Synergistic interactions - dm_patterns
motifs_filename=/data/kreiman/databh/dm_patterns/analysis/cooc/check/dm_patterns2.100.4.2.0.38.5000.5000.5000.check-ensembl.out.txt
consensus_filename=/data/kreiman/databh/dm_patterns/analysis/dm_patterns2.dm.80.consensus.txt
transcripts_filename=/data/kreiman/databh/dm_patterns/dm_patterns2.txt
number of transcripts = 13 [n_transcripts_cl]
number of motifs = 271 [n_motifs_cl]
maximum distance (bp) = 100 [max_distance]
minimum distance factor = 0.50 [min_dist_factor]
interactions of 2 motifs [max_n_motifs]
scan threshold column = 38 [thresh_column]
seqlengths_filename = /data/kreiman/databh/dm_patterns/upstream_sequences/dm_patterns2.dm.ensembl.lengths.txt and none
motifpos_filename = /data/kreiman/databh/dm_patterns/analysis/cooc/check/dm_patterns2.100.4.2.0.38.5000.5000.5000.check-ensembl.pos-cl.txt and none
seqs_filename = /data/kreiman/databh/dm_patterns/upstream_sequences/dm_patterns2.dm.ensembl.fasta and none
robustness_filename = /data/kreiman/databh/dm_patterns/analysis/cooc/check/compare_cooc_outputs.dm_patterns2.mul.2.txt
wm_filename = /data/kreiman/databh/dm_patterns/analysis/dm_patterns2.dm.80.matlab.txt
species = dm
max_n_motifs = 2
order constraint = false
number of modules = 95 [n_cooc]
number of modules after filter = 95 [n_cooc_actual]
Click on the motif ID numbers to get further information about the motifs.
Click on n_cooc_tr_cl (the number of transcripts with non-overlapping co-occurrences within the distance and order constraints) to see a list of the transcripts and positions
Click on p_binom_sp1 to see a plot of the occurrences of the motif cluster in each transcript (Figure legend)
Summary of results
i	id1	id2	consensus m1	consensus m2	ml1	ml2	map1	map2	r_oc_sp1	r_tr_sp1	n_cooc_all	n_cooc_tr_all	n_cooc_cl	n_cooc_tr_cl	p_binom
1	214	215	kdkcsksmmaw	ynncyckvkrnnannnk	11	17	8.24224	2.25513	524.58	524.58	8	8	4	4	8.40E-11
2	173	215	knsnnmnnnskcrkvnr	ynncyckvkrnnannnk	17	17	9.89915	2.25513	374.7	322.82	14	13	5	4	1.30E-10
3	93	268	tkkcmnwnaaaa	nnnyaaad	12	8	25.2437	8	29.01	21.63	434	388	12	8	4.10E-10
4	64	215	raaannrnvarar	ynncyckvkrnnannnk	13	17	8.72593	2.25513	114.75	97.14	64	54	7	5	7.50E-10
5	204	231	aaarrhvnnsrnar	tttttatk	14	8	10.8193	113.063	7.71	6.08	2992	2070	22	12	1.60E-09
6	100	268	kckmrnnnaandyk	nnnyaaad	14	8	2.20732	8	54.93	36.6	191	172	10	6	5.20E-09
7	270	270	vamnkrrtbd	vamnkrrtbd	10	10	10	10	33.84	15.32	1240	548	40	8	6.50E-09
8	35	212	dkccawaaam	vaaaahnnnnnnnnnnnnvnnnnaaa	10	26	44.4408	96.7282	13.12	8.43	1679	1245	21	10	8.20E-09
9	64	224	raaannrnvarar	vbsrnknnkkcnks	13	14	8.72593	3.10455	30.65	21.1	445	348	13	7	9.20E-09
10	233	268	yakktakv	nnnyaaad	8	8	124.29	8	37.57	20.75	391	354	14	7	1.00E-08
