Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017562.1 Corchorus olitorius cultivar O-4 contig17595, 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, 796

Length: 1328
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34


Found at i:745 original size:331 final size:334

Alignment explanation


    Indices: 11--759  Score: 1177
    Period size: 334  Copynumber: 2.3  Consensus size: 334

          1 AAAAATCAAA

                        *           **                                       
         11 GAAAAATCTTTCCGGTCAATTTTTTCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTT
          1 GAAAAATCTTTCGGGTCAATTTTTGGAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTT

            *                  *        *             *       *              
         76 CAGGCTAAAAACGCGTTCTGGTGGCCCGCCTAAGTTTTGAATTATTTTTGGCGCCAAGACTCCTT
         66 TAGGCTAAAAACGCGTTCTAGTGGCCCGACTAAGTTTTGAATGATTTTTGACGCCAAGACTCCTT

             *            *            *   *                                 
        141 GGAATATCTATTTTGATCTAACCAAATCTCAGCAATGATGGACTTAAGGATTTGTTTTTACGAGC
        131 GAAATATCTATTTTCATCTAACCAAATATCAACAATGATGGACTTAAGGATTTGTTTTTACGAGC

                *                                                            
        206 ATCTGAATGTTGTGTCGATTTAATTTAGAAAACAATTAAGAAATAAAAAAGAAAAACGATATCAG
        196 ATCTAAATGTTGTGTCGATTTAATTTAGAAAACAATTAAGAAATAAAAAAGAAAAACGATATCAG

                                 *       *                                   
        271 AAGCGTGAAAATCCCTCCAATCTTTTTGGTGTTGAATTATATATTTTTTATGAGTATTCTAAGAA
        261 AAGCGTGAAAATCCCTCCAATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTCTAAGAA

                     
        336 AAAATTGAG
        326 AAAATTGAG

                                               *                             
        345 GAAAAATCTTTCGGGTCAATTTTTGGAAAATTTTAACCGAAATCGTGTACTAACCATCACGGTTT
          1 GAAAAATCTTTCGGGTCAATTTTTGGAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTT

                                                   *         *               
        410 TAGGCTAAAAACGCGTTCTAGTGGCCCGACTAAGTTTTGCATGATTTTTTACGCCAAGACTCCTT
         66 TAGGCTAAAAACGCGTTCTAGTGGCCCGACTAAGTTTTGAATGATTTTTGACGCCAAGACTCCTT

                                *                     *                 **   
        475 GAAATATCTATTTTCATCTAGCCAAATATCAACAATGATGGATTTAAGGATTT-TTTTGTTTGAG
        131 GAAATATCTATTTTCATCTAACCAAATATCAACAATGATGGACTTAAGGATTTGTTTT-TACGAG

                           *                  *                             *
        539 CATCTAAAT-TATGTTTCGATTTAATTTAGAAAATAATTAAG-AA-AAAAAAGAAAAACGATATT
        195 CATCTAAATGT-TGTGTCGATTTAATTTAGAAAACAATTAAGAAATAAAAAAGAAAAACGATATC

                           * *                                               
        601 AGAAAG-GTGAAAA-GCGTCCAATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTCTAA
        259 AG-AAGCGTGAAAATCCCTCCAATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTCTAA

                        
        664 GAAAAAATTGAG
        323 GAAAAAATTGAG

                                                                         *   
        676 GAAAAATCTTTCGGGTCAATTTTTGGAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTT
          1 GAAAAATCTTTCGGGTCAATTTTTGGAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTT

                               
        741 TAGGCTAAAAACGCGTTCT
         66 TAGGCTAAAAACGCGTTCT

        760 GGCGCCAAGC


Statistics
Matches: 383,  Mismatches: 29, Indels: 9
        0.91            0.07        0.02

Matches are distributed among these distances:
 331  140  0.37
 332   27  0.07
 333   10  0.03
 334  206  0.54

ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34


Consensus pattern (334 bp):   
GAAAAATCTTTCGGGTCAATTTTTGGAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTT
TAGGCTAAAAACGCGTTCTAGTGGCCCGACTAAGTTTTGAATGATTTTTGACGCCAAGACTCCTT
GAAATATCTATTTTCATCTAACCAAATATCAACAATGATGGACTTAAGGATTTGTTTTTACGAGC
ATCTAAATGTTGTGTCGATTTAATTTAGAAAACAATTAAGAAATAAAAAAGAAAAACGATATCAG
AAGCGTGAAAATCCCTCCAATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTCTAAGAA
AAAATTGAG

