Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023369.1 Corchorus olitorius cultivar O-4 contig23402, 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: 5343
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28


Found at i:307 original size:154 final size:154

Alignment explanation


    Indices: 3--1501  Score: 2242
    Period size: 154  Copynumber: 9.7  Consensus size: 154

          1 GA

                                   *                 *      *                
          3 TTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGTCCCGAATGGCCCAAAATAACAAG
          1 TTTGCCAAATCGAAGACGA--TTCAAAACCGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAG

                                                            *                
         68 TGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATAATTATAGTTAGGCCAT
         64 TGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCAT

                                      
        133 AAACAATGGAAAGAAAAGCATTGTCG
        129 AAACAATGGAAAGAAAAGCATTGTCG

                                 *                            *              
        159 TTTGCCAAATCGAAGACGATTGAAAACCGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTG
          1 TTTGCCAAATCGAAGACGATTCAAAACCGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTG

                                   *             *                   *       
        224 TTCAAAATGAGCTAAAAACTTCATAGTGGACTAATCTCACCAAAATGATTATAGTTACGCCATAA
         66 TTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAA

                                 ** 
        289 ACAATGGAAAGAAAAGCATTGAGG
        131 ACAATGGAAAGAAAAGCATTGTCG

                              *     *     *               *                  
        313 TTTGCCAAATCGAAGACGTTTCAATA-CGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGT
          1 TTTGCCAAATCGAAGACGATTCAAAACCG-AACTAATGGGCCCCGAAAGGCCCAAAATAACAAGT

                *          *   *                  *                          
        377 GTTCCAAATGAGCTACAAATTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATA
         65 GTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATA

                           *      ** 
        442 AACAATGGAAAGAAACGCATTGAGG
        130 AACAATGGAAAGAAAAGCATTGTCG

                                          *                                  
        467 TTTGCCAAATCGAAGACGATTCAAAACCGATCTAATGGGCCCCGAAAGGCCCAAAATAACAAGTG
          1 TTTGCCAAATCGAAGACGATTCAAAACCGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTG

                       *                                                   * 
        532 TTCAAAATGAGTTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATTA
         66 TTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAA

                            *   * * 
        597 ACAATGGAAAGAAAAGTATTATGG
        131 ACAATGGAAAGAAAAGCATTGTCG

                                                        *                    
        621 TTTGCCAAATCGAAGACCG-TTCAAAACCGAACTAATGGGCCCCTAAAGGCCCAAAATAACAAGT
          1 TTTGCCAAATCGAAGA-CGATTCAAAACCGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGT

                                                           *                 
        685 GTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATAATTATAGTTAGGCCATA
         65 GTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATA

                                 *   
        750 AACAATGGAAAGAAAAGCATTTTCG
        130 AACAATGGAAAGAAAAGCATTGTCG

                                                              *              
        775 TTTGCCAAATCGAAGACGATTCAAAACCGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTG
          1 TTTGCCAAATCGAAGACGATTCAAAACCGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTG

               *                        *     **           *                 
        840 TTCGAAATGAGCTAAAAACTTCACAGTGAACTAAAATTACCAAAATGTTTATAGTTAGGCCATAA
         66 TTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAA

                        *      *      
        905 ACAATGGAAAAACAAAAGCTTTGT-G
        131 ACAATGG--AAAGAAAAGCATTGTCG

                                    *                 *      *               
        930 ATTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGTCCCGAATGGCCCAAAATAACAA
          1 -TTTGCCAAATCGAAGACGA--TTCAAAACCGAACTAATGGGCCCCGAAAGGCCCAAAATAACAA

                                                             *               
        995 GTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATAATTATAGTTAGGCCA
         63 GTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCA

                                       
       1060 TAAACAATGGAAAGAAAAGCATTGTCG
        128 TAAACAATGGAAAGAAAAGCATTGTCG

                                 * *       *              *        *         
       1087 TTTGCCAAATCGAAGACGATTGACAACCGAAGTAATGGGCCCCGAATGGCCCAAATTAACAAGTG
          1 TTTGCCAAATCGAAGACGATTCAAAACCGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTG

                                                     *                       
       1152 TTCAAAATGAGCTAAAAACTTCACAGTGGA-TGAATCTTACAAAAATGATTATAGTTAGGCCATA
         66 TTCAAAATGAGCTAAAAACTTCACAGTGGACT-AATCTTACCAAAATGATTATAGTTAGGCCATA

                      *              
       1216 AACAATGGAATGAAAAGCATTGTCG
        130 AACAATGGAAAGAAAAGCATTGTCG

                                                              *              
       1241 TTTGCCAAATCGAAGACGATTCAAAACCGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTG
          1 TTTGCCAAATCGAAGACGATTCAAAACCGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTG

                                   * *  *      *  *                          
       1306 TTCAAAATGAGCTAAAAACTTCATAATGAACTAATATTTCCAAAATGATTATAGTTAGGCCATAA
         66 TTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAA

                *     *      *      
       1371 ACAAAGGAAACAAAAGCTTTGT-G
        131 ACAATGGAAAGAAAAGCATTGTCG

                               *  *                 *      * *               
       1394 ATTTGCCAAATCG-A-A-GTTTTAAAACCGAACTAATGGGTCCCGAATGACCCAAAATAACAAGT
          1 -TTTGCCAAATCGAAGACGATTCAAAACCGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGT

                               *                      *    
       1456 GTTCAAAATGAGCT-AAAATTTCACAGTGGACTAATCTTACCCAAAT
         65 GTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAAT

       1502 TGATGTGCCA


Statistics
Matches: 1225,  Mismatches: 105, Indels: 32
        0.90            0.08        0.02

Matches are distributed among these distances:
 150   25  0.02
 151   55  0.04
 152    1  0.00
 153    7  0.01
 154  940  0.77
 155    6  0.00
 156   82  0.07
 157    1  0.00
 158  108  0.09

ACGTcount: A:0.41, C:0.19, G:0.18, T:0.23


Consensus pattern (154 bp):   
TTTGCCAAATCGAAGACGATTCAAAACCGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTG
TTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAA
ACAATGGAAAGAAAAGCATTGTCG

Done.