Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006403.1 Corchorus olitorius cultivar O-4 contig06428, 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, 674

Length: 1124
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31


Found at i:950 original size:333 final size:332

Alignment explanation


    Indices: 225--1111  Score: 1197
    Period size: 333  Copynumber: 2.7  Consensus size: 332

        215 TCAATTTTAG

                    *                            **      ***     *        *  
        225 AAAAATCACACAAAACTGAGCCGGGGCCCCGGAACGCACTTTTAGTTAAAAACTGTGATGTTTTT
          1 AAAAATCATACAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACAGTGATG--ATT

                            *   *  *            *       *                   *
        290 AGCACACGATTTTGGTGAAGGTTCTGCAAAAATTGAACCGAATGGTTTTTCCTCAATTTTTGGCT
         64 AGCACACGATTTTGGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCC

               *                          *                                  
        355 AAACTACTCATAAAAAATATATAAATCATCACCAAAAAGATTGAAGGGTTTTTCACGCTTCGAAG
        129 AAAATACTCATAAAAAATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTCACGCTTCGAAG

                                     *                            *          
        420 ATCG-TTTTCCTATGTTTTCCGAATTAATTTCCAAATAAATCGAAACTAGATTCTGATGCTCGTA
        194 ATCGTTTTTCCTATGTTTTCCGAATGAATTTCCAAATAAATCGAAACTAGATTCCGATGCTCGTA

                             *                    *  * *     *               
        484 AAAACAAATCTTTAAATTTTATGTGGCTGAGATTTGGGTAGTTGAATATGGATATTCCAAGGAGT
        259 AAAACAAATCTTTAAATCTTATGTGGCTGAGATTTGGGAAGATAAATATAGATATTCCAAGGAGT

                 *   
        549 CTTGGTGCC
        324 CTTGGCGCC

                                 **  *    **                            *    
        558 AAAAATCATACAAAACTGAGCATGGTCCCCAAAACGCGTTTTTAGCCGAAAACAGTGATGGTTAG
          1 AAAAATCATACAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACAGTGATGATTAG

                *                                 *                          
        623 CACATGATTTTGGTCAAGATTTTGCAAAAATTGACCCGGATGATTTTTCCTCAATTTTTGGCCAA
         66 CACACGATTTTGGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAA

                               *                 *                    *      
        688 AATACTCATAAAAAATATACAAATCATCGCCAAAAAGGTTGAAGGGTTTTTCACGCTTTGAAGAT
        131 AATACTCATAAAAAATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTCACGCTTCGAAGAT

                      *                          *          *                
        753 CGTTTTTCCTGTGCTTTTCCGAATGAATTT-CAAATTCAATCGAAACTGGATTCCGATGCTCGTA
        196 CGTTTTTCCTATG-TTTTCCGAATGAATTTCCAAA-TAAATCGAAACTAGATTCCGATGCTCGTA

                         *                                          *        
        817 AAAACAAATCTTTCAATCTTATGTGGCTGAGATTTGGGAAGATAAATATAGATATTTCAAGGAGT
        259 AAAACAAATCTTTAAATCTTATGTGGCTGAGATTTGGGAAGATAAATATAGATATTCCAAGGAGT

                      
        882 C-TGGACGCC
        324 CTTGG-CGCC

                            *                   *                            
        891 AAAAA-CAATACAAAAATGAGCCGGGGCCCCGGAACACGTTTTTAGCCGAAAACAGTGATGATTA
          1 AAAAATC-ATACAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACAGTGATGATTA

                  *    *   *                * *  *           *          *    
        955 GCACACAATTTCGGTTAAGATTTTGCAAAAATAGTCCAGAATGATTTTTACTCAATTTTTCGCCA
         65 GCACACGATTTTGGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCA

                                                            *                
       1020 AAATACTCATAGAAAATATATATAAATCATCGCCAAAAAGATTGAAGGATTTTTCACGCTTCGAA
        130 AAATACTCATA-AAAA-ATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTCACGCTTCGAA

                       *               
       1085 GATCGTTTTTCTTATGTTTTTCCGAAT
        193 GATCGTTTTTCCTATG-TTTTCCGAAT

       1112 TACTTTTTCA


Statistics
Matches: 483,  Mismatches: 64, Indels: 12
        0.86            0.11        0.02

Matches are distributed among these distances:
 331  123  0.25
 332   17  0.04
 333  271  0.56
 334    4  0.01
 335   68  0.14

ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31


Consensus pattern (332 bp):   
AAAAATCATACAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACAGTGATGATTAG
CACACGATTTTGGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAA
AATACTCATAAAAAATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTCACGCTTCGAAGAT
CGTTTTTCCTATGTTTTCCGAATGAATTTCCAAATAAATCGAAACTAGATTCCGATGCTCGTAAA
AACAAATCTTTAAATCTTATGTGGCTGAGATTTGGGAAGATAAATATAGATATTCCAAGGAGTCT
TGGCGCC
Done.