Found at i:1010 original size:301 final size:302

Alignment explanation


    Indices: 461--1028  Score: 876
    Period size: 301  Copynumber: 1.9  Consensus size: 302

        451 TGATTTTTTA

                                              *                     *        
        461 CGCCAAGACTCCTTGAAATATCTATTTTCATCTAGCCAAATATCAACAATGATGGATTTAAGGAT
          1 CGCCAAGACTCCTTGAAATATCTATTTTCATCTAACCAAATATCAACAATGATGGACTTAAGGAT

                    **                 *         *                           
        526 TTTTTTGTTTGAGCATCTAAATTATGTTTCGATTTAATTTAGAAAATAATTAAGAAAAAAAAGAA
         66 TTTTTTGTACGAGCATCTAAATTATGTGTCGATTTAAATTAGAAAATAATTAAGAAAAAAAAGAA

                     *             * *                                       
        591 AAACGATATTAGAAAGGTGAAAAGCGTCCAATATTTTTGGCGTTGAATTATATATTTTTTATGAG
        131 AAACGATATCAGAAAGGTGAAAACCCTCCAATATTTTTGGCGTTGAATTATATATTTTTTATGAG

                                              *                              
        656 TATTCTAAGAAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGGAAAA-TTTTAGCCGAAATC
        196 TATTCTAAGAAAAAATTGAGGAAAAATCTTTCGGCTCAATTTTTGGAAAATTTTTAGCCGAAATC

                                                      
        720 GTGTACTAACCATCACGATTTTAGGCTAAAAACGCGTTCTGG
        261 GTGTACTAACCATCACGATTTTAGGCTAAAAACGCGTTCTGG

                   *       *            *            *   *         *         
        762 CGCCAAGCCTCCTTGGAATATCTATTTTGATCTAACCAAATCTCAGCAATGATGGGCTTAAGGAT
          1 CGCCAAGACTCCTTGAAATATCTATTTTCATCTAACCAAATATCAACAATGATGGACTTAAGGAT

                               *                                             
        827 TTGTTTT-TACGAGCATCTGAATGT-TGTGTCGATTTAAATTAGAAAATAATTAAGAAAAAAAAA
         66 TT-TTTTGTACGAGCATCTAAAT-TATGTGTCGATTTAAATTAGAAAATAATTAAG-AAAAAAAA

                                                 *                           
        890 GAAAAACGATATCAG-AAGCGTGAAAATCCCTCCAATCTTTTTGGCGTTGAATTATATATTTTTT
        128 GAAAAACGATATCAGAAAG-GTGAAAA-CCCTCCAATATTTTTGGCGTTGAATTATATATTTTTT

                                                              *   *          
        954 ATGAGTATTCTAAG-AAAAATTGAGGAAAAATCTTTCGGCTCAATTTTTGCAAATTTTTTAGCCG
        191 ATGAGTATTCTAAGAAAAAATTGAGGAAAAATCTTTCGGCTCAATTTTTGGAAAATTTTTAGCCG

                       
       1018 AAATCGTGTAC
        256 AAATCGTGTAC

       1029 GTCACGGTTT


Statistics
Matches: 241,  Mismatches: 20, Indels: 10
        0.89            0.07        0.04

Matches are distributed among these distances:
 301  102  0.42
 302   71  0.29
 303   68  0.28

ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34


Consensus pattern (302 bp):   
CGCCAAGACTCCTTGAAATATCTATTTTCATCTAACCAAATATCAACAATGATGGACTTAAGGAT
TTTTTTGTACGAGCATCTAAATTATGTGTCGATTTAAATTAGAAAATAATTAAGAAAAAAAAGAA
AAACGATATCAGAAAGGTGAAAACCCTCCAATATTTTTGGCGTTGAATTATATATTTTTTATGAG
TATTCTAAGAAAAAATTGAGGAAAAATCTTTCGGCTCAATTTTTGGAAAATTTTTAGCCGAAATC
GTGTACTAACCATCACGATTTTAGGCTAAAAACGCGTTCTGG
Done.