Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011036.1 Corchorus olitorius cultivar O-4 contig11069, 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, 627

Length: 1045
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.42


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

Alignment explanation


    Indices: 1--1045  Score: 1731
    Period size: 155  Copynumber: 6.8  Consensus size: 154

                       *                *                                    
          1 TTTGAATCGTCATCGATTTGGCAACCCTTGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
          1 TTTGAATCGTCTTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA

                                 ** *                       *                
         66 ATCATTTTGGTGAGATTAGTCTTCAGTGAAGTTTTTAGCTCATTTGGAGCACTTGTTATTTTAGG
         66 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTAGG

                   *                
        131 CCTTTCGAGGCCCATTAGCTCTGT
        131 CCTTTCGGGGCCCATTAGCTCTGT

                      *  *                                      *            
        155 TTTGAATCGTTTTGGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTAAGGCCTAACTATA
          1 TTTGAATCGTCTTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA

                                                                             
        220 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTAGG
         66 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTAGG

                                    
        285 CCTTTCGGGGCCCATTAGCTCTGT
        131 CCTTTCGGGGCCCATTAGCTCTGT

                         *            *                           *          
        309 TTTGAATCGT-TTGGATTTGGCAACCGTCGATGCGTTTTCTTTCCGATTGTTTAAGGCCTAACTA
          1 TTTGAATCGTCTTCGATTTGGCAACCCTCGATGC-TTTTCTTTCC-ATTGTTTATGGCCTAACTA

                                                                             
        373 TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTA
         64 TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTA

              *                       
        438 GGTCTTTCGGGGCCCATTAGCTCTGT
        129 GGCCTTTCGGGGCCCATTAGCTCTGT

                                                                             
        464 TTTGAATCGTCTTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
          1 TTTGAATCGTCTTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA

                                                       *                     
        529 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATCTGGAACACTTGTTATTTTA-G
         66 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTAGG

                                    
        593 CCTTTCGGGGCCCATTAGCTCTGT
        131 CCTTTCGGGGCCCATTAGCTCTGT

                      *  *                                                   
        617 TTTGAATCGTTTTGGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
          1 TTTGAATCGTCTTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA

                                                                          *  
        682 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGG
         66 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTAGG

               *           *     *    
        747 CCTATCGGGGCCCGAATAG-TGTCGT
        131 CCTTTCGGGGCCC-ATTAGCTCT-GT

                       *                *                                    
        772 TTTGAATCGTCATCGATTTGGCAACCCTTGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
          1 TTTGAATCGTCTTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA

                                   *     *                                   
        837 ATCATTTTGGTGAGATTAGTCCATTGTGATGTTTTTAGCTCATTTGGAACACTTGTTATTTTAGG
         66 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTAGG

                              *   * 
        902 CCTTTCGGGG-CCATTAGTTCTAT
        131 CCTTTCGGGGCCCATTAGCTCTGT

                      *                       *                  *           
        925 TTTGAATCGTATTCGATTTGGCAACCCTCGATG-GTTTCTTTCCATTGTTTATCGCCTAACTATA
          1 TTTGAATCGTCTTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA

                      *                                              
        989 ATCATTTTGCTTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
         66 ATCATTTTG-GTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT


Statistics
Matches: 840,  Mismatches: 43, Indels: 17
        0.93            0.05        0.02

Matches are distributed among these distances:
 152   38  0.05
 153  249  0.30
 154  265  0.32
 155  267  0.32
 156   21  0.03

ACGTcount: A:0.20, C:0.19, G:0.20, T:0.42


Consensus pattern (154 bp):   
TTTGAATCGTCTTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTAGG
CCTTTCGGGGCCCATTAGCTCTGT

Found at i:824 original size:308 final size:308

Alignment explanation


    Indices: 1--1045  Score: 1731
    Period size: 308  Copynumber: 3.4  Consensus size: 308

