/space23/rsat/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0.tab 
 dyad-analysis  -v 1 -return occ,proba,rank -expfreq $RSAT/public_html/data/taxon_frequencies/Gammaproteobacteria/dyads_3nt_sp0-20_upstream-noorf_Gammaproteobacteria-noov-2str.freq -accept $RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_filter_dyads.tab -lth occ 1 -lth occ_sig 0 -uth rank 50 -i $RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_seq_purged.fasta -l 3 -sp 0-20 -2str -noov -sort -o $RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0.tab
 Citation: van Helden et al. (2000). Nucleic Acids Res. 28(8):1808-18.
 Program version              	1.78
 Input file                   	$RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_seq_purged.fasta
 Accepted dyad file           	$RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_filter_dyads.tab
 Accepted dyads               	3469
 Sequence type                	DNA
 Output file                  	$RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0.tab
 default return values        	freq,occ
 return values                	proba,occ,exp_freq,exp_occ,rank
 Discard overlapping matches
 Counted on both strands
 	grouped by pairs of reverse complements
 Monad parameters             
 	monad size                  	3
 	monad positions              368958
 	    valid                    	79978
 	    discarded                	288980 (contain other letters than ACGT)
 	distinct monads              64
 Dyad parameters              
 	dyad type                    any dyad
 	minimal spacing              0
 	maximal spacing              20
 	distinct dyads               	43680
 	dyads tested for significance	1757
	Dyad counts per spacing
		spacing	max_pos	occ	ovlps	ovl+occ	ACGT	nonACGT
		sp 0	361414	5742	106	5848	77439	283975
		sp 1	358922	5298	113	5411	76642	282280
		sp 2	356430	5209	138	5347	75869	280561
		sp 3	353938	5023	102	5125	75112	278826
		sp 4	351447	5123	124	5247	74366	277081
		sp 5	348956	5415	127	5542	73633	275323
		sp 6	346465	5089	149	5238	72908	273557
		sp 7	343975	4982	183	5165	72192	271783
		sp 8	341486	5177	179	5356	71484	270002
		sp 9	338997	4501	376	4877	70783	268214
		sp 10	336508	4286	126	4412	70110	266398
		sp 11	334019	4404	199	4603	69449	264570
		sp 12	331530	3882	100	3982	68798	262732
		sp 13	329041	3884	89	3973	68154	260887
		sp 14	326552	3645	131	3776	67518	259034
		sp 15	324063	3529	133	3662	66887	257176
		sp 16	321574	3664	200	3864	66265	255309
		sp 17	319085	3730	193	3923	65652	253433
		sp 18	316596	3644	281	3925	65044	251552
		sp 19	314107	3301	230	3531	64439	249668
		sp 20	311618	3242	191	3433	63842	247776
 Estimation of expected dyad frequencies
	Background model	exp_freq_file
