Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011636.1 Corchorus olitorius cultivar O-4 contig11669, 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: 2036
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38


Found at i:505 original size:153 final size:154

Alignment explanation


    Indices: 1--1497  Score: 2151
    Period size: 154  Copynumber: 9.8  Consensus size: 154

                       *          *                                     *    
          1 TCTTCGATTTGACAAACCTCAAGGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCAATTTG
          1 TCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG

                                      *             *              *         
         66 GTGAGATTAGTCCACTGTGAAG--TTAAGGCTCATTTGGATCACTTGTTATTTTGAGCCTATCGG
         66 GTGAGATTAGTCCACTGTGAAGTTTTTA-GCTCATTTGGAACACTTGTTATTTTGGGCCTATCGG

                       **            
        129 GGCCCATTAGTTCCGTTTTGAATCG
        130 GGCCCATTAGTGACGTTTTGAATCG

              ** *                    *       *                              
        154 TCCACAATTTGGCAAACCTCAAAGCTATTCTTT-AAGTTGTTTATGGCCTAACTATAATCATTTT
          1 TCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCA-TTGTTTATGGCCTAACTATAATCATTTT

             *                       *                                       
        218 GATGAGATTAGTCCACTGTGAAGTTCTTAGCTCAATTT-GAACACTTGTTATTTTGGGCCTATCG
         65 GGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC-ATTTGGAACACTTGTTATTTTGGGCCTATCG

                          *            
        282 GGGCCCATTAGAT-TCGTTTTGAATCG
        129 GGGCCCATTAG-TGACGTTTTGAATCG

                                                          *                  
        308 TCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTG
          1 TCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG

                                                *                            
        373 GTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTA-TTTGGGCCTATCGGG
         66 GTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGG

                         *          
        437 GCCCATTAGTGACATTTTGAATCG
        131 GCCCATTAGTGACGTTTTGAATCG

                 *                *                                     *    
        461 TCTTCAATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCAATTTG
          1 TCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG

                                      *             *                        
        526 GTGAGATTAGTCCACTGTGAAG--TTAAGGCTCATTTGGATCACTTG-TATTTTGGGCCTATCGG
         66 GTGAGATTAGTCCACTGTGAAGTTTTTA-GCTCATTTGGAACACTTGTTATTTTGGGCCTATCGG

                          *          
        588 GGCCCATTAGTGACATTTTGAATCG
        130 GGCCCATTAGTGACGTTTTGAATCG

                       *          *                                          
        613 TCTTCGATTTGACAAACCTCAAGGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG
          1 TCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG

                              *                      *                 *     
        678 GTGAGATTAGTCCACTGTAAAGTTTATT-GCTCATTTGGAATACTTGTTATTTTGGGCCCATCGG
         66 GTGAGATTAGTCCACTGTGAAGTTT-TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGG

                     * **            
        742 GGCCCATTACTTCCGTTTTGAATCG
        130 GGCCCATTAGTGACGTTTTGAATCG

                 *          *         *       *                            * 
        767 TCTTCAATTTGGCAAATCTCAAAGCTATTCTTT-AAGTTGTTTATGGCCTAACTATAATCATTGT
          1 TCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCA-TTGTTTATGGCCTAACTATAATCATTTT

             *               *       *                  *            *       
        831 GATGAGATTAGTCCACTATGAAGTTCTTAGCTCAATTT-GAACAGTTGTTATTTTGGTCCTATCG
         65 GGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC-ATTTGGAACACTTGTTATTTTGGGCCTATCG

                        **            
        895 GGGCCCATTAGTTTCGTTTTGAATCG
        129 GGGCCCATTAGTGACGTTTTGAATCG

                             *                    *       *      *           
        921 TCTTCGATTTGGCAAACTTCAAAGCTTTTCTTTCCATTTTTTATGGACTAACTTTAATCATTTTG
          1 TCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG

                            *                                                
        986 GTGAGATTAGTCCACTATGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGG
         66 GTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGG

                     *   *          
       1051 GCCCATTAGAGACATTTTGAATCG
        131 GCCCATTAGTGACGTTTTGAATCG

                           *   *  *                            *        *    
       1075 TCTTCGATTTGGCAAGCCTTAAGGCTTTTCTTTCCATTGTTTATGGCCTAAGTATAATCAATTTG
          1 TCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG

