Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010997.1 Corchorus olitorius cultivar O-4 contig11029, 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:0.22, C:0.20, G:0.18, T:0.40


Found at i:281 original size:154 final size:154

Alignment explanation


    Indices: 1--1079  Score: 1776
    Period size: 154  Copynumber: 7.0  Consensus size: 154

                                                                             
          1 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
          1 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT

                  *                                                          
         66 AGCTCACTTGGAACACTTGTTATTTTGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCT
         66 AGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCT

                                    
        131 TCGATTTGGCAACCCTCAATGCTT
        131 TCGATTTGGCAACCCTCAATGCTT

                     *             *                *                        
        155 TTCTTTCCAATGTTTATGGCCTAGCTATAATCATTTTGGTAAGATTAGTCCACTGTGAAGTTTTT
          1 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT

                                          *                                  
        220 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGACCATTAGTTCCGTTTTGAATCGTCT
         66 AGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCT

                                    
        285 TCGATTTGGCAACCCTCAATGCTT
        131 TCGATTTGGCAACCCTCAATGCTT

                                                    *                        
        309 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTGTGAAGTTTTT
          1 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT

                                          *  *  *  *  *                      
        374 AGCTCATTTGGAACACTTGTTATTTTGGGCCTAACGGGGCCCTTTAGTTCCG-TTTGAATCGTCT
         66 AGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCT

                          *          
        438 TCGAGTTTGGCAACACTCAATGCTT
        131 TCGA-TTTGGCAACCCTCAATGCTT

            *                                                                
        463 CTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG-TTTT
          1 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT

                          *                                                  
        527 AGCTCATTTGGAACCCTTG-TATTTTGGGCATATCGAGGACCATTAG-TCCGTTTTGAATCGTCT
         66 AGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCT

                                    
        590 TCGATTTGGCAACCCTCAATGC-T
        131 TCGATTTGGCAACCCTCAATGCTT

                                              *                   *          
        613 TTCTTTCCATTGTTTATGGCCTAACTATAATCATATTGGTGAGATTAGTCCACTCTGAAGTTTTT
          1 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT

                                                               *   *     *   
        678 AGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACCATTAGTTCCATTTAGAATCATCT
         66 AGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCT

                                    
        743 TCGATTTGGCAACCCTCAATGCTT
        131 TCGATTTGGCAACCCTCAATGCTT

               *       *                                   *                 
        767 TTCGTTCCATTATTTATGGCCTAACTATAATCA-TTTGGTGAGATT-TTCCACTGTGAAGTTTTT
          1 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT

                              *                            *                 
        830 AGCTCATTTGGAACACTTTTTATTTTGGGCATATCGAGGACCATTAGCTCCGTTTTGAATCGTCT
         66 AGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCT

                   *     *        * 
        895 TCGATTTCGCAACACTCAATGCAT
        131 TCGATTTGGCAACCCTCAATGCTT

                     *           *              **  *             *          
        919 TTCTTTCCAATGTTTATGGCCCAACTATAATCATTTCCGTAAGATTAGTCCACTTTGAAGTTTTT
          1 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT

                     *                                              *        
        984 AGCTCATTTCGAACACTTGTTATTTTGGGCATATCGAGGACCATTAGTTCCGTTTTTAATCGTCT
         66 AGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCT

                    *               
       1049 TCGATTTGACAACCCTCAATGCTT
        131 TCGATTTGGCAACCCTCAATGCTT

                   
       1073 TTCTTTC
          1 TTCTTTC


Statistics
Matches: 859,  Mismatches: 58, Indels: 16
        0.92            0.06        0.02

Matches are distributed among these distances:
 150   58  0.07
 151   43  0.05
 152  191  0.22
 153   94  0.11
 154  473  0.55

ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40


Consensus pattern (154 bp):   
TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
AGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCT
TCGATTTGGCAACCCTCAATGCTT

Found at i:1011 original size:458 final size:461

Alignment explanation


    Indices: 1--1079  Score: 1794
    Period size: 458  Copynumber: 2.3  Consensus size: 461

                                                                             
          1 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
          1 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT

                  *                                                          
         66 AGCTCACTTGGAACACTTGTTATTTTGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCT
         66 AGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCT

                                                           *          *      
        131 TCGATTTGGCAACCCTCAATGCTTTTCTTTCCAATGTTTATGGCCTAGCTATAATCATTTTGGTA
        131 TCGATTTGGCAACCCTCAATGCTTTTCTTTCCAATGTTTATGGCCTAACTATAATCATATTGGTA

                         *                                        *          
        196 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGAC
        196 AGATTAGTCCACTCTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGAC

                      *   *     *                              *       *     
        261 CATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTAT
        261 CATTAGTTCCATTTAGAATCATCTTCGATTTGGCAACCCTCAATGCTTTTCGTTCCATTATTTAT

                                                                             
        326 GGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACT
        326 GGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACT

                         *     *  *  *    *                        *         
        391 TGTTATTTTGGGCCTAACGGGGCCCTTTAGTTCCGTTTGAATCGTCTTCGAGTTTGGCAACACTC
        391 TGTTATTTTGGGCATAACGAGGACCATTAGCTCCGTTTGAATCGTCTTCGAGTTTCGCAACACTC

                  
        456 AATGCT
        456 AATGCT

                                                                             
        462 TCTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG-TTT
          1 T-TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT

                           *                                                 
        526 TAGCTCATTTGGAACCCTTG-TATTTTGGGCATATCGAGGACCATTAG-TCCGTTTTGAATCGTC
         65 TAGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTC

                                              *                              
        589 TTCGATTTGGCAACCCTCAATGC-TTTCTTTCCATTGTTTATGGCCTAACTATAATCATATTGGT
        130 TTCGATTTGGCAACCCTCAATGCTTTTCTTTCCAATGTTTATGGCCTAACTATAATCATATTGGT

            *                                                                
        653 GAGATTAGTCCACTCTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGA
        195 AAGATTAGTCCACTCTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGA

                                                                             
        718 CCATTAGTTCCATTTAGAATCATCTTCGATTTGGCAACCCTCAATGCTTTTCGTTCCATTATTTA
        260 CCATTAGTTCCATTTAGAATCATCTTCGATTTGGCAACCCTCAATGCTTTTCGTTCCATTATTTA

                                    *      *                                 
        783 TGGCCTAACTATAATCA-TTTGGTGAGATT-TTCCACTGTGAAGTTTTTAGCTCATTTGGAACAC
        325 TGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACAC

              *              *                                               
        846 TTTTTATTTTGGGCATATCGAGGACCATTAGCTCCGTTTTGAATCGTCTTCGA-TTTCGCAACAC
        390 TTGTTATTTTGGGCATAACGAGGACCATTAGCTCCG-TTTGAATCGTCTTCGAGTTTCGCAACAC

                     
        910 TCAATGCAT
        454 TCAATGC-T

                     *           *              **  *             *          
        919 TTCTTTCCAATGTTTATGGCCCAACTATAATCATTTCCGTAAGATTAGTCCACTTTGAAGTTTTT
          1 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT

                     *                                              *        
        984 AGCTCATTTCGAACACTTGTTATTTTGGGCATATCGAGGACCATTAGTTCCGTTTTTAATCGTCT
         66 AGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCT

                    *                      
       1049 TCGATTTGACAACCCTCAATGCTTTTCTTTC
        131 TCGATTTGGCAACCCTCAATGCTTTTCTTTC


Statistics
Matches: 578,  Mismatches: 33, Indels: 15
        0.92            0.05        0.02

Matches are distributed among these distances:
 456  132  0.23
 457   50  0.09
 458  204  0.35
 459   76  0.13
 460   35  0.06
 461   22  0.04
 462   59  0.10

ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40


Consensus pattern (461 bp):   
TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
AGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCT
TCGATTTGGCAACCCTCAATGCTTTTCTTTCCAATGTTTATGGCCTAACTATAATCATATTGGTA
AGATTAGTCCACTCTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGAC
CATTAGTTCCATTTAGAATCATCTTCGATTTGGCAACCCTCAATGCTTTTCGTTCCATTATTTAT
GGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACT
TGTTATTTTGGGCATAACGAGGACCATTAGCTCCGTTTGAATCGTCTTCGAGTTTCGCAACACTC
AATGCT
Done.