Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016420.1 Corchorus capsularis cultivar CVL-1 contig16441, 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, 682

Length: 1137
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29


Found at i:152 original size:61 final size:61

Alignment explanation


    Indices: 3--190  Score: 259
    Period size: 61  Copynumber: 3.0  Consensus size: 61

          1 GG

                                         *           *         *             
          3 TCGCTAAGTTGAAAATCCTGCAAAGGACGACTTAGGCAAAAGTTCAGTCAACCAAAAAAAAAAAA
          1 TCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAACTT-AG---AGC--AAAAAAAAAA

              
         68 GC
         60 GC

                                                     *                *  
         70 TCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCAAAAAAAAAGGC
          1 TCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAACTTAGAGCAAAAAAAAAAGC

                            *                                           
        131 TCGCTAAGTTGAAAATTCTGCAAAGGACGGCTTAGGCAAAACTTAGAGCACAAAAAAAAA
          1 TCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAACTTAGAGCA-AAAAAAAAA

        191 TAGAATGAAC


Statistics
Matches: 114,  Mismatches: 6, Indels: 7
        0.90            0.05        0.06

Matches are distributed among these distances:
  61   59  0.52
  62    8  0.07
  63    2  0.02
  66    2  0.02
  67   43  0.38

ACGTcount: A:0.45, C:0.18, G:0.21, T:0.17


Consensus pattern (61 bp):   
TCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAACTTAGAGCAAAAAAAAAAGC

Found at i:962 original size:16 final size:16

Alignment explanation


    Indices: 941--975  Score: 70
    Period size: 16  Copynumber: 2.2  Consensus size: 16

        931 ACAATTCAGA

                            
        941 AAGCAGAAAAGCTCTG
          1 AAGCAGAAAAGCTCTG

                            
        957 AAGCAGAAAAGCTCTG
          1 AAGCAGAAAAGCTCTG

               
        973 AAG
          1 AAG

        976 TATTTCAGAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   19  1.00

ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11


Consensus pattern (16 bp):   
AAGCAGAAAAGCTCTG
Done.