Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023732.1 Corchorus olitorius cultivar O-4 contig23765, 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: 12289
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30


Found at i:4228 original size:27 final size:27

Alignment explanation


    Indices: 4197--4255  Score: 82
    Period size: 27  Copynumber: 2.2  Consensus size: 27

       4187 CCCGTAGTTT

                    *     * *          
       4197 CTGGGATAGTATTGTTGCCCCTGATTC
          1 CTGGGATAATATTGCTCCCCCTGATTC

            *                          
       4224 TTGGGATAATATTGCTCCCCCTGATTC
          1 CTGGGATAATATTGCTCCCCCTGATTC

                 
       4251 CTGGG
          1 CTGGG

       4256 CTAAAATCTG


Statistics
Matches: 27,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  27   27  1.00

ACGTcount: A:0.15, C:0.24, G:0.25, T:0.36


Consensus pattern (27 bp):   
CTGGGATAATATTGCTCCCCCTGATTC

Found at i:9663 original size:31 final size:30

Alignment explanation


    Indices: 9599--9655  Score: 96
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       9589 ACTTGACCAA

                                     *    
       9599 TTAATTTCCCAAAATCTTCTTTTGGGTATC
          1 TTAATTTCCCAAAATCTTCTTTTGGATATC

                   *                   
       9629 TTAATTTTCCAAAATCTTCTTTTGGAT
          1 TTAATTTCCCAAAATCTTCTTTTGGAT

       9656 TTGCTTAAGA


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  30   25  1.00

ACGTcount: A:0.25, C:0.18, G:0.09, T:0.49


Consensus pattern (30 bp):   
TTAATTTCCCAAAATCTTCTTTTGGATATC

Found at i:10695 original size:16 final size:15

Alignment explanation


    Indices: 10657--10698  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

      10647 ACAGAGATTG

                   *       
      10657 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
      10672 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
      10687 ACTAGAAAACAA
          1 AC-AGAAAACAA

      10699 AGCAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.