Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011890.1 Corchorus olitorius cultivar O-4 contig11923, 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: 2821
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25


Found at i:984 original size:21 final size:21

Alignment explanation


    Indices: 960--1072  Score: 158
    Period size: 21  Copynumber: 5.4  Consensus size: 21

        950 CTTAGGCATT

                         *       
        960 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
        981 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *          * 
       1002 TCCAATGAACTTGGAACCTGC
          1 TCCAATGAGCTTGGAACCTTC

                                  
       1023 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                                  
       1044 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
       1065 TCCAATGA
          1 TCCAATGA

       1073 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:1461 original size:154 final size:154

Alignment explanation


    Indices: 1181--2279  Score: 1704
    Period size: 154  Copynumber: 7.1  Consensus size: 154

       1171 GCGCATCAGT

                 *           *                      **                       
       1181 TTGCCTAATCGAAGACGTTTCAAAACGGAACTAATGGGCCTTGATAGGCCCAAAATAA-AATGTG
          1 TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAA-GTG

                                     *                                       
       1245 TTCCAAATGAGCTAAAAACTTCACACTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAA
         65 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAA

                 *        *        * 
       1310 ACAATCGAAAGAAAGGCATTGAGTG
        130 ACAATGGAAAGAAAAGCATTGAGGG

                                       **              *                     
       1335 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGTTAGGCCCAAAATAACAAGTGT
          1 TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT

             **     *                                                        
       1400 TGAAAATGGGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
         66 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA

                   *               *
       1465 CAATGGATAGAAAAGCATTGAGGT
        131 CAATGGAAAGAAAAGCATTGAGGG

                 *                                  **                       
       1489 TTGCCTAATCGAAGACGATTCAAAACGGAACTAATGGGCCTTGATAGGCCCAAAATAA-AATGTG
          1 TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAA-GTG

                                     *                                       
       1553 TTCCAAATGAGCTAAAAACTTCACACTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAA
         65 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAA

                *                    
       1618 ACAAAGGAAAGAAAAGCATTGAGGG
        130 ACAATGGAAAGAAAAGCATTGAGGG

                                       **                    *               
       1643 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCTCAAAATAACAAGTGT
          1 TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT

                              *                                              
       1708 TCCAAATGAGC-AAAAACATCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
         66 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA

                   *               *
       1772 CAATGGATAGAAAAGCATTGAGGT
        131 CAATGGAAAGAAAAGCATTGAGGG

                 *          *        *          *                            
       1796 TTGCCTAATCGAAGACAATTCAAAATGGAACTAATGTGCCCCGATAGGCCCAAAATAACAAGTGT
          1 TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT

                           *                                                 
       1861 TCCAAATGAGCTAAAGACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
         66 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA

                                    
       1926 CAATGGAAAG-AAAGCATTGAGGG
        131 CAATGGAAAGAAAAGCATTGAGGG

                                       **                 ** *          *    
       1949 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAAACTCAAAATAACAGGTGT
          1 TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT

                              *   *     *                                    
       2014 TCCAAATGAGCT-AAAACATCATAGTGGGCTAATCTACACCAAAATGATTATAGTTAGGCCATAA
         66 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT-CACCAAAATGATTATAGTTAGGCCATAA

                               *      
       2078 ACAATGGAAAGAAAAGCGACTGAGGG
        130 ACAATGGAAAGAAAAGC-ATTGAGGG

                         *                            *                      
       2104 TTGCCAAATCGAAAACGATTCAAAACGGAACTAATGGGCCCCTATAGGCCCAAAATAACAAGTGT
          1 TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT

                                    *                                        
       2169 TCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
         66 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA

               *         *          
       2234 CAACGGAAAGAAAGGCATTGAGGG
        131 CAATGGAAAGAAAAGCATTGAGGG

                                  
       2258 TTGCCAAATCGAAGACGATTCA
          1 TTGCCAAATCGAAGACGATTCA

       2280 TCATGTCTCA


Statistics
Matches: 855,  Mismatches: 82, Indels: 16
        0.90            0.09        0.02

Matches are distributed among these distances:
 152   19  0.02
 153  261  0.31
 154  433  0.51
 155  123  0.14
 156   19  0.02

ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21


Consensus pattern (154 bp):   
TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
CAATGGAAAGAAAAGCATTGAGGG

Done.