Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011093.1 Corchorus olitorius cultivar O-4 contig11126, 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, 792

Length: 1321
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21


Found at i:355 original size:154 final size:154

Alignment explanation


    Indices: 16--1321  Score: 2075
    Period size: 154  Copynumber: 8.5  Consensus size: 154

          6 GATACGTCCG

                                                                             
         16 AAATAAC-AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
          1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA

                                                                            *
         80 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTT-CCAAATCGAAGACGATTCAAAACGT
         66 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGG

            *                       
        144 CACTAATGGGCCCCGATAGGCCCA
        131 AACTAATGGGCCCCGATAGGCCCA

                  *                            *             * *             
        168 AAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTTATCAAAATGATTATA
          1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA

                           *             *                                   
        233 GTTAGGCCATAAACATTGGAAAGAAAAGCGTTGAGGGTTGCCAAATCGAAGACGATTCAAAACGG
         66 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGG

                     *         *    
        298 AACTAATGGTCCCCGATAGTCCCA
        131 AACTAATGGGCCCCGATAGGCCCA

                  *             *                    *                       
        322 AAATAAAAAGTGTTCCAAATCAGCTAAAAACTTCACAGTGGTCTAATCTCACCAAAATGATTATA
          1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA

                   *                                                 *      *
        387 GTTAGGCAATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTGAAAACGT
         66 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGG

            *      *                 
        452 CACTAATCGGCCCC-ATTAGGCCCA
        131 AACTAATGGGCCCCGA-TAGGCCCA

                       *                    *  *    *                        
        476 AAATAACAAGTATTCCAAATGAGCTAAAAACTACATAGTGTACTAATCTCACCAAAATGATTATA
          1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA

                                        *                                    
        541 GTTAGGCCATAAACAATGGAAAGAAAAGAATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGG
         66 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGG

                        **          
        606 AACTAATGGGCCTTGATAGGCCCA
        131 AACTAATGGGCCCCGATAGGCCCA

                                                           *                 
        630 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATATCACCAAAATGA-TATA
          1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA

            *                           *   *                                
        694 ATTAGGCCATAAACAATGGAAAGAAAAGAATTTAGGGTTGCCAAATCGAAGACGATTCAAAACGG
         66 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGG

                *       *           
        759 AACTGATGGGCCTCGATAGG-CCA
        131 AACTAATGGGCCCCGATAGGCCCA

                                            *       *                        
        782 AAATAACAAGTGTTCCAAATGAGCTAAAAACTACACAGTGTACTAATCTCACCAAAATGATTATA
          1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA

                                                              *             *
        847 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAAACGATTCAAAACGT
         66 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGG

            *      *                 
        912 CACTAATCGGCCCC-ATTAGGCCCA
        131 AACTAATGGGCCCCGA-TAGGCCCA

                                            *  *    *                        
        936 AAATAACAAGTGTTCCAAATGAGCTAAAAACTACATAGTGTACTAATCTCACCAAAATGATTATA
          1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA

                                                                             
       1001 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGG
         66 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGG

                        *           
       1066 AACTAATGGGCCTCGATAGGCCCA
        131 AACTAATGGGCCCCGATAGGCCCA

                                            *  *    *                 *      
       1090 AAATAACAAGTGTTCCAAATGAGCTAAAAACTACAAAGTGCACTAATCTCACCAAAATAATTATA
          1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA

                * *        *                              *  *               
       1155 GTTAAGTCATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATTGAGGACGATTCAAAACGG
         66 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGG

                     *  *           
       1220 AACTAATGGACCTCGATAGGCCCA
        131 AACTAATGGGCCCCGATAGGCCCA

                                                                             
       1244 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
          1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA

             *           
       1309 GGTAGGCCATAAA
         66 GTTAGGCCATAAA


Statistics
Matches: 1064,  Mismatches: 82, Indels: 14
        0.92            0.07        0.01

Matches are distributed among these distances:
 152   67  0.06
 153  255  0.24
 154  740  0.70
 155    2  0.00

ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21


Consensus pattern (154 bp):   
AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGG
AACTAATGGGCCCCGATAGGCCCA

Found at i:1190 original size:614 final size:615

Alignment explanation


    Indices: 16--1321  Score: 2131
    Period size: 614  Copynumber: 2.1  Consensus size: 615

          6 GATACGTCCG

                                                                             
         16 AAATAAC-AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
          1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA

                                        *                                  **
         80 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTCCAAATCGAAGACGATTCAAAACGTC
         66 GTTAGGCCATAAACAATGGAAAGAAAAGAATTGAGGGTTCCAAATCGAAGACGATTCAAAACGGA

                                                                   *         
        145 ACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGA
        131 ACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTACAAAGTGGA

