Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011053.1 Corchorus olitorius cultivar O-4 contig11086, 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, 643

Length: 1073
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39


Found at i:398 original size:154 final size:154

Alignment explanation


    Indices: 37--1073  Score: 1657
    Period size: 154  Copynumber: 6.7  Consensus size: 154

         27 TGGCACATCA

                                              *                              
         37 CATTTTGGTGAGATTAGTCCACTGTGAAGTTCTTAAGACTCATTTGGAACACTTGTTATTTTGGG
          1 CATTTTGGTGAGATTAGTCCACTGTGAAGTT-TTTAG-CTCATTTGGAACACTTGTTATTTTGGG

                      *        **                              *             
        102 CCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGC-TTTCTT
         64 CCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTT

                                      
        166 TCCATTGTTTATGGCCTAACTATAAT
        129 TCCATTGTTTATGGCCTAACTATAAT

                                            *                                
        192 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTCTAGCTCATTTGGAACACTTGTTATTTTGGGCC
          1 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCC

               **     *                                                      
        257 TATTTGGGCCAATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTC
         66 TATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTC

                                    
        322 CATTGTTTATGGCCTAACTATAAT
        131 CATTGTTTATGGCCTAACTATAAT

                                        ** *   *                        *    
        346 CATTTTGGTGAGATTAGTCCACTGTGAACATCTTAACTCATTTGGAACACTTGTTATTTTAGGCC
          1 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCC

                    *        **      *                       *               
        411 TATCGGGGACCATTAGTGACGTTTTAAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTC
         66 TATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTC

                                    
        476 CATTGTTTATGGCCTAACTATAAT
        131 CATTGTTTATGGCCTAACTATAAT

                 *                                           *               
        500 CATTTGGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACAATTGTTATTTTGGGCC
          1 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCC

             *           *   **                              *               
        565 TGTCGGGGCCCATCAGTGACGTTTTGAATCGTCTTCGATTTGGCAAA-CGCAATGCTTTTCTTTC
         66 TATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTC

                     *              
        629 CATTGTTTAAGGCCTAACTATAAT
        131 CATTGTTTATGGCCTAACTATAAT

                  *    *                                   *                 
        653 CA-TTTCGTGAAATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAAACTTGTTATTTTGGGCC
          1 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCC

                                  *                                          
        717 TATCGGGGCCCATTAGTTCCGTCTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTC
         66 TATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTC

                                    
        782 CATTGTTTATGGCCTAACTATAAT
        131 CATTGTTTATGGCCTAACTATAAT

                                                                             
        806 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCC
          1 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCC

                      *           *                                          
        871 TATCGGGGCCAATTAGTTCCGTCTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTC
         66 TATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTC

                                    
        936 CATTGTTTATGGCCTAACTATAAT
        131 CATTGTTTATGGCCTAACTATAAT

            *        *                                      *                
        960 TATTTTGGTCAGATTAGTCCACTGTGAAGTTTTTAGTCTCATTTGGAAGACTTGTTTATTTTTTG
          1 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG-CTCATTTGGAACACTTG-TTA--TTTTG

             *                                               
       1025 GTCCTATCGGGGCCCATTAGTTCCGTTTTTGAATCGTCTTCGATTTGGC
         62 GGCCTATCGGGGCCCATTAGTTCCG-TTTTGAATCGTCTTCGATTTGGC


Statistics
Matches: 816,  Mismatches: 58, Indels: 12
        0.92            0.07        0.01

Matches are distributed among these distances:
 152   99  0.12
 153  160  0.20
 154  457  0.56
 155   47  0.06
 156    3  0.00
 158   28  0.03
 159   22  0.03

ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40


Consensus pattern (154 bp):   
CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCC
TATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTC
CATTGTTTATGGCCTAACTATAAT

Found at i:808 original size:306 final size:309

Alignment explanation


    Indices: 37--1073  Score: 1679
    Period size: 306  Copynumber: 3.4  Consensus size: 309

