Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016455.1 Corchorus olitorius cultivar O-4 contig16488, 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: 3471
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33


Found at i:691 original size:324 final size:322

Alignment explanation


    Indices: 1--923  Score: 1234
    Period size: 324  Copynumber: 2.8  Consensus size: 322

                                             *       *            *          
          1 GATAATTTTTTACGAGCATCTGAATTATGTTTCAATTTAATCAGAAATTAATTCTGAAAATAGGA
          1 GATAATTTTTTACGAGCATCTGAATTATGTTTCGATTTAATTAGAAATTAATTCGGAAAATAGGA

                                  *                   *     *                
         66 AAAATTATATTAGAAGCCTGAAGAGCCCTTAAATTTTATTGGTGTTGAATTATATATTTTTTATG
         66 AAAATTATATTAGAAGCCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTATATATTTTTTATG

                  *          *                                               
        131 AGTATTTTGGCCAAAAAGTGA-GAAAATATTTTTCGGGACT-GTTTTTGCAAAATTTTGGCCGAA
        131 AGTATTGTGGCCAAAAATTGAGGAAAAT-TTTTT-GGGA-TAGTTTTTGCAAAATTTTGGCCGAA

                 *    *                      *      *  *     * *             
        194 ATCGTATAGTAAACATCACTGTTTTTTGCTAAAGACGCGCATTATG-GGGCACGACTTAGTTTTG
        193 ATCGTGTAGTTAACATCACTG-TTTTTGCTAAAAACGCG-TTTCTGTGGCCCCGACTTAGTTTTG

            *                            *                                   
        258 TATGATTTTTGGCAGCAAGACTCCTTAAATTATTTATATTAATCTAACCAAATCTCACCCACAAT
        256 AATGATTTTT----G---GACTCCTTAAAATATTTATATTAATCTAACCAAATCTCACCCACAAT

                     
        323 GGATTTAAG
        314 GGATTTAAG

            *                           *         *                          
        332 AATAATTTTTTACGAGCATCTGAATTATATTTCGATTTGATTA-AAATTAATTCGGAAAATAGGA
          1 GATAATTTTTTACGAGCATCTGAATTATGTTTCGATTTAATTAGAAATTAATTCGGAAAATAGG-

                 **      *    *                       *   *          *       
        396 AAAAACGATATTATAAGCATGAAAAGCCCTTAAATATTT-TTAGCGATGAGTTATATGTTTTTTA
         65 AAAAATTATATTAGAAGCCTGAAAAGCCCTTAAAT-TTTATTGGCGTTGAGTTATATATTTTTTA

                                                                             
        460 TGAGTATTGTGGCCAAAAATTGAGGAAAATTTTTTGGGATAGTTTTTGCAAAATTTTGGCCGAAA
        129 TGAGTATTGTGGCCAAAAATTGAGGAAAATTTTTTGGGATAGTTTTTGCAAAATTTTGGCCGAAA

                                                                            *
        525 TCGTGTACGTTAACATCACTGATTTTTGCTAAAAACGCGTTTCTGTGGCCCCGACTTAGTTTTGC
        194 TCGTGTA-GTTAACATCACTG-TTTTTGCTAAAAACGCGTTTCTGTGGCCCCGACTTAGTTTTGA

                                            *              * *               
        590 ATGATTTTTGGACTCCTTAAAATATTTATATTCATCTAACCAAATCTTAGCCACAATGGATTTAA
        257 ATGATTTTTGGACTCCTTAAAATATTTATATTAATCTAACCAAATCTCACCCACAATGGATTTAA

             
        655 G
        322 G

                *                                      *                     
        656 GATATTTTTTTACGAGCATCTGAATTATGTTTCGATTTAATTATAAATTAATTCGGAAAATAGGA
          1 GATAATTTTTTACGAGCATCTGAATTATGTTTCGATTTAATTAGAAATTAATTCGGAAAATAGGA

                                                                 *           
        721 AAAATTATATTAGAAGCCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTATTTATTTTTTATG
         66 AAAATTATATTAGAAGCCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTATATATTTTTTATG

                                             **                              
        786 AGTATTGTGGCCAAAAATTGAGGAAAAATTTTTCAGGATAGTTTTTGCAAAATTTTGGCCGAAAT
        131 AGTATTGTGGCCAAAAATTGAGG-AAAATTTTTTGGGATAGTTTTTGCAAAATTTTGGCCGAAAT

                      *                                 *    *       *       
        851 CGTGTA--TACCATCACTGTTTTTGGCTAAAAACGCATGTTTC-ATGGCGCC-AGCTCAGTTTTG
        195 CGTGTAGTTAACATCACTGTTTTT-GCTAAAAACGC--GTTTCTGTGGCCCCGA-CTTAGTTTTG

                        
        912 AATGATTTTTGG
        256 AATGATTTTTGG

        924 CAGAAAGACT


Statistics
Matches: 529,  Mismatches: 50, Indels: 34
        0.86            0.08        0.06

Matches are distributed among these distances:
 321    5  0.01
 322   22  0.04
 323   29  0.05
 324  173  0.33
 325   65  0.12
 327    1  0.00
 329    1  0.00
 330   57  0.11
 331  167  0.32
 332    9  0.02

ACGTcount: A:0.33, C:0.13, G:0.17, T:0.38


Consensus pattern (322 bp):   
GATAATTTTTTACGAGCATCTGAATTATGTTTCGATTTAATTAGAAATTAATTCGGAAAATAGGA
AAAATTATATTAGAAGCCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTATATATTTTTTATG
AGTATTGTGGCCAAAAATTGAGGAAAATTTTTTGGGATAGTTTTTGCAAAATTTTGGCCGAAATC
GTGTAGTTAACATCACTGTTTTTGCTAAAAACGCGTTTCTGTGGCCCCGACTTAGTTTTGAATGA
TTTTTGGACTCCTTAAAATATTTATATTAATCTAACCAAATCTCACCCACAATGGATTTAAG

Found at i:3369 original size:62 final size:62

Alignment explanation


    Indices: 3272--3471  Score: 350
    Period size: 62  Copynumber: 3.3  Consensus size: 62

       3262 ACACGACAGA

                                                                          
       3272 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
          1 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG

                  *                                                       
       3334 CACGAATGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
          1 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG

                         *                                           *    
       3396 CACGAAGGTACACAAGAAG--AGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGG
          1 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG

                *           
       3456 CACGGAGGTACACGAG
          1 CACGAAGGTACACGAG


Statistics
Matches: 132,  Mismatches: 6, Indels: 2
        0.94            0.04        0.01

Matches are distributed among these distances:
  60   54  0.41
  62   78  0.59

ACGTcount: A:0.34, C:0.23, G:0.39, T:0.04


Consensus pattern (62 bp):   
CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG

Done.