Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011672.1 Corchorus olitorius cultivar O-4 contig11705, 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, 629

Length: 1049
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41


Found at i:298 original size:154 final size:155

Alignment explanation


    Indices: 1--1049  Score: 1562
    Period size: 154  Copynumber: 6.8  Consensus size: 155

                                            *                         * *    
          1 TTAGTCCACTGTGAAGTTTTTTAGCTCATTTGAAACACTTGTTATTTTGGGCCTATCGAGACCCA
          1 TTAGTCCACTGTGAAG-TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCA

                    *                                 *                      
         66 TTAGAT-ATGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATG
         65 TTAG-TGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATG

              *                *       
        130 GCATAACTATAATCATTTTAG-TGAGA
        129 GCCTAACTATAATCATTTTGGTTGAGA

                                                 *                           
        156 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACATGTTATTTTGGGCCTATCGGGGCCCAT
          1 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCAT

                **                                                           
        221 TAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGC
         66 TAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGC

                 *       *       * * 
        286 CTAACCATAATCAATTTGG-TCATA
        131 CTAACTATAATCATTTTGGTTGAGA

                    *      *         *        *                              
        310 TTAGTCCATTGTGAAATTTTTAGCTTATTTGGAAAACTTGTTATTTTGGGCCTATCGGGGCCCAT
          1 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCAT

                     *  *                      *                             
        375 TAGTGACGTATTAAATCGTCTTCGATTTGGCAAACTTCAATGCTTTTCTTTCCATTGTTTATGGC
         66 TAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGC

                                     
        440 CTAACTATAATCATTTTGG-TGAGA
        131 CTAACTATAATCATTTTGGTTGAGA

                                                                             
        464 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGACGGCCC
          1 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGG--GGCCC

                   *                           *       *                     
        529 ATTAGT-TCTGTTTTGAATCGTCTTCGATTTGGCAGACCTCAAAGCTTTTCTTTCCATTGTTTAT
         64 ATTAGTGAC-GTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTAT

                                    *   
        593 GGCCTAACTATAATCATTTT-GTTTAGA
        128 GGCCTAACTATAATCATTTTGGTTGAGA

                           *                  *                              
        620 TTAGTCCACTGTG-ACTTTTTAGCTCATTTGGAATACTTG-TATTTTGGGCCTATCGGGGCCCAT
          1 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCAT

                       *                                            *        
        683 TACGTGACCGTATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCACTGTTTATG
         66 TA-GTGA-CGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATG

                                        
        748 GCCTAACTATAATCATTTTGGTTGAGTA
        129 GCCTAACTATAATCATTTTGGTTGAG-A

                            *                  *                             
        776 TTAGTCCACTGTGTAACTTTTTAGCTCATTTGGAATACTTGTTATTTTGGGCCTATTC-GGGCCC
          1 TTAGTCCACTGTG-AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTA-TCGGGGCCC

                       *                                            *        
        840 ATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCACTGTTTATG
         64 ATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATG

                                       
        905 GCCTAACTATAATCA-TTTGGTTGAGA
        129 GCCTAACTATAATCATTTTGGTTGAGA

                                           *                    *      * *   
        931 TTAGTCCACTGTGTAAGTTTTTAGCTCATTTCGAACACTTGTTATTTTGGGCTTATCGGTGACCA
          1 TTAGTCCACTGTG-AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCA

                                *                   *              
        996 TTAGTGACGTTTTGAATCGTTTTCGATTTGG-AAACCTTCGATGCTTTTCTTTCC
         65 TTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACC-TCAATGCTTTTCTTTCC


Statistics
Matches: 823,  Mismatches: 55, Indels: 32
        0.90            0.06        0.04

Matches are distributed among these distances:
 152    9  0.01
 153    3  0.00
 154  412  0.50
 155  150  0.18
 156  122  0.15
 157   72  0.09
 158   30  0.04
 159   23  0.03
 160    2  0.00

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


Consensus pattern (155 bp):   
TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCAT
TAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGC
CTAACTATAATCATTTTGGTTGAGA

Done.