                      **                *                                    
          1 TTTGAATCGTCATCGATTTGGCAACCCTTGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
          1 TTTGAATCGTTTTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA

                                 ** *                       *                
         66 ATCATTTTGGTGAGATTAGTCTTCAGTGAAGTTTTTAGCTCATTTGGAGCACTTGTTATTTTAGG
         66 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTAGG

                   *                          *  *                           
        131 CCTTTCGAGGCCCATTAGCTCTGTTTTGAATCGTTTTGGATTTGGCAACCCTCGATGCTTTTCTT
        131 CCTTTCGGGGCCCATTAGCTCTGTTTTGAATCGTCTTCGATTTGGCAACCCTCGATGCTTTTCTT

                       *                                                     
        196 TCCATTGTTTAAGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
        196 TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC

                                                            
        261 ATTTGGAACACTTGTTATTTTAGGCCTTTCGGGGCCCATTAGCTCTGT
        261 ATTTGGAACACTTGTTATTTTAGGCCTTTCGGGGCCCATTAGCTCTGT

                         *            *                           *          
        309 TTTGAATCG-TTTGGATTTGGCAACCGTCGATGCGTTTTCTTTCCGATTGTTTAAGGCCTAACTA
          1 TTTGAATCGTTTTCGATTTGGCAACCCTCGATGC-TTTTCTTTCC-ATTGTTTATGGCCTAACTA

                                                                             
        373 TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTA
         64 TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTA

              *                                                              
        438 GGTCTTTCGGGGCCCATTAGCTCTGTTTTGAATCGTCTTCGATTTGGCAACCCTCGATGCTTTTC
        129 GGCCTTTCGGGGCCCATTAGCTCTGTTTTGAATCGTCTTCGATTTGGCAACCCTCGATGCTTTTC

                                                                             
        503 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
        194 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC

                *                                             
        568 TCATCTGGAACACTTGTTATTTTA-GCCTTTCGGGGCCCATTAGCTCTGT
        259 TCATTTGGAACACTTGTTATTTTAGGCCTTTCGGGGCCCATTAGCTCTGT

                         *                                                   
        617 TTTGAATCGTTTTGGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
          1 TTTGAATCGTTTTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA

                                                                          *  
        682 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGG
         66 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTAGG

               *           *     *               *                *          
        747 CCTATCGGGGCCCGAATAG-TGTCGTTTTGAATCGTCATCGATTTGGCAACCCTTGATGCTTTTC
        131 CCTTTCGGGGCCC-ATTAGCTCT-GTTTTGAATCGTCTTCGATTTGGCAACCCTCGATGCTTTTC

                                                             *     *         
        811 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCATTGTGATGTTTTTAGC
        194 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC

                                                        *   * 
        876 TCATTTGGAACACTTGTTATTTTAGGCCTTTCGGGG-CCATTAGTTCTAT
        259 TCATTTGGAACACTTGTTATTTTAGGCCTTTCGGGGCCCATTAGCTCTGT

                      *                       *                  *           
        925 TTTGAATCGTATTCGATTTGGCAACCCTCGATG-GTTTCTTTCCATTGTTTATCGCCTAACTATA
          1 TTTGAATCGTTTTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA

                      *                                              
        989 ATCATTTTGCTTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
         66 ATCATTTTG-GTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT


Statistics
Matches: 695,  Mismatches: 35, Indels: 14
        0.93            0.05        0.02

Matches are distributed among these distances:
 307  154  0.22
 308  280  0.40
 309  261  0.38

ACGTcount: A:0.20, C:0.19, G:0.20, T:0.42


Consensus pattern (308 bp):   
TTTGAATCGTTTTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTAGG
CCTTTCGGGGCCCATTAGCTCTGTTTTGAATCGTCTTCGATTTGGCAACCCTCGATGCTTTTCTT
TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
ATTTGGAACACTTGTTATTTTAGGCCTTTCGGGGCCCATTAGCTCTGT
Done.