Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017548.1 Corchorus olitorius cultivar O-4 contig17581, 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, 900

Length: 1500
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30


Found at i:676 original size:332 final size:332

Alignment explanation


    Indices: 56--1495  Score: 2104
    Period size: 332  Copynumber: 4.4  Consensus size: 332

         46 CTGAGCCGGG

                                                      *        *            *
         56 GTACACGATTTCGGCAAAAATTTTGCAAAAATTGA-CCGAAATATTTTTCCTCAATTTTTAACCG
          1 GTACACGATTTCGGCAAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCCCAATTTTTAACCA

                         * *                    *                            
        120 CAATACTCGTAAATAGTATATAATTCAACGCCAAAACGATTGAAGGGCTTTGCACGCTTCTAATA
         66 CAATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTGCACGCTTCTAATA

                                                  *                          
        185 TCATTTTTTTTTTAAA-TTTTCCGAATTAATTTGCGATCAAATCGAAACATGATTCAAATGCTCG
        131 TCA---TTTTTTTAAATTTTTCCGAATTAATTTGCGATTAAATCGAAACATGATTCAAATGCTCG

                                *                                            
        249 TAAAATCAAATATTTACATCAAAGGTGGCTGAAATTTGGGATGATGAATATAGATAATTCAATGA
        193 TAAAATCAAATATTTACATCCAAGGTGGCTGAAATTTGGGATGATGAATATAGATAATTCAATGA

              *   *                *                                         
        314 GTTTTGTGGCCAAAAATCATGCAGAACTGAGCC-GGGCCCCGGAACGCGTTTTCAGCCAAAAATC
        258 GTCTTGGGGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTCAGCCAAAAATC

                      
        378 ATGATAGTTA
        323 ATGATAGTTA

                                                                             
        388 GTACACGATTTCGGCAAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCCCAATTTTTAACCA
          1 GTACACGATTTCGGCAAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCCCAATTTTTAACCA

                                                           *            *    
        453 CAATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTGCACGCTTCAAATA
         66 CAATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTGCACGCTTCTAATA

                                                      *                      
        518 TCATTTTTTTAAAATTTTTCCGAATTAATTTGCGATTAAATCAAAACATGATTCAAATGCTCGTA
        131 TCATTTTTTT-AAATTTTTCCGAATTAATTTGCGATTAAATCGAAACATGATTCAAATGCTCGTA

                                        *                                    
        583 AAATCAAATATTTACATCCAAGGTGGCTAAAATTTGGGATGATGAATATAGATAATTCAATGAGT
        195 AAATCAAATATTTACATCCAAGGTGGCTGAAATTTGGGATGATGAATATAGATAATTCAATGAGT

                    *     * *                     *            *             
        648 CTTGGGGCAAAAAAACTTGCAAAACTGAGCCGGGGCCCTGGAACGCGTTTTAAGCC----A--A-
        260 CTTGGGGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTCAGCCAAAAATCAT

                   *
        706 GA-A--TC
        325 GATAGTTA

                                                                           * 
        711 GT-CACGATTTCGGCAAAAATTTTGCAAAAATTGACTCC-AAAGATTTTTCCCCAATTTTTAAAC
          1 GTACACGATTTCGGCAAAAATTTTGCAAAAATTGAC-CCGAAAGATTTTTCCCCAATTTTTAACC

                 *   *                       *                  *  * *  *    
        774 ACAATTCTCATAAAAAATATATAATTCAACGCCGAAAAGATTGAAGGGCTTTTCATGGTTGTAAT
         65 ACAATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTGCACGCTTCTAAT

                        *     *                    *             *           
        839 ATCATTTTTTT-TATTTTGCCGAATTAATTTGCGATTAATTCGAAACATGATTAAAATGCTCGTA
        130 ATCATTTTTTTAAATTTTTCCGAATTAATTTGCGATTAAATCGAAACATGATTCAAATGCTCGTA

                     **             *                     *                  
        903 AAATCAAATCCTTACATCCAAGGTAGCTGAAATTTGGGATGATGAACATAGATAATTCAATGAGT
        195 AAATCAAATATTTACATCCAAGGTGGCTGAAATTTGGGATGATGAATATAGATAATTCAATGAGT

               *                        *                           *      * 
        968 CTTAGGGCCAAAAATCATGCAAAACTGATCCGGGGCCCCGGAACGCGTTTTCAGCCCAAAATCGT
        260 CTTGGGGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTCAGCCAAAAATCAT

               *    
       1033 GATGGTTA
        325 GATAGTTA

                        *        *                              *   *        
       1041 GTACACGATTTCAGCAAAAATGTTGCAAAAATTGACCC-AACAGATTTTTCCGCAAGTTTTAACC
          1 GTACACGATTTCGGCAAAAATTTTGCAAAAATTGACCCGAA-AGATTTTTCCCCAATTTTTAACC

                          *                  *                               
       1105 ACAATACTCGTAAATAATATATAATTCAACGCCGAAAAGATTGAAGGGCTTTGCACGCTTCTAAT
         65 ACAATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTGCACGCTTCTAAT

                       **                                                    
       1170 ATCATTTTTTTTTATTTTTCCGAATTAATTTGCGATTAAATCGAAACATGATTCAAATGCTCGTA
        130 ATCATTTTTTTAAATTTTTCCGAATTAATTTGCGATTAAATCGAAACATGATTCAAATGCTCGTA

                                                 *                           
       1235 AAATCAAATATTTACATCCAAGGTGGCTGAAATTTGGAATGATGAATATAGATAATTCAATGAGT
        195 AAATCAAATATTTACATCCAAGGTGGCTGAAATTTGGGATGATGAATATAGATAATTCAATGAGT

                      *             *    *     * *                         * 
       1300 CTTGGGGCCAGAAATCATGCAAAATTGAGTCGGGGTCACGGAACGCGTTTTCAGCCAAAAATCGT
        260 CTTGGGGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTCAGCCAAAAATCAT

             * *    
       1365 GTTGGTTA
        325 GATAGTTA

                    *                                 *     *      *        *
       1373 GTACACGAATTCGGCAAAAATTTTGCAAAAATTGACCCGAAATATTTTCCCCCAAATTTTAACCT
          1 GTACACGATTTCGGCAAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCCCAATTTTTAACCA

             *                                         *        *     
       1438 CCATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGATGGGCTTTGTACGCT
         66 CAATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTGCACGCT

       1496 ACTGA


Statistics
Matches: 996,  Mismatches: 93, Indels: 38
        0.88            0.08        0.03

Matches are distributed among these distances:
 320  157  0.16
 322  124  0.12
 323    5  0.01
 324    1  0.00
 325    1  0.00
 326    2  0.00
 327    3  0.00
 329    1  0.00
 330   14  0.01
 331  123  0.12
 332  452  0.45
 333  113  0.11

ACGTcount: A:0.36, C:0.17, G:0.16, T:0.30


Consensus pattern (332 bp):   
GTACACGATTTCGGCAAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCCCAATTTTTAACCA
CAATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTGCACGCTTCTAATA
TCATTTTTTTAAATTTTTCCGAATTAATTTGCGATTAAATCGAAACATGATTCAAATGCTCGTAA
AATCAAATATTTACATCCAAGGTGGCTGAAATTTGGGATGATGAATATAGATAATTCAATGAGTC
TTGGGGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTCAGCCAAAAATCATG
ATAGTTA

Done.