Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009378.1 Corchorus olitorius cultivar O-4 contig09409, 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, 603

Length: 1005
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22


Found at i:646 original size:155 final size:154

Alignment explanation


    Indices: 1--1005  Score: 1561
    Period size: 154  Copynumber: 6.6  Consensus size: 154

                                                                             
          1 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAAACTTCACAGTGGACTAATCTCACTAAAATGAT
          1 CCAAAATAACAAGTGTTCCAAATGAGCT-AAAAACTTCACAGTGGACTAATCTCACTAAAATGAT

                         *                *                *                 
         66 TATAGTTAGGCCAAAAACAATGGAAAGAAAGGCATTGAGGTTTGCCAGATCGAAGACGATTCAAA
         65 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAA

                                      
        131 ACGTCACTAATGGGCC-CTGATAGGC
        130 ACGTCACTAATGGGCCTC-GATAGGC

                                       *         *                 *         
        156 CCAAAAT-ACAAGTGTTCCAAATGAGCAAAAAACTT-TCAGTGGACTAATCTCACCAAAATGATT
          1 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATT

                                         *    *                              
        219 ATAGTTAGGCCATAAAC-ATGGAAAG-AAGGCATCGATGG-TTGCCAAATCGAAGACGATTCAAA
         66 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GGTTTGCCAAATCGAAGACGATTCAAA

                         *           
        281 ACGTCACTAATGGTCCTCGATAGGC
        130 ACGTCACTAATGGGCCTCGATAGGC

                                             *                     *         
        306 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGACTAATCTCACCAAAATGATT
          1 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATT

                                           *         *            *          
        371 ATAGTTAGGCCATAAACAATGGAAAGAAAAGAATTGAGGTTGGCCAAATCGAAGTCGATTCAAAA
         66 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAA

              **       *   *        
        436 CGGAACTAATGAGCCCCGATAGGC
        131 CGTCACTAATGGGCCTCGATAGGC

                                                                             
        460 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATT
          1 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATT

                   *                         *                               
        525 ATAGTTATGCCATAAACAATGGAAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAA
         66 ATAGTTAGGCCATAAACAATGG-AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAA

               **                    
        590 ACGGAACTAATGGGCCTCGATAGGC
        130 ACGTCACTAATGGGCCTCGATAGGC

                                             *                               
        615 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGACTAATCTACACTAAAATGAT
          1 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT-CACTAAAATGAT

              *                                                          *  *
        680 TACAGTTAGGCCAT-AACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTTAAT
         65 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAA

                            *        
        744 ACGTCACTAATGGGCCCCGATAGGC
        130 ACGTCACTAATGGGCCTCGATAGGC

                          *        *                                         
        769 CCAAAATAACAAGTTTTCCAAATAAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATT
          1 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATT

                            *                                                
        834 ATAGTTA-GCCATAAAAAATGGAAAGAAAAGCA-T----TTTGCCAAATCGAAGACGATTCAAAA
         66 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAA

                        *           
        893 CGTCACTAATGGCCCT-GATAGGC
        131 CGTCACTAATGGGCCTCGATAGGC

                                *               *                  *         
        916 CCAAAATAACAAGTGTTCCATATGAGCTAAAAACTTTACAGTGGACTAATCTCACCAAAATGATT
          1 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATT

                                     
        981 ATAGTTAGGCCATAAACAATGGAAA
         66 ATAGTTAGGCCATAAACAATGGAAA


Statistics
Matches: 786,  Mismatches: 53, Indels: 29
        0.91            0.06        0.03

Matches are distributed among these distances:
 147   74  0.09
 148   54  0.07
 150   61  0.08
 151   37  0.05
 152   92  0.12
 153   55  0.07
 154  262  0.33
 155  127  0.16
 156   24  0.03

ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22


Consensus pattern (154 bp):   
CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATT
ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAA
CGTCACTAATGGGCCTCGATAGGC

Found at i:664 original size:309 final size:305

Alignment explanation


    Indices: 1--1005  Score: 1573
    Period size: 309  Copynumber: 3.3  Consensus size: 305

