Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009270.1 Corchorus olitorius cultivar O-4 contig09299, 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, 706

Length: 1178
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21


Found at i:288 original size:155 final size:154

Alignment explanation


    Indices: 5--1178  Score: 1852
    Period size: 154  Copynumber: 7.6  Consensus size: 154

          1 ACAT

                                                                      *    * 
          5 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTC-AAACGGAACTAATGGTCCTTAC
          1 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCC--CC

                *            *      *                                   *    
         69 GATATGCCCAAAATAACGAGTGTTGCAAATGAGCTAAAAACTT-AACAGTGGACTAATCTCACCA
         64 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAA-AGTGGACTAATCTTACCA

                                      *
        133 AAATGATTATAGTTAGGCCATAAACAT
        128 AAATGATTATAGTTAGGCCATAAACAA

                                                                             
        160 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA
          1 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA

                                            **                               
        225 TAGGCCCAAAATAACAAGTGTTCCAAATGACGAAAAAAACTTCAAAGTGGACTAATCTTACCAAA
         66 TAGGCCCAAAATAACAAGTGTTCCAAATGA-GCTAAAAACTTCAAAGTGGACTAATCTTACCAAA

                                     *
        290 ATGATTATAGTTAGGCCCATAAACAT
        130 ATGATTATAGTTAGG-CCATAAACAA

                                                                       *  *  
        316 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAATGGTCCTCG
          1 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACT-AATGGGCCCCG

                *                              *                             
        381 ACTATGCCCAAAATAACAAGTGTTCCAAATGA-CAAAAAAACTTCAAAGTGGACTAATCTTACCA
         65 A-TAGGCCCAAAATAACAAGTGTTCCAAATGAGC-TAAAAACTTCAAAGTGGACTAATCTTACCA

                                       
        445 AAATGATTATAGTTAGGCCATAAACAA
        128 AAATGATTATAGTTAGGCCATAAACAA

                                                                      *  **  
        472 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGTCCTTGA
          1 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA

                 *                      *                 *             *    
        537 TATCGACCCAAAATAACAAGTGTTCCAAGTGAGACTAAAAACTTCACAGTGGACTAATCTCACCA
         66 TA--GGCCCAAAATAACAAGTGTTCCAAATGAG-CTAAAAACTTCAAAGTGGACTAATCTTACCA

                                       
        602 AAATGATTATAGTTAGGCCATAAACAA
        128 AAATGATTATAGTTAGGCCATAAACAA

                                *   *                                     *  
        629 TGGAAAGAAAAGCATTGAGGTTTGTCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCTGA
          1 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA

                                                                            *
        694 TAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAG
         66 TAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAA

                                    
        759 TGATTATAGTTAGGCCATAAACAA
        131 TGATTATAGTTAGGCCATAAACAA

                                                                      *  *   
        783 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGTCCTCGA
          1 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA

              *                        *                *             *      
        848 TATGCCCAAAATAACAAGTAGTTCCAAGTGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
         66 TAGGCCCAAAATAACAAGT-GTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAA

                                     
        913 ATGATTATAGTTAGGCCATAAACAA
        130 ATGATTATAGTTAGGCCATAAACAA

                                                                             
        938 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA
          1 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA

                                       *           *                         
       1003 TAGGCCCAAAATAACAAGTGTTCCAAAGGAGCTAAAAACATCAAAGTGGACTAATCTTACCAAAA
         66 TAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAA

                        *          *
       1068 TGATTATAGTTAAGCCATAAACAT
        131 TGATTATAGTTAGGCCATAAACAA

                                                *           **               
       1092 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGATGATTCAAAACGTCACTAATGGGCCCCGA
          1 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA

             *                     
       1157 TTGGCCCAAAATAA-AGAGTGTT
         66 TAGGCCCAAAATAACA-AGTGTT


Statistics
Matches: 953,  Mismatches: 53, Indels: 27
        0.92            0.05        0.03

Matches are distributed among these distances:
 153    1  0.00
 154  309  0.32
 155  270  0.28
 156  169  0.18
 157  174  0.18
 158   30  0.03

ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21


Consensus pattern (154 bp):   
TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA
TAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAA
TGATTATAGTTAGGCCATAAACAA

Found at i:1014 original size:309 final size:309

Alignment explanation


    Indices: 5--1178  Score: 1876
    Period size: 309  Copynumber: 3.8  Consensus size: 309

          1 ACAT

                                                                      *    * 
          5 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTC-AAACGGAACTAATGGTCCTTAC
          1 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCC--CC

                *            *      *                                   *    
         69 GATATGCCCAAAATAACGAGTGTTGCAAATGAGCTAAAAACTT-AACAGTGGACTAATCTCACCA
         64 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAA-AGTGGACTAATCTTACCA

                                      *                                      
        133 AAATGATTATAGTTAGGCCATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACG
        128 AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACG

                                          *                       *     **   
        198 ATTCAAAACGGAACTAATGGGCCCCGATA-GGCCCAAAATAACAAGTGTTCCAAATGACGAAAAA
        193 ATTCAAAACGGAACTAATGGGCCCCGATATCGCCCAAAATAACAAGTGTTCCAAGTGA-GCTAAA

                   *             *                               *
        262 AACTTCAAAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCCATAAACAT
        257 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG-CCATAAACAA

                                                                       *  *  
        316 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAATGGTCCTCG
          1 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACT-AATGGGCCCCG

                *                              *                             
        381 ACTATGCCCAAAATAACAAGTGTTCCAAATGA-CAAAAAAACTTCAAAGTGGACTAATCTTACCA
         65 A-TAGGCCCAAAATAACAAGTGTTCCAAATGAGC-TAAAAACTTCAAAGTGGACTAATCTTACCA

                                                                             
        445 AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACG
        128 AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACG

                                *  **                                        
        510 ATTCAAAACGGAACTAATGGTCCTTGATATCGACCCAAAATAACAAGTGTTCCAAGTGAGACTAA
        193 ATTCAAAACGGAACTAATGGGCCCCGATATCG-CCCAAAATAACAAGTGTTCCAAGTGAG-CTAA

                                                                  
        575 AAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
        256 AAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA

                                *   *                                     *  
        629 TGGAAAGAAAAGCATTGAGGTTTGTCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCTGA
          1 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA

                                                                            *
        694 TAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAG
         66 TAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAA

                                                                             
        759 TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATT
        131 TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATT

                             *  *                                            
        824 CAAAACGGAACTAATGGTCCTCGATAT-GCCCAAAATAACAAGTAGTTCCAAGTGAGCTAAAAAC
        196 CAAAACGGAACTAATGGGCCCCGATATCGCCCAAAATAACAAGT-GTTCCAAGTGAGCTAAAAAC

                                                              
        888 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
        260 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA

                                                                             
        938 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA
          1 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA

                                       *           *                         
       1003 TAGGCCCAAAATAACAAGTGTTCCAAAGGAGCTAAAAACATCAAAGTGGACTAATCTTACCAAAA
         66 TAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAA

                        *          *                                    *    
       1068 TGATTATAGTTAAGCCATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGATGATT
        131 TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATT

                   **                  *                    
       1133 CAAAACGTCACTAATGGGCCCCGAT-TGGCCCAAAATAA-AGAGTGTT
        196 CAAAACGGAACTAATGGGCCCCGATATCGCCCAAAATAACA-AGTGTT


Statistics
Matches: 813,  Mismatches: 38, Indels: 27
        0.93            0.04        0.03

Matches are distributed among these distances:
 308    5  0.01
 309  294  0.36
 310   13  0.02
 311  197  0.24
 312  163  0.20
 313   72  0.09
 314   69  0.08

ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21


Consensus pattern (309 bp):   
TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA
TAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAA
TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATT
CAAAACGGAACTAATGGGCCCCGATATCGCCCAAAATAACAAGTGTTCCAAGTGAGCTAAAAACT
TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
Done.