Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011078.1 Corchorus olitorius cultivar O-4 contig11111, 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, 647

Length: 1079
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22


Found at i:545 original size:154 final size:154

Alignment explanation


    Indices: 2--1079  Score: 1587
    Period size: 154  Copynumber: 7.0  Consensus size: 154

          1 G

                                     * ** *                **                
          2 TTGCCAAATCGAAGACGATTCAAAATGGAATTAATGGGTCCC-GATATACCCAAAATAGA-AAGT
          1 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGG-CCCGGATAGGCCCAAAATA-ACAAGT

                        *            *                                       
         65 GTTCCAAATGAGATAA-AACTTACAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
         64 GTTCCAAATGAGCTAAGAACTT-CACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT

                 *           * *      *
        129 AAACAGTGGAAAGAAAAACATTGAGGA
        128 AAACAATGGAAAGAAAAGCTTTGAGGT

                                       **       *    *                 *     
        156 TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGAGCCCCGATAGGCCCAAAAATAAAAAGTG
          1 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCGGATAGGCCC-AAAATAACAAGTG

                           *  *                                       *      
        221 TTCCAAATGAGCTAAAAATTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAA
         65 TTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAA

             *                       
        286 AAAATGGAAAGAAAAGCTTTGAGGT
        130 ACAATGGAAAGAAAAGCTTTGAGGT

                                                                             
        311 TTAGCCAAATCGAAGACGATTCAAAACGTCACTAATGGG-CCGCGATAGGCCCAAAATAACAAGT
          1 TT-GCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCG-GATAGGCCCAAAATAACAAGT

                                                         *    *              
        375 GTTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACCAAATTGATCATAGTTAGGCCATA
         64 GTTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATA

                            *         
        440 AACAATGGAAAGAAAAACTTTGAGGT
        129 AACAATGGAAAGAAAAGCTTTGAGGT

                                                                             
        466 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCGGATAGGCCCAAAATAACAAGTGT
          1 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCGGATAGGCCCAAAATAACAAGTGT

                               *                  *                          
        531 TCCAAATGAGCTAAGAACTGCACAGTGGACTAATCTCATCAAAATGATTATAGTTAGGCCATAAA
         66 TCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA

                  *                  
        596 CAACT-TAAAGAAAAGCTTTGAGGT
        131 CAA-TGGAAAGAAAAGCTTTGAGGT

                         *   *                       *                       
        620 TTGCCAAATCGAAAACGTTTCAAAACGTCACTAATGGGCCCAGATAGGCCCAAAATAACAAGTGT
          1 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCGGATAGGCCCAAAATAACAAGTGT

                          *                                  *       *       
        685 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTGTAGTTAGTCCATAAA
         66 TCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA

            *                  *    
        750 TAATGGAAAGAAAAGCTTTAAGGT
        131 CAATGGAAAGAAAAGCTTTGAGGT

                  *                    **            *                       
        774 TTGCCACATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
          1 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCGGATAGGCCCAAAATAACAAGTGT

            *                 *   *                    *             *       
        839 ACCAAATGAGCTAAGAACATCATAGTGGACTAATCTCACCAAATTGATTATAGTTAGTCCATAAA
         66 TCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA

                               *    
        904 CAATGGAAAGAAAA-CTTTAAGGT
        131 CAATGGAAAGAAAAGCTTTGAGGT

                                                                             
        927 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCGGATAGGCCCAAAAT-ACAAGTGT
          1 TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCGGATAGGCCCAAAATAACAAGTGT

                               *                    *                        
        991 TCCAAATGAGCTAAGAACTGCACAGTGGACTAATCTCATCAAAAATGATTATAGTTAGGCCATAA
         66 TCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCA-CCAAAATGATTATAGTTAGGCCATAA

                   *                 
       1056 ACAACT-TAAAGAAAAGCTTTGAGG
        130 ACAA-TGGAAAGAAAAGCTTTGAGG


Statistics
Matches: 843,  Mismatches: 69, Indels: 24
        0.90            0.07        0.03

Matches are distributed among these distances:
 152   42  0.05
 153  100  0.12
 154  463  0.55
 155  192  0.23
 156   46  0.05

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


Consensus pattern (154 bp):   
TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCGGATAGGCCCAAAATAACAAGTGT
TCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
CAATGGAAAGAAAAGCTTTGAGGT

Done.