Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013074.1 Corchorus capsularis cultivar CVL-1 contig13095, 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: 10256
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:7078 original size:2 final size:2

Alignment explanation


    Indices: 7071--7107  Score: 65
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       7061 AATTTAAGTC

                                                            *      
       7071 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       7108 AAGAACAATA


Statistics
Matches: 33,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
AT

Found at i:7122 original size:14 final size:14

Alignment explanation


    Indices: 7105--7143  Score: 57
    Period size: 11  Copynumber: 3.0  Consensus size: 14

       7095 ATATATATTT

                          
       7105 ATAAAGAACAATAA
          1 ATAAAGAACAATAA

                          
       7119 ATAAAG---AATAA
          1 ATAAAGAACAATAA

                          
       7130 ATAAAGAACAATAA
          1 ATAAAGAACAATAA

       7144 CAATGAGAAG


Statistics
Matches: 22,  Mismatches: 0, Indels: 6
        0.79            0.00        0.21

Matches are distributed among these distances:
  11   11  0.50
  14   11  0.50

ACGTcount: A:0.72, C:0.05, G:0.08, T:0.15


Consensus pattern (14 bp):   
ATAAAGAACAATAA

Found at i:7287 original size:126 final size:126

Alignment explanation


    Indices: 7132--7383  Score: 486
    Period size: 126  Copynumber: 2.0  Consensus size: 126

       7122 AAGAATAAAT

                                                                             
       7132 AAAGAACAATAACAATGAGAAGTGAAAGGACTAAAAAACCGCCCTAAAGAATTCCTCTCATTGAT
          1 AAAGAACAATAACAATGAGAAGTGAAAGGACTAAAAAACCGCCCTAAAGAATTCCTCTCATTGAT

                                                                         
       7197 TTATGTCATAACTGAGTTGGGTTTTATTGTCATTTCGACCTCATTAAATTTTTGATGGATA
         66 TTATGTCATAACTGAGTTGGGTTTTATTGTCATTTCGACCTCATTAAATTTTTGATGGATA

                                            *                 *              
       7258 AAAGAACAATAACAATGAGAAGTGAAAGGACTCAAAAACCGCCCTAAAGAGTTCCTCTCATTGAT
          1 AAAGAACAATAACAATGAGAAGTGAAAGGACTAAAAAACCGCCCTAAAGAATTCCTCTCATTGAT

                                                                         
       7323 TTATGTCATAACTGAGTTGGGTTTTATTGTCATTTCGACCTCATTAAATTTTTGATGGATA
         66 TTATGTCATAACTGAGTTGGGTTTTATTGTCATTTCGACCTCATTAAATTTTTGATGGATA

       7384 CAAGCTCCCA


Statistics
Matches: 124,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 126  124  1.00

ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32


Consensus pattern (126 bp):   
AAAGAACAATAACAATGAGAAGTGAAAGGACTAAAAAACCGCCCTAAAGAATTCCTCTCATTGAT
TTATGTCATAACTGAGTTGGGTTTTATTGTCATTTCGACCTCATTAAATTTTTGATGGATA
Done.