11	35	268	dkccawaaam	nnnyaaad	10	8	44.4408	8	15.94	14.13	724	594	11	8	1.20E-08
12	100	212	kckmrnnnaandyk	vaaaahnnnnnnnnnnnnvnnnnaaa	14	26	2.20732	96.7282	19.29	20.12	435	365	8	7	1.30E-08
13	35	177	dkccawaaam	tdnnmhhnammaaaa	10	15	44.4408	1.84039	16.53	13.34	698	629	11	8	1.90E-08
14	95	135	shynhtkkccka	rntykkccavnnks	12	14	6.2064	3.37689	27.48	18.22	420	403	11	7	2.60E-08
15	102	243	tnttknnndnwnaawaa	kkkrttty	17	8	35.9758	95.1165	28.8	27.61	255	228	7	6	2.90E-08
16	100	231	kckmrnnnaandyk	tttttatk	14	8	2.20732	113.063	43.71	46.42	120	113	5	5	3.80E-08
17	95	244	shynhtkkccka	krttycyk	12	8	6.2064	92.3561	99.92	99.92	42	42	4	4	4.20E-08
18	208	214	kskrknrrknkvk	kdkcsksmmaw	13	11	4.55535	8.24224	40.98	44.08	128	119	5	5	5.00E-08
19	48	246	maawksvaaa	kymtacck	10	8	5.02275	78.5479	20.79	14.93	555	492	11	7	1.00E-07
20	144	201	rvdhkmtkckaw	vnnbnnnvkcakckr	12	15	2.70818	14.5729	44.64	38.01	141	138	6	5	1.10E-07
21	98	121	skksnnkkkknrd	atbkccksbk	13	10	1.48853	7.23416	88.91	80.7	59	52	5	4	1.10E-07
22	182	214	kdkckrnnndnannnnnnknbnk	kdkcsksmmaw	23	11	3.26998	8.24224	92.03	79.18	57	53	5	4	1.20E-07
23	189	220	kkrnnnkbkknnnknkk	rmknncrvdarnck	17	14	2.08843	2.19853	47.08	36.43	156	144	7	5	1.30E-07
24	72	205	rmaaanvkcnkmnm	ynkcdknkmbynkc	14	14	10.4987	8.69747	84.61	76.3	62	55	5	4	1.40E-07
25	95	270	shynhtkkccka	vamnkrrtbd	12	10	6.2064	10	71.13	76.3	59	55	4	4	1.40E-07
26	64	171	raaannrnvarar	kcnkshnrncranns	13	15	8.72593	5.68814	19.08	14.02	660	524	12	7	1.60E-07
27	174	205	kcsrkckvsm	ynkcdknkmbynkc	10	14	8.96466	8.69747	81.97	73.62	64	57	5	4	1.60E-07
28	41	163	vakhrarhkrk	snnnnncnbnssmnndnnskynks	11	24	22.0843	7.68625	51.04	34.74	185	151	9	5	1.70E-07
29	101	102	aawdwnhnnnnaawaaw	tnttknnndnwnaawaa	17	17	37.1278	35.9758	6.59	4.99	3660	2314	23	11	1.80E-07
30	98	205	skksnnkkkknrd	ynkcdknkmbynkc	13	14	1.48853	8.69747	62.64	69.94	67	60	4	4	2.00E-07
31	163	205	snnnnncnbnssmnndnnskynks	ynkcdknkmbynkc	24	14	7.68625	8.69747	36.18	33.2	174	158	6	5	2.10E-07
32	113	231	aaarnndkraaa	tttttatk	12	8	0.542878	113.063	13.3	13.35	631	550	8	7	2.20E-07
33	179	233	kcnkmranrannnnna	yakktakv	16	8	6.16361	124.29	29.98	32.58	175	161	5	5	2.30E-07
34	74	237	cnkvkakcrkc	hckctcrc	11	8	4.09333	101.351	22.93	19.37	366	325	8	6	2.40E-07
35	35	143	dkccawaaam	vmaaancvaam	10	11	44.4408	3.87667	10.15	9.64	1137	871	11	8	2.50E-07
36	185	197	rnkwktktkyr	kkckkcmmwnr	11	11	29.4071	9.50267	25.1	30.5	209	172	5	5	3.30E-07
37	73	214	dnbnknnkksnnrkkk	kdkcsksmmaw	16	11	9.28687	8.24224	73.88	61.71	71	68	5	4	3.40E-07
38	258	269	rtaaaaar	ntttttrnbnb	8	11	102.496	11	7.92	7.11	1590	1328	12	9	3.70E-07
39	189	225	kkrnnnkbkknnnknkk	mkcrsnndvrkcks	17	14	2.08843	1.65577	63.2	59.95	83	70	5	4	3.80E-07
