Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000410.1 Corchorus capsularis cultivar CVL-1 contig00410, 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: 8340
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31


Found at i:345 original size:42 final size:42

Alignment explanation


    Indices: 293--374  Score: 128
    Period size: 42  Copynumber: 2.0  Consensus size: 42

        283 TGTTGACACA

                            *         *        *      
        293 TACCCCACCTGATAATTGATTATGTATTTAATATTTAAAACC
          1 TACCCCACCTGATAATCGATTATGTAGTTAATATTGAAAACC

                *                                   
        335 TACCTCACCTGATAATCGATTATGTAGTTAATATTGAAAA
          1 TACCCCACCTGATAATCGATTATGTAGTTAATATTGAAAA

        375 TTAATATCTA


Statistics
Matches: 36,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  42   36  1.00

ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37


Consensus pattern (42 bp):   
TACCCCACCTGATAATCGATTATGTAGTTAATATTGAAAACC

Found at i:619 original size:16 final size:16

Alignment explanation


    Indices: 600--657  Score: 57
    Period size: 16  Copynumber: 3.6  Consensus size: 16

        590 AACCTGCCCA

                            
        600 ACCCGAGACCTGGTAG
          1 ACCCGAGACCTGGTAG

                      * * * 
        616 ACCCGAGACCCGATTG
          1 ACCCGAGACCTGGTAG

                              
        632 ACCCG-GAACCT-GTATG
          1 ACCCGAG-ACCTGGTA-G

                      
        648 ACCCGAGACC
          1 ACCCGAGACC

        658 CGACTGACCA


Statistics
Matches: 33,  Mismatches: 6, Indels: 6
        0.73            0.13        0.13

Matches are distributed among these distances:
  15    2  0.06
  16   30  0.91
  17    1  0.03

ACGTcount: A:0.26, C:0.36, G:0.26, T:0.12


Consensus pattern (16 bp):   
ACCCGAGACCTGGTAG

Found at i:665 original size:16 final size:16

Alignment explanation


    Indices: 615--750  Score: 107
    Period size: 16  Copynumber: 8.6  Consensus size: 16

        605 AGACCTGGTA

                          * 
        615 GACCCGAGACCCGATT
          1 GACCCGAGACCCGAAT

                        * *  
        631 GACCCG-GAACCTGTAT
          1 GACCCGAG-ACCCGAAT

                          * 
        647 GACCCGAGACCCGACT
          1 GACCCGAGACCCGAAT

                *  *  *  ** 
        663 GACCAGAAACTCGTGT
          1 GACCCGAGACCCGAAT

                      *     
        679 GACCCGAGACTCGAAT
          1 GACCCGAGACCCGAAT

                   *        
        695 GACCCGAAACCCGAAT
          1 GACCCGAGACCCGAAT

            *   *            
        711 AACCTGA-ACCC-AGAT
          1 GACCCGAGACCCGA-AT

                   *        
        726 GACCCGAAACCCGAAT
          1 GACCCGAGACCCGAAT

                     
        742 GACCCGAGA
          1 GACCCGAGA

        751 AAACTGCCTG


Statistics
Matches: 93,  Mismatches: 22, Indels: 10
        0.74            0.18        0.08

Matches are distributed among these distances:
  14    1  0.01
  15   12  0.13
  16   78  0.84
  17    2  0.02

ACGTcount: A:0.32, C:0.35, G:0.23, T:0.11


Consensus pattern (16 bp):   
GACCCGAGACCCGAAT

Found at i:1421 original size:33 final size:33

Alignment explanation


    Indices: 1379--1451  Score: 119
    Period size: 33  Copynumber: 2.2  Consensus size: 33

       1369 AGTAAATCCG

                                      *      
       1379 AACCTGTTTTGAGTGTTGTTTGCGATGACACTA
          1 AACCTGTTTTGAGTGTTGTTTGCGATAACACTA

                                        *    
       1412 AACCTGTTTTGAGTGTTGTTTGCGATAATACTA
          1 AACCTGTTTTGAGTGTTGTTTGCGATAACACTA

              *    
       1445 AATCTGT
          1 AACCTGT

       1452 GATACGGGGA


Statistics
Matches: 37,  Mismatches: 3, Indels: 0
        0.93            0.08        0.00

Matches are distributed among these distances:
  33   37  1.00

ACGTcount: A:0.23, C:0.14, G:0.22, T:0.41


Consensus pattern (33 bp):   
AACCTGTTTTGAGTGTTGTTTGCGATAACACTA

Found at i:3636 original size:164 final size:165

Alignment explanation


    Indices: 3352--3681  Score: 583
    Period size: 164  Copynumber: 2.0  Consensus size: 165

       3342 CTCATGCTTG

                *                                       *                    
       3352 TTAGTTGAAGACTATTACCACTTACCACTCCAATTAATCACATGTTTTTTTTGTCTCATCAAATC
          1 TTAGGTGAAGACTATTACCACTTACCACTCCAATTAATCACATGATTTTTTTGTCTCATCAAATC

                                     *                                       
       3417 TTTTTAAGTAAAAGAAATAAAACTTTATGATAAACACTTAAGGTAAGACTTTCAAGAGTAAATGT
         66 TTTTTAAGTAAAAGAAATAAAACTTAATGATAAACACTTAAGGTAAGACTTTCAAGAGTAAATGT

                 *       *                     
       3482 GTTGCGTTAATTAGAGAGTTGAATTGGTAAGATAT
        131 GTTGCCTTAATTAAAGAGTTGAATTGGTAAGATAT

                                                                             
       3517 TTAGGTGAAGACTATTACCACTTACCACTCCAATTAATCACAT-ATTTTTTTGTCTCATCAAATC
          1 TTAGGTGAAGACTATTACCACTTACCACTCCAATTAATCACATGATTTTTTTGTCTCATCAAATC

                                                             *               
       3581 TTTTTAAGTAAAAGAAATAAAACTTAATGATAAACA-TCTAAGGTAAGATTTTCAAGAGTAAATG
         66 TTTTTAAGTAAAAGAAATAAAACTTAATGATAAACACT-TAAGGTAAGACTTTCAAGAGTAAATG

                                                
       3645 TGTTGCCTTAATTAAAGAGTTGAATTGGTAAGATAT
        130 TGTTGCCTTAATTAAAGAGTTGAATTGGTAAGATAT

             
       3681 T
          1 T

       3682 AGACCTCTAT


Statistics
Matches: 158,  Mismatches: 6, Indels: 3
        0.95            0.04        0.02

Matches are distributed among these distances:
 163    1  0.01
 164  115  0.73
 165   42  0.27

ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36


Consensus pattern (165 bp):   
TTAGGTGAAGACTATTACCACTTACCACTCCAATTAATCACATGATTTTTTTGTCTCATCAAATC
TTTTTAAGTAAAAGAAATAAAACTTAATGATAAACACTTAAGGTAAGACTTTCAAGAGTAAATGT
GTTGCCTTAATTAAAGAGTTGAATTGGTAAGATAT
Done.