Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013229.1 Corchorus olitorius cultivar O-4 contig13262, 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: 3800
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35


Found at i:900 original size:153 final size:154

Alignment explanation


    Indices: 414--1582  Score: 1831
    Period size: 154  Copynumber: 7.6  Consensus size: 154

        404 ATTCGTATCA

                                         *                                 * 
        414 CTAACTATAATCATTTTGGTGAGATTAGTGCACTGTGAAGTTTTTAGCTCATTTGGAACACTTAT
          1 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT

                                           *           *                     
        479 TATTTTGGGCCTATCGGGGCCCATTAGTTCCATTTTGAATCGTATTCGATTTGGCAACCCTCAAT
         66 TATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAAT

                                    
        544 GCTTTTCTTTCCATTGTTTATGGC
        131 GCTTTTCTTTCCATTGTTTATGGC

                *                   *                                        
        568 CTAAGTATAATCATTTTGGTGAGAATAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
          1 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT

                                         **                                  
        633 TATTTTGGGCCTATCGGGGCCCATTAGTTTTGTTTTGAATCGTCTTCGATTTGGCAACCCTCAAT
         66 TATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAAT

              *                     
        698 GCATTTCTTTCCATTGTTTATGGC
        131 GCTTTTCTTTCCATTGTTTATGGC

                                       *                                     
        722 CTAACTATAATCATTTTGGTGAGATTATTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
          1 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT

                                          *                            * *   
        787 TATTTTGGGCCTATCGGGGCCCATTAGTT-TGTTTTGAATCGTCTTCGATTTGGCAACCTTTAAT
         66 TATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAAT

                                    
        851 GCTTTTCTTTCCATTGTTTATGGC
        131 GCTTTTCTTTCCATTGTTTATGGC

               *        *       *             *                *   *       * 
        875 CTAGCTATAATCCTTTTGGTAAGATTAGTCCACTATGAAGTTTTTAGCTCAATTGAAACACTTTT
          1 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT

                           *               *   *     *                       
        940 TATTTTGGGCCTATCAGGGCCCATTAGTTCCATTTGGAATCATCTTCGATTTGGCAACCCTCAAT
         66 TATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAAT

                         *     *  * 
       1005 GCTTTTCTTTCCAATGTTTTTGAC
        131 GCTTTTCTTTCCATTGTTTATGGC

                               **             *                            * 
       1029 CTAACTATAATCATTTTGGAAAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTTT
          1 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT

                            *           ****               *           *     
       1094 TATTTTGGGCCTATCGTGGCCCATTAGTGATTTTTTGAATCGTCTTCTATTT-GCAACCTTCAAT
         66 TATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAAT

                                    
       1158 GCTTTTCTTTCCATTGTTTATGGC
        131 GCTTTTCTTTCCATTGTTTATGGC

                                              * *              *   *       * 
       1182 CTAACTATAATCATTTTGGTGAGATTAGTCCACTATTAAGTTTTTAGCTCAATTGAAACACTTTT
          1 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT

                           *                   *     *                       
       1247 TATTTTGGGCCTATCAGGGCCCATTAGTTCCGTTTGGAATCATCTTCGATTTGGCAACCCTCAAT
         66 TATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAAT

                                  * 
       1312 GCTTTTCTTTCCATTGTTTATGAC
        131 GCTTTTCTTTCCATTGTTTATGGC

                                *             *   *                          
       1336 CTAACTATAATCATTTTGGTAAGATTAGTCCACTTTGATGTTTTTAGCTCATTTGGAACACTTGT
          1 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT

                                           *                                 
       1401 TATTTTGGGCCTATCGGGGCCCATTAGTTCCATTTTGAATCGTCTTCGATTTGGC-ACCCTCAAT
         66 TATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAAT

                                    
       1465 GCTTTTCTTTCCATTGTTTATGGC
        131 GCTTTTCTTTCCATTGTTTATGGC

                                                              *         *    
       1489 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCGTTTGGAACAGTTGT
          1 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT

                             *           
       1554 TATTTTGGGCCTATCGGTGCCCATTAGTT
         66 TATTTTGGGCCTATCGGGGCCCATTAGTT

       1583 TGGCGGGTCA


Statistics
Matches: 926,  Mismatches: 87, Indels: 5
        0.91            0.09        0.00

Matches are distributed among these distances:
 153  395  0.43
 154  531  0.57

ACGTcount: A:0.21, C:0.19, G:0.18, T:0.42


Consensus pattern (154 bp):   
CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
TATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAAT
GCTTTTCTTTCCATTGTTTATGGC

Found at i:988 original size:307 final size:308

Alignment explanation


    Indices: 414--1582  Score: 1869
    Period size: 307  Copynumber: 3.8  Consensus size: 308

        404 ATTCGTATCA

                                *        *                                 * 
        414 CTAACTATAATCATTTTGGTGAGATTAGTGCACTGTGAAGTTTTTAGCTCATTTGGAACACTTAT
          1 CTAACTATAATCATTTTGGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT

                                                       *                     
        479 TATTTTGGGCCTATCGGGGCCCATTAGTTCCATTTTGAATCGTATTCGATTTGGCAACCCTCAAT
         66 TATTTTGGGCCTATCGGGGCCCATTAGTTCCATTTTGAATCGTCTTCGATTTGGCAACCCTCAAT

                                        *                   *         *      
        544 GCTTTTCTTTCCATTGTTTATGGCCTAAGTATAATCATTTTGGTGAGAATAGTCCACTGTGAAGT
        131 GCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTATGAAGT

                      *   *                        *             **    *     
        609 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTTTGTTTTGAATC
        196 TTTTAGCTCAATTGAAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTTCCGTTTGGAATC

            *                         *                   * 
        674 GTCTTCGATTTGGCAACCCTCAATGCATTTCTTTCCATTGTTTATGGC
        261 ATCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGAC

                                *      *                                     
        722 CTAACTATAATCATTTTGGTGAGATTATTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
          1 CTAACTATAATCATTTTGGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT

                                          **                           * *   
        787 TATTTTGGGCCTATCGGGGCCCATTAGTT-TGTTTTGAATCGTCTTCGATTTGGCAACCTTTAAT
         66 TATTTTGGGCCTATCGGGGCCCATTAGTTCCATTTTGAATCGTCTTCGATTTGGCAACCCTCAAT

                                       *        *       *                    
        851 GCTTTTCTTTCCATTGTTTATGGCCTAGCTATAATCCTTTTGGTAAGATTAGTCCACTATGAAGT
        131 GCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTATGAAGT

                                  *                                *         
        916 TTTTAGCTCAATTGAAACACTTTTTATTTTGGGCCTATCAGGGCCCATTAGTTCCATTTGGAATC
        196 TTTTAGCTCAATTGAAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTTCCGTTTGGAATC

                                                 *     *    
        981 ATCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCAATGTTTTTGAC
        261 ATCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGAC

                               *              *                            * 
       1029 CTAACTATAATCATTTTGGAAAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTTT
          1 CTAACTATAATCATTTTGGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT

                            *           ****               *           *     
       1094 TATTTTGGGCCTATCGTGGCCCATTAGTGATTTTTTGAATCGTCTTCTATTT-GCAACCTTCAAT
         66 TATTTTGGGCCTATCGGGGCCCATTAGTTCCATTTTGAATCGTCTTCGATTTGGCAACCCTCAAT

                                                                        *    
       1158 GCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTATTAAGT
        131 GCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTATGAAGT

                                  *                                          
       1223 TTTTAGCTCAATTGAAACACTTTTTATTTTGGGCCTATCAGGGCCCATTAGTTCCGTTTGGAATC
        196 TTTTAGCTCAATTGAAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTTCCGTTTGGAATC

                                                            
       1288 ATCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGAC
        261 ATCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGAC

                                              *   *                          
       1336 CTAACTATAATCATTTTGGTAAGATTAGTCCACTTTGATGTTTTTAGCTCATTTGGAACACTTGT
          1 CTAACTATAATCATTTTGGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT

                                                                             
       1401 TATTTTGGGCCTATCGGGGCCCATTAGTTCCATTTTGAATCGTCTTCGATTTGGC-ACCCTCAAT
         66 TATTTTGGGCCTATCGGGGCCCATTAGTTCCATTTTGAATCGTCTTCGATTTGGCAACCCTCAAT

                                                                      *      
       1465 GCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGT
        131 GCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTATGAAGT

                     **   *    *                                  
       1530 TTTTAGCTCGTTTGGAACAGTTGTTATTTTGGGCCTATC-GGTGCCCATTAGTT
        196 TTTTAGCTCAATTGAAACACTTGTTATTTTGGGCCTATCAGG-GCCCATTAGTT

       1583 TGGCGGGTCA


Statistics
Matches: 797,  Mismatches: 61, Indels: 7
        0.92            0.07        0.01

Matches are distributed among these distances:
 306    2  0.00
 307  682  0.86
 308  113  0.14

ACGTcount: A:0.21, C:0.19, G:0.18, T:0.42


Consensus pattern (308 bp):   
CTAACTATAATCATTTTGGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
TATTTTGGGCCTATCGGGGCCCATTAGTTCCATTTTGAATCGTCTTCGATTTGGCAACCCTCAAT
GCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTATGAAGT
TTTTAGCTCAATTGAAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTTCCGTTTGGAATC
ATCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGAC

Found at i:2765 original size:21 final size:21

Alignment explanation


    Indices: 2741--2853  Score: 158
    Period size: 21  Copynumber: 5.4  Consensus size: 21

       2731 CTTAGGCATT

                         *       
       2741 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
       2762 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *          * 
       2783 TCCAATGAACTTGGAACCTGC
          1 TCCAATGAGCTTGGAACCTTC

                                  
       2804 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                                  
       2825 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
       2846 TCCAATGA
          1 TCCAATGA

       2854 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

Done.