Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012132.1 Corchorus olitorius cultivar O-4 contig12165, 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, 766

Length: 1277
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21


Found at i:366 original size:154 final size:154

Alignment explanation


    Indices: 1--1277  Score: 1975
    Period size: 154  Copynumber: 8.2  Consensus size: 154

                                               *                    *      * 
          1 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAACTCGAAGACGATTCAAAACG-GATCTAACG
          1 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCA-CTAATG

             *                      *                         *              
         65 GGCCCCGATAGGCCCAAAATAACATGTGTTCCAAATGAGCTAAAAACTTCGCAGTGGACTAATGC
         65 GACCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT-C

                                      
        130 TCACCAAAATGATTATAGTTAGGCCA
        129 TCACCAAAATGATTATAGTTAGGCCA

                                                                             
        156 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC-ATATG
          1 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTA-ATG

                                                             *               
        220 GACCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTTACAGTGGACTAATCT
         65 GACCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT

             *                   *   
        285 CGCCAAAATGATTATAGTTAGTCCA
        130 CACCAAAATGATTATAGTTAGGCCA

                                                       *       *             
        310 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAAGATTCAATACGTCACTAATGG
          1 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGG

            *   *    *                *                        *             
        375 GCCCGGATAAGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTTCACGGTGGACTAATCTC
         66 ACCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC

                                    
        440 ACCAAAATGATTATAGTTAGGCCA
        131 ACCAAAATGATTATAGTTAGGCCA

                                                                   **        
        464 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGG
          1 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGG

                         *                          *     *   *   *          
        529 ACCCCGATAGGCCAAAAATAACAAGTGTTCCAAATGAGCTTAAAACATCAAAGTCGACTAATCTC
         66 ACCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC

                                    
        594 ACCAAAATGATTATAGTTAGGCCA
        131 ACCAAAATGATTATAGTTAGGCCA

                  *                                    *           **        
        618 TAAACAGTGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAAACGGAACTAATGG
          1 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGG

               *                                                             
        683 ACCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC
         66 ACCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC

                                    
        748 ACCAAAATGATTATAGTTAGGCCA
        131 ACCAAAATGATTATAGTTAGGCCA

                                                                       *     
        772 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACAAATGG
          1 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGG

               *                                                             
        837 ACCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC
         66 ACCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC

                           *        
        902 ACCAAAATGATTATAATTAGGCCA
        131 ACCAAAATGATTATAGTTAGGCCA

                                           *                              *  
        926 TAAACAATGGAAAGAAAAAGCATTGAGGTTTTCCAAATCGAAGACGATTCAAAAACGTCACAAAA
          1 TAAACAATGGAAAG-AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTC-AAAACGTCAC-TAA

                             *            *                         *        
        991 TGGACCCCCGATAGGCCAAAAATAACAAGTTTTCCCAAATGAGACTAAAAACTTCAAAGTGGACT
         63 TGGA-CCCCGATAGGCCCAAAATAACAAGTGTT-CCAAATGAG-CTAAAAACTTCACAGTGGACT

                *                         
       1056 AATCACA-CAAAATGATTATAGTTAGGCCA
        125 AATCTCACCAAAATGATTATAGTTAGGCCA

                                                         *            **     
       1085 TAAACAATGGAAAGAAAAGCATTGAGGTTTTGACCAAATCGAAGAAGATTACAAAACGGAACTAA
          1 TAAACAATGGAAAGAAAAGCATTGAGG-TTTG-CCAAATCGAAGACGATT-CAAAACGTCACTAA

                                               * *                           
       1150 TCGGACCCCGATACGGACCCAAAATAACAAGTGATACTAAATGAGACTAAAAACTTCACAGTGGA
         63 T-GGACCCCGATA-GG-CCCAAAATAACAAGTG-TTCCAAATGAG-CTAAAAACTTCACAGTGGA

                                            
       1215 CTAATCTCACCAAAATGATTATAGTTAGGCCA
        123 CTAATCTCACCAAAATGATTATAGTTAGGCCA

                *   *       *              
       1247 TAAATAATCGAAAGAATAGCATTGAGGTTTG
          1 TAAACAATGGAAAGAAAAGCATTGAGGTTTG


Statistics
Matches: 1037,  Mismatches: 68, Indels: 28
        0.92            0.06        0.02

Matches are distributed among these distances:
 154  616  0.59
 155  151  0.15
 156   11  0.01
 157    7  0.01
 158   38  0.04
 159   58  0.06
 160   55  0.05
 161   54  0.05
 162   47  0.05

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


Consensus pattern (154 bp):   
TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGG
ACCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC
ACCAAAATGATTATAGTTAGGCCA

Done.