         27 TGGCACATCA

                                              *                              
         37 CATTTTGGTGAGATTAGTCCACTGTGAAGTTCTTAAGACTCATTTGGAACACTTGTTATTTTGGG
          1 CATTTTGGTGAGATTAGTCCACTGTGAAGTT-TTTAGACTCATTTGGAACACTTGTTATTTTGGG

                                                                             
        102 CCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGC-TTTCTT
         65 CCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTT

                                                                      *      
        166 TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTCTAGCTC
        130 TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC

                                         **                                  
        231 ATTTGGAACACTTGTTATTTTGGGCCTATTTGGGCCAATTAGTTCCGTTTTGAATCGTCTTCGAT
        195 ATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCAATTAGTTCCGTTTTGAATCGTCTTCGAT

                                                              
        296 TTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT
        260 TTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT

                                        ** *                             *   
        346 CATTTTGGTGAGATTAGTCCACTGTGAACATCTTA-ACTCATTTGGAACACTTGTTATTTTAGGC
          1 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGACTCATTTGGAACACTTGTTATTTTGGGC

                                      *                                      
        410 CTATCGGGGACCATTAGTGACGTTTTAAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTT
         66 CTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTT

                                          *                                  
        475 CCATTGTTTATGGCCTAACTATAATCATTTGGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCA
        131 CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCA

                     *                *        *  *   **                     
        540 TTTGGAACAATTGTTATTTTGGGCCTGTCGGGGCCCATCAGTGACGTTTTGAATCGTCTTCGATT
        196 TTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCAATTAGTTCCGTTTTGAATCGTCTTCGATT

                     *                        *              
        605 TGGCAAA-CGCAATGCTTTTCTTTCCATTGTTTAAGGCCTAACTATAAT
        261 TGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT

                  *    *                                    *                
        653 CA-TTTCGTGAAATTAGTCCACTGTGAAGTTTTTAG-CTCATTTGGAAAACTTGTTATTTTGGGC
          1 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGACTCATTTGGAACACTTGTTATTTTGGGC

                     *        **   *                          *              
        716 CTATCGGGGCCCATTAGTTCCGTCTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTT
         66 CTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTT

                                                                             
        781 CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCA
        131 CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCA

                                                           *                 
        846 TTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCAATTAGTTCCGTCTTGAATCGTCTTCGATT
        196 TTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCAATTAGTTCCGTTTTGAATCGTCTTCGATT

                                                             
        911 TGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT
        261 TGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT

            *        *                          *           *                
        960 TATTTTGGTCAGATTAGTCCACTGTGAAGTTTTTAGTCTCATTTGGAAGACTTGTTTATTTTTTG
          1 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGACTCATTTGGAACACTTG-TTA--TTTTG

             *          *        **                          
       1025 GTCCTATCGGGGCCCATTAGTTCCGTTTTTGAATCGTCTTCGATTTGGC
         63 GGCCTATCGGGGACCATTAGTGACG-TTTTGAATCGTCTTCGATTTGGC


Statistics
Matches: 671,  Mismatches: 48, Indels: 14
        0.92            0.07        0.02

Matches are distributed among these distances:
 306  241  0.36
 307  165  0.25
 308  166  0.25
 309   45  0.07
 310    3  0.00
 312   29  0.04
 313   22  0.03

ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40


Consensus pattern (309 bp):   
CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGACTCATTTGGAACACTTGTTATTTTGGGC
CTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTT
CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCA
TTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCAATTAGTTCCGTTTTGAATCGTCTTCGATT
TGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT

Found at i:936 original size:460 final size:462

Alignment explanation


    Indices: 37--1073  Score: 1686
    Period size: 460  Copynumber: 2.2  Consensus size: 462

         27 TGGCACATCA

                                              *                              
         37 CATTTTGGTGAGATTAGTCCACTGTGAAGTTCTTAAGACTCATTTGGAACACTTGTTATTTTGGG
          1 CATTTTGGTGAGATTAGTCCACTGTGAAGTT-TTTAGACTCATTTGGAACACTTGTTATTTTGGG

                      *                                        *             
        102 CCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTCTTT
         65 CCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCGCAATGCTTTCTTT

