; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/08/11/retrieve-seq_2026-08-11.184937_DRw5uO.fasta.fasta.purged -format fasta -lth occ_sig 0 -uth rank 50 -return occ,proba,rank -2str -noov -quick_if_possible -seqtype dna -bg upstream-noorf -org Arabidopsis_thaliana.TAIR10.60 -pseudo 0.01 -l 6 -o $RSAT/public_html/tmp/www-data/2026/08/11/oligo-analysis_2026-08-11.184952_9l9pFk_6nt.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/www-data/2026/08/11/retrieve-seq_2026-08-11.184937_DRw5uO.fasta.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/08/11/oligo-analysis_2026-08-11.184952_9l9pFk_6nt.tab
; Discard overlapping matches
; Counted on both strands
; grouped by pairs of reverse complements
; Background model upstream-noorf
; Organism Arabidopsis_thaliana.TAIR10.60
; Background estimation method Frequency file
; Expected frequency file $RSAT/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.60/oligo-frequencies/6nt_upstream-noorf_Arabidopsis_thaliana.TAIR10.60-noov-2str.freq
; Pseudo-frequency 0.01
; Pseudo-frequency per oligo 4.80769230769231e-06
; Sequence type DNA
; Nb of sequences 316
; Sum of sequence lengths 626253
; 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 602960
; total overlapping occurrences 14159
; total non overlapping occ 588801
; alphabet size 4
; nb possible oligomers 2080
; oligomers tested for significance 2080
;
; column headers
; 1 seq oligomer sequence
; 2 id 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 id exp_freq occ exp_occ occ_P occ_E occ_sig rank ovl_occ forbocc
gtcaac gtcaac|gttgac 0.0004297171609 409 259.10 5.4e-18 1.1e-14 13.95 1 0 2045
agtcaa agtcaa|ttgact 0.0007630976254 655 460.12 7.5e-18 1.6e-14 13.80 2 4 3275
gtcaaa gtcaaa|tttgac 0.0009646070372 767 581.62 1.3e-13 2.7e-10 9.58 3 0 3835
cacgtg cacgtg|cacgtg 0.0001768199621 190 106.62 2.2e-13 4.6e-10 9.34 4 0 950
ggtcaa ggtcaa|ttgacc 0.0004673981908 398 281.82 4.1e-11 8.6e-08 7.07 5 0 1990
aagtca aagtca|tgactt 0.0007169314601 574 432.28 4.7e-11 9.8e-08 7.01 6 4 2870
acgcgt acgcgt|acgcgt 0.0000541871632 76 32.67 7.1e-11 1.5e-07 6.83 7 0 380
aataat aataat|attatt 0.0028732101965 1998 1732.43 2.3e-10 4.9e-07 6.31 8 179 9990
acacgt acacgt|acgtgt 0.0003548069721 311 213.93 3e-10 6.2e-07 6.21 9 14 1555
acgtgg acgtgg|ccacgt 0.0002373957950 218 143.14 3.7e-09 7.7e-06 5.11 10 10 1090
aacgcg aacgcg|cgcgtt 0.0000792409060 92 47.78 9e-09 1.9e-05 4.73 11 19 460
tgacca tgacca|tggtca 0.0004691303634 383 282.87 9e-09 1.9e-05 4.73 12 0 1915
tacgaa tacgaa|ttcgta 0.0004328049468 356 260.96 1.4e-08 2.9e-05 4.54 13 1 1780
aaagtc aaagtc|gacttt 0.0007280023023 559 438.96 2.1e-08 4.4e-05 4.36 14 0 2795
aaaaaa aaaaaa|tttttt 0.0047025601837 3126 2835.46 3.9e-08 8.0e-05 4.10 15 4209 15630
actaat actaat|attagt 0.0012350770014 894 744.70 6e-08 1.2e-04 3.91 16 2 4470