                                              *                     *        
          1 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAAACTTCACAGTGGACTAATCTCACTAAAATGAT
          1 CCAAAATAACAAGTGTTCCAAATGAGCT-AAAAATTTCACAGTGGACTAATCTCACCAAAATGAT

                         *                *                *                 
         66 TATAGTTAGGCCAAAAACAATGGAAAGAAAGGCATTGAGGTTTGCCAGATCGAAGACGATTCAAA
         65 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAA

                             *                                  *         *  
        131 ACGTCACTAATGGGCCCTGATAGGCCCAAAAT-ACAAGTGTTCCAAATGAGCAAAAAACTT-TCA
        130 ACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA

                           *                                      *          
        194 GTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC-ATGGAAAG-AAGGCATCGATGG
        195 GTGGACTAATCTCACTAAAATGATTATAGTTA-GCCATAAACAATGGAAAGAAAAGC-T-GA-GG

                                                  *           
        257 -TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCTCGATAGGC
        256 TTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGCCCTCGATAGGC

                                                                             
        306 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGACTAATCTCACCAAAATGATT
          1 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGACTAATCTCACCAAAATGATT

                                           *         *            *          
        371 ATAGTTAGGCCATAAACAATGGAAAGAAAAGAATTGAGGTTGGCCAAATCGAAGTCGATTCAAAA
         66 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAA

              **       *                                                     
        436 CGGAACTAATGAGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
        131 CGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG

                                                                             
        501 TGGACTAATCTCACTAAAATGATTATAGTTATGCCATAAACAATGGAAAAGAAAAGCTTTGAGGT
        196 TGGACTAATCTCACTAAAATGATTATAGTTA-GCCATAAACAATGG-AAAGAAAAGC--TGAGGT

                                       **        *           
        566 TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCTCGATAGGC
        257 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGCCCTCGATAGGC

                                                                    *        
        615 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGACTAATCTACACTAAAATGAT
          1 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGACTAATCT-CACCAAAATGAT

              *                                                          *  *
        680 TACAGTTAGGCCAT-AACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTTAAT
         65 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAA

                                                   *        *                
        744 ACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTTTTCCAAATAAGCTAAAAACTTCACA
        130 ACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA

                                                    *                   *    
        809 GTGGACTAATCTCACTAAAATGATTATAGTTAGCCATAAAAAATGGAAAGAAAAGC--A-TTTTG
        195 GTGGACTAATCTCACTAAAATGATTATAGTTAGCCATAAACAATGGAAAGAAAAGCTGAGGTTTG

                                                          
        871 CCAAATCGAAGACGATTCAAAACGTCACTAATGGCCCT-GATAGGC
        260 CCAAATCGAAGACGATTCAAAACGTCACTAATGGCCCTCGATAGGC

                                *                                            
        916 CCAAAATAACAAGTGTTCCATATGAGCTAAAAACTTT-ACAGTGGACTAATCTCACCAAAATGAT
          1 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAA-TTTCACAGTGGACTAATCTCACCAAAATGAT

                                      
        980 TATAGTTAGGCCATAAACAATGGAAA
         65 TATAGTTAGGCCATAAACAATGGAAA


Statistics
Matches: 649,  Mismatches: 41, Indels: 24
        0.91            0.06        0.03

Matches are distributed among these distances:
 300   24  0.04
 301   65  0.10
 302   42  0.06
 303    1  0.00
 304  121  0.19
 305   55  0.08
 306   42  0.06
 307   14  0.02
 308   19  0.03
 309  241  0.37
 310   25  0.04

ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22


Consensus pattern (305 bp):   
CCAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGACTAATCTCACCAAAATGATT
ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAA
CGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
TGGACTAATCTCACTAAAATGATTATAGTTAGCCATAAACAATGGAAAGAAAAGCTGAGGTTTGC
CAAATCGAAGACGATTCAAAACGTCACTAATGGCCCTCGATAGGC
Done.