; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/07/10/tmp_sequence_2026-07-10.105849_MwFmTr.fasta.purged -format fasta -lth occ_sig 0 -uth rank 50 -return freq,occ,proba,rank,ratio,zscore -2str -noov -quick_if_possible -seqtype dna -bg upstream-noorf -org Homo_sapiens_GRCh38 -pseudo 0.01 -l 4 -o $RSAT/public_html/tmp/www-data/2026/07/10/oligo-analysis_2026-07-10.105849_yMrI9W_4nt.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 4
; Input file $RSAT/public_html/tmp/www-data/2026/07/10/tmp_sequence_2026-07-10.105849_MwFmTr.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/07/10/oligo-analysis_2026-07-10.105849_yMrI9W_4nt.tab
; Discard overlapping matches
; Counted on both strands
; grouped by pairs of reverse complements
; Background model upstream-noorf
; Organism Homo_sapiens_GRCh38
; Background estimation method Frequency file
; Expected frequency file $RSAT/public_html/data/genomes/Homo_sapiens_GRCh38/oligo-frequencies/4nt_upstream-noorf_Homo_sapiens_GRCh38-noov-2str.freq
; Pseudo-frequency 0.01
; Pseudo-frequency per oligo 7.35294117647059e-05
; Sequence type DNA
; Nb of sequences 5062
; Sum of sequence lengths 1399185
; 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 1186561
; total overlapping occurrences 44037
; total non overlapping occ 1142524
; alphabet size 4
; nb possible oligomers 136
; oligomers tested for significance 136
;
; column headers
; 1 seq oligomer sequence
; 2 id oligomer identifier
; 3 obs_freq observed relative frequency
; 4 exp_freq expected relative frequency
; 5 occ observed occurrences
; 6 exp_occ expected occurrences
; 7 occ_P occurrence probability (binomial)
; 8 occ_E E-value for occurrences (binomial)
; 9 occ_sig occurrence significance (binomial)
; 10 rank rank
; 11 ovl_occ number of overlapping occurrences (discarded from the count)
; 12 forbocc forbidden positions (to avoid self-overlap)
; 13 zscore z-score (Gaussian approximation)
; 14 exp_var estimation of the variance on occurrences
; 15 ratio observed/expected ratio
#seq id obs_freq exp_freq occ exp_occ occ_P occ_E occ_sig rank ovl_occ forbocc zscore exp_var ratio
ccgc ccgc|gcgg 0.0106071242861 0.0027877686570 12586 3307.86 0 0e+00 350.00 1 1116 37758 161.32 3307.858 3.8049
cccg cccg|cggg 0.0104335133213 0.0032878994693 12380 3901.29 0 0e+00 350.00 2 760 37140 135.75 3901.293 3.1733
cgcc cgcc|ggcg 0.0102169210011 0.0033514748720 12123 3976.73 0 0e+00 350.00 3 1128 36369 129.18 3976.729 3.0485
cggc cggc|gccg 0.0081378032819 0.0024277739276 9656 2880.70 0 0e+00 350.00 4 1158 28968 126.23 2880.702 3.3520
cgcg cgcg|cgcg 0.0037756170985 0.0007447827586 4480 883.73 0 0e+00 350.00 5 1004 13440 120.97 883.730 5.0694
cgga cgga|tccg 0.0062171266374 0.0018482367403 7377 2193.05 0 0e+00 350.00 6 275 22131 110.70 2193.046 3.3638
agcg agcg|cgct 0.0062533658194 0.0019033684787 7420 2258.46 0 0e+00 350.00 7 278 22260 108.61 2258.463 3.2854
gcgc gcgc|gcgc 0.0045408537783 0.0012202293268 5388 1447.88 0 0e+00 350.00 8 1066 16164 103.55 1447.877 3.7213
cgca cgca|tgcg 0.0054771731078 0.0017084024734 6499 2027.12 0 0e+00 350.00 9 288 19497 99.32 2027.124 3.2060
ccgg ccgg|ccgg 0.0049116733147 0.0015379841764 5828 1824.91 0 0e+00 350.00 10 0 17484 93.71 1824.912 3.1936
cgac cgac|gtcg 0.0037916297603 0.0010606045480 4499 1258.47 0 0e+00 350.00 11 95 13497 91.35 1258.472 3.5750
gcga gcga|tcgc 0.0049310570632 0.0016340766693 5851 1938.93 0 0e+00 350.00 12 124 17553 88.84 1938.932 3.0176
acgc acgc|gcgt 0.0050844415079 0.0017116649615 6033 2030.99 0 0e+00 350.00 13 129 18099 88.80 2030.995 2.9705
gccc gccc|gggc 0.0141846900412 0.0073316745028 16831 8699.48 0 0e+00 350.00 14 759 50493 87.18 8699.479 1.9347
accg accg|cggt 0.0045231555731 0.0014742147491 5367 1749.25 0 0e+00 350.00 15 95 16101 86.50 1749.246 3.0682
cgtc cgtc|gacg 0.0046377725208 0.0015337443790 5503 1819.88 0 0e+00 350.00 16 253 16509 86.34 1819.881 3.0238
ccga ccga|tcgg 0.0051198379182 0.0018350574380 6075 2177.41 0 0e+00 350.00 17 0 18225 83.53 2177.408 2.7900