aacacg aacacg|cgtgtt 0.0002839636234 245 171.22 6.8e-08 1.4e-04 3.85 17 0 1225
aaataa aaataa|ttattt 0.0040521921345 2707 2443.31 7.7e-08 1.6e-04 3.79 18 153 13535
aaaata aaaata|tatttt 0.0048463807170 3207 2922.17 1e-07 2.1e-04 3.67 19 95 16035
taataa taataa|ttatta 0.0024299999480 1666 1465.19 1.4e-07 3.0e-04 3.52 20 102 8330
aatttg aatttg|caaatt 0.0019534014450 1358 1177.82 1.5e-07 3.2e-04 3.50 21 56 6790
aattat aattat|ataatt 0.0027147038522 1845 1636.86 2.3e-07 4.8e-04 3.32 22 116 9225
acgata acgata|tatcgt 0.0003551835314 292 214.16 2.6e-07 5.4e-04 3.27 23 0 1460
atacta atacta|tagtat 0.0009587578167 702 578.09 3.3e-07 6.8e-04 3.17 24 8 3510
aataaa aataaa|tttatt 0.0037761239893 2517 2276.85 3.7e-07 7.7e-04 3.11 25 130 12585
attata attata|tataat 0.0022289173034 1529 1343.95 4e-07 8.3e-04 3.08 26 111 7645
cgtata cgtata|tatacg 0.0003656518788 294 220.47 1.4e-06 2.8e-03 2.55 27 13 1470
aatact aatact|agtatt 0.0009607912367 696 579.32 1.4e-06 2.9e-03 2.54 28 0 3480
aaatta aaatta|taattt 0.0034545925895 2295 2082.98 2.4e-06 5.0e-03 2.30 29 39 11475
aaaaat aaaaat|attttt 0.0051362811390 3351 3096.97 3.2e-06 6.7e-03 2.17 30 5 16755
acgtat acgtat|atacgt 0.0003822706941 301 230.49 5.1e-06 1.1e-02 1.98 31 20 1505
aattag aattag|ctaatt 0.0013044894249 912 786.55 6.7e-06 1.4e-02 1.86 32 20 4560
tagtca tagtca|tgacta 0.0005396724646 407 325.40 7.2e-06 1.5e-02 1.82 33 1 2035
acaaat acaaat|atttgt 0.0019601544078 1333 1181.89 8.5e-06 1.8e-02 1.75 34 4 6665
aaaagt aaaagt|actttt 0.0019884465602 1350 1198.95 9.8e-06 2.0e-02 1.69 35 0 6750
gaccaa gaccaa|ttggtc 0.0005713034425 427 344.47 9.8e-06 2.0e-02 1.69 36 0 2135
acgtga acgtga|tcacgt 0.0002991013056 240 180.35 1.3e-05 2.7e-02 1.57 37 16 1200
cgcgta cgcgta|tacgcg 0.0000622455314 66 37.53 1.7e-05 3.5e-02 1.46 38 8 330
gacaaa gacaaa|tttgtc 0.0010662027255 751 642.88 1.7e-05 3.6e-02 1.45 39 0 3755
taatta taatta|taatta 0.0014275740949 985 860.77 1.8e-05 3.8e-02 1.42 40 62 4925
gaccca gaccca|tgggtc 0.0002521569180 206 152.04 1.8e-05 3.8e-02 1.42 41 0 1030
ataata ataata|tattat 0.0023943774420 1603 1443.71 1.9e-05 4.0e-02 1.40 42 162 8015
atacga atacga|tcgtat 0.0004124456429 316 248.69 2.3e-05 4.8e-02 1.32 43 1 1580
gtccaa gtccaa|ttggac 0.0004356667971 331 262.69 2.8e-05 5.8e-02 1.24 44 0 1655
gtatta gtatta|taatac 0.0008432796438 602 508.46 2.9e-05 6.1e-02 1.21 45 1 3010
cacacg cacacg|cgtgtg 0.0001930371142 162 116.39 3.7e-05 7.7e-02 1.11 46 1 810
acgcgg acgcgg|ccgcgt 0.0000528315498 57 31.86 3.8e-05 7.8e-02 1.11 47 0 285
aagaaa aagaaa|tttctt 0.0030888029247 2034 1862.42 4.5e-05 9.4e-02 1.03 48 69 10170
gtctaa gtctaa|ttagac 0.0004854479313 361 292.71 6.3e-05 1.3e-01 0.88 49 0 1805
caaaaa caaaaa|tttttg 0.0033137092185 2169 1998.03 8.1e-05 1.7e-01 0.77 50 0 10845
; Host name rsat
; Job started 2026-08-11.184954
; Job done 2026-08-11.184955
; Seconds 0.51
; user 0.51
; system 0.02
; cuser 0.17
; csystem 0.02