Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014920.1 Corchorus olitorius cultivar O-4 contig14953, 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, 838

Length: 1397
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:914 original size:330 final size:332

Alignment explanation


    Indices: 1--1362  Score: 1881
    Period size: 333  Copynumber: 4.1  Consensus size: 332

                *                          *                                 
          1 GGGTTAATTTTTGCAAAATCTTGACCGAAATTGTGTGCTAACCATCACAGTTTTCGGCTTAAAAA
          1 GGGTCAATTTTTGCAAAATCTTGACCGAAATCGTGTGCTAACCATCACAGTTTTCGGC-T-AAAA

             **       *             *                               *        
         66 ATACGTTCCGAGG-CTCCGGCTCATTTTTGTATGATTTTTGGCGCCAAGACTCCTTTGAATATCT
         64 ACGCGTTCCGGGGCCT-CGGC-CAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTAGAATATCT

                      *  *            *   *     *                    **      
        130 ATATTCATCTGCCTAAATCTCAGCCATATATGATTTGAAGATTTATTTTTACGAGCATTAGAAGT
        127 ATATTCATCTACCCAAATCTCAGCCACATAAGATTTAAAGATTTATTTTTACGAGCACCAGAAGT

                                               *                       * *   
        195 CAGTTTCGATTTAATTGGAAATTAATTCGGAAAAGTATAGGAAAAACGATATTCGAAGCTTTAAA
        192 CAGTTTCGATTTAATTGGAAATTAATTCGGAAAAGCATAGGAAAAACGATATTCGAAGCGTGAAA

                       *               *                          *          
        260 AACCCTTCAATCTTTTTGGAGATGATTCATATATTTTTTATGAGTATTTTGGCTGAAAATTTAGG
        257 AACCCTTCAATATTTTTGGAGATGATTTATATATTTTTTATGAGTATTTTGGCTAAAAATTTAGG

                       
        325 AAAAATCATTC
        322 AAAAATCATTC

                *                  *              * *       *                
        336 GGGTGAATTTTTGCAAAATCTTGGCCGAAATCGTGTGTGTTA-CATCATAGTTTTCGGCTAAAAA
          1 GGGTCAATTTTTGCAAAATCTTGACCGAAATCGTGTG-CTAACCATCACAGTTTTCGGCTAAAAA

               *                                   *  *            *         
        400 CGCATTCCGGGGACC-CGGCTCAGTTTTGTATGATTTTTTGCACCAAGACTCCTTCGAATATCTA
         65 CGCGTTCCGGGG-CCTCGGC-CAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTAGAATATCTA

                                                     * *                     
        464 TATTCATCTACCCAAATCTCAGCCACATAAGATTTAAAGATATGTTTTTACGAGCACCAGAA-TC
        128 TATTCATCTACCCAAATCTCAGCCACATAAGATTTAAAGATTTATTTTTACGAGCACCAGAAGT-

                                                                             
        528 CAGTTTCGATTTAATTGGAAATTAATTCGGAAAAGCATAGGAAAAACGATATTCGAAGCGTGAAA
        192 CAGTTTCGATTTAATTGGAAATTAATTCGGAAAAGCATAGGAAAAACGATATTCGAAGCGTGAAA

                        **                                                *  
        593 AACCCTTCAATAAATTTGGAGATGATTTATATATTTTTTATGAGTATTTTGG-TCAAAAATTGAG
        257 AACCCTTCAATATTTTTGGAGATGATTTATATATTTTTTATGAGTATTTTGGCT-AAAAATTTAG

                       *
        657 GAAAAATCATTT
        321 GAAAAATCATTC

              *                                                              
        669 GGTTCAATTTTTGCAAAATCTTGACCGAAATCGTGTGCTAACCATCACAGTTTTCGGCTAAAAAC
          1 GGGTCAATTTTTGCAAAATCTTGACCGAAATCGTGTGCTAACCATCACAGTTTTCGGCTAAAAAC

                                                *   *                        
        734 GCGTTCCGGGGCCTCGG-C-GTTTTGTATGATTTTTTGCGGCAAGACTCCTTAGAATATCTATAT
         66 GCGTTCCGGGGCCTCGGCCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTAGAATATCTATAT

