Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014862.1 Corchorus capsularis cultivar CVL-1 contig14883, 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: 7371
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:2325 original size:10 final size:10

Alignment explanation


    Indices: 2310--2361  Score: 50
    Period size: 10  Copynumber: 4.8  Consensus size: 10

       2300 TCGACACCAA

                      
       2310 GCCATGCCCG
          1 GCCATGCCCG

                        
       2320 GCCATGTCCGCG
          1 GCCATG-CC-CG

             *       * 
       2332 CACCATGCCTG
          1 -GCCATGCCCG

                      
       2343 GCCATGCCCG
          1 GCCATGCCCG

                     
       2353 GCCAATGCC
          1 GCC-ATGCC

       2362 ATGCCATCCG


Statistics
Matches: 34,  Mismatches: 4, Indels: 7
        0.76            0.09        0.16

Matches are distributed among these distances:
  10   17  0.50
  11    8  0.24
  12    4  0.12
  13    5  0.15

ACGTcount: A:0.13, C:0.46, G:0.27, T:0.13


Consensus pattern (10 bp):   
GCCATGCCCG

Found at i:5533 original size:12 final size:13

Alignment explanation


    Indices: 5508--5541  Score: 52
    Period size: 12  Copynumber: 2.7  Consensus size: 13

       5498 ATAATTATTG

                         
       5508 TTTGCTTTATTAA
          1 TTTGCTTTATTAA

                         
       5521 TTTGCTTTA-TAA
          1 TTTGCTTTATTAA

             *       
       5533 TCTGCTTTA
          1 TTTGCTTTA

       5542 GATTTAGATT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  12   11  0.55
  13    9  0.45

ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59


Consensus pattern (13 bp):   
TTTGCTTTATTAA

Found at i:7016 original size:21 final size:21

Alignment explanation


    Indices: 6992--7031  Score: 53
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       6982 GCGACATGGA

                                 
       6992 GATTCCAAACAAAAGCAAGGC
          1 GATTCCAAACAAAAGCAAGGC

                *   *   *      
       7013 GATTTCAACCAAGAGCAAG
          1 GATTCCAAACAAAAGCAAG

       7032 AAAGATCAAC


Statistics
Matches: 16,  Mismatches: 3, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  21   16  1.00

ACGTcount: A:0.45, C:0.23, G:0.20, T:0.12


Consensus pattern (21 bp):   
GATTCCAAACAAAAGCAAGGC
Done.