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