Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020945.1 Corchorus olitorius cultivar O-4 contig20978, 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: 4107
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:775 original size:32 final size:31

Alignment explanation


    Indices: 673--775  Score: 109
    Period size: 32  Copynumber: 3.2  Consensus size: 31

        663 AAAAATAAAG

                 *                     *     
        673 AAAATATTTTTTTTTCTAAAAACGCAGGAACAA
          1 AAAATTTTTTTTTTTC-AAAAACGCA-AAACAA

            *                                
        706 GAAATTTTTTTTTTAT-AGAAAACGCAAAACAA
          1 AAAATTTTTTTTTT-TCA-AAAACGCAAAACAA

                                  *         
        738 AAAATTTTTTTTTTTCAAAAACACAAAACTAA
          1 AAAATTTTTTTTTTTCAAAAACGCAAAAC-AA

            *     
        770 TAAATT
          1 AAAATT

        776 AAAAACGCAA


Statistics
Matches: 60,  Mismatches: 6, Indels: 9
        0.80            0.08        0.12

Matches are distributed among these distances:
  31   12  0.20
  32   27  0.45
  33   20  0.33
  34    1  0.02

ACGTcount: A:0.48, C:0.11, G:0.06, T:0.36


Consensus pattern (31 bp):   
AAAATTTTTTTTTTTCAAAAACGCAAAACAA

Found at i:808 original size:28 final size:25

Alignment explanation


    Indices: 776--829  Score: 81
    Period size: 25  Copynumber: 2.0  Consensus size: 25

        766 CTAATAAATT

                                        
        776 AAAAACGCAAGAAAACCCTTTTTTTATG
          1 AAAAACGC-A-AAAA-CCTTTTTTTATG

                                     
        804 AAAAACGCAAAAACCTTTTTTTATG
          1 AAAAACGCAAAAACCTTTTTTTATG

             
        829 A
          1 A

        830 TGCAGAAACA


Statistics
Matches: 26,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  25   13  0.50
  26    4  0.15
  27    1  0.04
  28    8  0.31

ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30


Consensus pattern (25 bp):   
AAAAACGCAAAAACCTTTTTTTATG
Done.