Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010929.1 Corchorus olitorius cultivar O-4 contig10961, 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: 1987
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34


Found at i:848 original size:106 final size:105

Alignment explanation


    Indices: 711--1204  Score: 719
    Period size: 106  Copynumber: 4.7  Consensus size: 105

        701 ATGTTCAAAG

                           *   *     *        **                             
        711 TTTCAGTTTGACCCAAGGCAGTC-TCCATTCAGTAAATTTCAGTTGACCCAGGGCGGTCTTTCTT
          1 TTTCAG-TTGACCCAGGGCGGTCTTTC-TTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTT

                                                   *   
        775 CAGTTCATTTCAGTTGACCCAGGGCGGTCTTTCTTCAAGATTA
         64 CAGTTCATTTCAGTTGACCCAGGGCGGTCTTTCTTC-AGTTTA

                                                                 *           
        818 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCAGTCTTTCTTCA
          1 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCA

               *                                    
        883 GTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA
         66 GTTCATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA

                                     *                *                *     
        923 TTTCAGTTGACCCAGGGCGGTCTTTTTTCAGTTTATTTCAGTAGACCCAGGGCGGTCTTCCTTCA
          1 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTC-

                                                      
        988 AGATT-ATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA
         65 AG-TTCATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA

                                        *  *                                 
       1029 TTTCAGTTGACCCAGGGCGGTC-TTC--AAGATTATTTCAGTTGACCCAGGGCGGTCTTTCTTCA
          1 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCA

               *  *                                 
       1091 GTTTATCTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA
         66 GTTCATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA

                       *  *               *  *                             * 
       1131 TTTCAGTTGACTCATGGCGGTCTTTCTTCAATTCATTTCAGTTGACCCAGGGCGGTCTTTCTTTA
          1 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCA

            *        
       1196 ATTCATTTC
         66 GTTCATTTC

       1205 TAAGATCCAG


Statistics
Matches: 352,  Mismatches: 28, Indels: 16
        0.89            0.07        0.04

Matches are distributed among these distances:
 101    2  0.01
 102   57  0.16
 103   35  0.10
 105  105  0.30
 106  143  0.41
 107   10  0.03

ACGTcount: A:0.17, C:0.23, G:0.21, T:0.38


Consensus pattern (105 bp):   
TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCA
GTTCATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA

Found at i:1204 original size:35 final size:35

Alignment explanation


    Indices: 711--1193  Score: 731
    Period size: 35  Copynumber: 13.8  Consensus size: 35

        701 ATGTTCAAAG

                           *   *     *        ** 
        711 TTTCAGTTTGACCCAAGGCAGTC-TCCATTCAGTAAA
          1 TTTCAG-TTGACCCAGGGCGGTCTTTC-TTCAGTTTA

                                             * 
        747 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTCA
          1 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA

                                            *   
        782 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAAGATTA
          1 TTTCAGTTGACCCAGGGCGGTCTTTCTTC-AGTTTA

                                               
        818 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA
          1 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA

                              *                
        853 TTTCAGTTGACCCAGGGCAGTCTTTCTTCAGTTTA
          1 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA

                                               
        888 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA
          1 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA

                                     *         
        923 TTTCAGTTGACCCAGGGCGGTCTTTTTTCAGTTTA
          1 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA

                   *                *       *   
        958 TTTCAGTAGACCCAGGGCGGTCTTCCTTCAAGATTA
          1 TTTCAGTTGACCCAGGGCGGTCTTTCTTC-AGTTTA

                                               
        994 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA
          1 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA

                                        *  *   
       1029 TTTCAGTTGACCCAGGGCGGTC-TTC--AAGATTA
          1 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA

                                               
       1061 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA
          1 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA

             *                                 
       1096 TCTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA
          1 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA

                       *  *               *  * 
       1131 TTTCAGTTGACTCATGGCGGTCTTTCTTCAATTCA
          1 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA

                                        
       1166 TTTCAGTTGACCCAGGGCGGTCTTTCTT
          1 TTTCAGTTGACCCAGGGCGGTCTTTCTT

       1194 TAATTCATTT


Statistics
Matches: 411,  Mismatches: 30, Indels: 13
        0.91            0.07        0.03

Matches are distributed among these distances:
  32   27  0.07
  33    3  0.01
  34    3  0.01
  35  305  0.74
  36   73  0.18

ACGTcount: A:0.17, C:0.23, G:0.22, T:0.38


Consensus pattern (35 bp):   
TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA

Done.