Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001027.1 Corchorus capsularis cultivar CVL-1 contig01027, 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: 14860
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31


Found at i:12943 original size:18 final size:18

Alignment explanation


    Indices: 12922--12960  Score: 51
    Period size: 18  Copynumber: 2.2  Consensus size: 18

      12912 AATAAGATCC

                           *  
      12922 AAAAAAAAAAAAAGAGAG
          1 AAAAAAAAAAAAAGAAAG

                 *   *        
      12940 AAAAAGAAAGAAAGAAAG
          1 AAAAAAAAAAAAAGAAAG

               
      12958 AAA
          1 AAA

      12961 GAAAGAAGAG


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00


Consensus pattern (18 bp):   
AAAAAAAAAAAAAGAAAG

Found at i:12949 original size:4 final size:4

Alignment explanation


    Indices: 12942--12967  Score: 52
    Period size: 4  Copynumber: 6.5  Consensus size: 4

      12932 AAAGAGAGAA

                                            
      12942 AAAG AAAG AAAG AAAG AAAG AAAG AA
          1 AAAG AAAG AAAG AAAG AAAG AAAG AA

      12968 GAGATCCATT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   22  1.00

ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00


Consensus pattern (4 bp):   
AAAG

Found at i:14109 original size:4 final size:4

Alignment explanation


    Indices: 14100--14157  Score: 62
    Period size: 4  Copynumber: 14.5  Consensus size: 4

      14090 TCAAACATGA

                                            *    *    *    *       *   
      14100 ATAT ATAT ATAT ATAT ATAT ATAT ATGT ATGT ATGT ATGT ATAT GTAT
          1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT

              *         
      14148 ATGT ATAT AT
          1 ATAT ATAT AT

      14158 GCATGAATCA


Statistics
Matches: 48,  Mismatches: 6, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
   4   48  1.00

ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50


Consensus pattern (4 bp):   
ATAT

Found at i:14111 original size:6 final size:6

Alignment explanation


    Indices: 14100--14157  Score: 62
    Period size: 6  Copynumber: 9.7  Consensus size: 6

      14090 TCAAACATGA

                                          *    *   *    *      *   
      14100 ATATAT ATATAT ATATAT ATATAT ATGTAT GTATGT ATGTAT ATGTAT
          1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT

              *        
      14148 ATGTAT ATAT
          1 ATATAT ATAT

      14158 GCATGAATCA


Statistics
Matches: 44,  Mismatches: 8, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
   6   44  1.00

ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50


Consensus pattern (6 bp):   
ATATAT

Done.