Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010967.1 Corchorus olitorius cultivar O-4 contig10999, 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: 1995
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.25


Found at i:547 original size:21 final size:21

Alignment explanation


    Indices: 523--635  Score: 158
    Period size: 21  Copynumber: 5.4  Consensus size: 21

        513 CTTAGGCATT

                         *       
        523 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
        544 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *          * 
        565 TCCAATGAACTTGGAACCTGC
          1 TCCAATGAGCTTGGAACCTTC

                                  
        586 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                                  
        607 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
        628 TCCAATGA
          1 TCCAATGA

        636 ACTTCTAGCA


Statistics
Matches: 85,  Mismatches: 6, Indels: 2
        0.91            0.06        0.02

Matches are distributed among these distances:
  20    2  0.02
  21   83  0.98

ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Found at i:1081 original size:154 final size:154

Alignment explanation


    Indices: 742--1995  Score: 1950
    Period size: 154  Copynumber: 8.1  Consensus size: 154

        732 TGGCGCATCA

                    *                                                        
        742 GATAGGCCAAAAATAACAAGTGTTCCAAATGAGCATAAAAACTTCACAGTGGACTAATCTCACCA
          1 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGC-TAAAAACTTCACAGTGGACTAATCTCACCA

              *   *      *           *                 *                     
        807 AAGTGAATATAGTAAGGCCATAAACTATGGAAAGAAAAGCATTTAGGTTTGCCAAATCGAAGACG
         65 AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACG

                                     
        872 ATTCAAAACGGAACTAATGGGCCCC
        130 ATTCAAAACGGAACTAATGGGCCCC

            *                                       *      * *               
        897 CATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAGTTCACAATCGACTAATCTCACCAA
          1 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA

                               *          *                  *               
        962 AATGATTATAGTTAGGCACTTAAACAACT-TAAAGAAAAGC-TTCGAGGATTGCCAAATCGAAGA
         66 AATGATTATAGTTAGGC-CATAAACAA-TGGAAAGAAAAGCATT-GAGGTTTGCCAAATCGAAGA

            *                          
       1025 TGATTCAAAACGGAACTAAT-GGCCCC
        128 CGATTCAAAACGGAACTAATGGGCCCC

                *                            *                  **           
       1051 GATATGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGAAAAATCTCACCAA
          1 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA

                                                                             
       1116 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
         66 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA

               *             *      
       1181 TTCTAAACGGAACTAATTGGCCCC
        131 TTCAAAACGGAACTAATGGGCCCC

                                             *           *                   
       1205 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTACTCAGTGGACTAATCTCACCA
          1 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT-CACAGTGGACTAATCTCACCA

                                                                             
       1270 AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACG
         65 AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACG

                                   * 
       1335 ATTCAAAACGGAACTAATGGGCCTC
        130 ATTCAAAACGGAACTAATGGGCCCC

                                                   *                        *
       1360 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAGCTTCACAGTGGACTAATCTCACCAT
          1 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA

                                                      *                      
       1425 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTTAGGTTTGCCAAATCGAAGACGA
         66 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA

                                    
       1490 TTCAAAACGGAACTAATGGGCCCC
        131 TTCAAAACGGAACTAATGGGCCCC

                                                           * *               
       1514 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATCGACTAATCTCACCAA
          1 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA

                                          *                  *               
       1579 AATGATTATAGTTAGGCCATAAACAACT--TAAGAAAAG-ACTTCGAGGATTGCCAAATCGAAGA
         66 AATGATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCA-TT-GAGGTTTGCCAAATCGAAGA

            *               *          
       1641 TGATTCAAAACGGAACCAATGGGCCCC
        128 CGATTCAAAACGGAACTAATGGGCCCC

                    *                        *                          *    
       1668 GATAGGCCTAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTCTCCAA
          1 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA

                                                           *               * 
       1733 AATGATTATAGTTAGGCCATAAACAATGGAAA-AAAAGC-TTCGAGGATTGCCAAATCGAAGATG
         66 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT-GAGGTTTGCCAAATCGAAGACG

                                     
       1796 ATTCAAAACGGAACTAATGGGCCCC
        130 ATTCAAAACGGAACTAATGGGCCCC

                                             *                               
       1821 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTCACCAA
          1 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA

                    *                           *     *             *      * 
       1886 AATGATTACAGTTAGGCCATAAACAATGGAAAGAAATGCATTTAGGTTTGCCAAATGGAAGACAA
         66 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA

             *   *                  
       1951 TGCAATACGGAACTAAT-GGCCCC
        131 TTCAAAACGGAACTAATGGGCCCC

                                  
       1974 TGATAGGCCCAAAATAACAAGT
          1 -GATAGGCCCAAAATAACAAGT


Statistics
Matches: 1016,  Mismatches: 67, Indels: 33
        0.91            0.06        0.03

Matches are distributed among these distances:
 152    2  0.00
 153  215  0.21
 154  561  0.55
 155  237  0.23
 156    1  0.00

