Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000020.1 Corchorus olitorius cultivar O-4 contig00020, 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: 2169
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37


Found at i:1552 original size:331 final size:329

Alignment explanation


    Indices: 525--1610  Score: 1191
    Period size: 332  Copynumber: 3.3  Consensus size: 329

        515 TTGTTTTTAG

                             *    * *     *   *        * *             * *  *
        525 AAGCGTGAAAAG-CCTTTCAATCTATTTGGGGTTGAATTATATGTTTTTTATGAGTATTGTGGCT
          1 AAGCGTGAAAAGTCC-TCCAATATTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTAGCC

                             *    **          *      *      *              * 
        589 AAAAATTGAGGAAAAATATTTCGGGTCATTTTTTACAAAATATTAGCCAAAATCGTGTAACATCA
         65 AAAAATTGAGGAAAAATTTTTCCAGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGT-AC-TAA

             *      ***                           *            *            *
        654 CGAT-ATTTTTTTTGTTTGCTAAAAACGCGTTCCGAT-ACCCCGGGTCAGTATTGCATGATTTTC
        128 CCATCA--CGATTT-TTTGCTAAAAACGCGTTCCG-TGGCCCCGGGTCAGTTTTGCATGATTTTT

                        *            *        *                              
        717 GGCGCCAAGACACCTTGA-ACTATCTATATTCATATAATCAAATCTCAGTCACATTGGATTTAAT
        189 GGCGCCAAGAC-TCTTGAGA-TATCCATATTCATCTAATCAAATCTCAGTCACATTGGATTTAA-

                                 *                                *         *
        781 GATTTGTTTTTATGAGCATCAAAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAGTAG
        251 GATTTGTTTTTATGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCTGAAAAA-TAT

                         **
        846 GAAAAACGATATTGG
        315 GAAAAACGATATTAA

                  *    **   *           *    *   *       *           *       
        861 AAGCGTAAAAACCCCTTCAATATTTTTGCCGTTGAATGATATATTTTTTTATGA-TAATTTAG-C
          1 AAGCGTGAAAAGTCCTCCAATATTTTTGGCGTTAAATTATATA-TATTTTATGAGTATTTTAGCC

                           *  *          *                              *   *
        924 AAAAACTTGAGGAAATATCTTTCCAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAAT
         65 AAAAA-TTGAGGAAAAATTTTTCCAGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAAC

                   *     *        *       *                  *               
        989 CATCACGGTTTTTGGCTAAAAATGCGTTCCATGGCCCCGGGTCAGTTTTACATGATTTTTGGCGC
        129 CATCACGATTTTTTGCTAAAAACGCGTTCCGTGGCCCCGGGTCAGTTTTGCATGATTTTTGGCGC

            *  *      *               *                     *   *   *        
       1054 TAAAACTACTAGAGATATCCACTATTTATCTAATCAAATCTCAGTCACGTTGCATTAAAGGATTT
        194 CAAGACT-CTTGAGATATCCA-TATTCATCTAATCAAATCTCAGTCACATTGGATTTAA-GATTT

                 *         *       *                                         
       1119 GTTTTAATGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATT-TAGAAAAATATGAAAA
        256 GTTTTTATGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCT-GAAAAATATGAAAA

             *     *  
       1183 ATGATATGAA
        320 ACGATATTAA

                                                            *    *           
       1193 AAGCGTGAAAAGTCCTCCAATATTTTTGGCGTTAAATTATATATATTTCATGATTATTTTAGCCA
          1 AAGCGTGAAAAGTCCTCCAATATTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTAGCCA

                                 *                       *              *    
       1258 AAAATTGAGGAAAAATTTTTCTAGTCATTTTTTGCAAAATTTTAGGCGAAATCGTGTACTGACCA
         66 AAAATTGAGGAAAAATTTTTCCAGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCA

                                      *           *  *                 *     
       1323 TCACGATTTTTTGCTAAAAACGCGTTTCGTGGCCCCGGCTCTGTTTTGCATGATTTTTGCCGCCA
        131 TCACGATTTTTTGCTAAAAACGCGTTCCGTGGCCCCGGGTCAGTTTTGCATGATTTTTGGCGCCA

                                                                           * 
       1388 AGACTCTTTGAGATATCCATATTCATCTAATCAAATCTCA-TCTACATTGGATTTAAGAATTTAT
        196 AGACTC-TTGAGATATCCATATTCATCTAATCAAATCTCAGTC-ACATTGGATTTAAG-ATTTGT

                 *       *                        *                          
       1452 TTTTACGAGCATCCGAATCTTGTTTCGATTTAATTAGATATTAATTCTGAAAAATATGAAAAACG
        258 TTTTATGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCTGAAAAATATGAAAAACG

                   
       1517 ATATTAA
        323 ATATTAA

                                 *                                           
       1524 AAGCGTGAAAAGTCCTCCAATCTTTTTGGCGTTAAATTATATATATTTTATGAGTA-TTTATGCC
          1 AAGCGTGAAAAGTCCTCCAATATTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTA-GCC

                  *          *     
       1588 AAAAAAATGATGGAAAATTTTTT
         65 -AAAAATTGA-GGAAAAATTTTT

       1611 GACACCAAGA


Statistics
Matches: 630,  Mismatches: 102, Indels: 39
        0.82            0.13        0.05

Matches are distributed among these distances:
 330    7  0.01
 331  164  0.26
 332  246  0.39
 333  108  0.17
 334    4  0.01
 335    7  0.01
 336   82  0.13
 337   12  0.02

ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37


Consensus pattern (329 bp):   
AAGCGTGAAAAGTCCTCCAATATTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTAGCCA
AAAATTGAGGAAAAATTTTTCCAGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCA
TCACGATTTTTTGCTAAAAACGCGTTCCGTGGCCCCGGGTCAGTTTTGCATGATTTTTGGCGCCA
AGACTCTTGAGATATCCATATTCATCTAATCAAATCTCAGTCACATTGGATTTAAGATTTGTTTT
TATGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCTGAAAAATATGAAAAACGATA
TTAA
Done.