Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004482.1 Corchorus capsularis cultivar CVL-1 contig04490, 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, 634

Length: 1058
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.32


Found at i:612 original size:321 final size:318

Alignment explanation


    Indices: 1--1058  Score: 1212
    Period size: 321  Copynumber: 3.3  Consensus size: 318

                    *      *         *                      * *      *       
          1 CGAAACGCATTTCTAGCAAAAAACAGTGATGGTTAGTACAC-ATTTTCGGTTAAAAATTAACCCG
          1 CGAAACGCGTTTCTAACAAAAAACAATGATGGTTAGTACACGA-TTTCAGCTAAAAACTAACCCG

                              *     **        *      *                       
         65 AAAAGGTTTTTTCTCAATATTT-TAAAAAATATTGAGAAAATATATATAATTCAACGCCAAAAAG
         65 -AAA-GTTTTTTCTCAATTTTTCTGGAAAATATTCAGAAAAAATATATAATTCAACGCCAAAAAG

                                                           *                 
        129 ATTGACAGGCTTTTCACG-TATCTAATATCG---TTT--TTTTTTTCAAATTTATTTCAAATTAA
        128 ATTGACAGGCTTTTCACGCT-TCTAATATCGTTTTTTCATTTTTTTCGAATTTATTTCAAATTAA

                     *     *     *                      *                    
        188 ATCGAAACACGATTCCGATGCTTGTAAAAACAAATCCTTAAATCTATTGTGACTGAGATTTGGTT
        192 ATCGAAACAAGATTCAGATGCAT-TAAAAACAAATCCTTAAATCCATTGTGACTGAGATTTGGTT

                                                               **    *       
        253 AGATGAATATAGATA-TTAAAAGGAGTCTTTCTGCCAAAAATACTGCAAAACAGAGCCGGAGCCC
        256 AGATGAATATAGATATTTAAAA-GAGTCTTTCTGCCAAAAATACTGCAAAATTGAGCAGG-GCCC

              *  *                         *               *        *        
        317 CGTAATGCGTTTCTAACAAAAAACAATGATGTTTAGTACACGATTTCGGCTAAAAATTAACCCGA
          1 CGAAACGCGTTTCTAACAAAAAACAATGATGGTTAGTACACGATTTCAGCTAAAAACTAACCCGA

                                    *     *              *        *          
        382 AATGTTTTTTTCTCAATTTTT-TGCAAAATGTTCAGAAAAAATATGTAATTCAATGCCAAAAAGA
         66 AA-G-TTTTTTCTCAATTTTTCTGGAAAATATTCAGAAAAAATATATAATTCAACGCCAAAAAGA

                  *                 *                      *  *    *         
        446 TTGACACGCTTTTCACGCTTCTAACATCGTTTTTTCATTTTTTTCGACTTAATTTAAAATTAAAT
        129 TTGACAGGCTTTTCACGCTTCTAATATCGTTTTTTCATTTTTTTCGAATTTATTTCAAATTAAAT

                          *     *                                            
        511 CGAAACAAGATTCAAATGCGCTTAAAAACAAATCCTTAAATCCATTGTGACTGAGATTTGGTTAG
        194 CGAAACAAGATTCAGATGC-ATTAAAAACAAATCCTTAAATCCATTGTGACTGAGATTTGGTTAG

                                         *                                 
        576 ATGAATATAGATATTTAAAAGAGTCTTTCAGCCAAAAAT-CATGCAAAATTGAGCAGTGGCCC
        258 ATGAATATAGATATTTAAAAGAGTCTTTCTGCCAAAAATAC-TGCAAAATTGAGCAG-GGCCC

                           * *      **              *       *         *      
        638 CGAAACGCGTTTCTATCCAAAAACCGTGATGGTTAGTACATGATTTCAACTAAAAACTGACCCGA
          1 CGAAACGCGTTTCTAACAAAAAACAATGATGGTTAGTACACGATTTCAGCTAAAAACTAACCCGA

                                                               *  *       *  
        703 AGAG-TTTTTCTCAATTTTTCTGGAAAATA-TCAG-AAAAATATATAATTCCACACCAAAAACAT
         66 A-AGTTTTTTCTCAATTTTTCTGGAAAATATTCAGAAAAAATATATAATTCAACGCCAAAAAGAT

               **  *                   *                                     
        765 TGATGGGTTTTTCACGCTTCTAATATCATTTTTTCAATTTTTTTCGAATTTATTTCAAATTAAAT
        130 TGACAGGCTTTTCACGCTTCTAATATCGTTTTTTC-ATTTTTTTCGAATTTATTTCAAATTAAAT

             *   *             * *                        *     *      *     
        830 CAAAAAAAGATTCAGATGTTAGTAAAAACAAATCCTTAAATCCATTATGACTTAGATTTTGTTAG
        194 CGAAACAAGATTCAGATG-CATTAAAAACAAATCCTTAAATCCATTGTGACTGAGATTTGGTTAG

                     *      *        *                   *                 
        895 ATGAATATAAATATTTCAAAGAGTCGTTCTGCCAAAAATCAC-GCGAAATTGAGCAGGGGCCC
        258 ATGAATATAGATATTTAAAAGAGTCTTTCTGCCAAAAAT-ACTGCAAAATTGAGCA-GGGCCC

                  *            *       *             *                   *   
        957 CGAAACACGTTTCTAGCCAAAAAAAACCATGATGGTTAGTAAACGATTTCAGCTAAAAACTGACC
          1 CGAAACGCGTTTCTA---ACAAAAAACAATGATGGTTAGTACACGATTTCAGCTAAAAACTAACC

                   *                              
       1022 C-AAAGAGTTTTTCTCAATTTTTCTGGAAAATATTCAG
         63 CGAAAG-TTTTTTCTCAATTTTTCTGGAAAATATTCAG


Statistics
Matches: 636,  Mismatches: 81, Indels: 43
        0.84            0.11        0.06

Matches are distributed among these distances:
 315    4  0.01
 316  131  0.21
 317    2  0.00
 318   53  0.08
 319  169  0.27
 320   11  0.02
 321  187  0.29
 322   75  0.12
 323    4  0.01

ACGTcount: A:0.37, C:0.16, G:0.14, T:0.32


Consensus pattern (318 bp):   
CGAAACGCGTTTCTAACAAAAAACAATGATGGTTAGTACACGATTTCAGCTAAAAACTAACCCGA
AAGTTTTTTCTCAATTTTTCTGGAAAATATTCAGAAAAAATATATAATTCAACGCCAAAAAGATT
GACAGGCTTTTCACGCTTCTAATATCGTTTTTTCATTTTTTTCGAATTTATTTCAAATTAAATCG
AAACAAGATTCAGATGCATTAAAAACAAATCCTTAAATCCATTGTGACTGAGATTTGGTTAGATG
AATATAGATATTTAAAAGAGTCTTTCTGCCAAAAATACTGCAAAATTGAGCAGGGCCC

Done.