                            *                      *                         
       1140 GTGAGATTAGTCCACTATGAAG-TTTTAGCTCATTTGGATCACTTGTTATTTTGGGCCTATCGGG
         66 GTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGG

                         *          
       1204 GCCCATTAGTGACATTTTGAATCG
        131 GCCCATTAGTGACGTTTTGAATCG

                                  *                                          
       1228 TCTTCGATTTGGCAAACCTCAACGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG
          1 TCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG

                     *        *                                       *  *   
       1293 GTGAGATTAATCCACTGTAAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCCATAGGG
         66 GTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGG

                                    
       1358 GCCCATTAGTGACGTTTTGAATCG
        131 GCCCATTAGTGACGTTTTGAATCG

                 *                    *       *                              
       1382 TCTTCAATTTGGCAAACCTCAAAGCTATTCTTT-AAGTTGTTTATGGCCTAACTATAATCATTTT
          1 TCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCA-TTGTTTATGGCCTAACTATAATCATTTT

             *               *       *                     *     
       1446 GATGAGATTAGTCCACTATGAAGTTCTTAGCTCAATTT-GAACACTTCTTATT
         65 GGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC-ATTTGGAACACTTGTTATT

       1498 GATGCGCCAA


Statistics
Matches: 1211,  Mismatches: 111, Indels: 43
        0.89            0.08        0.03

Matches are distributed among these distances:
 151    5  0.00
 152  139  0.11
 153  365  0.30
 154  684  0.56
 155   18  0.01

ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39


Consensus pattern (154 bp):   
TCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG
GTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGG
GCCCATTAGTGACGTTTTGAATCG

Found at i:1318 original size:307 final size:308

Alignment explanation


    Indices: 1--1497  Score: 2266
    Period size: 307  Copynumber: 4.9  Consensus size: 308

                       *          *                                     *    
          1 TCTTCGATTTGACAAACCTCAAGGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCAATTTG
          1 TCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG

                                      *             *              *         
         66 GTGAGATTAGTCCACTGTGAAG--TTAAGGCTCATTTGGATCACTTGTTATTTTGAGCCTATCGG
         66 GTGAGATTAGTCCACTGTGAAGTTTTTA-GCTCATTTGGAACACTTGTTATTTTGGGCCTATCGG

                       **              **                                    
        129 GGCCCATTAGTTCCGTTTTGAATCGTCCACAATTTGGCAAACCTCAAAGCTATTCTTTAAGTTGT
        130 GGCCCATTAGTGACGTTTTGAATCGTCTTCAATTTGGCAAACCTCAAAGCTATTCTTTAAGTTGT

                                *                    *                       
        194 TTATGGCCTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTCTTAGCTCAATTTGAA
        195 TTATGGCCTAACTATAATCAATTTGATGAGATTAGTCCACTATGAAGTTCTTAGCTCAATTTGAA

                                                 * *          
        259 CACTTGTTATTTTGGGCCTATCGGGGCCCATTAGAT-TCGTTTTGAATCG
        260 CACTTGTTATTTTGGGCCTATCGGGGCCCATTAG-TGACATTTTGAATCG

                                                          *                  
        308 TCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTG
          1 TCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG

                                                *                            
        373 GTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTA-TTTGGGCCTATCGGG
         66 GTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGG

                         *                                *   *       *      
        437 GCCCATTAGTGACATTTTGAATCGTCTTCAATTTGGCAAACCTCAATGCTTTTCTTTCCA-TTGT
        131 GCCCATTAGTGACGTTTTGAATCGTCTTCAATTTGGCAAACCTCAAAGCTATTCTTT-AAGTTGT

                                     *               *         *             
        501 TTATGGCCTAACTATAATCAATTTGGTGAGATTAGTCCACTGTGAAG-T-TAAGGCTC-ATTTGG
        195 TTATGGCCTAACTATAATCAATTTGATGAGATTAGTCCACTATGAAGTTCTTA-GCTCAATTT-G

             *                                                 
        563 ATCACTTG-TATTTTGGGCCTATCGGGGCCCATTAGTGACATTTTGAATCG
        258 AACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACATTTTGAATCG

                       *          *                                          
        613 TCTTCGATTTGACAAACCTCAAGGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG
          1 TCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG

