Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011574.1 Corchorus olitorius cultivar O-4 contig11607, 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, 765

Length: 1276
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22


Found at i:284 original size:154 final size:154

Alignment explanation


    Indices: 4--1276  Score: 1881
    Period size: 154  Copynumber: 8.3  Consensus size: 154

          1 CCT

                                *               *   *                        
          4 AAATAACAAGTGTTCCAAATTAGCTAAAAACTTCACGGTGTACTAATCTCACCAAAATGATTATA
          1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA

                                 *         *                 *               
         69 GTTAGTCCATAAACAATGGAAGGAAAAGCATCGAGGTTTGCCAAATCGAGGACGATTCAAAACAG
         66 GTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-G

                           *         
        134 -AACTAATGGGCCCCAATAGGCCCA
        130 TAACTAATGGGCCCCGATAGGCCCA

                                       *                       *             
        158 AAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCATCAAAATGATTATA
          1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA

                 *             *          *                    *             
        223 GTTAGGCCATAAACAACT-TAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAAACGATTCAAAACG
         66 GTTAGTCCATAAACAA-TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG

             *            *          
        287 TCACTAATGGGCCCAGATAGGCCCA
        130 TAACTAATGGGCCCCGATAGGCCCA

               *                   *       *                               * 
        312 AAACAACAAGTGTTCCAAATGAGATAAAAACATCACAGTGGACTAATCTCACCAAAATGATTACA
          1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA

                         *                                                  *
        377 GTTAGTCCATAAATAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGG
         66 GTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGT

                         *      *  *
        442 AACTAATGGGCCCTGATAGGTCCT
        131 AACTAATGGGCCCCGATAGGCCCA

                                *               *   *                        
        466 AAATAACAAGTGTTCCAAATTAGCTAAAAACTTCACGGTGTACTAATCTCACCAAAATGATTATA
          1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA

                                               *                *         * *
        531 GTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGTTTTGCCAAATCGAAGATGATTCAAAATGG
         66 GTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGT

                 *                  
        596 AACTAGTGGGCCCCGATAGGCCCA
        131 AACTAATGGGCCCCGATAGGCCCA

                                                                             
        620 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
          1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA

                                                                          *  
        685 GTTAGTCCATAAACAATGGAAAGAAAAG-ATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGT
         66 GTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGT

            *                       
        749 CACTAATGGGCCCCGATAGGCCCA
        131 AACTAATGGGCCCCGATAGGCCCA

                      * *              *                            *        
        773 AAATAACAAGCGATCCAAATGAGCTAACAACTTCACAGTGGACTAATCTCACCAAATTGATTATA
          1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA

                 *          ***        * *         *                         
        838 GTTAGGCCATAAACAACATAAAGAAAAACTTTGAGGTTTACCAAATC-AAGGACGATTCAAAACG
         66 GTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAA-GACGATTCAAAACG

             *          *          * 
        902 TCACTAATGGGCACCGATAGGCCAA
        130 TAACTAATGGGCCCCGATAGGCCCA

                                              *                             *
        927 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCGCAGTGGACTAATCTCACCAAAATGATTATT
          1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA

                         *              **                                  *
        992 GTTAGTCCATAAAAAATGGAAAGAAAAGGTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGG
         66 GTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGT

                                    
       1057 AACTAATGGGCCCCGATAGGCCCA
        131 AACTAATGGGCCCCGATAGGCCCA

                                       *                       *            *
       1081 AAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCATCAAAATGATTATG
          1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA

                 *             *          *                    *             
       1146 GTTAGGCCATAAACAACT-TAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAAACGATTCAAAACG
         66 GTTAGTCCATAAACAA-TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG

             *      *     *       *  
       1210 TCACTAATTGGCCCAGATAGGCTCA
        130 TAACTAATGGGCCCCGATAGGCCCA

                                           *          
       1235 AAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGA
          1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA


Statistics
Matches: 1010,  Mismatches: 102, Indels: 14
        0.90            0.09        0.01

Matches are distributed among these distances:
 153  143  0.14
 154  863  0.85
 155    4  0.00

ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22


Consensus pattern (154 bp):   
AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
GTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGT
AACTAATGGGCCCCGATAGGCCCA

Found at i:1188 original size:615 final size:616

Alignment explanation


    Indices: 4--1276  Score: 2016
    Period size: 615  Copynumber: 2.1  Consensus size: 616

          1 CCT

                                *               *   *                        
          4 AAATAACAAGTGTTCCAAATTAGCTAAAAACTTCACGGTGTACTAATCTCACCAAAATGATTATA
          1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA

                                 *                           *               
         69 GTTAGTCCATAAACAATGGAAGGAAAAGCATCGAGGTTTGCCAAATCGAGGACGATTCAAAACAG
         66 GTTAGTCCATAAACAATGGAAAGAAAAGCATCGAGGTTTGCCAAATCGAAGACGATTCAAAACAG

