Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012065.1 Corchorus olitorius cultivar O-4 contig12098, 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: 9676
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34


Found at i:4114 original size:33 final size:33

Alignment explanation


    Indices: 4072--4141  Score: 131
    Period size: 33  Copynumber: 2.1  Consensus size: 33

       4062 GAGGACTTGT

                               *             
       4072 CATTAACAAGATCACCATTGATTATAGATTCCC
          1 CATTAACAAGATCACCATTCATTATAGATTCCC

                                             
       4105 CATTAACAAGATCACCATTCATTATAGATTCCC
          1 CATTAACAAGATCACCATTCATTATAGATTCCC

                
       4138 CATT
          1 CATT

       4142 CCACGGCTTG


Statistics
Matches: 36,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  33   36  1.00

ACGTcount: A:0.36, C:0.26, G:0.07, T:0.31


Consensus pattern (33 bp):   
CATTAACAAGATCACCATTCATTATAGATTCCC

Found at i:4142 original size:18 final size:18

Alignment explanation


    Indices: 4086--4142  Score: 57
    Period size: 18  Copynumber: 3.3  Consensus size: 18

       4076 AACAAGATCA

                 *            
       4086 CCATTGATTATAGATTCC
          1 CCATTCATTATAGATTCC

                   **        *
       4104 CCATT-AACA-AGA-TCA
          1 CCATTCATTATAGATTCC

                              
       4119 CCATTCATTATAGATTCC
          1 CCATTCATTATAGATTCC

                  
       4137 CCATTC
          1 CCATTC

       4143 CACGGCTTGA


Statistics
Matches: 30,  Mismatches: 6, Indels: 6
        0.71            0.14        0.14

Matches are distributed among these distances:
  15    7  0.23
  16    5  0.17
  17    5  0.17
  18   13  0.43

ACGTcount: A:0.32, C:0.28, G:0.07, T:0.33


Consensus pattern (18 bp):   
CCATTCATTATAGATTCC

Found at i:7843 original size:154 final size:154

Alignment explanation


    Indices: 7358--9676  Score: 3654
    Period size: 154  Copynumber: 15.1  Consensus size: 154

       7348 CCCCGTATCA

                                         *                     *  *          
       7358 CTTTCCATTGTTTATGGACTAACTATAATAATTTTGGTGAGATTAGTCCACAGTAAAGTTTTTAG
          1 CTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG

                                              *                              
       7423 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTC
         66 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTC

                                    
       7488 GATTTGGCAAACCTCAATGCTTTT
        131 GATTTGGCAAACCTCAATGCTTTT

                             *                 *            *                
       7512 CTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGTGAGATTAGTCAACTGTGAAGTTTTTAG
          1 CTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG

                                                                           * 
       7577 CTCATTTGGAACTACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCAT
         66 CTCATTTGGAAC-ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTT

                    *         * *    
       7642 CGATTTGGAAAACCTCAAAGTTTTT
        130 CGATTTGGCAAACCTCAATGCTTTT

                                    *   *                                    
       7667 CTTTCCATTGTTTATGGACTAACTGTAAGCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG
          1 CTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG

                                            **            **         *       
       7732 CTCATTTGGAACACTTGTTATTTTGGGCCTATAAGGGCCCATTAGTTCCGTTTTGAAACGTCTTC
         66 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTC

            *  * *                  
       7797 AATCTCGCAAACCTCAATGCTTTT
        131 GATTTGGCAAACCTCAATGCTTTT

                             *                                  *            
       7821 CTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTATGAAGTTTTTAG
          1 CTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG

                        *              *      *      *    **                 
       7886 CTCATTTGGAACCCTTGTTATTTTGGGTCTATCGAGGCCCAATAGTTCCGTTTTGAATCGTCTTC
         66 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTC

                                    
       7951 GATTTGGCAAACCTCAATGCTTTT
        131 GATTTGGCAAACCTCAATGCTTTT

                *                       *                                    
       7975 CTTTGCATTGTTTATGGACTAACTATAAGCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG
          1 CTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG

                                            **  *         **                 
       8040 CTCATTTGGAACACTTGTTATTTTGGGCCTATAAGGACCCATTAGTTCCGTTTTGAATCGTCTTC
         66 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTC

                                    
       8105 GATTTGGCAAACCTCAATGCTTTT
        131 GATTTGGCAAACCTCAATGCTTTT

                             *                      *           *            
       8129 CTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGATATTAGTCCACTATGAAGTTTTTAG
          1 CTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG

