Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011007.1 Corchorus olitorius cultivar O-4 contig11039, 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: 3330
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29


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

Alignment explanation


    Indices: 1--1053  Score: 1725
    Period size: 154  Copynumber: 6.8  Consensus size: 154

                                     **                           **         
          1 AAACAATGGAAAGAAAAGCATTGAGAATTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGG
          1 AAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGG

                *  *   *                                                     
         66 CCCCAATGGGCTCAAAGA-AA-AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC
         66 CCCCGATAGGCCCAAA-ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC

                           *    *    
        129 ACCAAAATGATTATATTTAGACCAT
        130 ACCAAAATGATTATAATTAGGCCAT

                                                                             
        154 AAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGG
          1 AAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGG

                                                                             
        219 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
         66 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA

                          *    *    
        284 CCAAAATGATTATATTTAGACCAT
        131 CCAAAATGATTATAATTAGGCCAT

                                                                             
        308 AAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGG
          1 AAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGG

                                                                          *  
        373 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCACA
         66 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA

            *                       
        438 TCAAAATGATTATAATTAGGCCAT
        131 CCAAAATGATTATAATTAGGCCAT

                                     **         **  *                        
        462 AAACAATGGAAAGAAAAGCATTGAGATTTGCCAAATATAATACGATTCAAAACGTCACTAATGGG
          1 AAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGG

                                                            *                
        527 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCTCAGTGGACTAATCTCA
         66 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA

                          *         
        592 CCAAAATGATTATAGTTAGGCCAT
        131 CCAAAATGATTATAATTAGGCCAT

                                  *         *                                
        616 AAACAATGGAAAGAAAAGCATTAAGGGTTGCCCAATCGAAGACGATTCAAAACGTCACTAATGGG
          1 AAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGG

                                                             *               
        681 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCA
         66 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA

                                    
        746 CCAAAATGATTATAATTAGGCCAT
        131 CCAAAATGATTATAATTAGGCCAT

                                     **         *   *             **         
        770 AAACAATGGAAAGAAAAGCATTGAGTTTTGCCAAATTGAATACGATTCAAAACGGAACTAATGGG
          1 AAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGG

             * *                                                             
        835 CTCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
         66 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA

                          *         
        900 CCAAAATGATTATAGTTAGGCCAT
        131 CCAAAATGATTATAATTAGGCCAT

                       **             *                                    * 
        924 AAACAATGGAACTAAAAGCATTGA-GATATGCCAAATCGAAGACGATTCAAAACGTCACTAATTG
          1 AAACAATGGAAAGAAAAGCATTGAGGGT-TGCCAAATCGAAGACGATTCAAAACGTCACTAATGG

                              *                              *               
        988 GCCCCGATAGGCCCAAAACAACAAGTGTTCCAAATGAGCTAAAAACTTCTCAGTGGACTAATCTC
         65 GCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC

             
       1053 A
        130 A

       1054 TGATGCGCCA


Statistics
Matches: 842,  Mismatches: 55, Indels: 5
        0.93            0.06        0.01

Matches are distributed among these distances:
 152    1  0.00
 153   77  0.09
 154  764  0.91

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


Consensus pattern (154 bp):   
AAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGG
CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
CCAAAATGATTATAATTAGGCCAT

Found at i:1186 original size:21 final size:21

Alignment explanation


    Indices: 1160--1272  Score: 149
    Period size: 21  Copynumber: 5.4  Consensus size: 21

       1150 TGCTAGAAGT

                                 
       1160 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                                 
       1181 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                       *   *    *
       1202 TCATTGGAGCAGGTTACAAGT
          1 TCATTGGAGCAAGTTCCAAGC

                                 *
       1223 TCATTGGAG-AAGGTTCCAAGA
          1 TCATTGGAGCAA-GTTCCAAGC

                            *     
       1244 TCATTGGAG-AAGGTTTCAAGC
          1 TCATTGGAGCAA-GTTCCAAGC

                    
       1265 TCATTGGA
          1 TCATTGGA

       1273 AATGCCTAAG


Statistics
Matches: 83,  Mismatches: 8, Indels: 2
        0.89            0.09        0.02

Matches are distributed among these distances:
  20    1  0.01
  21   82  0.99

ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGCAAGTTCCAAGC

Done.