                                              * *              *             
        134 AACTAATGGGCCCCAATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGG
        131 AACTAATGGGCCCCAATAGGCCCAAAATAACAAGCGATCCAAATGAGCTAACAACTTCACAGTGG

                      *                              *         *           * 
        199 ACTAATCTCATCAAAATGATTATAGTTAGGCCATAAACAACTTAAAGAAAAGCTTTGAGGTTTGC
        196 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACATAAAGAAAAACTTTGAGGTTTAC

                                                          *                  
        264 CAAATCGAAAACGATTCAAAACGTCACTAATGGGCCCAGATAGGCCCAAAACAACAAGTGTTCCA
        261 CAAATCGAAAACGATTCAAAACGTCACTAATGGGCCCAGATAGGCCAAAAACAACAAGTGTTCCA

                                                                         *   
        329 AATGAGATAAAAACATCACAGTGGACTAATCTCACCAAAATGATTACAGTTAGTCCATAAATAAT
        326 AATGAGATAAAAACATCACAGTGGACTAATCTCACCAAAATGATTACAGTTAGTCCATAAAAAAT

                                                                         *   
        394 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCTGAT
        391 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAT

               *  *                    *               *   *                 
        459 AGGTCCTAAATAACAAGTGTTCCAAATTAGCTAAAAACTTCACGGTGTACTAATCTCACCAAAAT
        456 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT

                        *                             *              * *     
        524 GATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGTTTTGCCAAATCGAAGATGATTC
        521 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAAACGATTC

                *       *       *          
        589 AAAATGGAACTAGTGGGCCCCGATAGGCCCA
        586 AAAACGGAACTAATGGGCCCAGATAGGCCCA

                                                                             
        620 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
          1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA

                                           *                               * 
        685 GTTAGTCCATAAACAATGGAAAGAAAAG-ATTGAGGTTTGCCAAATCGAAGACGATTCAAAA-TG
         66 GTTAGTCCATAAACAATGGAAAGAAAAGCATCGAGGTTTGCCAAATCGAAGACGATTCAAAACAG

             *             *                                                 
        748 TCACTAATGGGCCCCGATAGGCCCAAAATAACAAGCGATCCAAATGAGCTAACAACTTCACAGTG
        131 -AACTAATGGGCCCCAATAGGCCCAAAATAACAAGCGATCCAAATGAGCTAACAACTTCACAGTG

                            *                                                
        813 GACTAATCTCACCAAATTGATTATAGTTAGGCCATAAACAACATAAAGAAAAACTTTGAGGTTTA
        195 GACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACATAAAGAAAAACTTTGAGGTTTA

                       *                                          *          
        878 CCAAATC-AAGGACGATTCAAAACGTCACTAATGGGCACC-GATAGGCCAAAAATAACAAGTGTT
        260 CCAAATCGAA-AACGATTCAAAACGTCACTAATGGGC-CCAGATAGGCCAAAAACAACAAGTGTT

                     *       *  *                            **              
        941 CCAAATGAGCTAAAAACTTCGCAGTGGACTAATCTCACCAAAATGATTATTGTTAGTCCATAAAA
        323 CCAAATGAGATAAAAACATCACAGTGGACTAATCTCACCAAAATGATTACAGTTAGTCCATAAAA

                          **                                                 
       1006 AATGGAAAGAAAAGGTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
        388 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC

                                                 *                       *   
       1071 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCATCAA
        453 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA

                     *                   *          *                        
       1136 AATGATTATGGTTAGGCCATAAACAACT-TAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAAACG
        518 AATGATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAAACG

                      **      *             *  
       1200 ATTCAAAACGTCACTAATTGGCCCAGATAGGCTCA
        582 ATTCAAAACGGAACTAATGGGCCCAGATAGGCCCA

                                           *          
       1235 AAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGA
          1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA


Statistics
Matches: 602,  Mismatches: 51, Indels: 9
        0.91            0.08        0.01

Matches are distributed among these distances:
 614    3  0.00
 615  507  0.84
 616   92  0.15

ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22


Consensus pattern (616 bp):   
AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
GTTAGTCCATAAACAATGGAAAGAAAAGCATCGAGGTTTGCCAAATCGAAGACGATTCAAAACAG
AACTAATGGGCCCCAATAGGCCCAAAATAACAAGCGATCCAAATGAGCTAACAACTTCACAGTGG
ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACATAAAGAAAAACTTTGAGGTTTAC
CAAATCGAAAACGATTCAAAACGTCACTAATGGGCCCAGATAGGCCAAAAACAACAAGTGTTCCA
AATGAGATAAAAACATCACAGTGGACTAATCTCACCAAAATGATTACAGTTAGTCCATAAAAAAT
GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAT
AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAAACGATTC
AAAACGGAACTAATGGGCCCAGATAGGCCCA
Done.