                        *                          * *      *     *  *   *   
       8194 CTCATTTGGAACTCTTGTTATTTTGGGCCTATCGGGGCCAAGTAGTGATGTTTTTAACCGTTTTC
         66 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTC

                   *         *      
       8259 GATTTGGAAAACCTCAAAGCTTTT
        131 GATTTGGCAAACCTCAATGCTTTT

                                    *    *                    *              
       8283 CTTTCCATTGTTTATGGACTAACTGTAATTATTTTGGTGAGATTAGTCCAATGTGAAGTTTTTAG
          1 CTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG

                          *                   *                              
       8348 CTCATTTGGAACACCTGTTATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTC
         66 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTC

            *                       
       8413 TATTTGGCAAACCTCAATGCTTTT
        131 GATTTGGCAAACCTCAATGCTTTT

                *                        *                                  *
       8437 CTTTTCATTGTTTAT-G----ACTATAATTATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAA
          1 CTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG

                                              *                              
       8497 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTC
         66 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTC

            *                        
       8562 TATTTGGCAAACCTCAATGCTTTTT
        131 GATTTGGCAAACCTCAATGC-TTTT

                *                        *                       *          *
       8587 CTTTTCATTGTTTAT-G----ACTATAATTATTTTGGTGAGATTAGTCCACTGAGAAGTTTTTAA
          1 CTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG

                                                                             
       8647 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTC
         66 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTC

                                    
       8712 GATTTGGCAAACCTCAATGCTTTT
        131 GATTTGGCAAACCTCAATGCTTTT

                       *                                                     
       8736 CTTTCCATTGTGTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG
          1 CTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG

                       *                         *                           
       8801 CTCATTTGGAAAACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTC
         66 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTC

                            *    *   
       8866 GATTTGGC-AACCTTCGATGCCTTT
        131 GATTTGGCAAACC-TCAATGCTTTT

                             *                                  *            
       8890 CTTTCCATTGTTTATGGCCT-ACATATAATCATTTTGGTGAGATTAGTCCACAGTGAAGTTTTTA
          1 CTTTCCATTGTTTATGGACTAAC-TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTA

                                             *    ***        *     *    *    
       8954 GCTCATTTGGAACACTTGTTATTTTGGGCCTATTGGGGATTATTAGTGAAGTTTTAAATCATCTT
         65 GCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTT

                                     
       9019 CGATTTGGCAAACCTCAATGCTTTT
        130 CGATTTGGCAAACCTCAATGCTTTT

                * *    *     *           *                                   
       9044 CTTTACGTTGTGTATGGCCTAACTATAATTATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG
          1 CTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG

                                       *                    **             * 
       9109 CTCATTTGGAACACTTTAGTTATTTTGTGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTAT
         66 CTCATTTGGAACAC-TT-GTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCT

                                      
       9174 TCGATTTGGCAAACCTCAATGCTTTT
        129 TCGATTTGGCAAACCTCAATGCTTTT

                             *                    *                          
       9200 CTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTTAGATTAGTCCACTGTGAAGTTTTTAG
          1 CTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG

                                     *                                       
       9265 CTCATTTGGAACACTTGTTATTTTGTGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTC
         66 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTC

                                    
       9330 GATTTGGCAAACCTCAATGCTTTT
        131 GATTTGGCAAACCTCAATGCTTTT

                                                                             
       9354 CTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG
          1 CTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG

                                     *                                       
       9419 CTCATTTGGAACACTTGTTATTTTGTGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTC
         66 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTC

                                    
       9484 GATTTGGCAAACCTCAATGCTTTT
        131 GATTTGGCAAACCTCAATGCTTTT

                                    *      *                                 
       9508 CTTTCCATTGTTTATGGACTAACTGTAATCACTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG
          1 CTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG

                            *                                             *  
       9573 CTCATTTGGAACACTTTTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCATC
         66 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTC

                                    
       9638 GATTTGGCAAACCTCAATGCTTTT
        131 GATTTGGCAAACCTCAATGCTTTT

                           
       9662 CTTTCCATTGTTTAT
          1 CTTTCCATTGTTTAT


Statistics
Matches: 2002,  Mismatches: 150, Indels: 26
        0.92            0.07        0.01

Matches are distributed among these distances:
 149  142  0.07
 150  147  0.07
 153    7  0.00
 154  1416  0.71
 155  154  0.08
 156  136  0.07

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


Consensus pattern (154 bp):   
CTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG
CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTC
GATTTGGCAAACCTCAATGCTTTT

Done.