                              *                      *                 *     
        678 GTGAGATTAGTCCACTGTAAAGTTTATT-GCTCATTTGGAATACTTGTTATTTTGGGCCCATCGG
         66 GTGAGATTAGTCCACTGTGAAGTTT-TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGG

                     * **                            *                       
        742 GGCCCATTACTTCCGTTTTGAATCGTCTTCAATTTGGCAAATCTCAAAGCTATTCTTTAAGTTGT
        130 GGCCCATTAGTGACGTTTTGAATCGTCTTCAATTTGGCAAACCTCAAAGCTATTCTTTAAGTTGT

                                                                             
        807 TTATGGCCTAACTATAATC-ATTGTGATGAGATTAGTCCACTATGAAGTTCTTAGCTCAATTTGA
        195 TTATGGCCTAACTATAATCAATT-TGATGAGATTAGTCCACTATGAAGTTCTTAGCTCAATTTGA

               *            *                   ** *          
        871 ACAGTTGTTATTTTGGTCCTATCGGGGCCCATTAGTTTCGTTTTGAATCG
        259 ACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACATTTTGAATCG

                             *                    *       *      *           
        921 TCTTCGATTTGGCAAACTTCAAAGCTTTTCTTTCCATTTTTTATGGACTAACTTTAATCATTTTG
          1 TCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG

                            *                                                
        986 GTGAGATTAGTCCACTATGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGG
         66 GTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGG

                     *   *               *         *   *  *   *       *      
       1051 GCCCATTAGAGACATTTTGAATCGTCTTCGATTTGGCAAGCCTTAAGGCTTTTCTTTCCA-TTGT
        131 GCCCATTAGTGACGTTTTGAATCGTCTTCAATTTGGCAAACCTCAAAGCTATTCTTT-AAGTTGT

                       *             *                                       
       1115 TTATGGCCTAAGTATAATCAATTTGGTGAGATTAGTCCACTATGAAGTT-TTAGCTC-ATTTGGA
        195 TTATGGCCTAACTATAATCAATTTGATGAGATTAGTCCACTATGAAGTTCTTAGCTCAATTT-GA

            *                                                 
       1178 TCACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACATTTTGAATCG
        259 ACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACATTTTGAATCG

                                  *                                          
       1228 TCTTCGATTTGGCAAACCTCAACGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG
          1 TCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG

                     *        *                                       *  *   
       1293 GTGAGATTAATCCACTGTAAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCCATAGGG
         66 GTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGG

                                                                             
       1358 GCCCATTAGTGACGTTTTGAATCGTCTTCAATTTGGCAAACCTCAAAGCTATTCTTTAAGTTGTT
        131 GCCCATTAGTGACGTTTTGAATCGTCTTCAATTTGGCAAACCTCAAAGCTATTCTTTAAGTTGTT

                               *                                             
       1423 TATGGCCTAACTATAATCATTTTGATGAGATTAGTCCACTATGAAGTTCTTAGCTCAATTTGAAC
        196 TATGGCCTAACTATAATCAATTTGATGAGATTAGTCCACTATGAAGTTCTTAGCTCAATTTGAAC

                *     
       1488 ACTTCTTATT
        261 ACTTGTTATT

       1498 GATGCGCCAA


Statistics
Matches: 1070,  Mismatches: 99, Indels: 41
        0.88            0.08        0.03

Matches are distributed among these distances:
 304    1  0.00
 305  153  0.14
 306  129  0.12
 307  483  0.45
 308  293  0.27
 309   11  0.01

ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39


Consensus pattern (308 bp):   
TCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG
GTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGG
GCCCATTAGTGACGTTTTGAATCGTCTTCAATTTGGCAAACCTCAAAGCTATTCTTTAAGTTGTT
TATGGCCTAACTATAATCAATTTGATGAGATTAGTCCACTATGAAGTTCTTAGCTCAATTTGAAC
ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACATTTTGAATCG

Found at i:1632 original size:21 final size:21

Alignment explanation


    Indices: 1606--1647  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1596 TAAGGAAGAA

                                 
       1606 GTTTCAAGCTCATCAGAGTTG
          1 GTTTCAAGCTCATCAGAGTTG

                          *      
       1627 GTTTCAAGCTCATCGGAGTTG
          1 GTTTCAAGCTCATCAGAGTTG

       1648 CCTAAGATGC


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33


Consensus pattern (21 bp):   
GTTTCAAGCTCATCAGAGTTG
Done.