Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014448.1 Corchorus capsularis cultivar CVL-1 contig14469, 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, 865

Length: 1442
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36


Found at i:637 original size:332 final size:331

Alignment explanation


    Indices: 1--1256  Score: 1497
    Period size: 332  Copynumber: 3.8  Consensus size: 331

                         *                  *    *     **                    
          1 TCCTTGAAATATCGATATTCATCTAACCAAATGTCAGTCAAAATACATTTAAGAATTTATTTTTA
          1 TCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCAAAACGCATTTAAGAATTTATTTTTA

                       *             *             *           *             
         66 -AGAG-CATCAAAATCTTGTTTCGACTAACTAGAAATTATTTCGGAAAAAATTAGGAAAAACGAT
         66 CA-AGTCATCAGAATCTTGTTTCGATTAACTAGAAATTAATTCGGAAAAAAATAGGAAAAACGAT

                                   *         *                         *     
        129 ATTAGAAGCGTGAAAATCCATTCGATATTTTTGGAGTTGAATTATATAATTTTTTATGATTATTG
        130 ATTAGAAGCGTGAAAATCCATTCAATATTTTTGTAGTTGAATTATAT-ATTTTTTATGAGTATTG

                                    *     *        *     *                   
        194 TGGCAAAAAATTGAAAGAAAAATTCTGGTTTAATTTTTGTAAAATTTTAGCCGAAATCGTGTACT
        194 TGGCAAAAAATTGAAAGAAAAATTTTGGTTCAATTTTTGCAAAATATTAGCCGAAATCGTGTACT

                    * *     *       *  *         *              *            
        259 AACCATCATGATTTTTTGCTAAAAATGTGTTCTGGGAACCTGGCTCAGTTTTACATGATTTTTGT
        259 AACCATCACGGTTTTTGGCTAAAACTGCGTTCTGGG-TCCTGGCTCAGTTTTGCATGATTTTTGT

                  *  
        324 CGCCAACAC
        323 CGCCAAGAC

                  *               *  *                          *            
        333 TCCTTGTAATATCTATATTCATTTAGCCAAATCTCAGCCAAAACGCATTTAATAATTTATTTTTA
          1 TCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCAAAACGCATTTAAGAATTTATTTTTA

                                                                        *    
        398 CAAG-CATCAGAATCTTGTTTCGATTAACTAGAAATTAATTCGGAAAAAAATAGGAAAAATGATA
         66 CAAGTCATCAGAATCTTGTTTCGATTAACTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATA

            *     ***        *                                    *          
        462 CTAGAAATTTGAAAATCAATTCAATATTTTTGTAGTTGAATTATATATTTTTTAAGAGTATTGTG
        131 TTAGAAGCGTGAAAATCCATTCAATATTTTTGTAGTTGAATTATATATTTTTTATGAGTATTGTG

                *                                       *           *     *  
        527 GCAAGAAATTGAAAGAAAAACTTTTGGTTCAATTTTTGCAAAATTTTAGCCGAAATTGTGTAATA
        196 GCAAAAAATTGAAAGAAAAA-TTTTGGTTCAATTTTTGCAAAATATTAGCCGAAATCGTGTACTA

                       **                   *     *             *           *
        592 ACCATCACGGTGCTTGGCTAAAACTGCGTTACAGGGTCATGGCTCAGTTTTGTATGATTTTTGTT
        260 ACCATCACGGTTTTTGGCTAAAACTGCGTT-CTGGGTCCTGGCTCAGTTTTGCATGATTTTTGTC

                    
        657 GCCAAGAC
        324 GCCAAGAC

                      *      *    *           *     * ** *                   
        665 TCCTTGAAATCTCTATAGTCATTTAACCAAATCTTAGCCACATTGAATTTAAGAATTTATTTTTA
          1 TCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCAAAACGCATTTAAGAATTTATTTTTA

             *                    *     *              *        *     *  *   
        730 CGAGTC-TCAGAATCTTGTTTCAATTAATTAGAAATTAATTC-AAAAAAAATTGGAAAGACAATA
         66 CAAGTCATCAGAATCTTGTTTCGATTAACTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATA

                             *   *             *                      *      
        793 TTAGAAGCGTGAAAATCTATTTAATATTTTTGGT-TTTGAATTATATATTTTTTATGATTATTGT
        131 TTAGAAGCGTGAAAATCCATTCAATATTTTT-GTAGTTGAATTATATATTTTTTATGAGTATTGT

                                                             **        *     
        857 GGCAAAAAATTGAAAGAAAAATTTTTGGTTCAATTTTTGCAAAATATTAATCGAAATCGGGTACT
        195 GGCAAAAAATTGAAAGAAAAA-TTTTGGTTCAATTTTTGCAAAATATTAGCCGAAATCGTGTACT

                 *           *          *        *     *           *      *  
        922 AACCACCACGGTTTTTGTCTAAAAAC-GGGTTCTTGGCTCCTGTCTCAGTTTTGCGTGATTTATG
        259 AACCATCACGGTTTTTGGCT-AAAACTGCGTTC-TGGGTCCTGGCTCAGTTTTGCATGATTTTTG

            *         
        986 GCGCCAAGAC
        322 TCGCCAAGAC

                *              *                     *                 *     
        996 TCCTCGAAATATCTATATTTATCTAACCAAATCTCAGCC-ATACTGCATTTAAGAATTTTTTTTT
          1 TCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCAAAAC-GCATTTAAGAATTTATTTTT

               *    *                *     *                               * 
       1060 AAAAAAGTAAT-AGAATCTTGTTTCCATTAAATAGAAATTAATTCGG-AAAAAATAGGAAAAATG
         65 --ACAAGTCATCAGAATCTTGTTTCGATTAACTAGAAATTAATTCGGAAAAAAATAGGAAAAACG

             *                          *      **   *                        
       1123 AAATTAGAAGCGTGAAAATCCATTCAATCTTTTTGCCGTTAAATTATATATTTTTTATGAGTATT
        128 ATATTAGAAGCGTGAAAATCCATTCAATATTTTTGTAGTTGAATTATATATTTTTTATGAGTATT

                   *         *                              *                
       1188 GTGGCAAGAAATTGAAATAAAAAGTTTTGGTTCAATTTTTGCAAAATACTAGCCGAAATCGTGTA
        193 GTGGCAAAAAATTGAAAGAAAAA-TTTTGGTTCAATTTTTGCAAAATATTAGCCGAAATCGTGTA

                
       1253 CTAA
        257 CTAA

       1257 ATGTCAGTCA


Statistics
Matches: 782,  Mismatches: 129, Indels: 25
        0.84            0.14        0.03

Matches are distributed among these distances:
 330    1  0.00
 331  265  0.34
 332  344  0.44
 333  171  0.22
 334    1  0.00

ACGTcount: A:0.36, C:0.13, G:0.15, T:0.37


Consensus pattern (331 bp):   
TCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCAAAACGCATTTAAGAATTTATTTTTA
CAAGTCATCAGAATCTTGTTTCGATTAACTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATA
TTAGAAGCGTGAAAATCCATTCAATATTTTTGTAGTTGAATTATATATTTTTTATGAGTATTGTG
GCAAAAAATTGAAAGAAAAATTTTGGTTCAATTTTTGCAAAATATTAGCCGAAATCGTGTACTAA
CCATCACGGTTTTTGGCTAAAACTGCGTTCTGGGTCCTGGCTCAGTTTTGCATGATTTTTGTCGC
CAAGAC

Done.