	exp. freq. file       	$RSAT/public_html/data/taxon_frequencies/Gammaproteobacteria/dyads_3nt_sp0-20_upstream-noorf_Gammaproteobacteria-noov-2str.freq
 column headers
	1	sequence       	
	2	identifier             	
	3	expected_freq  	
	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
	11	all_occ        	number of non-overlapping + overlapping occurrences
	12	ov_coef        	overlap coefficient
	13	remark         	remark (dir_rep=direct repeat; rc_pal=reverse complementary palindrom)
sequence identifier expected_freq occ exp_occ occ_P occ_E occ_sig rank ovl_occ all_occ ov_coef remark
ctgn{10}cag ctgn{10}cag|ctgn{10}cag 0.0003456874153 314 1.48 4.5e-226 8.0e-223 222.10 1 0 314 1.0000 rc_pal
ctgn{9}aca ctgn{9}aca|tgtn{9}cag 0.0005083601722 346 2.29 4.1e-208 7.2e-205 204.14 2 195 541 1.0000
ctgn{8}tac ctgn{8}tac|gtan{8}cag 0.0003739946179 281 1.94 3.7e-179 6.5e-176 175.18 3 8 289 1.0010
tgtn{8}aca tgtn{8}aca|tgtn{8}aca 0.0002933554708 246 1.52 9.2e-168 1.6e-164 163.79 4 0 246 1.0000 rc_pal
actn{11}cag actn{11}cag|ctgn{11}agt 0.0004108612830 264 1.81 2.8e-155 4.8e-152 151.32 5 61 325 1.0000
atan{0}cag atan{0}cag|ctgn{0}tat 0.0005080478754 300 2.92 5.7e-154 1.0e-150 150.00 6 0 300 1.0000
ctgn{1}ata ctgn{1}ata|tatn{1}cag 0.0005906601121 316 3.13 1.3e-151 2.3e-148 147.63 7 0 316 1.0000
tatn{0}aca tatn{0}aca|tgtn{0}ata 0.0004887765724 282 2.81 2.2e-142 3.9e-139 138.41 8 15 297 1.0000
gtan{7}aca gtan{7}aca|tgtn{7}tac 0.0003742870433 242 1.86 1.9e-139 3.3e-136 135.48 9 25 267 1.0000
atan{6}cag atan{6}cag|ctgn{6}tat 0.0005962825672 275 3.03 3.5e-122 6.1e-119 118.21 10 1 276 1.0000
ctgn{7}ata ctgn{7}ata|tatn{7}cag 0.0005710708062 259 2.85 1.6e-114 2.7e-111 110.56 11 4 263 1.0000
actn{0}gta actn{0}gta|tacn{0}agt 0.0003689572643 215 2.12 8.2e-110 1.4e-106 105.84 12 0 215 1.0010
tatn{6}aca tatn{6}aca|tgtn{6}ata 0.0006914357351 259 3.52 7.2e-96 1.3e-92 91.90 13 9 268 1.0000
actn{2}ata actn{2}ata|tatn{2}agt 0.0005473261470 222 2.85 1.5e-85 2.6e-82 81.58 14 4 226 1.0010
atan{1}aca atan{1}aca|tgtn{1}tat 0.0007268155597 250 3.85 5.9e-81 1.0e-77 76.98 15 6 256 1.0010
actn{1}tat actn{1}tat|atan{1}agt 0.0005888404156 222 3.12 4.5e-79 7.9e-76 75.10 16 3 225 1.0000
atan{5}aca atan{5}aca|tgtn{5}tat 0.0007718740120 247 4.18 2.5e-77 4.3e-74 73.36 17 5 252 1.0010
atan{0}tac atan{0}tac|gtan{0}tat 0.0004714560800 195 2.71 2.6e-75 4.6e-72 71.34 18 63 258 1.0000
atan{2}cag atan{2}cag|ctgn{2}tat 0.0006594312496 227 3.43 1.6e-74 2.8e-71 70.55 19 1 228 1.0000
ctgn{3}ata ctgn{3}ata|tatn{3}cag 0.0006483049960 208 3.26 3.2e-64 5.7e-61 60.25 20 12 220 1.0000
tatn{0}ata tatn{0}ata|tatn{0}ata 0.0004010086656 165 2.30 1e-63 1.8e-60 59.74 21 5 170 1.0664 rc_pal
cctn{11}cag cctn{11}cag|ctgn{11}agg 0.0004347873990 162 1.91 3.8e-63 6.7e-60 59.17 22 5 167 1.0000
ctgn{5}ata ctgn{5}ata|tatn{5}cag 0.0005996195247 191 3.25 6.2e-60 1.1e-56 55.96 23 2 193 1.0000
