Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011464.1 Corchorus olitorius cultivar O-4 contig11497, 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, 783

Length: 1305
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.24


Found at i:281 original size:154 final size:154

Alignment explanation


    Indices: 1--866  Score: 1349
    Period size: 154  Copynumber: 5.7  Consensus size: 154

                    *             *             *                            
          1 TGAGGGTTCCCAAATCGAAGACAATTCAAAACGGAATTAATGGGCCCCGATAGGCCCAAAATAAC
          1 TGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAC

                                      *   *                                 *
         66 AAGTGTTCCAAATGAGCTAAAAACTTGACAATGGACTAATCTCACCAAAATGATTATAGTTAGGT
         66 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC

            *        *    *         
        131 TATAAACAACGGAACGAAAAGCAT
        131 CATAAACAATGGAAAGAAAAGCAT

                                                     *                       
        155 TGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATTGGCCCCGATAGGCCCAAAATAAC
          1 TGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAC

                                   *                                        *
        220 AAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGT
         66 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC

                                    
        285 CATAAACAATGGAAAGAAAAGCAT
        131 CATAAACAATGGAAAGAAAAGCAT

                                           *    *      *  *                  
        309 TGAGGGTTGCCAAATCGAAGACGATTCAAAATGGAAGTAATGGTCCTCGATAGGCCCAAAATAAC
          1 TGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAC

                         *                            *  *                   
        374 AAGTGTTCCAAATTAGCTAAAAACTTCACAGTGGACTAATCTTACTAAAATGATTATAGTTAGGC
         66 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC

                  **         *      
        439 CATAAATTATGGAAAGACAAGCAT
        131 CATAAACAATGGAAAGAAAAGCAT

                            *             *                                  
        463 TGAGGGTTGCCAAATCCAA-A--A--C--ATC---ACTAATGGGCCCCGATAGGCCCAAAATAAC
          1 TGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAC

              *                          *     *                             
        518 AACTGTTCCAAATGAGCTAAAAACTTCACTGTGGATTAATCTCACCAAAATGATTATAGTTAGGC
         66 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC

                                    
        583 CATAAACAATGGAAAGAAAAGCAT
        131 CATAAACAATGGAAAGAAAAGCAT

                                             **                     *      * 
        607 TGAGGGTTG-CAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCTAAAATAGC
          1 TGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAC

                                                                             
        671 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
         66 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC

                                    
        736 CATAAACAATGGAAAGAAAAGCAT
        131 CATAAACAATGGAAAGAAAAGCAT

                                                          *                  
        760 TGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCTCGATAGGCCCAAAATAAC
          1 TGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAC

                     *                          *     
        825 AAGTGTTCCCAATGAGCTAAAAACTTCACAGTGGACCAATCT
         66 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT

        867 GATACGAATC


Statistics
Matches: 649,  Mismatches: 52, Indels: 22
        0.90            0.07        0.03

Matches are distributed among these distances:
 143    8  0.01
 144  117  0.18
 146    1  0.00
 147    1  0.00
 148    1  0.00
 149    1  0.00
 150    2  0.00
 151    1  0.00
 153  124  0.19
 154  393  0.61

ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22


Consensus pattern (154 bp):   
TGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAC
AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
CATAAACAATGGAAAGAAAAGCAT

Found at i:757 original size:153 final size:154

Alignment explanation


    Indices: 479--866  Score: 670
    Period size: 153  Copynumber: 2.5  Consensus size: 154

        469 TTGCCAAATC

                  *                                  *                       
        479 CAAAACATCACTAATGGGCCCCGATAGGCCCAAAATAACAACTGTTCCAAATGAGCTAAAAACTT
          1 CAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT

               *     *                                                       
        544 CACTGTGGATTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG
         66 CACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG

                                    
        609 AGGGTTG-CAAATCGAAGACGATT
        131 AGGGTTGCCAAATCGAAGACGATT

                                          *      *                           
        632 CAAAACGTCACTAATGGGCCCCGATAGGCCTAAAATAGCAAGTGTTCCAAATGAGCTAAAAACTT
          1 CAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT

                                                                             
        697 CACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG
         66 CACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG

                                    
        762 AGGGTTGCCAAATCGAAGACGATT
        131 AGGGTTGCCAAATCGAAGACGATT

                   **           *                           *                
        786 CAAAACGGAACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCCAATGAGCTAAAAACTT
          1 CAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT

                      *     
        851 CACAGTGGACCAATCT
         66 CACAGTGGACTAATCT

        867 GATACGAATC


Statistics
Matches: 221,  Mismatches: 13, Indels: 1
        0.94            0.06        0.00

Matches are distributed among these distances:
 153  131  0.59
 154   90  0.41

ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21


Consensus pattern (154 bp):   
CAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT
CACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG
AGGGTTGCCAAATCGAAGACGATT
Done.