Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011088.1 Corchorus capsularis cultivar CVL-1 contig11109, 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: 42519
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34


Found at i:30155 original size:30 final size:32

Alignment explanation


    Indices: 30113--30202  Score: 93
    Period size: 30  Copynumber: 3.0  Consensus size: 32

      30103 TTGAGAAGTT

                                            
      30113 TGGTAAGG-TTGTGAAAGTTGA-GAAAAAGAA
          1 TGGTAAGGTTTGTGAAAGTTGACGAAAAAGAA

                                   *   * *   
      30143 TGGT-AGGTTTGTGAGAA-TTGAGGAAGATG-A
          1 TGGTAAGGTTTGTGA-AAGTTGACGAAAAAGAA

                                     *     
      30173 TGGTAAGGTTTG-GAAAGTTGACGAGAAAGA
          1 TGGTAAGGTTTGTGAAAGTTGACGAAAAAGA

      30203 TGAGGAAAAG


Statistics
Matches: 48,  Mismatches: 6, Indels: 11
        0.74            0.09        0.17

Matches are distributed among these distances:
  29    5  0.10
  30   29  0.60
  31   14  0.29

ACGTcount: A:0.37, C:0.01, G:0.37, T:0.26


Consensus pattern (32 bp):   
TGGTAAGGTTTGTGAAAGTTGACGAAAAAGAA

Found at i:41716 original size:11 final size:11

Alignment explanation


    Indices: 41694--41743  Score: 50
    Period size: 11  Copynumber: 4.6  Consensus size: 11

      41684 GACAGCATAG

                       
      41694 CAAAAACAAAA
          1 CAAAAACAAAA

             *     *   
      41705 CGAAAACGAAA
          1 CAAAAACAAAA

                       
      41716 CAAAAACAAAA
          1 CAAAAACAAAA

                 *      
      41727 -AACAGA-AAAA
          1 CAA-AAACAAAA

                   
      41737 CAAAAAC
          1 CAAAAAC

      41744 GATACCAAAC


Statistics
Matches: 30,  Mismatches: 6, Indels: 6
        0.71            0.14        0.14

Matches are distributed among these distances:
  10    8  0.27
  11   22  0.73

ACGTcount: A:0.76, C:0.18, G:0.06, T:0.00


Consensus pattern (11 bp):   
CAAAAACAAAA

Found at i:41847 original size:14 final size:14

Alignment explanation


    Indices: 41828--41854  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

      41818 AAAGTGCCAC

                          
      41828 AAAAAATAAAAATA
          1 AAAAAATAAAAATA

                         
      41842 AAAAAATAAAAAT
          1 AAAAAATAAAAAT

      41855 GAAATTAGAA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15


Consensus pattern (14 bp):   
AAAAAATAAAAATA
Done.