Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011128.1 Corchorus olitorius cultivar O-4 contig11161, 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, 675

Length: 1126
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22


Found at i:539 original size:154 final size:154

Alignment explanation


    Indices: 1--1126  Score: 1715
    Period size: 154  Copynumber: 7.3  Consensus size: 154

                                             *        *                      
          1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAATCATTGAGGTTTGCCAAATCGAAGACGATTCA
          1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCA

                 **        *                         *                * *    
         66 AAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTTTTCCAAATGAGCTAAAAATTTCA
         66 AAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAATACTTCA

                                    
        131 CAGTGGACTAATCTCACCAAAATG
        131 CAGTGGACTAATCTCACCAAAATG

                                  *              *  *    * *                 
        155 ATTATAGTTAGGCCATAAACAACGGAAAG-AAAGCATCGAAGGTTTCAAAATCGAAGACGATTCA
          1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCA

               *                      *         *                     *  *   
        219 AAATGGAACTAATGGGCCCCGATAGGGCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACATCA
         66 AAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAATACTTCA

            *                *       
        284 TAGTGGACTAATCTCAATCAAAATG
        131 CAGTGGACTAATCTC-ACCAAAATG

                       *                          *                  *    *  
        309 ATTATAGTTAGCCCATAAACAATGGAAAGAAAAGCATTTAGGGTTGCCAAATCGAA-TCTGAATC
          1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGAC-GATTC

                         *       *                                     *     
        373 AAAACGGAACTAAGGGGCCCCTATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
         65 AAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAATACTTC

                                     
        438 ACAGTGGACTAATCTCACCAAAATG
        130 ACAGTGGACTAATCTCACCAAAATG

                                       *         *                           
        463 ATTATAGTTAGGCCATAAACAATGGAAGGAAAAGCATAGAGGGTTGCCAAATCGAAGACGATTCA
          1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCA

                ***                    *                                     
        528 AAACTTCACTAATGGGCCCCGATAGGCTCAAAATAACAAGTGTTCCAAATGAGCTAAATACTTCA
         66 AAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAATACTTCA

                        *           
        593 CAGTGGACTAATTTCACCAAAATG
        131 CAGTGGACTAATCTCACCAAAATG

                                                       *             *       
        617 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAAGCATTGAGGTTTGCCAAATCGAAAACGATTC
          1 ATTATAGTTAGGCCATAAACAATGGAAAG-AAAAGCATTGAGGGTTGCCAAATCGAAGACGATTC

                    *                                           *            
        682 AAAA-GGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATAAGCTAAATACTT
         65 AAAACGG-AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAATACTT

                          *           
        746 CACAGTGGACTAATTTCACCAAAATG
        129 CACAGTGGACTAATCTCACCAAAATG

                                                       *                     
        772 ATTATAGTTAGGCCATAAACAATGG-AAGAAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTC
          1 ATTATAGTTAGGCCATAAACAATGGAAAG-AAAAGCATTGAGGGTTGCCAAATCGAAGACGATTC

                                                                             
        836 AAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAATACTTC
         65 AAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAATACTTC

                                      
        901 ACAGTGGACTAATCTCACCAAAATTG
        130 ACAGTGGACTAATCTCACCAAAA-TG

                                                                         *   
        927 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGAATCA
          1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCA

                         *                                            *      
        992 AAACGGAACTAAGGGGGCCCCGATAGGCCCAAAATAACAAGTGTT-CAAATGAGCTAAGTACTTC
         66 AAACGGAACTAA-TGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAATACTTC

                                     
       1056 ACAGTGGACTAATCTCACC-AAATG
        130 ACAGTGGACTAATCTCACCAAAATG

                         * *                        *      
       1080 ATTAGTAGTTAGGTCGTAAACAATGGAAAGTAAAAGCATTTAGGGTT
          1 ATTA-TAGTTAGGCCATAAACAATGGAAAG-AAAAGCATTGAGGGTT


Statistics
Matches: 892,  Mismatches: 68, Indels: 23
        0.91            0.07        0.02

Matches are distributed among these distances:
 153  105  0.12
 154  384  0.43
 155  369  0.41
 156   34  0.04

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


Consensus pattern (154 bp):   
ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCA
AAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAATACTTCA
CAGTGGACTAATCTCACCAAAATG

Found at i:715 original size:309 final size:307

Alignment explanation


    Indices: 1--1118  Score: 1681
    Period size: 309  Copynumber: 3.6  Consensus size: 307

