Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006845.1 Corchorus capsularis cultivar CVL-1 contig06866, 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: 12424
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32


Found at i:3396 original size:21 final size:21

Alignment explanation


    Indices: 3370--3422  Score: 63
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       3360 GCACTGGAGT

                       * *       
       3370 ACATGGGGCGCGAGGCAAACC
          1 ACATGGGGCGCCAAGCAAACC

                    *        *   
       3391 ACATGGGGTGCCAAGCATACC
          1 ACATGGGGCGCCAAGCAAACC

                        
       3412 ACAT-GGGCGCC
          1 ACATGGGGCGCC

       3423 CAGCGCTAAT


Statistics
Matches: 27,  Mismatches: 5, Indels: 1
        0.82            0.15        0.03

Matches are distributed among these distances:
  20    6  0.22
  21   21  0.78

ACGTcount: A:0.26, C:0.30, G:0.34, T:0.09


Consensus pattern (21 bp):   
ACATGGGGCGCCAAGCAAACC

Found at i:5440 original size:181 final size:178

Alignment explanation


    Indices: 5092--5487  Score: 506
    Period size: 181  Copynumber: 2.2  Consensus size: 178

       5082 AAGATGATTT

                    *                                                        
       5092 AAGTGTCTATTAAAAGACTGTTTCATGATCTACAACTTTCATGAAGAACTCAAAAACTAAATTTA
          1 AAGTGTCTCTTAAAAGACTGTTTCATGATCTACAACTTTCATGAAGAACTCAAAAACTAAATTTA

                  *      *          *                     *                  
       5157 ATGTTTCAAGTATCAAAAATGCTTCCAAAAAATTAGTTGTTTCAGTTAACGGAAATGGACGGTCC
         66 ATGTTTAAAGTATAAAAAATGCTTACAAAAAATTAGTTGTTTCAGTGAACGGAAATGGACGGTCC

                                    *     *                  
       5222 ACTTAATATTACATAACTTTTGCTTCAGATGTCTGATTGAG-GTAATCC
        131 ACTTAATATTACATAACTTTTGCTCCAGATATCTGATTGAGAG-AATCC

                            **        *            *      *    *   *         
       5270 AAGTGTCTCTTAAAAGGTTGTTTCATTATCTACAACTTTTATGAAGGACTCGAAAGCTAAATTTA
          1 AAGTGTCTCTTAAAAGACTGTTTCATGATCTACAACTTTCATGAAGAACTCAAAAACTAAATTTA

                     *                   *  *    *             *   *    *    
       5335 ATGTTTAAATTATAAAATAAAATGCTTACGAAGAATTTGTTGTTTCAGTGAGCGGGAATGTACGG
         66 ATGTTTAAAGTAT--AA-AAAATGCTTACAAAAAATTAGTTGTTTCAGTGAACGGAAATGGACGG

              *                *          *               *  * 
       5400 TCTACTTAATATTACATAATTTTTGCTCCATATATCTGATTGAGAGGATTC
        128 TCCACTTAATATTACATAACTTTTGCTCCAGATATCTGATTGAGAGAATCC

                           *                     
       5451 AAGTGTCTCTTAAAAAACTGTTTCATGATCTACAACT
          1 AAGTGTCTCTTAAAAGACTGTTTCATGATCTACAACT

       5488 GAAATTTTGT


Statistics
Matches: 184,  Mismatches: 30, Indels: 5
        0.84            0.14        0.02

Matches are distributed among these distances:
 178   68  0.37
 180    1  0.01
 181  114  0.62
 182    1  0.01

ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36


Consensus pattern (178 bp):   
AAGTGTCTCTTAAAAGACTGTTTCATGATCTACAACTTTCATGAAGAACTCAAAAACTAAATTTA
ATGTTTAAAGTATAAAAAATGCTTACAAAAAATTAGTTGTTTCAGTGAACGGAAATGGACGGTCC
ACTTAATATTACATAACTTTTGCTCCAGATATCTGATTGAGAGAATCC

Found at i:7417 original size:2 final size:2

Alignment explanation


    Indices: 7410--7435  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       7400 TTGCATAACG

                                                  
       7410 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

       7436 TGTAATTTGC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.