Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001590.1 Corchorus olitorius cultivar O-4 contig01590, 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, 682

Length: 1137
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30


Found at i:532 original size:28 final size:28

Alignment explanation


    Indices: 500--599  Score: 166
    Period size: 28  Copynumber: 3.6  Consensus size: 28

        490 GCACTTGAAG

                                        
        500 TGACCAAAATGCCCCTGGATATGCAAAA
          1 TGACCAAAATGCCCCTGGATATGCAAAA

                                  *     
        528 TGACCAAAATGCCCCTGGATATACAAAA
          1 TGACCAAAATGCCCCTGGATATGCAAAA

                                         
        556 TGACCAAAATGCCCCTGG-TCATGCAAAA
          1 TGACCAAAATGCCCCTGGAT-ATGCAAAA

               *            
        584 TGATCAAAATGCCCCT
          1 TGACCAAAATGCCCCT

        600 TTAAGTGACC


Statistics
Matches: 68,  Mismatches: 3, Indels: 2
        0.93            0.04        0.03

Matches are distributed among these distances:
  27    1  0.01
  28   67  0.99

ACGTcount: A:0.38, C:0.27, G:0.16, T:0.19


Consensus pattern (28 bp):   
TGACCAAAATGCCCCTGGATATGCAAAA

Found at i:894 original size:35 final size:35

Alignment explanation


    Indices: 855--1118  Score: 330
    Period size: 35  Copynumber: 7.5  Consensus size: 35

        845 TGGGTTCATA

                            *        *       * 
        855 TTGAAGATGCTACACCAAGTCATCTAAATTCGTTT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTCGTCT

                            *        *       * 
        890 TTGAAGATGCTACACCAAGTCATCTAAATTCGTTT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTCGTCT

                                  *          * 
        925 TTGAAGATGCTACACCGAGTCACCTGAATTCGTTT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTCGTCT

                    *      *      *        *   
        960 TTGAAGATACTACACTGAGTCACCTGAATTCATCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTCGTCT

                            *         *   **   
        995 TTGAAGATGCTACACCAAGTCATCTGGATTTATCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTCGTCT

                                      *   *    
       1030 TTGAAGATGCTACACCGAGTCATCTGGATTTGTCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTCGTCT

                                 *    *   **   
       1065 TTGAAGATGCTACACCGAGTCGTCTGGATTTATCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTCGTCT

                               
       1100 TTGAAGATGCTACACCGAG
          1 TTGAAGATGCTACACCGAG

       1119 CCGTCTGGAT


Statistics
Matches: 212,  Mismatches: 17, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  35  212  1.00

ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33


Consensus pattern (35 bp):   
TTGAAGATGCTACACCGAGTCATCTGAATTCGTCT

Found at i:1126 original size:105 final size:105

Alignment explanation


    Indices: 855--1137  Score: 368
    Period size: 105  Copynumber: 2.7  Consensus size: 105

        845 TGGGTTCATA

                            *        *     * *                          **   
        855 TTGAAGATGCTACACCAAGTCATCTAAATTCGTTTTTGAAGATGCTACACCAAGTCATCTAAATT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCTTTGAAGATGCTACACCAAGTCATCTGGATT

            ** *                                  * 
        920 CGTTTTTGAAGATGCTACACCGAGTCACCTGAATTCGTTT
         66 TATCTTTGAAGATGCTACACCGAGTCACCTGAATTCGTCT

                    *      *      *                                          
        960 TTGAAGATACTACACTGAGTCACCTGAATTCATCTTTGAAGATGCTACACCAAGTCATCTGGATT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCTTTGAAGATGCTACACCAAGTCATCTGGATT

                                       *   *   *    
       1025 TATCTTTGAAGATGCTACACCGAGTCATCTGGATTTGTCT
         66 TATCTTTGAAGATGCTACACCGAGTCACCTGAATTCGTCT

                                 *    *   *                    *  * *        
       1065 TTGAAGATGCTACACCGAGTCGTCTGGATTTATCTTTGAAGATGCTACACCGAGCCGTCTGGATT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCTTTGAAGATGCTACACCAAGTCATCTGGATT

                    
       1130 TATCTTTG
         66 TATCTTTG


Statistics
Matches: 153,  Mismatches: 25, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
 105  153  1.00

ACGTcount: A:0.27, C:0.21, G:0.19, T:0.34


Consensus pattern (105 bp):   
TTGAAGATGCTACACCGAGTCATCTGAATTCATCTTTGAAGATGCTACACCAAGTCATCTGGATT
TATCTTTGAAGATGCTACACCGAGTCACCTGAATTCGTCT
Done.