Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012225.1 Corchorus olitorius cultivar O-4 contig12258, 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: 3286
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30


Found at i:2852 original size:154 final size:154

Alignment explanation


    Indices: 2572--3286  Score: 1062
    Period size: 154  Copynumber: 4.7  Consensus size: 154

       2562 CCGTATTAGA

                                             *                               
       2572 TCACAGTGGACTAATCTCACCAAAATGATTATATTTAGGCCATAAACAATGGAAAGAAAAGCATT
          1 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT

                                                  *       **                 
       2637 GAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTATTGGGCCCTTATAGGCCCAAAATAA-A
         66 GAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACA

                                     
       2701 ATGTGTTCCAAATGAGCTAAAAACT
        131 A-GTGTTCCAAATGAGCTAAAAACT

                 *                                           *         *     
       2726 TCACACTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACGGAAAGAAAGGCATT
          1 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT

                                            **                               
       2791 GAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACA
         66 GAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACA

                  **           *    
       2856 AGTGTTGAAAATGAGCTAATAACT
        131 AGTGTTCCAAATGAGCTAAAAACT

                                                  *           *  *           
       2880 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGCCCATAAAC-ATTGATAGAAAAGCATT
          1 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT

                *     *                                   **                 
       2944 GAGGTTTGCCTAATCGAAGACGATTCAAAACGGAACTAATGGGCCCAAATAGGCCCAAAATAA-A
         66 GAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACA

                                     
       3008 ATGTGTTCCAAATGAGCTAAAAACT
        131 A-GTGTTCCAAATGAGCTAAAAACT

               **                                            *         *     
       3033 TCATTGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACGGAAAGAAAGGCATT
          1 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT

                         *                  **      *             *          
       3098 GAGGGTTGCCAAAGCGAAGACGATTCAAAACGTCACTAATAGGCCCCGATAGGCTCAAAATAACA
         66 GAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACA

                                    
       3163 AGTGTTCCAAATGAGCTAAAAACT
        131 AGTGTTCCAAATGAGCTAAAAACT

                          *                         *                 *      
       3187 TCACAGTGGACTAACCTCACCAAAATGATTATAGTTAGGCTATAAACAATGGAAAG--GAGCATT
          1 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT

                *     *       *      *           
       3250 GAGGTTTGCCTAATCGAATACGATTTAAAACGGAACT
         66 GAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACT


Statistics
Matches: 500,  Mismatches: 57, Indels: 10
        0.88            0.10        0.02

Matches are distributed among these distances:
 152   37  0.07
 153  134  0.27
 154  325  0.65
 155    4  0.01

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


Consensus pattern (154 bp):   
TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
GAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACA
AGTGTTCCAAATGAGCTAAAAACT

Found at i:3127 original size:307 final size:306

Alignment explanation


    Indices: 2572--3286  Score: 1173
    Period size: 307  Copynumber: 2.3  Consensus size: 306

       2562 CCGTATTAGA

                                             *                   *           
       2572 TCACAGTGGACTAATCTCACCAAAATGATTATATTTAGGCCATAAACAATGGAAAGAAAAGCATT
          1 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC-AT-GATAGAAAAGCATT

                *     *                           *       **                 
       2637 GAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTATTGGGCCCTTATAGGCCCAAAATAAAA
         64 GAGGTTTGCCTAATCGAAGACGATTCAAAACGGAACTAATGGGCCCAAATAGGCCCAAAATAAAA

                                                                             
       2702 TGTGTTCCAAATGAGCTAAAAACTTCACACTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
        129 TGTGTTCCAAATGAGCTAAAAACTTCACACTGGACTAATCTCACCAAAATGATTATAGTTAGGCC

                                                 *                          *
       2767 ATAAACAACGGAAAGAAAGGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATG
        194 ATAAACAACGGAAAGAAAGGCATTGAGGGTTGCCAAAGCGAAGACGATTCAAAACGTCACTAATA

                                          *            *    
       2832 GGCCCCGATAGGCCCAAAATAACAAGTGTTGAAAATGAGCTAATAACT
        259 GGCCCCGATAGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACT

                                                  *                          
       2880 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGCCCATAAACATTGATAGAAAAGCATTG
          1 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA-TGATAGAAAAGCATTG

                                                                             
       2945 AGGTTTGCCTAATCGAAGACGATTCAAAACGGAACTAATGGGCCCAAATAGGCCCAAAATAAAAT
         65 AGGTTTGCCTAATCGAAGACGATTCAAAACGGAACTAATGGGCCCAAATAGGCCCAAAATAAAAT

                                      ***                                    
       3010 GTGTTCCAAATGAGCTAAAAACTTCATTGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
        130 GTGTTCCAAATGAGCTAAAAACTTCACACTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA

                                                                             
       3075 TAAACAACGGAAAGAAAGGCATTGAGGGTTGCCAAAGCGAAGACGATTCAAAACGTCACTAATAG
        195 TAAACAACGGAAAGAAAGGCATTGAGGGTTGCCAAAGCGAAGACGATTCAAAACGTCACTAATAG

                        *                 *                
       3140 GCCCCGATAGGCTCAAAATAACAAGTGTTCCAAATGAGCTAAAAACT
        260 GCCCCGATAGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACT

                          *                         *           *            
       3187 TCACAGTGGACTAACCTCACCAAAATGATTATAGTTAGGCTATAAACA--ATGGAAAGGAGCATT
          1 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACATGATAGAAA--AGCATT

                              *      *           
       3250 GAGGTTTGCCTAATCGAATACGATTTAAAACGGAACT
         64 GAGGTTTGCCTAATCGAAGACGATTCAAAACGGAACT


Statistics
Matches: 381,  Mismatches: 23, Indels: 8
        0.92            0.06        0.02

Matches are distributed among these distances:
 304    6  0.02
 306   41  0.11
 307  288  0.76
 308   46  0.12

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


Consensus pattern (306 bp):   
TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACATGATAGAAAAGCATTGA
GGTTTGCCTAATCGAAGACGATTCAAAACGGAACTAATGGGCCCAAATAGGCCCAAAATAAAATG
TGTTCCAAATGAGCTAAAAACTTCACACTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
AAACAACGGAAAGAAAGGCATTGAGGGTTGCCAAAGCGAAGACGATTCAAAACGTCACTAATAGG
CCCCGATAGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACT
Done.