Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017327.1 Corchorus olitorius cultivar O-4 contig17360, 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: 19595
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:6468 original size:59 final size:59

Alignment explanation


    Indices: 6376--6511  Score: 227
    Period size: 59  Copynumber: 2.3  Consensus size: 59

       6366 TTGCTTCGTA

                        *                                      *       
       6376 CTCGGTCGCACGACCTAGTGGGCATCCCCCACACGAGCAATAAAAACGATCGAGCATCC
          1 CTCGGTCGCACGGCCTAGTGGGCATCCCCCACACGAGCAATAAAAACGATCAAGCATCC

                                                       *               
       6435 CTCGGTCGCACGGCCTAGTGGGCATCCCCCACACGAGCAATAAGAACGATCAAGCATCC
          1 CTCGGTCGCACGGCCTAGTGGGCATCCCCCACACGAGCAATAAAAACGATCAAGCATCC

                *   *         
       6494 CTCGATCGTACGGCCTAG
          1 CTCGGTCGCACGGCCTAG

       6512 CATGCCTACA


Statistics
Matches: 72,  Mismatches: 5, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  59   72  1.00

ACGTcount: A:0.26, C:0.35, G:0.24, T:0.15


Consensus pattern (59 bp):   
CTCGGTCGCACGGCCTAGTGGGCATCCCCCACACGAGCAATAAAAACGATCAAGCATCC

Found at i:15651 original size:11 final size:11

Alignment explanation


    Indices: 15635--15682  Score: 52
    Period size: 11  Copynumber: 4.7  Consensus size: 11

      15625 GAAGTTCGTG

                       
      15635 TTTGAAGACTA
          1 TTTGAAGACTA

                        
      15646 TTTGAAGA-TAA
          1 TTTGAAGACT-A

                       
      15657 TTTGAAGAC--
          1 TTTGAAGACTA

                       
      15666 -TTGAAGACTA
          1 TTTGAAGACTA

                    
      15676 -TTGAAGA
          1 TTTGAAGA

      15683 ATTATTTCAA


Statistics
Matches: 33,  Mismatches: 0, Indels: 9
        0.79            0.00        0.21

Matches are distributed among these distances:
   8    8  0.24
  10    8  0.24
  11   17  0.52

ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33


Consensus pattern (11 bp):   
TTTGAAGACTA

Found at i:17020 original size:15 final size:15

Alignment explanation


    Indices: 17002--17030  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

      16992 GTTTCTAGTA

                           
      17002 TAATTGTTTTCTTTT
          1 TAATTGTTTTCTTTT

                          
      17017 TAATTGTTTTCTTT
          1 TAATTGTTTTCTTT

      17031 CAACCTCTGC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72


Consensus pattern (15 bp):   
TAATTGTTTTCTTTT

Found at i:17672 original size:2 final size:2

Alignment explanation


    Indices: 17667--17695  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      17657 CCTCTAACAA

                                                       
      17667 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 A

      17696 CTTAGCCCAC


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

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


Consensus pattern (2 bp):   
AT

Done.