Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010999.1 Corchorus olitorius cultivar O-4 contig11031, 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: 1704
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23


Found at i:304 original size:154 final size:154

Alignment explanation


    Indices: 1--1339  Score: 2108
    Period size: 154  Copynumber: 8.7  Consensus size: 154

                                 *                         *           *  *  
          1 GGAAAGAAAAGCATATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGTCCTCG
          1 GGAAAGAAAAGC--ATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCG

               *     *                                                       
         66 ATATGCCCATAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
         64 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA

                                      
        131 ATGATTATAGTTAGTCCATAAACAAT
        129 ATGATTATAGTTAGTCCATAAACAAT

                                                         * **     *     *    
        157 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAAAGGGCCGCGAT
          1 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGAT

                                                                  *          
        222 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATGTCACCAAAAT
         66 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT

                    *   *           
        287 GATTATAGATAGGCCATAAACAAT
        131 GATTATAGTTAGTCCATAAACAAT

                        *            *                     **                
        311 GGAAAGAAAAGCCTTGAGGTTTGCCTAATCGAAGACGATTCAAAATGTCACTAATGGGCCCCGAT
          1 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGAT

                             * *                       *                   * 
        376 AGGCCCAAAATAACAAGCGATCCAAATGAGCTAAAAACTTCACGGTGGACTAATCTCACCAAATT
         66 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT

              *                      
        441 GAATATAGTTACG-CCATAAACAAT
        131 GATTATAGTTA-GTCCATAAACAAT

                     *                                   * **            *   
        465 GGAAAGAAATGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCTGAT
          1 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGAT

               *                                                             
        530 AGGTCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
         66 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT

                                    
        595 GATTATAGTTAGTCCATAAACAAT
        131 GATTATAGTTAGTCCATAAACAAT

                                          *         *                        
        619 GGAAAGAAAAGCATTGAGGTTTGCCAAATCAAAGACGATTTAAAATGGAACTAATGGGCCCCGAT
          1 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGAT

            *                             *   *                *           * 
        684 TGGCCCAAAATAACAAGTGTTCC-AATGAGGTAAGAACTTCACAGTGGACTGATCTCACCAAATT
         66 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT

                                *   
        748 GATTATAGTTAGTCCATAAAAAAT
        131 GATTATAGTTAGTCCATAAACAAT

                                                                   *         
        772 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATCGGCCCCGAT
          1 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGAT

               *          *               *   *                            * 
        837 AGGACCAAAATAACGAGTGTTCCAAATGAGGTAAGAACTTCACAGTGGACTAATCTCACCAAATT
         66 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT

                                    
        902 GATTATAGTTAGTCCATAAACAAT
        131 GATTATAGTTAGTCCATAAACAAT

                        *                                  **                
        926 GGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAATGTCACTAATGGGCCCCGAT
          1 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGAT

                              * *                                            
        991 AGAG-CCAAAATAACAAGCGATCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAA
         66 AG-GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAA

                                 *   
       1055 TGATTATAGTTAGTCCATAAAAAAT
        130 TGATTATAGTTAGTCCATAAACAAT

                                                                         *   
       1080 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCGGAT
          1 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGAT

                                                        *                    
       1145 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAAT
         66 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT

              *                     
       1210 GAATATAGTTAGTCCATAAACAAT
        131 GATTATAGTTAGTCCATAAACAAT

                        *                  *             *               *   
       1234 GGAAAGAAAAGCTTTGAGGTTTGCCAAATCGGAGACGATTCAAAACGGAACTAATGGGCCCAGAT
          1 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGAT

                                              *      
       1299 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTC
         66 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC

       1340 TGATGCGCCA


Statistics
Matches: 1097,  Mismatches: 81, Indels: 12
        0.92            0.07        0.01

Matches are distributed among these distances:
 153  144  0.13
 154  939  0.86
 155    2  0.00
 156   12  0.01

ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22


Consensus pattern (154 bp):   
GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGAT
AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
GATTATAGTTAGTCCATAAACAAT

Found at i:1273 original size:615 final size:616

Alignment explanation


    Indices: 1--1339  Score: 2209
    Period size: 615  Copynumber: 2.2  Consensus size: 616

                                 *                                     *  *  
          1 GGAAAGAAAAGCATATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGTCCTCG
          1 GGAAAGAAAAGC-T-TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCG

                      *                          *                           
         66 ATAT-GCCCATAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
         64 AT-TGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACCAA

                                   *                                         
        130 AATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
        128 AATGATTATAGTTAGTCCATAAAAAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA

                     **      *    *       *                                  
        195 TTCAAAACGTCACTAAAGGGCCGCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAC
        193 TTCAAAACGGAACTAAACGGCCCCGATAGGACCAAAATAACAAGTGTTCCAAATGAGCTAAAAAC

