ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ggacgagGUUUUUAGGUAa 5' ||:|||||||| Target 5' caaaaggCAGAAATCCATt 3'	113 - 131	156.00	-13.00
2	miRNA 3' ggaCGAGGUUU----UUAGGUAa 5' | |::||: || |||| Target 5' gtgGATTTAAGAATTAAACCATt 3'	78 - 100	114.00	-6.60
3	miRNA 3' ggaCGAGGUUUUUAGGUAa 5' | | |: ::||||| Target 5' ccaGATGCGTTGGTCCATa 3'	364 - 382	112.00	-8.70

Mutant ID	Mutant Position	Mutant Source
COSN30480536	62	COSMIC
COSN30534644	82	COSMIC
COSN31606250	88	COSMIC
COSN31538182	100	COSMIC
COSN30109323	108	COSMIC
COSN30508817	108	COSMIC
COSN30493175	124	COSMIC
COSN32053869	134	COSMIC
COSN27004423	148	COSMIC
COSN31546363	193	COSMIC
COSN25422805	225	COSMIC
COSN28744083	245	COSMIC
COSN21205028	570	COSMIC
COSN22322017	1037	COSMIC
rs78337240	399	GWAS

Mutant ID	Mutant Position	Mutant Source
rs368352580	10	dbSNP
rs1468613117	14	dbSNP
rs771466002	16	dbSNP
rs1257385209	17	dbSNP
rs1210271221	19	dbSNP
rs745580593	22	dbSNP
rs1298512658	24	dbSNP
rs778674564	30	dbSNP
rs1028712099	33	dbSNP
rs1365769468	34	dbSNP
rs1296682286	43	dbSNP
rs1432616022	48	dbSNP
rs746901254	57	dbSNP
rs949125143	72	dbSNP
rs998213927	77	dbSNP
rs1355837648	80	dbSNP
rs186995427	81	dbSNP
rs773166264	84	dbSNP
rs1328360891	113	dbSNP
rs565484355	121	dbSNP
rs140288196	122	dbSNP
rs768662799	127	dbSNP
rs1441547875	128	dbSNP
rs774137482	129	dbSNP
rs1018823123	134	dbSNP
rs1004662822	137	dbSNP
rs886299680	142	dbSNP
rs1454458159	143	dbSNP
rs1048791991	149	dbSNP
rs937474730	158	dbSNP
rs930362163	163	dbSNP
rs1228979763	171	dbSNP
rs1352061888	173	dbSNP
rs1197509355	177	dbSNP
rs1482210930	184	dbSNP
rs113660412	199	dbSNP
rs1254335004	202	dbSNP
rs1233580057	210	dbSNP
rs1348663592	213	dbSNP
rs1282275776	225	dbSNP
rs1238206688	226	dbSNP
rs1376690264	227	dbSNP
rs182665037	229	dbSNP
rs1393652788	231	dbSNP
rs1359897744	232	dbSNP
rs1055159949	233	dbSNP
rs1336440369	235	dbSNP
rs1434871164	236	dbSNP
rs939007486	238	dbSNP
rs1455666598	239	dbSNP
rs1388064174	243	dbSNP
rs1059218	245	dbSNP
rs1473897210	259	dbSNP
rs978378715	260	dbSNP
rs1421997942	270	dbSNP
rs1181582080	277	dbSNP
rs1255453462	283	dbSNP
rs1211496785	290	dbSNP
rs945509704	291	dbSNP
rs1486062685	299	dbSNP
rs780247231	302	dbSNP
rs1214748916	305	dbSNP
rs1350173788	310	dbSNP
rs1280520758	315	dbSNP
rs1241698219	316	dbSNP
rs1339073994	318	dbSNP
rs192015805	325	dbSNP
rs368722392	328	dbSNP
rs1356842373	332	dbSNP
rs187285308	336	dbSNP
rs954244275	337	dbSNP
rs1266982763	341	dbSNP
rs183514931	347	dbSNP
rs1159922915	353	dbSNP
rs976685011	354	dbSNP
rs965381235	359	dbSNP
rs1331208538	361	dbSNP
rs78452980	362	dbSNP
rs533887228	367	dbSNP
rs556233716	371	dbSNP
rs867217351	372	dbSNP
rs1191527058	375	dbSNP
rs1027879338	377	dbSNP
rs1285301514	384	dbSNP
rs1207088631	390	dbSNP
rs1286157005	391	dbSNP
rs1047464755	396	dbSNP
rs78337240	399	dbSNP
rs1234478247	402	dbSNP
rs367780877	407	dbSNP