cccc cccc|gggg 0.0123356489890 0.0064110132776 14637 7607.06 0 0e+00 350.00 18 4624 43911 80.60 7607.058 1.9241
cgag cgag|ctcg 0.0057881558555 0.0023630703077 6868 2803.93 0 0e+00 350.00 19 200 20604 76.75 2803.927 2.4494
acgg acgg|ccgt 0.0047397478933 0.0018014768054 5624 2137.56 0 0e+00 350.00 20 0 16872 75.41 2137.562 2.6310
aacg aacg|cgtt 0.0038067996504 0.0013793870095 4517 1636.73 0 0e+00 350.00 21 131 13551 71.19 1636.727 2.7598
cacg cacg|cgtg 0.0053979525705 0.0024918307988 6405 2956.71 0 0e+00 350.00 22 322 19215 63.42 2956.709 2.1663
cgaa cgaa|ttcg 0.0034654771225 0.0013510953445 4112 1603.16 0 0e+00 350.00 23 94 12336 62.66 1603.157 2.5649
ggcc ggcc|ggcc 0.0068340355026 0.0038889302736 8109 4614.45 0 0e+00 350.00 24 0 24327 51.44 4614.453 1.7573
aggg aggg|ccct 0.0134843467803 0.0090085431169 16000 10689.19 0 0e+00 350.00 25 0 48000 51.37 10689.186 1.4968
ggac ggac|gtcc 0.0081487593137 0.0050367152895 9669 5976.37 0 0e+00 350.00 26 0 29007 47.77 5976.370 1.6179
acga acga|tcgt 0.0028746941792 0.0013461728678 3411 1597.32 0 0e+00 350.00 27 35 10233 45.38 1597.316 2.1355
cgta cgta|tacg 0.0022164895020 0.0009479984036 2630 1124.86 2e-319 3e-317 316.57 28 157 7890 44.88 1124.858 2.3381
gagc gagc|gctc 0.0098216610861 0.0068096835825 11654 8080.10 2e-306 2e-304 303.68 29 419 34962 39.76 8080.105 1.4423
ggga ggga|tccc 0.0138138705048 0.0102143486822 16391 12119.95 5e-300 6e-298 297.21 30 0 49173 38.80 12119.948 1.3524
accc accc|gggt 0.0095595590956 0.0067400502998 11343 7997.48 3e-273 3e-271 270.47 31 0 34029 37.41 7997.481 1.4183
acgt acgt|acgt 0.0019788278900 0.0009084964269 2348 1077.99 4e-245 6e-243 242.24 32 0 7044 38.68 1077.986 2.1781
gacc gacc|ggtc 0.0073026165532 0.0051155180322 8665 6069.87 3e-216 4e-214 213.42 33 0 25995 33.31 6069.874 1.4275
ctcc ctcc|ggag 0.0145420252309 0.0114687107067 17255 13608.32 2e-200 2e-198 197.61 34 665 51765 31.26 13608.325 1.2680
cctc cctc|gagg 0.0138568518601 0.0110413391293 16442 13101.22 1e-175 2e-173 172.76 35 627 49326 29.19 13101.222 1.2550
atcg atcg|cgat 0.0021591810282 0.0012314037082 2562 1461.14 2e-149 3e-147 146.57 36 85 7686 28.80 1461.136 1.7534
ctgc ctgc|gcag 0.0112939832002 0.0092424577695 13401 10966.74 5e-113 7e-111 110.19 37 1013 40203 23.24 10966.740 1.2220
ccac ccac|gtgg 0.0106467345547 0.0087252240456 12633 10353.01 3e-105 5e-103 102.34 38 327 37899 22.41 10353.011 1.2202
tcga tcga|tcga 0.0012776418574 0.0006976994493 1516 827.86 6e-102 9e-100 99.06 39 0 4548 23.92 827.863 1.8312
ggaa ggaa|ttcc 0.0118679107100 0.0099528609744 14082 11809.68 9.6e-93 1.3e-90 89.88 40 0 42246 20.91 11809.677 1.1924
agcc agcc|ggct 0.0112518446165 0.0095189069318 13351 11294.76 6.4e-80 8.7e-78 77.06 41 0 40053 19.35 11294.764 1.1821
cttc cttc|gaag 0.0105447591822 0.0089888819548 12512 10665.86 1.1e-68 1.5e-66 65.82 42 267 37536 17.88 10665.857 1.1731
gcac gcac|gtgc 0.0073127298133 0.0061167857105 8677 7257.94 2.4e-59 3.3e-57 56.49 43 280 26031 16.66 7257.939 1.1955
ccca ccca|tggg 0.0136200330198 0.0119844784667 16161 14220.31 4.5e-58 6.1e-56 55.21 44 0 48483 16.27 14220.315 1.1365
cagc cagc|gctg 0.0115771544826 0.0100927886606 13737 11975.71 1.5e-56 2.0e-54 53.70 45 927 41211 16.09 11975.709 1.1471
cacc cacc|ggtg 0.0096067543093 0.0085711972364 11399 10170.25 1.8e-33 2.4e-31 30.62 46 317 34197 12.18 10170.248 1.1208
gcca gcca|tggc 0.0094617975814 0.0084799625454 11227 10061.99 1.2e-30 1.6e-28 27.78 47 408 33681 11.61 10061.993 1.1158
aagg aagg|cctt 0.0101663547007 0.0091946486643 12063 10910.01 5.7e-28 7.7e-26 25.11 48 0 36189 11.04 10910.012 1.1057
acac acac|gtgt 0.0078175500459 0.0070330562304 9276 8345.15 5e-24 6.8e-22 21.17 49 1360 27828 10.19 8345.150 1.1115
aggc aggc|gcct 0.0110310384380 0.0101047032099 13089 11989.85 1.4e-23 1.9e-21 20.72 50 568 39267 10.04 11989.847 1.0917
; Host name rsat
; Job started 2026-07-10.105855
; Job done 2026-07-10.105855
; Seconds 0.46
; user 0.46
; system 0.03
; cuser 0.27
; csystem 0.03