATATACAAAG

       3125 ACATGGACGA


Statistics
Matches: 36,  Mismatches: 6, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  42   36  1.00

ACGTcount: A:0.42, C:0.12, G:0.23, T:0.24


Consensus pattern (42 bp):   
GAATGGATAATGCACGACCGATGCATGAACATATATACAAAG

Found at i:3131 original size:42 final size:42

Alignment explanation


    Indices: 3065--3159  Score: 133
    Period size: 42  Copynumber: 2.3  Consensus size: 42

       3055 TGACCTATGC

                                     *                 
       3065 ATGAACATATATACAAAGGAATGGATGATGCA-CGATGGATGT
          1 ATGAACATATATACAAAGGAATGGACGATGCATCGA-GGATGT

                                              *        
       3107 ATGAACATATATACAAA-GACATGGACGATGCATGGAGGATGT
          1 ATGAACATATATACAAAGGA-ATGGACGATGCATCGAGGATGT

                        
       3149 ATG-ACATATAT
          1 ATGAACATATAT

       3160 CAATGGATAT


Statistics
Matches: 49,  Mismatches: 2, Indels: 5
        0.88            0.04        0.09

Matches are distributed among these distances:
  41   10  0.20
  42   37  0.76
  43    2  0.04

ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24


Consensus pattern (42 bp):   
ATGAACATATATACAAAGGAATGGACGATGCATCGAGGATGT
Done.