; oligo-analysis -v 1 -quick -i $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/data/sequences/peak-motifs_test_maxlen1000_purged_ml30_mis0.fasta -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 100 -return occ,proba,rank -2str -noov -seqtype dna -l 6 -markov 3 -pseudo 0.01 -o $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3.tab
; Citation: van Helden et al. (1998). J Mol Biol 281(5), 827-42.
; Program version 1.169
; Quick counting mode
; Detection of over-represented words (right-tail test)
; Oligomer length 6
; Input file $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/data/sequences/peak-motifs_test_maxlen1000_purged_ml30_mis0.fasta
; Input format fasta
; Output file $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3.tab
; Discard overlapping matches
; Counted on both strands
; grouped by pairs of reverse complements
; Background model Markov
; Background estimation method Markov model estimated from input sequences
; Markov chain order 3
; Pseudo-frequency 0.01
; Pseudo-frequency per oligo 4.80769230769231e-06
; Sequence type DNA
; Nb of sequences 109
; Sum of sequence lengths 108923
; discarded residues NA (quick mode) (other letters than ACGT)
; discarded occurrences NA (quick mode) (contain discarded residues)
; nb possible positions NA (quick mode)
; total oligo occurrences 107326
; total overlapping occurrences 721
; total non overlapping occ 106605
; alphabet size 4
; nb possible oligomers 2080
; oligomers tested for significance 2077
;
; column headers
; 1 seq oligomer sequence
; 2 identifier oligomer identifier
; 3 exp_freq expected relative frequency
; 4 occ observed occurrences
; 5 exp_occ expected occurrences
; 6 occ_P occurrence probability (binomial)
; 7 occ_E E-value for occurrences (binomial)
; 8 occ_sig occurrence significance (binomial)
; 9 rank rank
; 10 ovl_occ number of overlapping occurrences (discarded from the count)
; 11 forbocc forbidden positions (to avoid self-overlap)
#seq identifier exp_freq occ exp_occ occ_P occ_E occ_sig rank ovl_occ forbocc
aagaga aagaga|tctctt 0.0004779345800 82 51.29 4.7e-05 9.9e-02 1.01 1 0 410
ctcttc ctcttc|gaagag 0.0004776162891 81 51.26 7.6e-05 1.6e-01 0.80 2 0 405
atcgac atcgac|gtcgat 0.0004342487485 75 46.61 7.9e-05 1.6e-01 0.79 3 0 375
acaaaa acaaaa|ttttgt 0.0011063622948 162 118.74 9.4e-05 2.0e-01 0.71 4 0 810
gctaaa gctaaa|tttagc 0.0005965451160 96 64.02 0.00011 2.4e-01 0.62 5 0 480
ggtaga ggtaga|tctacc 0.0003281869297 59 35.22 0.00016 3.2e-01 0.49 6 0 295
ggcaaa ggcaaa|tttgcc 0.0010448238142 152 112.14 0.00020 4.1e-01 0.39 7 0 760
agagat agagat|atctct 0.0004166579051 70 44.72 0.00028 5.9e-01 0.23 8 2 350
tcggca tcggca|tgccga 0.0005637646404 89 60.51 0.00036 7.4e-01 0.13 9 0 445
; Host name biow
; Job started 2014-09-05.202713
; Job done 2014-09-05.202714
; Seconds 0.8
; user 0.8
; system 0.02
; cuser 0.25
; csystem 0.02