Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016716.1 Corchorus olitorius cultivar O-4 contig16749, 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: 16715
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32


Found at i:8610 original size:29 final size:29

Alignment explanation


    Indices: 8568--8627  Score: 111
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       8558 ATGCCAATCA

                                         
       8568 TTCACTGTTTTTGCAGTAAGTTTGATGGC
          1 TTCACTGTTTTTGCAGTAAGTTTGATGGC

                                    *    
       8597 TTCACTGTTTTTGCAGTAAGTTTGTTGGC
          1 TTCACTGTTTTTGCAGTAAGTTTGATGGC

              
       8626 TT
          1 TT

       8628 GATGCTTTGG


Statistics
Matches: 30,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  29   30  1.00

ACGTcount: A:0.15, C:0.13, G:0.23, T:0.48


Consensus pattern (29 bp):   
TTCACTGTTTTTGCAGTAAGTTTGATGGC

Found at i:16550 original size:50 final size:49

Alignment explanation


    Indices: 16480--16612  Score: 150
    Period size: 50  Copynumber: 2.7  Consensus size: 49

      16470 TTTTACATTT

                                            *                  
      16480 CTTGCACCTTTTTCTCAATTTTTA-CAACAAAGTTGAATC-TTTAATTTTC
          1 CTTGCACCTTTTTCTCAATTTTTATCAA-AAAATTGAA-CATTTAATTTTC

                                      *                 *     
      16529 CTTGCACCTTTTTTCTCAATTTTTATGAAAAAATTGAACATTTACTTTTC
          1 CTTGCACC-TTTTTCTCAATTTTTATCAAAAAATTGAACATTTAATTTTC

            *            *                       
      16579 ATTGCA-CTTTTTATCAATTTTT-T-AACAAAATTGA
          1 CTTGCACCTTTTTCTCAATTTTTATCAA-AAAATTGA

      16613 TTGGCACGCT


Statistics
Matches: 75,  Mismatches: 5, Indels: 10
        0.83            0.06        0.11

Matches are distributed among these distances:
  46    2  0.03
  47    9  0.12
  48   14  0.19
  49   10  0.13
  50   38  0.51
  51    2  0.03

ACGTcount: A:0.29, C:0.17, G:0.06, T:0.47


Consensus pattern (49 bp):   
CTTGCACCTTTTTCTCAATTTTTATCAAAAAATTGAACATTTAATTTTC

Found at i:16681 original size:2 final size:2

Alignment explanation


    Indices: 16674--16708  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      16664 CAATTACTAT

                                                                
      16674 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      16709 TCTTCTT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Done.