                   * *                            *             *            
        210 CTAATCTTATCAAAATGATTATAGTTAGGCCATAAACATTGGAAAGAAAAGCGTTGAGGGTTGCC
        196 CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCC

                    *                                 *                      
        275 AAATCGAAGACGATTCAAAACGGAACTAATGGTCCCCGATAGTCCCAAAATAAAAAGTGTTCCAA
        261 AAATCGAAAACGATTCAAAACGGAACTAATGGTCCCCGATAGGCCCAAAATAAAAAGTGTTCCAA

                          *                                                  
        340 ATCAGCTAAAAACTTCACAGTGGTCTAATCTCACCAAAATGATTATAGTTAGGCAATAAACAATG
        326 ATCAGCTAAAAACTACACAGTGGTCTAATCTCACCAAAATGATTATAGTTAGGCAATAAACAATG

                                                   *      **                 
        405 GAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTGAAAACGTCACTAATCGGCCCCATTA
        391 GAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATCGGCCCCATTA

                                                     *    *                 *
        470 GGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTACATAGTGTACTAATCTCACCAAAATG
        456 GGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTACAAAGTGCACTAATCTCACCAAAATA

                      *                                                      
        535 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGAATTGAGGGTTGCCAAATCGAAGACGATTCA
        521 ATTATAGTTAAGCCATAAACAATGGAAAGAAAAGAATTGAGGGTTGCCAAATCGAAGACGATTCA

                           *   *          
        600 AAACGGAACTAATGGGCCTTGATAGGCCCA
        586 AAACGGAACTAATGGACCTCGATAGGCCCA

                                                           *                 
        630 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATATCACCAAAATGA-TATA
          1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA

            *                               *                                
        694 ATTAGGCCATAAACAATGGAAAGAAAAGAATTTAGGGTTGCCAAATCGAAGACGATTCAAAACGG
         66 GTTAGGCCATAAACAATGGAAAGAAAAGAATTGAGGGTT-CCAAATCGAAGACGATTCAAAACGG

                *       *                 *                            *    *
        759 AACTGATGGGCCTCGATAGG-CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTACACAGTGT
        130 AACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTACAAAGTGG

                                                                             
        823 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGC
        195 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGC

                                   **                               *        
        888 CAAATCGAAAACGATTCAAAACGTCACTAATCGG-CCCC-ATTAGGCCCAAAATAACAAGTGTTC
        260 CAAATCGAAAACGATTCAAAACGGAACTAAT-GGTCCCCGA-TAGGCCCAAAATAAAAAGTGTTC

                 *              *                                     *      
        951 CAAATGAGCTAAAAACTACATAGT-GTACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
        323 CAAATCAGCTAAAAACTACACAGTGGT-CTAATCTCACCAAAATGATTATAGTTAGGCAATAAAC

                                                                      *      
       1015 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCTC
        387 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATCGGCC-C

            *                     *                                          
       1080 GA-TAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTACAAAGTGCACTAATCTCACCA
        451 CATTAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTACAAAGTGCACTAATCTCACCA

                             *        *            *                 *  *    
       1144 AAATAATTATAGTTAAGTCATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATTGAGGACG
        516 AAATAATTATAGTTAAGCCATAAACAATGGAAAGAAAAGAATTGAGGGTTGCCAAATCGAAGACG

                                               
       1209 ATTCAAAACGGAACTAATGGACCTCGATAGGCCCA
        581 ATTCAAAACGGAACTAATGGACCTCGATAGGCCCA

                                                                             
       1244 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
          1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA

             *           
       1309 GGTAGGCCATAAA
         66 GTTAGGCCATAAA


Statistics
Matches: 640,  Mismatches: 45, Indels: 13
        0.92            0.06        0.02

Matches are distributed among these distances:
 613    3  0.00
 614  526  0.82
 615  111  0.17

ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21


Consensus pattern (615 bp):   
AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
GTTAGGCCATAAACAATGGAAAGAAAAGAATTGAGGGTTCCAAATCGAAGACGATTCAAAACGGA
ACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTACAAAGTGGA
CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCC
AAATCGAAAACGATTCAAAACGGAACTAATGGTCCCCGATAGGCCCAAAATAAAAAGTGTTCCAA
ATCAGCTAAAAACTACACAGTGGTCTAATCTCACCAAAATGATTATAGTTAGGCAATAAACAATG
GAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATCGGCCCCATTA
GGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTACAAAGTGCACTAATCTCACCAAAATA
ATTATAGTTAAGCCATAAACAATGGAAAGAAAAGAATTGAGGGTTGCCAAATCGAAGACGATTCA
AAACGGAACTAATGGACCTCGATAGGCCCA
Done.