                            *                                                
        260 TTCACAGTGGACTAATGTCACCAAAATGATTATAGATAGGCCATAAACAATGGAAAGAAAAGCCT
        258 TTCACAGTGGACTAATCTCACCAAAATGATTATAGATAGGCCATAAACAATGGAAAGAAAAGCCT

                       *                                                     
        325 TGAGGTTTGCCTAATCGAAGACGATTCAAAATGTCACTAATGGGCCCCGATAGGCCCAAAATAAC
        323 TGAGGTTTGCCAAATCGAAGACGATTCAAAATGTCACTAATGGGCCCCGATAGGCCCAAAATAAC

                                         *                   *               
        390 AAGCGATCCAAATGAGCTAAAAACTTCACGGTGGACTAATCTCACCAAATTGAATATAGTTACGC
        388 AAGCGATCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAATATAGTTACGC

                  *            *                                     **      
        455 CATAAACAATGGAAAGAAATGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAAT
        453 CATAAAAAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT

                  *      *                                        *          
        520 GGGCCCTGATAGGTCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
        518 GGGCCCGGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATC

                        *                     
        585 TCACCAAAATGATTATAGTTAGTCCATAAACAAT
        583 TCACCAAAATGAATATAGTTAGTCCATAAACAAT

                        *                 *         *    *                   
        619 GGAAAGAAAAGCATTGAGGTTTGCCAAATCAAAGACGATTTAAAATGGAACTAATGGGCCCCGAT
          1 GGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAT

                                          *                    *           * 
        684 TGGCCCAAAATAACAAGTGTTCC-AATGAGGTAAGAACTTCACAGTGGACTGATCTCACCAAATT
         66 TGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACCAAAAT

                                                                             
        748 GATTATAGTTAGTCCATAAAAAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTC
        131 GATTATAGTTAGTCCATAAAAAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTC

                *        *                        *               *   *      
        813 AAAATGGAACTAATCGGCCCCGATAGGACCAAAATAACGAGTGTTCCAAATGAGGTAAGAACTTC
        196 AAAACGGAACTAAACGGCCCCGATAGGACCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC

                                  *         *   *                       *    
        878 ACAGTGGACTAATCTCACCAAATTGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGA
        261 ACAGTGGACTAATCTCACCAAAATGATTATAGATAGGCCATAAACAATGGAAAGAAAAGCCTTGA

                                                                             
        943 GGTTTGCCAAATCGAAGACGATTCAAAATGTCACTAATGGGCCCCGATAGAG-CCAAAATAACAA
        326 GGTTTGCCAAATCGAAGACGATTCAAAATGTCACTAATGGGCCCCGATAG-GCCCAAAATAACAA

                                                               *             
       1007 GCGATCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA-GTCC
        390 GCGATCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAATATAGTTACG-CC

                                                                  *          
       1071 ATAAAAAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATG
        454 ATAAAAAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG

                                                                             
       1136 GGCCCGGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATCT
        519 GGCCCGGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATCT

                                             
       1201 CACCAAAATGAATATAGTTAGTCCATAAACAAT
        584 CACCAAAATGAATATAGTTAGTCCATAAACAAT

                                           *                             *   
       1234 GGAAAGAAAAGCTTTGAGGTTTGCCAAATCGGAGACGATTCAAAACGGAACTAATGGGCCCAGAT
          1 GGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAT

            *                                        
       1299 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTC
         66 TGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTC

       1340 TGATGCGCCA


Statistics
Matches: 668,  Mismatches: 49, Indels: 10
        0.92            0.07        0.01

Matches are distributed among these distances:
 614    1  0.00
 615  572  0.86
 616   83  0.12
 618   12  0.02

ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22


Consensus pattern (616 bp):   
GGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAT
TGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACCAAAAT
GATTATAGTTAGTCCATAAAAAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTC
AAAACGGAACTAAACGGCCCCGATAGGACCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
ACAGTGGACTAATCTCACCAAAATGATTATAGATAGGCCATAAACAATGGAAAGAAAAGCCTTGA
GGTTTGCCAAATCGAAGACGATTCAAAATGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAG
CGATCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAATATAGTTACGCCAT
AAAAAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGG
CCCGGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCA
CCAAAATGAATATAGTTAGTCCATAAACAAT

Found at i:1607 original size:20 final size:21

Alignment explanation


    Indices: 1579--1621  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       1569 CATCTTGAAG

                                 
       1579 ATTTAAAG-CCATCGGAGATC
          1 ATTTAAAGCCCATCGGAGATC

                *        *       
       1599 ATTTGAAGCCCATTGGAGATC
          1 ATTTAAAGCCCATCGGAGATC

              
       1620 AT
          1 AT

       1622 CAACAAACGG


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20    7  0.35
  21   13  0.65

ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28


Consensus pattern (21 bp):   
ATTTAAAGCCCATCGGAGATC

Done.