                      *       **                           *                 
        797 TCATCTACCCTAATCTCAATCACATAAGATTTAAAGATTTATTTTTATGAGCACCAGAA-TCCAG
        131 TCATCTACCCAAATCTCAGCCACATAAGATTTAAAGATTTATTTTTACGAGCACCAGAAGT-CAG

                                     **                                    * 
        861 TTTCGATTTAATTGGAAATTAATTCTAAAAAGCATAGGAAAAACGATATTCGAAGCGTGAAAAGC
        195 TTTCGATTTAATTGGAAATTAATTCGGAAAAGCATAGGAAAAACGATATTCGAAGCGTGAAAAAC

                    *       *           *          *                         
        926 CCTTCAATCTTTTTGGCGATGATTTATAAATTTTTTATGCGTATTTTGGCTAAAAATTTAGGAAA
        260 CCTTCAATATTTTTGGAGATGATTTATATATTTTTTATGAGTATTTTGGCTAAAAATTTAGGAAA

                   *
        991 AATCATTT
        325 AATCATTC

                                   *  *                                      
        999 GGGTCAA-TTTT-CAAACATCTTCACTGAAATCGTGTGCTAACTCATCACAGTTTT-GGCTAAAA
          1 GGGTCAATTTTTGCAAA-ATCTTGACCGAAATCGTGTGCTAAC-CATCACAGTTTTCGGCTAAAA

                    *      *        *                *       *     *      *  
       1061 ACGCGTTCTGGGGCCCCGGCCCAGATTTGTATGATTTTTGGAGCCAAGAGTCCTTGGAATATTTA
         64 ACGCGTTCCGGGGCCTCGG-CCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTAGAATATCTA

                *                        *             *            *        
       1126 TATTTATCTACCCAAATCTCAGCCACATAGGATTTAAAGA-TTGTTTTTACGAGCATCAGAAGTC
        128 TATTCATCTACCCAAATCTCAGCCACATAAGATTTAAAGATTTATTTTTACGAGCACCAGAAGTC

                                            *      *                    *    
       1190 AGTTTCGATTTAATTGGAAATTAATTCGGAAATGCATAGAAAAAACGATATTCGAAGCGTCAAAA
        193 AGTTTCGATTTAATTGGAAATTAATTCGGAAAAGCATAGGAAAAACGATATTCGAAGCGTGAAAA

                               *                                *        *   
       1255 ACCCTTCAATATTTTTGGATATGATTTATATA-TTTTTATGAGTATTTTGGCCAAAAATTTTGGA
        258 ACCCTTCAATATTTTTGGAGATGATTTATATATTTTTTATGAGTATTTTGGCTAAAAATTTAGGA

                      
       1319 AAAATCATTC
        323 AAAATCATTC

                                                
       1329 GGGTCAA-TTTTGCAAAATCTTG-CCGAAATCGTGT
          1 GGGTCAATTTTTGCAAAATCTTGACCGAAATCGTGT

       1363 AATACCATCA


Statistics
Matches: 917,  Mismatches: 95, Indels: 36
        0.88            0.09        0.03

Matches are distributed among these distances:
 328    4  0.00
 329   63  0.07
 330  298  0.32
 331  113  0.12
 332   77  0.08
 333  309  0.34
 334    1  0.00
 335   50  0.05
 336    2  0.00

ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35


Consensus pattern (332 bp):   
GGGTCAATTTTTGCAAAATCTTGACCGAAATCGTGTGCTAACCATCACAGTTTTCGGCTAAAAAC
GCGTTCCGGGGCCTCGGCCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTAGAATATCTATAT
TCATCTACCCAAATCTCAGCCACATAAGATTTAAAGATTTATTTTTACGAGCACCAGAAGTCAGT
TTCGATTTAATTGGAAATTAATTCGGAAAAGCATAGGAAAAACGATATTCGAAGCGTGAAAAACC
CTTCAATATTTTTGGAGATGATTTATATATTTTTTATGAGTATTTTGGCTAAAAATTTAGGAAAA
ATCATTC
Done.