Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015800.1 Corchorus olitorius cultivar O-4 contig15833, 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: 18279
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:2049 original size:2 final size:2

Alignment explanation


    Indices: 2042--2072  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       2032 ACTAAAAAGA

                                                          
       2042 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       2073 AAACTTTTTG


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:8226 original size:15 final size:15

Alignment explanation


    Indices: 8208--8259  Score: 77
    Period size: 15  Copynumber: 3.5  Consensus size: 15

       8198 GGTCGATGGT

                 *     *   
       8208 CTCTAAGTTGATGGC
          1 CTCTAGGTTGACGGC

                         * 
       8223 CTCTAGGTTGACGAC
          1 CTCTAGGTTGACGGC

                           
       8238 CTCTAGGTTGACGGC
          1 CTCTAGGTTGACGGC

                   
       8253 CTCTAGG
          1 CTCTAGG

       8260 CCGGCGAACT


Statistics
Matches: 33,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  15   33  1.00

ACGTcount: A:0.17, C:0.25, G:0.29, T:0.29


Consensus pattern (15 bp):   
CTCTAGGTTGACGGC

Found at i:8272 original size:30 final size:30

Alignment explanation


    Indices: 8208--8276  Score: 84
    Period size: 30  Copynumber: 2.3  Consensus size: 30

       8198 GGTCGATGGT

                 *     *          **     *
       8208 CTCTAAGTTGATGGCCTCTAGGTTGACGAC
          1 CTCTAGGTTGACGGCCTCTAGGCCGACGAA

                                     *    
       8238 CTCTAGGTTGACGGCCTCTAGGCCGGCGAA
          1 CTCTAGGTTGACGGCCTCTAGGCCGACGAA

                     
       8268 CTCTAGGTT
          1 CTCTAGGTT

       8277 AGAATTGATG


Statistics
Matches: 33,  Mismatches: 6, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  30   33  1.00

ACGTcount: A:0.17, C:0.26, G:0.29, T:0.28


Consensus pattern (30 bp):   
CTCTAGGTTGACGGCCTCTAGGCCGACGAA
Done.