tatn{2}aca tatn{2}aca|tgtn{2}ata 0.0008003481114 226 4.17 1.9e-59 3.3e-56 55.49 24 17 243 1.0000
gtan{1}ata gtan{1}ata|tatn{1}tac 0.0005564973169 181 2.95 9.9e-56 1.7e-52 51.76 25 64 245 1.0000
atan{4}cag atan{4}cag|ctgn{4}tat 0.0006338089480 189 3.25 1.4e-54 2.5e-51 50.61 26 12 201 1.0000
cctn{10}aca cctn{10}aca|tgtn{10}agg 0.0004405193135 148 1.89 5.2e-52 9.2e-49 48.04 27 3 151 1.0000
actn{12}agg actn{12}agg|cctn{12}agt 0.0003242987355 116 1.26 1.9e-44 3.3e-41 40.48 28 0 116 1.0000
cctn{9}tac cctn{9}tac|gtan{9}agg 0.0003293593663 117 1.48 2.3e-43 4.0e-40 39.40 29 0 117 1.0010
ctgn{9}cca ctgn{9}cca|tggn{9}cag 0.0004372000158 132 1.97 2.3e-41 4.0e-38 37.40 30 2 134 1.0000
tatn{4}aca tatn{4}aca|tgtn{4}ata 0.0007292375725 176 3.74 3.1e-39 5.5e-36 35.26 31 5 181 1.0000
tggn{8}aca tggn{8}aca|tgtn{8}cca 0.0003741727687 114 1.94 6e-36 1.1e-32 31.98 32 0 114 1.0000
gtan{3}aca gtan{3}aca|tgtn{3}tac 0.0003877729118 119 1.95 8.9e-36 1.6e-32 31.80 33 6 125 1.0000
aacn{12}cag aacn{12}cag|ctgn{12}gtt 0.0005532558071 136 2.15 9.2e-35 1.6e-31 30.79 34 7 143 1.0000
gtan{2}tac gtan{2}tac|gtan{2}tac 0.0001341736266 70 0.70 1.3e-34 2.2e-31 30.66 35 0 70 1.0000 rc_pal
cctn{8}ata cctn{8}ata|tatn{8}agg 0.0005024079917 130 2.60 7.7e-34 1.4e-30 29.87 36 0 130 1.0000
atan{12}ctg atan{12}ctg|cagn{12}tat 0.0005414740995 128 2.10 2.9e-31 5.1e-28 27.29 37 5 133 1.0000
atan{7}agg atan{7}agg|cctn{7}tat 0.0005135899914 126 2.56 2.3e-30 4.0e-27 26.40 38 0 126 1.0000
cagn{13}ata cagn{13}ata|tatn{13}ctg 0.0005599987026 126 2.18 3e-29 5.2e-26 25.28 39 10 136 1.0000
actn{4}ata actn{4}ata|tatn{4}agt 0.0005972642552 137 3.06 7.4e-29 1.3e-25 24.89 40 8 145 1.0010
actn{3}tat actn{3}tat|atan{3}agt 0.0006096237898 138 3.06 4.1e-28 7.1e-25 24.15 41 1 139 1.0000
gtgn{5}ata gtgn{5}ata|tatn{5}cac 0.0004598655572 115 2.49 7.5e-28 1.3e-24 23.88 42 1 116 1.0000
ctgn{11}aga ctgn{11}aga|tctn{11}cag 0.0004165660271 105 1.83 9.2e-28 1.6e-24 23.79 43 2 107 1.0000
actn{10}cca actn{10}cca|tggn{10}agt 0.0002994277595 88 1.28 1.1e-27 2.0e-24 23.70 44 0 88 1.0010
atan{3}aca atan{3}aca|tgtn{3}tat 0.0008723676684 169 4.38 1.2e-26 2.0e-23 22.69 45 12 181 1.0010
ctgn{4}tac ctgn{4}tac|gtan{4}cag 0.0003870569077 102 1.98 3e-26 5.3e-23 22.28 46 0 102 1.0010
actn{6}ata actn{6}ata|tatn{6}agt 0.0005931467013 128 3.02 1.5e-25 2.7e-22 21.57 47 4 132 1.0010
ctgn{8}cac ctgn{8}cac|gtgn{8}cag 0.0004163015311 101 2.16 1.2e-24 2.1e-21 20.68 48 0 101 1.0010
actn{2}cag actn{2}cag|ctgn{2}agt 0.0003557843559 95 1.85 2.3e-24 4.0e-21 20.39 49 9 104 1.0000
gtgn{7}aca gtgn{7}aca|tgtn{7}cac 0.0003353520622 89 1.67 3.7e-24 6.5e-21 20.19 50 2 91 1.0000 
 Host name	sinik
 Job started	2018-03-21.142932
 Job done	2018-03-21.142939
 Seconds	7.46
	user	7.46
	system	0.09
	cuser	0.03
;	csystem	0