Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023115.1 Corchorus olitorius cultivar O-4 contig23148, 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: 11570
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32


Found at i:393 original size:32 final size:32

Alignment explanation


    Indices: 327--400  Score: 105
    Period size: 32  Copynumber: 2.3  Consensus size: 32

        317 TGGCCTATAG

                 *                     *    
        327 GGCTTAGTAGTGGCGCGACTTTGGGCGCTAAT
          1 GGCTTGGTAGTGGCGCGACTTTGGGCGATAAT

                                             
        359 GGCTTGGTAGTGGCGCGACTTTGGGCGGAT-AT
          1 GGCTTGGTAGTGGCGCGACTTTGGGC-GATAAT

               *      
        391 GGCCTGGTAG
          1 GGCTTGGTAG

        401 AGACATAAGG


Statistics
Matches: 38,  Mismatches: 3, Indels: 2
        0.88            0.07        0.05

Matches are distributed among these distances:
  32   36  0.95
  33    2  0.05

ACGTcount: A:0.14, C:0.18, G:0.42, T:0.27


Consensus pattern (32 bp):   
GGCTTGGTAGTGGCGCGACTTTGGGCGATAAT

Found at i:604 original size:21 final size:21

Alignment explanation


    Indices: 566--605  Score: 53
    Period size: 21  Copynumber: 1.9  Consensus size: 21

        556 GCATTTGGCT

                  *   *          
        566 CGGATGGCGCGGAAGAAGGCG
          1 CGGATGACGCAGAAGAAGGCG

                         *     
        587 CGGATGACGCAGAGGAAGG
          1 CGGATGACGCAGAAGAAGG

        606 TACGGCTAGC


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:0.28, C:0.17, G:0.50, T:0.05


Consensus pattern (21 bp):   
CGGATGACGCAGAAGAAGGCG

Found at i:640 original size:21 final size:21

Alignment explanation


    Indices: 614--653  Score: 55
    Period size: 21  Copynumber: 1.9  Consensus size: 21

        604 GGTACGGCTA

                                  
        614 GCCGGGCATGGT-GCGCGGATG
          1 GCCGGGCA-GGTGGCGCGGATG

                  *            
        635 GCCGGGTAGGTGGCGCGGA
          1 GCCGGGCAGGTGGCGCGGA

        654 GGGTAGCGCT


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    3  0.18
  21   14  0.82

ACGTcount: A:0.10, C:0.23, G:0.55, T:0.12


Consensus pattern (21 bp):   
GCCGGGCAGGTGGCGCGGATG

Found at i:7287 original size:2 final size:2

Alignment explanation


    Indices: 7280--7305  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       7270 GGGTTTGGTA

                                                  
       7280 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

       7306 GGGTAAAATG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:7321 original size:13 final size:13

Alignment explanation


    Indices: 7303--7330  Score: 56
    Period size: 13  Copynumber: 2.2  Consensus size: 13

       7293 TATATATATA

                         
       7303 TATGGGTAAAATG
          1 TATGGGTAAAATG

                         
       7316 TATGGGTAAAATG
          1 TATGGGTAAAATG

              
       7329 TA
          1 TA

       7331 AATTTAAAGA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   15  1.00

ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32


Consensus pattern (13 bp):   
TATGGGTAAAATG
Done.