40	47	164	kcvaamkkrtw	dnrnnnknsrnnknknndknnnnnknv	11	27	6.25033	4.98522	67.25	59.95	78	70	5	4	3.80E-07
41	130	209	kkktkkkbkdnnrk	aaanwmnnnnnnnnnnnadnnnnndaa	14	27	1.81006	115.569	15.15	12.28	762	598	11	7	3.90E-07
42	166	188	rrvakcsaaa	aawthkcykb	10	10	0.683489	3.55742	19.13	17.58	384	358	7	6	4.30E-07
43	196	234	kybrnnnnmnnnkscrkh	tttctktt	18	8	12.6596	112.022	43.51	28.2	217	186	9	5	4.80E-07
44	177	244	tdnnmhhnammaaaa	krttycyk	15	8	1.84039	92.3561	10.6	11.37	693	646	7	7	6.60E-07
45	163	208	snnnnncnbnssmnndnnskynks	kskrknrrknkvk	24	13	7.68625	4.55535	21.27	16.35	444	385	9	6	6.70E-07
46	202	231	annkchkcnvhnnmr	tttttatk	15	8	14.5469	113.063	14.92	16.31	422	386	6	6	6.80E-07
47	64	173	raaannrnvarar	knsnnmnnnskcrkvnr	13	17	8.72593	9.89915	12.44	6.6	2024	1430	24	9	7.00E-07
48	209	236	aaanwmnnnnnnnnnnnadnnnnndaa	tcmtaatt	27	8	115.569	104.259	6.03	5.31	2609	1976	15	10	7.30E-07
49	87	267	kbmmaaankkc	hdaakcbb	11	8	8.52225	8	50.56	51.18	83	82	4	4	7.30E-07
50	208	261	kskrknrrknkvk	kcactcav	13	8	4.55535	105.574	28.65	15.54	476	405	13	6	9.00E-07
51	156	201	kntcrywkcka	vnnbnnnvkcakckr	11	15	2.46783	14.5729	48.24	48.24	87	87	4	4	9.40E-07
52	147	194	rnrkkdknnnnnkdnnnnkknnk	dnkcnkscnrncra	23	14	0.0171907	3.83721	77.31	47.15	95	89	7	4	1.00E-06
53	146	233	cmaamaarmr	yakktakv	10	8	0.120609	124.29	13.11	15.17	480	415	6	6	1.00E-06
54	64	194	raaannrnvarar	dnkcnkscnrncra	13	14	8.72593	3.83721	13.16	14.47	558	435	7	6	1.40E-06
55	201	203	vnnbnnnvkcakckr	vaaanknsvkcnsnr	15	15	14.5729	11.2875	51.43	43.26	102	97	5	4	1.50E-06
56	214	218	kdkcsksmmaw	ksksnnnnkbnkkndnnnnknnk	11	23	8.24224	6.3427	50.93	42.82	103	98	5	4	1.50E-06
57	196	205	kybrnnnnmnnnkscrkh	ynkcdknkmbynkc	18	14	12.6596	8.69747	54.27	40.74	116	103	6	4	1.90E-06
58	196	260	kybrnnnnmnnnkscrkh	ctaatyrh	18	8	12.6596	98.6907	38.86	40.74	108	103	4	4	1.90E-06
59	176	203	awhahawnnnhanwwwhanw	vaaanknsvkcnsnr	20	15	2.12932	11.2875	19.5	21.24	269	247	5	5	2.00E-06
60	247	261	yctstmkc	kcactcav	8	8	114.515	105.574	27.27	13.48	577	467	15	6	2.10E-06
61	180	196	vnaaannnnnnmamamd	kybrnnnnmnnnkscrkh	17	18	98.7525	12.6596	16.42	13.48	639	467	10	6	2.10E-06
62	45	101	kkbkrkcvkc	aawdwnhnnnnaawaaw	10	17	7.71919	37.1278	17.31	20.49	303	256	5	5	2.40E-06
63	150	269	aaaamkkkkk	ntttttrnbnb	10	11	10.9678	11	44.46	38.15	118	110	5	4	2.50E-06
64	41	241	vakhrarhkrk	ccmtttcs	11	8	22.0843	116.042	23.24	20.25	316	259	7	5	2.50E-06
65	74	124	cnkvkakcrkc	aamarmarva	11	10	4.09333	53.1201	31.32	37.47	134	112	4	4	2.70E-06
66	170	240	wnnsakmkannnhk	whastaac	14	8	6.50325	99.0364	20.91	20.02	301	262	6	5	2.70E-06
67	95	122	shynhtkkccka	cdkscakbnks	12	11	6.2064	7.16415	18.28	19.87	287	264	5	5	2.80E-06
68	89	256	aaaawtdrtk	amytarcc	10	8	2.36745	102.757	15.54	12.79	540	492	8	6	2.80E-06
