Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010513.1 Corchorus capsularis cultivar CVL-1 contig10534, 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: 33308
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33


Found at i:96 original size:31 final size:29

Alignment explanation


    Indices: 53--130  Score: 129
    Period size: 30  Copynumber: 2.6  Consensus size: 29

         43 ATAACAATGT

                                          
         53 AATTAAACTTGCAATGAAGGTCCAACAAAA
          1 AATTAAACTTGCAATGAAGG-CCAACAAAA

                             *            
         83 AATTAAACATTGCAATGGAGGCCAACAAAA
          1 AATTAAAC-TTGCAATGAAGGCCAACAAAA

                              
        113 AATTAAACTTGCAATGAA
          1 AATTAAACTTGCAATGAA

        131 AGATTTTTTA


Statistics
Matches: 45,  Mismatches: 2, Indels: 3
        0.90            0.04        0.06

Matches are distributed among these distances:
  29    9  0.20
  30   25  0.56
  31   11  0.24

ACGTcount: A:0.50, C:0.15, G:0.14, T:0.21


Consensus pattern (29 bp):   
AATTAAACTTGCAATGAAGGCCAACAAAA

Found at i:17129 original size:12 final size:12

Alignment explanation


    Indices: 17112--17137  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

      17102 AAAAGTCGTG

                        
      17112 TGAACATACATA
          1 TGAACATACATA

                        
      17124 TGAACATACATA
          1 TGAACATACATA

              
      17136 TG
          1 TG

      17138 GGGTTTATAC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27


Consensus pattern (12 bp):   
TGAACATACATA

Found at i:27187 original size:6 final size:6

Alignment explanation


    Indices: 27176--27214  Score: 53
    Period size: 6  Copynumber: 6.5  Consensus size: 6

      27166 TTTCAACTCA

                                             *            
      27176 AAAAAG AAAAAG AAAAAG AAAAA- AAAAAA AAGAAAG AAA
          1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AA-AAAG AAA

      27215 GACAATGATA


Statistics
Matches: 30,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
   5    5  0.17
   6   20  0.67
   7    5  0.17

ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00


Consensus pattern (6 bp):   
AAAAAG

Found at i:27199 original size:14 final size:14

Alignment explanation


    Indices: 27182--27216  Score: 52
    Period size: 14  Copynumber: 2.5  Consensus size: 14

      27172 CTCAAAAAAG

                          
      27182 AAAAAGAAAAAGAA
          1 AAAAAGAAAAAGAA

                 *        
      27196 AAAAAAAAAAAGAA
          1 AAAAAGAAAAAGAA

             *     
      27210 AGAAAGA
          1 AAAAAGA

      27217 CAATGATAAG


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

Matches are distributed among these distances:
  14   18  1.00

ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00


Consensus pattern (14 bp):   
AAAAAGAAAAAGAA
Done.