Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011595.1 Corchorus olitorius cultivar O-4 contig11628, 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: 2723
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26


Found at i:343 original size:154 final size:154

Alignment explanation


    Indices: 1--1839  Score: 2821
    Period size: 154  Copynumber: 12.0  Consensus size: 154

                                                            *                
          1 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATCGAAAGAAAAGCATTGA
          1 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA

                                           **                     **         
         66 GGTTTGCCAAATCGAAGACGATTTCAAAACGAAACTAATGGGCCCCGGA-AGGCATAAAATAACA
         66 GGTTTGCCAAATCGAAGACGA-TTCAAAACGTCACTAATGGGCCCC-GATAGGCCCAAAATAACA

                                      
        130 AGTGTTCCAAATGAGCTAAAAACTTC
        129 AGTGTTCCAAATGAGCTAAAAACTTC

                                                            *                
        156 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATCGAAAGAAAAGCATTGA
          1 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA

                                        *                                    
        221 GGTTTGCCAAATCGAAGACGATTCAAAATGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAG
         66 GGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAG

                 *               *  
        286 TGTTCAAAATGAGCTAAAAACATC
        131 TGTTCCAAATGAGCTAAAAACTTC

                                                            *                
        310 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATCGAAAGAAAAGCATTGA
          1 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA

                                                                             
        375 GGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAG
         66 GGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAG

                    *    *          
        440 TGTTCCAATTGAGTTAAAAACTTC
        131 TGTTCCAAATGAGCTAAAAACTTC

                           * *           *      *                         *  
        464 ACAGTGGACTAATCTTAGCAAAATGATTACAGTTAGCCCATAAACAATGGAAAGAAAAGCATCGA
          1 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA

              *                           **      *        *     *           
        529 GGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATAGGCCCCGAAAGGCCTAAAATAACAAG
         66 GGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAG

                                    
        594 TGTTCCAAATGAGCTAAAAACTTC
        131 TGTTCCAAATGAGCTAAAAACTTC

                                                                 *        *  
        618 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAACAAAAGCATCGA
          1 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA

              *  *      *  *              **  *                   *          
        683 GGGTTACCAAATTGATGACGATTCAAAACGAAACGAATGGGCCCCGGA-AGGCCTAAAATAACAA
         66 GGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCC-GATAGGCCCAAAATAACAA

                                     
        747 GTGTTCCAAATGAGCT-AAAACTTC
        130 GTGTTCCAAATGAGCTAAAAACTTC

               *             *                                            ** 
        771 ACATTGGACTAATCTCAGCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCAA
          1 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA

              *                           **                                 
        836 GGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA-AGGCCCAAAATAACAAG
         66 GGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAG

                                    
        900 TGTTCCAAATGAGCTAAAAACTTC
        131 TGTTCCAAATGAGCTAAAAACTTC

                                                        *               *    
        924 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAAAATGGAAAGAAAAGCTTTGA
          1 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA

            *                             **            *                    
        989 AGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCTGATAGGCCCAAAATAACAAG
         66 GGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAG

               *             *   *  
       1054 TGTACCAAATGAGCTAAGAACATC
        131 TGTTCCAAATGAGCTAAAAACTTC

             *             *                                  *        *    *
       1078 ATAGTGGACTAATCTAACCAAAATGATTATAGTTAGGCCATAAACAACT-TAAA-AAAAACATTT
          1 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCATTG

                              ***                                            
       1141 AGGTTTGCCAAATCGAAGGTTATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAA
         65 AGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAA

                *  *     *           
       1206 GTGTACCGAATGACCTAAAAACTTC
        130 GTGTTCCAAATGAGCTAAAAACTTC

                           *      *                       *             *    
       1231 ACAGTGGACTAATCTTACCAAATTGATTATAGTTAGGCCATAAACATTGGAAAGAAAAGCCTTGA
          1 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA

                               *                                             
       1296 GGTTTGCCAAATCGAAGACAATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAG
         66 GGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAG

                                    
       1361 TGTTCCAAATGAGCTAAAAACTTC
        131 TGTTCCAAATGAGCTAAAAACTTC

                               *  *                       *             *    
       1385 ACAGTGGACTAATCTCACCGAATTGATTATAGTTAGGCCATAAACATTGGAAAGAAAAGCCTTGA
          1 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA

                                                                             
       1450 GGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAG
         66 GGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAG

                             *       
       1515 TGTTCCAAATGAGCTAAGAACTGT-
        131 TGTTCCAAATGAGCTAAAAACT-TC

               *             *                                *          *   
       1539 ACAATGGACTAATCTCATCAAAATGATTATAGTTAGGCCATAAACAACT-TAAAGAAAAGCTTTG
          1 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCATTG

                             *                                           *   
       1603 AGGTTTGCCAAATCGAAAACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAGCAA
         65 AGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAA

              *                      
       1668 GTATTCCAAATGAGCTAAAAACTTC
        130 GTGTTCCAAATGAGCTAAAAACTTC

                              *   *                                          
       1693 ACAGTGGACTAATCTCACTAAATTGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA
          1 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA

                                     *                 *                    *
       1758 GGTTTGCCAAATCGAAGACGATTCAGAACGTCACTAATGGGCCGCGATAGGCCCAAAATAACAAT
         66 GGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAG

                      *      
       1823 TGTTCCAAATTAGCTAA
        131 TGTTCCAAATGAGCTAA

       1840 TGATTGAGCC


Statistics
Matches: 1554,  Mismatches: 119, Indels: 23
        0.92            0.07        0.01

Matches are distributed among these distances:
 152   34  0.02
 153  356  0.23
 154  1073  0.69
 155   91  0.06

ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21


Consensus pattern (154 bp):   
ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA
GGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAG
TGTTCCAAATGAGCTAAAAACTTC

Done.