Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014989.1 Corchorus capsularis cultivar CVL-1 contig15010, 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: 19655
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:7439 original size:12 final size:12

Alignment explanation


    Indices: 7419--7470  Score: 61
    Period size: 12  Copynumber: 4.3  Consensus size: 12

       7409 TAGCAGAAAT

                        
       7419 TCGAGTTCGAGC
          1 TCGAGTTCGAGC

                *      * 
       7431 TCGAATTCGATAC
          1 TCGAGTTCGA-GC

                        
       7444 -CGAGTTCGAGC
          1 TCGAGTTCGAGC

                 *      
       7455 TCGAGCTCGAGC
          1 TCGAGTTCGAGC

                
       7467 TCGA
          1 TCGA

       7471 CAGTTATATA


Statistics
Matches: 33,  Mismatches: 5, Indels: 4
        0.79            0.12        0.10

Matches are distributed among these distances:
  11    1  0.03
  12   31  0.94
  13    1  0.03

ACGTcount: A:0.21, C:0.27, G:0.29, T:0.23


Consensus pattern (12 bp):   
TCGAGTTCGAGC

Found at i:15857 original size:2 final size:2

Alignment explanation


    Indices: 15845--15920  Score: 66
    Period size: 2  Copynumber: 37.5  Consensus size: 2

      15835 GGAGGCCAAC

                                        *             *                   
      15845 TA TA TA GTA TA TA TA TA TA AA T- TGA TA TC TA -A CTA TA TA TA
          1 TA TA TA -TA TA TA TA TA TA TA TA T-A TA TA TA TA -TA TA TA TA

             * *                              *                 
      15886 TC CA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      15921 TATCAATTAA


Statistics
Matches: 59,  Mismatches: 10, Indels: 10
        0.75            0.13        0.13

Matches are distributed among these distances:
   1    2  0.03
   2   53  0.90
   3    4  0.07

ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46


Consensus pattern (2 bp):   
TA

Found at i:18398 original size:164 final size:165

Alignment explanation


    Indices: 18121--18450  Score: 644
    Period size: 164  Copynumber: 2.0  Consensus size: 165

      18111 CACTTGGCAG

                                                                             
      18121 TGGGGATCGTGCAGCAGCGGTATGTTATTTACAAAATTGCCCCTATAAAGTGAAATACCCAAAAT
          1 TGGGGATCGTGCAGCAGCGGTATGTTATTTACAAAATTGCCCCTATAAAGTGAAATACCCAAAAT

                                                                             
      18186 ACCCCTGACTTTTATTTGAAATAGCCTATGATAAATAGTGAAAAGACACAACTTGCCCTCGAAGT
         66 ACCCCTGACTTTTATTTGAAATAGCCTATGATAAATAGTGAAAAGACACAACTTGCCCTCGAAGT

                                               
      18251 TTAGTCCCTATGTCGCTGCTGACTCCCAGTAATAA
        131 TTAGTCCCTATGTCGCTGCTGACTCCCAGTAATAA

                                                                             
      18286 TGGGG-TCGTGCAGCAGCGGTATGTTATTTACAAAATTGCCCCTATAAAGTGAAATACCCAAAAT
          1 TGGGGATCGTGCAGCAGCGGTATGTTATTTACAAAATTGCCCCTATAAAGTGAAATACCCAAAAT

                                                                             
      18350 ACCCCTGACTTTTATTTGAAATAGCCTATGATAAATAGTGAAAAGACACAACTTGCCCTCGAAGT
         66 ACCCCTGACTTTTATTTGAAATAGCCTATGATAAATAGTGAAAAGACACAACTTGCCCTCGAAGT

                                           *   
      18415 TTAGTCCCTATGTCGCTGCTGACTCCCAGTAGTAA
        131 TTAGTCCCTATGTCGCTGCTGACTCCCAGTAATAA

             
      18450 T
          1 T

      18451 TTATAGGGAG


Statistics
Matches: 164,  Mismatches: 1, Indels: 1
        0.99            0.01        0.01

Matches are distributed among these distances:
 164  159  0.97
 165    5  0.03

ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28


Consensus pattern (165 bp):   
TGGGGATCGTGCAGCAGCGGTATGTTATTTACAAAATTGCCCCTATAAAGTGAAATACCCAAAAT
ACCCCTGACTTTTATTTGAAATAGCCTATGATAAATAGTGAAAAGACACAACTTGCCCTCGAAGT
TTAGTCCCTATGTCGCTGCTGACTCCCAGTAATAA
Done.