Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000755.1 Corchorus capsularis cultivar CVL-1 contig00755, 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: 11588
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:8 original size:2 final size:2

Alignment explanation


    Indices: 2--72  Score: 142
    Period size: 2  Copynumber: 35.5  Consensus size: 2

          1 T

                                                                          
          2 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                                                       
         44 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T

         73 GCCTCGTCAT


Statistics
Matches: 69,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   69  1.00

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


Consensus pattern (2 bp):   
TC

Found at i:2248 original size:79 final size:79

Alignment explanation


    Indices: 2117--2272  Score: 285
    Period size: 79  Copynumber: 2.0  Consensus size: 79

       2107 TGTAACAAGT

                                          *        *                         
       2117 TTACACCAAGGATAAACTTAATTGGCTGTTTGTGAAAGTGGGATGTAAATCTTGTTGTGTAAGGG
          1 TTACACCAAGGATAAACTTAATTGGCTGTTCGTGAAAGTAGGATGTAAATCTTGTTGTGTAAGGG

                          
       2182 TAAGCATGTAACGG
         66 TAAGCATGTAACGG

                 *                                                           
       2196 TTACAGCAAGGATAAACTTAATTGGCTGTTCGTGAAAGTAGGATGTAAATCTTGTTGTGTAAGGG
          1 TTACACCAAGGATAAACTTAATTGGCTGTTCGTGAAAGTAGGATGTAAATCTTGTTGTGTAAGGG

                        
       2261 TAAGCATGTAAC
         66 TAAGCATGTAAC

       2273 AGGACAGTCT


Statistics
Matches: 74,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  79   74  1.00

ACGTcount: A:0.31, C:0.10, G:0.27, T:0.31


Consensus pattern (79 bp):   
TTACACCAAGGATAAACTTAATTGGCTGTTCGTGAAAGTAGGATGTAAATCTTGTTGTGTAAGGG
TAAGCATGTAACGG

Found at i:7491 original size:13 final size:13

Alignment explanation


    Indices: 7473--7499  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       7463 GCTTAATGAG

                         
       7473 AAAAAAGAAAGAA
          1 AAAAAAGAAAGAA

                         
       7486 AAAAAAGAAAGAA
          1 AAAAAAGAAAGAA

             
       7499 A
          1 A

       7500 GAAATTTTCA


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

Matches are distributed among these distances:
  13   14  1.00

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


Consensus pattern (13 bp):   
AAAAAAGAAAGAA
Done.