Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000577.1 Corchorus olitorius cultivar O-4 contig00577, 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: 2618
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35


Found at i:655 original size:330 final size:329

Alignment explanation


    Indices: 46--1358  Score: 1426
    Period size: 330  Copynumber: 4.0  Consensus size: 329

         36 TGGGATTTGG

                  *                      *      *         *     *   *    *   
         46 TTAGATTAATATAGATATTTCAAGGAGTCACGGCGCGAAAAATCATTCAAAATTGAACCGGTGCC
          1 TTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCC

             *                       **      *   *             *   *  *      
        111 CGGAATA--CGTTTTTAGCCAAAAATAGTGATGCTTATTACACGATTTCGGGTAACATATTGCAA
         66 CCGAA-ACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAA

                          *      *               *      *                    
        174 AAATTGACCCGAAAGTATTTCATCAATTTTT-AGTCATAATACTTATAAAAAGAATATATAATTC
        130 AAATTGACCCGAAAATATTTCCTCAATTTTTGA-T-AAAATACTCAT-AAAA-AATATATAATTC

                                                                       *     
        238 AACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTT-ATATTTTTTCTGAATTA
        191 AACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTC-AAATTA

                                      *                            *         
        302 ATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAAAAAATCCTTAAATGCAATGTGGC
        255 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAAATCCTTAAATCCAATGTGGC

                    * 
        367 TAAGATTTTA
        320 TAAGATTTAA

                                        *                  *                 
        377 TTAGATGAATATAGATATTTCAAGGAGTGTCGGCGCCAAAAATCATGTAAAACTGAGCCGGGGCC
          1 TTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCC

                             *                             *        *        
        442 CCGAAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAACTTTGCAAA
         66 CCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAA

              *            *      * *                         *          *  *
        507 AAATGACCCGAAAATTTGTTCCCCTATTTCTTGATAAAATACTCATAAAATATATATAATTTAAT
        131 AATTGACCCGAAAATAT-TTCCTCAATTT-TTGATAAAATACTCATAAAAAATATATAATTCAAC

            *            *  *        *                                       
        572 ACC-AAAAGATTGGAGAACTTTTCATGCTTTTAATATCGTTTTTCATA-TTTTTCAGAATTAATT
        194 GCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCA-AATTAATT

                  *                  *     *       *    *               *  * 
        635 TCTAATAAAATCGAAACAAGATTCATATGCTTGTAAAAACAAATTCTTAAATCCAATGTGTCTGA
        258 TCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAAATCCTTAAATCCAATGTGGCTAA

                 * 
        700 GATTTGA
        323 GATTTAA

                        *     *           *                                  
        707 TTAGATGAATATGGATATCTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCC
          1 TTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCC

                      *               *        * *                        *  
        772 CC-AGAACGCTTTTTTAGCCAAAAACTGTGATGGTCATTACACGATTTCGGCTAAAATTTTGTAA
         66 CCGA-AACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAA

              *    ***               *      * *         * *                  
        836 AAGTTGATTAGAAAAATATTTCCTCGATTTTAGGCTAAAATACTTACAAAAAATATATAATTCAA
        130 AAATTGACCCG-AAAATATTTCCTCAATTTT-TGATAAAATACTCATAAAAAATATATAATTCAA

                              *     *        *         *   *       *         
        901 CGCCAAAAAGATTGAAGGGCTTTTGACG-TTTCCAATATCGTTCTTCCTATTTTTCCAAATTAAT
        193 CGCCAAAAAGATTGAAGGACTTTTCACGCTTT-TAATATCGTTTTTCATATTTTTTCAAATTAAT

              *                                     *                        
        965 TTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTA
        257 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAAATCCTTAAATCCAATGTGGCTA

                    
       1030 AGATTTAA
        322 AGATTTAA

                 **                 *  *  *  *  *               *    *    * *
       1038 TTAGACAAATATAGATATTTCAAGTAGCCTTGGAGCAAAAAATCATGCAAAATTGAGTCGGGTCT
          1 TTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCC

             * *                                       * *                   
       1103 CTGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTTGTTAGTATATGATTTCGGCTAAAATTTTG
         66 CCGAAACGCGTTTTTAGCCAAAAACCGTGAT-G---GTTAGTACACGATTTCGGCTAAAATTTTG

                    *  *      *                   *     *                    
       1168 CAAAAATTTACAC-AAAAGATTTCTCCTCAATTTTTGGCTAAAACACTCAT-AAAAATATATAAT
        127 CAAAAATTGACCCGAAAATA-TT-TCCTCAATTTTT-GATAAAATACTCATAAAAAATATATAAT

                   *                *    *                *    *             
       1231 TCAACGCAAAAAAGATTGAAGTG-GTTTTTACGCTTTTAATATCGTATTTCTTATTTTTTCTAAA
        189 TCAACGCCAAAAAGATTGAAG-GACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTC-AAA

                              *          *     * *            *              
       1295 TTAATTTCTAATTAAATCAAAACAAGATTAAGATGTTTGT-AAAAAAAATTCTTAAATCCAATGT
        252 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAAATCCTTAAATCCAATGT

       1359 TGCAAAAATT


Statistics
Matches: 819,  Mismatches: 139, Indels: 45
        0.82            0.14        0.04

Matches are distributed among these distances:
 329    2  0.00
 330  275  0.34
 331  266  0.32
 332   72  0.09
 333   22  0.03
 334   86  0.11
 335   96  0.12

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


Consensus pattern (329 bp):   
TTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCC
CCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAA
AATTGACCCGAAAATATTTCCTCAATTTTTGATAAAATACTCATAAAAAATATATAATTCAACGC
CAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCAAATTAATTTCT
AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAAATCCTTAAATCCAATGTGGCTAAGAT
TTAA

Found at i:2358 original size:15 final size:16

Alignment explanation


    Indices: 2340--2369  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

       2330 ATAAATAATA

                            
       2340 ATATTATAAT-TAAAT
          1 ATATTATAATCTAAAT

                           
       2355 ATATTATAATCTAAA
          1 ATATTATAATCTAAA

       2370 AATAATTATT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15   10  0.71
  16    4  0.29

ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43


Consensus pattern (16 bp):   
ATATTATAATCTAAAT
Done.