ACGTcount: A:0.41, C:0.19, G:0.18, T:0.21


Consensus pattern (154 bp):   
GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
TTCAAAACGGAACTAATGGGCCCC

Found at i:1632 original size:463 final size:460

Alignment explanation


    Indices: 742--1995  Score: 1964
    Period size: 463  Copynumber: 2.7  Consensus size: 460

        732 TGGCGCATCA

                                              *                              
        742 GATAGGCCAAAAATAACAAGTGTTCCAAATGAGCATAAAAACTTCACAGTGGACTAATCTCACCA
          1 GATAGGCCAAAAATAACAAGTGTTCCAAATGAG-TTAAAAACTTCACAGTGGACTAATCTCACCA

              *   *      *           *                 *                     
        807 AAGTGAATATAGTAAGGCCATAAACTATGGAAAGAAAAGCATTTAGGTTTGCCAAATCGAAGACG
         65 AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACG

                                     *                                       
        872 ATTCAAAACGGAACTAATGGGCCCCCATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAA
        130 ATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT-AAAA

                    * *                                  *          *        
        937 G-TTCACAATCGACTAATCTCACCAAAATGATTATAGTTAGGCACTTAAACAACT-TAAAGAAAA
        194 GCTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC-CATAAACAA-TGGAAAGAAAA

                  *   *               *                             *        
       1000 GC-TTCGAGGATTGCCAAATCGAAGATGATTCAAAACGGAACTAATGGCCCCGATATGCCCAAAA
        257 GCATT-TAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGCCCCGATAGGCCCAAAA

                                *             * *                            
       1064 TAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGAAAAATCTCACCAAAATGATTATAGTT
        321 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATCGAAAAATCTCACCAAAATGATTATAGTT

                                             *                     *         
       1129 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCTAAACGGAAC
        386 AGGCCATAAACAAT-GAAAGAAAAGCATTGAGGATTGCCAAATCGAAGACGATTCAAAACGGAAC

            *   *      
       1194 TAATTGGCCCC
        450 CAATGGGCCCC

                    *                                    *                   
       1205 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTACTCAGTGGACTAATCTCACCA
          1 GATAGGCCAAAAATAACAAGTGTTCCAAATGAGTTAAAAACTT-CACAGTGGACTAATCTCACCA

                                                                             
       1270 AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACG
         65 AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACG

                                   *                                         
       1335 ATTCAAAACGGAACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAG
        130 ATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAG

                                    *                                        
       1400 CTTCACAGTGGACTAATCTCACCATAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
        195 CTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA

                                                                             
       1465 TTTAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
        260 TTTAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT-GGCCCCGATAGGCCCAAAATAA

                                                **                           
       1530 CAAGTGTTCCAAATGAGCTAAAAACTTCACAATCGACTAATCTCACCAAAATGATTATAGTTAGG
        324 CAAGTGTTCCAAATGAGCTAAAAACTTCACAATCGAAAAATCTCACCAAAATGATTATAGTTAGG

                         *                                  *                
       1595 CCATAAACAACT-TAAGAAAAG-ACTTCGAGGATTGCCAAATCGAAGATGATTCAAAACGGAACC
        389 CCATAAACAA-TGAAAGAAAAGCA-TT-GAGGATTGCCAAATCGAAGACGATTCAAAACGGAACC

                      
       1658 AATGGGCCCC
        451 AATGGGCCCC

                    *                                                   *    
       1668 GATAGGCCTAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTCTCCAA
          1 GATAGGCCAAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTCACCAA

                                                           *               * 
       1733 AATGATTATAGTTAGGCCATAAACAATGGAAA-AAAAGC-TTCGAGGATTGCCAAATCGAAGATG
         66 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT-GAGGTTTGCCAAATCGAAGACG

                                                                      *     *
       1796 ATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAA
        130 ATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAG

                                             *                           *   
       1861 CTTCACAGTGGACTAATCTCACCAAAATGATTACAGTTAGGCCATAAACAATGGAAAGAAATGCA
        195 CTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA

                            *      *  *   *                                  
       1926 TTTAGGTTTGCCAAATGGAAGACAATGCAATACGGAACTAATGGCCCCTGATAGGCCCAAAATAA
        260 TTTAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGCCCC-GATAGGCCCAAAATAA

                 
       1991 CAAGT
        324 CAAGT


Statistics
Matches: 736,  Mismatches: 45, Indels: 22
        0.92            0.06        0.03

Matches are distributed among these distances:
 460    8  0.01
 461  211  0.29
 462  131  0.18
 463  385  0.52
 464    1  0.00

ACGTcount: A:0.41, C:0.19, G:0.18, T:0.21


Consensus pattern (460 bp):   
GATAGGCCAAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTCACCAA
AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
TTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAGC
TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
TTAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGCCCCGATAGGCCCAAAATAACA
AGTGTTCCAAATGAGCTAAAAACTTCACAATCGAAAAATCTCACCAAAATGATTATAGTTAGGCC
ATAAACAATGAAAGAAAAGCATTGAGGATTGCCAAATCGAAGACGATTCAAAACGGAACCAATGG
GCCCC
Done.