Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022322.1 Corchorus olitorius cultivar O-4 contig22355, 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: 2289
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.33


Found at i:285 original size:154 final size:154

Alignment explanation


    Indices: 1--935  Score: 1437
    Period size: 154  Copynumber: 6.1  Consensus size: 154

                                       *                *                *   
          1 TTGGGCCTATCGGGGCCCATTAGTGACATTTTGAATCGTCTTCGGTTTGGCAAACCTCAATTCTT
          1 TTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTT

               *                                                             
         66 TTCATTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
         66 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT

                 *                  
        131 AGCTCTTTTGGAACACTTGTTATT
        131 AGCTCATTTGGAACACTTGTTATT

               *       **            *           *                    *      
        155 TTGTGCCTATCAAGGCCCATTAGT-TCTGTTTTGAATTGTCTTCGATTTGGCAAACCTTAATGCT
          1 TTGGGCCTATCGGGGCCCATTAGTGAC-GTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCT

                *             *                            *      *          
        219 TTTCATTCCATTGTTTATCGCCTAACTATAATCATTTTGGTGAGATTTGTCCACCGTGAAGTTTT
         65 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT

                                     
        284 TAGCTCATTTGGAACACTTGTTATT
        130 TAGCTCATTTGGAACACTTGTTATT

                            *   *                                  *         
        309 TTGGGCCTATCGGGGCGCATCAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACTTCAATGTCT
          1 TTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG-C-

                                                        *                    
        374 TTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGGGATTAGTCCACTGTGAAGTT
         64 -TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT

                *                      
        439 TTTAACTCATTTGGAACACTTGTTATT
        128 TTTAGCTCATTTGGAACACTTGTTATT

                           *                                             *   
        466 TTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATTCTT
          1 TTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTT

                           *       *                                         
        531 TTCTTTCCATTGTTTTTGGCCTATCTATAATCATTTT-GTGAGATTAGTCCACTGTGAAGTTTTT
         66 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT

                *                   
        595 AGCTTATTTGGAACACTTGTTATT
        131 AGCTCATTTGGAACACTTGTTATT

              **        *           **          **                 *      *  
        619 TTCTGCCTATCGAGGCCCATTAGTTCCGTTTTGAATTATCTTCGATTTGGCAAACGTCAATTCCT
          1 TTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAA-TGCT

                                                              *              
        684 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGATG-TTAGACCACTGTGAAGTTT
         65 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGA-GATTAGTCCACTGTGAAGTTT

                                      
        748 TTAGCTCATTTGGAACACTTGTTATT
        129 TTAGCTCATTTGGAACACTTGTTATT

                           *    *                                            
        774 TTGGGCCTATCGGGGACCATCAGTGACGTTTTGAATCGTCTTCGATTT-GCAAACCTCAATGCTT
          1 TTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTT

                                                              *              
        838 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCTACTGTGAAGTTTTT
         66 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT

                                  * 
        903 AGCTCATTTGGAACACTTGTTAGT
        131 AGCTCATTTGGAACACTTGTTATT

                     
        927 TTGGGCCTA
          1 TTGGGCCTA

        936 ACCACAACAA


Statistics
Matches: 706,  Mismatches: 66, Indels: 19
        0.89            0.08        0.02

Matches are distributed among these distances:
 152    1  0.00
 153  197  0.28
 154  276  0.39
 155   88  0.12
 156    2  0.00
 157  142  0.20

ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42


Consensus pattern (154 bp):   
TTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTT
TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
AGCTCATTTGGAACACTTGTTATT

Done.