                                             *        *             *    *   
          1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAATCATTGAGGTTTGCCAAATCGAAGACGATTCA
          1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAAACGAATCA

                 **     *  *                         *                  *    
         66 AAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTTTTCCAAATGAGCTAAAAATTTCA
         66 AAACGGAACTAAGGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA

                                                          *    *         *  *
        131 CAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACGGAAAG-AAAGCATCGAA
        131 CAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAGGAAAAGCATAGAG

                * *                                                      *   
        195 GGTTTCAAAATCGAAGACGATTCAAAA-TGGAACTAATGGGCCCCGATAGGGCCAAAATAAAAAG
        196 GGTTGCCAAATCGAAGACGATTCAAAACT-GAACTAATGGGCCCCGATA-GGCCAAAATAACAAG

                              *  *   *                *       
        259 TGTTCCAAATGAGCTAAAAACATCATAGTGGACTAATCTCAATCAAAATG
        259 TGTTCCAAATGAGCTAAATACTTCACAGTGGACTAATCTC-ACCAAAATG

                       *                          *                  *       
        309 ATTATAGTTAGCCCATAAACAATGGAAAGAAAAGCATTTAGGGTTGCCAAATCG-AATCTGAATC
          1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAAAC-GAATC

                                 *                                           
        373 AAAACGGAACTAAGGGGCCCCTATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
         65 AAAACGGAACTAAGGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC

                                                                             
        438 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAGGAAAAGCATAGA
        130 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAGGAAAAGCATAGA

                                          **                                 
        503 GGGTTGCCAAATCGAAGACGATTCAAAACTTCACTAATGGGCCCCGATAGGCTCAAAATAACAAG
        195 GGGTTGCCAAATCGAAGACGATTCAAAACTGAACTAATGGGCCCCGATAGGC-CAAAATAACAAG

                                                 *           
        568 TGTTCCAAATGAGCTAAATACTTCACAGTGGACTAATTTCACCAAAATG
        259 TGTTCCAAATGAGCTAAATACTTCACAGTGGACTAATCTCACCAAAATG

                                                       *                  *  
        617 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAAGCATTGAGGTTTGCCAAATCGAAAACGATTC
          1 ATTATAGTTAGGCCATAAACAATGGAAAG-AAAAGCATTGAGGGTTGCCAAATCGAAAACGAATC

                    *     *                                     *       *    
        682 AAAA-GGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATAAGCTAAATACTT
         65 AAAACGG-AACTAAGGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT

                          *                                       *        * 
        746 CACAGTGGACTAATTTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAGAAAAAGCATTG
        129 CACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAGGAAAAGCATAG

               *                          *                                  
        811 AGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAA
        194 AGGGTTGCCAAATCGAAGACGATTCAAAACTGAACTAATGGGCCCCGATAGG-CCAAAATAACAA

                                                               
        876 GTGTTCCAAATGAGCTAAATACTTCACAGTGGACTAATCTCACCAAAATTG
        258 GTGTTCCAAATGAGCTAAATACTTCACAGTGGACTAATCTCACCAAAA-TG

                                                                    *        
        927 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGAATCA
          1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAAACGAATCA

                                                                      **     
        992 AAACGGAACTAAGGGGGCCCCGATAGGCCCAAAATAACAAGTGTT-CAAATGAGCTAAGTACTTC
         66 AAACGGAACTAA-GGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC

                                                  * *              *        
       1056 ACAGTGGACTAATCTCACC-AAATGATTAGTAGTTAGGTCGTAAACAATGGAAAGTAAAAGCAT
        130 ACAGTGGACTAATCTCACCAAAATGATTA-TAGTTAGGCCATAAACAATGG-AAGGAAAAGCAT

       1119 TTAGGGTT


Statistics
Matches: 740,  Mismatches: 57, Indels: 24
        0.90            0.07        0.03

Matches are distributed among these distances:
 307    2  0.00
 308  214  0.29
 309  444  0.60
 310   80  0.11

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


Consensus pattern (307 bp):   
ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAAACGAATCA
AAACGGAACTAAGGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
CAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAGGAAAAGCATAGAG
GGTTGCCAAATCGAAGACGATTCAAAACTGAACTAATGGGCCCCGATAGGCCAAAATAACAAGTG
TTCCAAATGAGCTAAATACTTCACAGTGGACTAATCTCACCAAAATG
Done.