                      *                    *    *                            
        167 CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTCTAGCTCA
        130 CCATTGTTTAAGGCCTAACTATAATCATTTTCGTGAAATTAGTCCACTGTGAAGTTTCTAGCTCA

                   *                    **                 *                 
        232 TTTGGAACACTTGTTATTTTGGGCCTATTTGGGCCAATTAGTTCCGTTTTGAATCGTCTTCGATT
        195 TTTGGAAAACTTGTTATTTTGGGCCTATCGGGGCCAATTAGTTCCGTCTTGAATCGTCTTCGATT

                                                                             
        297 TGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTA
        260 TGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTA

                                                                             
        362 GTCCACTGTGAACATCTTAACTCATTTGGAACACTTGTTATTTTAGGCCTATCGGGGACCATTAG
        325 GTCCACTGTGAACATCTTAACTCATTTGGAACACTTGTTATTTTAGGCCTATCGGGGACCATTAG

                  *                          *                               
        427 TGACGTTTTAAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTA
        390 TGACGTCTTAAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTA

                    
        492 ACTATAAT
        455 ACTATAAT

                 *                                            *              
        500 CATTTGGGTGAGATTAGTCCACTGTGAAGTTTTTAG-CTCATTTGGAACAATTGTTATTTTGGGC
          1 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGACTCATTTGGAACACTTGTTATTTTGGGC

              *           *                                                  
        564 CTGTCGGGGCCCATCAGTGACGTTTTGAATCGTCTTCGATTTGGCAAA-CGCAATGCTTTTCTTT
         66 CTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCGCAATGC-TTTCTTT

                                                                     *       
        628 CCATTGTTTAAGGCCTAACTATAATCA-TTTCGTGAAATTAGTCCACTGTGAAGTTTTTAGCTCA
        130 CCATTGTTTAAGGCCTAACTATAATCATTTTCGTGAAATTAGTCCACTGTGAAGTTTCTAGCTCA

                                               *                             
        692 TTTGGAAAACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTCTTGAATCGTCTTCGATT
        195 TTTGGAAAACTTGTTATTTTGGGCCTATCGGGGCCAATTAGTTCCGTCTTGAATCGTCTTCGATT

                                                                             
        757 TGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTA
        260 TGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTA

                        ** *   *                        *                    
        822 GTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGG-CCAATTA
        325 GTCCACTGTGAACATCTTAACTCATTTGGAACACTTGTTATTTTAGGCCTATCGGGGACC-ATTA

              **      *                                                      
        886 GTTCCGTCTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCT
        389 GTGACGTCTTAAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCT

                     
        951 AACTATAAT
        454 AACTATAAT

            *        *                          *           *                
        960 TATTTTGGTCAGATTAGTCCACTGTGAAGTTTTTAGTCTCATTTGGAAGACTTGTTTATTTTTTG
          1 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGACTCATTTGGAACACTTG-TTA--TTTTG

             *                   **                          
       1025 GTCCTATCGGGGCCCATTAGTTCCGTTTTTGAATCGTCTTCGATTTGGC
         63 GGCCTATCGGGGCCCATTAGTGACG-TTTTGAATCGTCTTCGATTTGGC


Statistics
Matches: 531,  Mismatches: 36, Indels: 12
        0.92            0.06        0.02

Matches are distributed among these distances:
 459    2  0.00
 460  324  0.61
 461  120  0.23
 462    7  0.01
 463   30  0.06
 464   25  0.05
 465   23  0.04

ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40


Consensus pattern (462 bp):   
CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGACTCATTTGGAACACTTGTTATTTTGGGC
CTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCGCAATGCTTTCTTTC
CATTGTTTAAGGCCTAACTATAATCATTTTCGTGAAATTAGTCCACTGTGAAGTTTCTAGCTCAT
TTGGAAAACTTGTTATTTTGGGCCTATCGGGGCCAATTAGTTCCGTCTTGAATCGTCTTCGATTT
GGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
TCCACTGTGAACATCTTAACTCATTTGGAACACTTGTTATTTTAGGCCTATCGGGGACCATTAGT
GACGTCTTAAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAA
CTATAAT
Done.