Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012302.1 Corchorus capsularis cultivar CVL-1 contig12323, 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: 8869
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30


Found at i:4075 original size:10 final size:10

Alignment explanation


    Indices: 4060--4085  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

       4050 AGTTGCTGCC

                      
       4060 AAATTCCAGA
          1 AAATTCCAGA

                      
       4070 AAATTCCAGA
          1 AAATTCCAGA

                  
       4080 AAATTC
          1 AAATTC

       4086 TAGAGTCCTC


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   16  1.00

ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23


Consensus pattern (10 bp):   
AAATTCCAGA

Found at i:7915 original size:18 final size:18

Alignment explanation


    Indices: 7892--7928  Score: 65
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       7882 TGTCTGTCGA

                     *        
       7892 CACTCTTATTTATATTCC
          1 CACTCTTATCTATATTCC

                              
       7910 CACTCTTATCTATATTCC
          1 CACTCTTATCTATATTCC

             
       7928 C
          1 C

       7929 CTGTTCGATC


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.22, C:0.32, G:0.00, T:0.46


Consensus pattern (18 bp):   
CACTCTTATCTATATTCC

Found at i:8364 original size:10 final size:10

Alignment explanation


    Indices: 8349--8400  Score: 59
    Period size: 10  Copynumber: 4.8  Consensus size: 10

       8339 TCGAAACCAA

                      
       8349 GCCATGCCCG
          1 GCCATGCCCG

                        
       8359 GCCATGTCCGCG
          1 GCCATG-CC-CG

             *         
       8371 CACCATGCCCG
          1 -GCCATGCCCG

                      
       8382 GCCATGCCCG
          1 GCCATGCCCG

                     
       8392 GCCAATGCC
          1 GCC-ATGCC

       8401 ATGACATCCG


Statistics
Matches: 36,  Mismatches: 2, Indels: 7
        0.80            0.04        0.16

Matches are distributed among these distances:
  10   18  0.50
  11    9  0.25
  12    4  0.11
  13    5  0.14

ACGTcount: A:0.13, C:0.48, G:0.27, T:0.12


Consensus pattern (10 bp):   
GCCATGCCCG
Done.