69	178	182	ssnnnnnknnknnsnnknkskc	kdkckrnnndnannnnnnknbnk	22	23	19.3435	3.26998	22.95	19.65	320	267	7	5	3.00E-06
70	64	205	raaannrnvarar	ynkcdknkmbynkc	13	14	8.72593	8.69747	18.57	19.01	339	276	6	5	3.50E-06
71	122	171	cdkscakbnks	kcnkshnrncranns	11	15	7.16415	5.68814	17.6	18.8	298	279	5	5	3.70E-06
72	84	229	aaawnanhantttna	ttaskttt	15	8	5.31045	106.258	18.27	17.96	402	292	7	5	4.60E-06
73	163	253	snnnnncnbnssmnndnnskynks	ccccyhcc	24	8	7.68625	111.806	20.51	17.78	358	295	7	5	4.80E-06
74	85	100	wdwaawnwnaahnnntt	kckmrnnnaandyk	17	14	76.6851	2.20732	31.55	32.28	133	130	4	4	4.90E-06
75	233	270	yakktakv	vamnkrrtbd	8	10	124.29	10	34.76	17.2	332	305	11	5	5.70E-06
76	182	261	kdkckrnnndnannnnnnknbnk	kcactcav	23	8	3.26998	105.574	25.25	17.14	374	306	9	5	5.80E-06
77	45	98	kkbkrkcvkc	skksnnkkkknrd	10	13	7.71919	1.48853	35.21	30.86	149	136	5	4	5.80E-06
78	9	174	bvvhwaaran	kcsrkckvsm	10	10	I_HB_01	8.96466	27.25	29.55	154	142	4	4	7.00E-06
79	194	207	dnkcnkscnrncra	bkssnnknnknnnrkkk	14	17	3.83721	6.40808	21.3	15.8	394	332	8	5	8.70E-06
80	196	212	kybrnnnnmnnnkscrkh	vaaaahnnnnnnnnnnnnvnnnnaaa	18	26	12.6596	96.7282	20.52	15.66	409	335	8	5	9.10E-06
81	146	163	cmaamaarmr	snnnnncnbnssmnndnnskynks	10	24	0.120609	7.68625	13.42	15.43	391	340	5	5	9.80E-06
82	71	268	knnnscnnnnnnnntkkcmanv	nnnyaaad	22	8	11.4903	8	24.98	26.73	168	157	4	4	1.00E-05
83	64	225	raaannrnvarar	mkcrsnndvrkcks	13	14	8.72593	1.65577	25.59	26.07	205	161	5	4	1.20E-05
84	85	220	wdwaawnwnaahnnntt	rmknncrvdarnck	17	14	76.6851	2.19853	27.46	24.54	191	171	5	4	1.50E-05
85	69	178	tktkwktkyb	ssnnnnnknnknnsnnknkskc	10	22	77.704	19.3435	36.54	24.26	201	173	7	4	1.50E-05
86	170	188	wnnsakmkannnhk	aawthkcykb	14	10	6.50325	3.55742	27.76	24.12	189	174	5	4	1.60E-05
87	180	225	vnaaannnnnnmamamd	mkcrsnndvrkcks	17	14	98.7525	1.65577	18.9	23.84	222	176	4	4	1.70E-05
88	81	227	kynkscakcsm	kksnknbdnnnndnnnkckks	11	21	5.18876	16.9015	16.99	13.84	494	379	8	5	1.70E-05
89	187	201	ckctkbkwdns	vnnbnnnvkcakckr	11	15	4.07677	14.5729	17.87	13.7	411	383	7	5	1.70E-05
90	45	64	kkbkrkcvkc	raaannrnvarar	10	13	7.71919	8.72593	16.99	13.59	494	386	8	5	1.80E-05
91	150	268	aaaamkkkkk	nnnyaaad	10	8	10.9678	8	27.18	22.93	193	183	5	4	1.90E-05
92	76	213	aannnnnnraaamnnrwa	kwktnnkwtkbdknt	18	15	49.0637	14.1138	11.42	9.04	919	696	10	6	2.10E-05
93	256	264	amytarcc	aayccktt	8	8	102.757	114.762	18.37	12.46	457	421	8	5	2.80E-05
94	146	259	cmaamaarmr	ckrwwkck	10	8	0.120609	100.498	5.61	7.9	1495	797	8	6	4.60E-05
95	207	220	bkssnnknnknnnrkkk	rmknncrvdarnck	17	14	6.40808	2.19853	14.78	17.49	284	240	4	4	5.70E-05
i	id1	id2	consensus m1	consensus m2	ml1	ml2	map1	map2	r_oc_sp1	r_tr_sp1	n_cooc_all	n_cooc_tr_all	n_cooc_cl	n_cooc_tr_cl	p_binom
Questions? --> kreiman@mit.edu
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