Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004148.1 Corchorus capsularis cultivar CVL-1 contig04156, 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: 3160
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32


Found at i:125 original size:14 final size:14

Alignment explanation


    Indices: 106--132  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

         96 CAACAATATA

                          
        106 AATAATAACAAAAT
          1 AATAATAACAAAAT

                         
        120 AATAATAACAAAA
          1 AATAATAACAAAA

        133 CACTGAAAAA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19


Consensus pattern (14 bp):   
AATAATAACAAAAT

Found at i:872 original size:17 final size:17

Alignment explanation


    Indices: 850--884  Score: 61
    Period size: 17  Copynumber: 2.1  Consensus size: 17

        840 AAATACATAG

                             
        850 AACTATCTAGTGTAACA
          1 AACTATCTAGTGTAACA

                    *        
        867 AACTATCTCGTGTAACA
          1 AACTATCTAGTGTAACA

             
        884 A
          1 A

        885 CTTTACAAAT


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29


Consensus pattern (17 bp):   
AACTATCTAGTGTAACA

Found at i:3132 original size:79 final size:79

Alignment explanation


    Indices: 3001--3157  Score: 262
    Period size: 79  Copynumber: 2.0  Consensus size: 79

       2991 CACGTTTGGC

                                        **          *              *         
       3001 TGATTTCATCACTCCCTCCTCAAGTTGGTGCGTGAAAATTTGCAACGCCCAACTTGAACACTAAT
          1 TGATTTCATCACTCCCTCCTCAAGTTGGCACGTGAAAATTAGCAACGCCCAACTTAAACACTAAT

                          
       3066 GATTCAAATCGATT
         66 GATTCAAATCGATT

                                                                             
       3080 TGATTTCATCACTCCCTCCTCAAGTTGGCACGT-AAAGATTAGCAACGCCCAACTTAAACACTAA
          1 TGATTTCATCACTCCCTCCTCAAGTTGGCACGTGAAA-ATTAGCAACGCCCAACTTAAACACTAA

                          
       3144 TGATTCAAATCGAT
         65 TGATTCAAATCGAT

       3158 CCT


Statistics
Matches: 73,  Mismatches: 4, Indels: 2
        0.92            0.05        0.03

Matches are distributed among these distances:
  78    3  0.04
  79   70  0.96

ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29


Consensus pattern (79 bp):   
TGATTTCATCACTCCCTCCTCAAGTTGGCACGTGAAAATTAGCAACGCCCAACTTAAACACTAAT
GATTCAAATCGATT
Done.