rs896261425	410	dbSNP
rs1321369041	414	dbSNP
rs1429484676	416	dbSNP
rs1326499024	423	dbSNP
rs752047653	424	dbSNP
rs745732968	425	dbSNP
rs927471719	440	dbSNP
rs1054916625	444	dbSNP
rs1406268943	451	dbSNP
rs1003208066	459	dbSNP
rs1475149464	467	dbSNP
rs577025920	479	dbSNP
rs1195633673	487	dbSNP
rs759036183	497	dbSNP
rs1214640381	502	dbSNP
rs1185016388	516	dbSNP
rs947634262	517	dbSNP
rs913475409	532	dbSNP
rs1339541629	540	dbSNP
rs558806193	546	dbSNP
rs1042649826	553	dbSNP
rs1230645430	560	dbSNP
rs988810606	565	dbSNP
rs1326155267	566	dbSNP
rs933303021	567	dbSNP
rs75527287	570	dbSNP
rs770708911	571	dbSNP
rs1486582004	576	dbSNP
rs1054321974	577	dbSNP
rs1169660673	578	dbSNP
rs571211433	585	dbSNP
rs1016521923	589	dbSNP
rs1394765960	592	dbSNP
rs373645660	593	dbSNP
rs548295895	594	dbSNP
rs976842288	596	dbSNP
rs1204466866	597	dbSNP
rs1291846593	605	dbSNP
rs1438857952	609	dbSNP
rs867454791	610	dbSNP
rs965338232	614	dbSNP
rs535914380	615	dbSNP
rs1198169764	622	dbSNP
rs908524082	623	dbSNP
rs982766855	628	dbSNP
rs1298616439	629	dbSNP
rs896167945	635	dbSNP
rs1278699251	636	dbSNP
rs1442846866	638	dbSNP
rs368431407	642	dbSNP
rs867006356	643	dbSNP
rs1027581727	648	dbSNP
rs1293433059	660	dbSNP
rs1374891389	662	dbSNP
rs903567589	664	dbSNP
rs1455708081	666	dbSNP
rs1378887561	668	dbSNP
rs1176916002	669	dbSNP
rs995071276	670	dbSNP
rs959274538	679	dbSNP
rs1235168323	691	dbSNP
rs1437851779	693	dbSNP
rs1485087301	697	dbSNP
rs1280358585	714	dbSNP
rs1033410120	715	dbSNP
rs1350970700	718	dbSNP
rs1283314033	728	dbSNP
rs868035727	731	dbSNP
rs867955108	732	dbSNP
rs1414064344	741	dbSNP
rs147153186	743	dbSNP
rs1313515308	752	dbSNP
rs550267567	753	dbSNP
rs1042051448	754	dbSNP
rs1158637703	758	dbSNP
rs1401693408	761	dbSNP
rs933542975	766	dbSNP
rs1009237757	767	dbSNP
rs1190546656	770	dbSNP
rs894013542	783	dbSNP
rs532857237	784	dbSNP
rs1189379681	785	dbSNP
rs1270982415	789	dbSNP
rs1241223430	792	dbSNP
rs565211315	793	dbSNP
rs1202680880	800	dbSNP
rs766051149	814	dbSNP
rs1341234458	820	dbSNP
rs1287405415	821	dbSNP
rs1232635067	822	dbSNP
rs1335321756	824	dbSNP
rs932808250	827	dbSNP
rs1293996403	830	dbSNP
rs760474034	839	dbSNP
rs546819189	842	dbSNP
rs1416762302	856	dbSNP
rs1359920236	857	dbSNP
rs528648699	858	dbSNP
rs1041213260	860	dbSNP
rs943484579	864	dbSNP
rs1461394405	867	dbSNP
rs1167736651	870	dbSNP
rs1275557660	871	dbSNP
rs1260402793	879	dbSNP
rs944104070	884	dbSNP
rs909297506	890	dbSNP
rs561088332	894	dbSNP
rs908638047	914	dbSNP
rs1310485604	917	dbSNP
rs113663369	918	dbSNP
rs1220299450	925	dbSNP
rs1468738204	937	dbSNP
rs950567251	941	dbSNP
rs1216699965	948	dbSNP
rs868488590	951	dbSNP
rs1026123457	958	dbSNP
rs931366106	959	dbSNP
rs920505911	963	dbSNP
rs1321568003	965	dbSNP
rs973368181	971	dbSNP
rs371062651	974	dbSNP
rs959454543	975	dbSNP
rs1328574122	978	dbSNP
rs10917034	981	dbSNP
rs368701503	982	dbSNP
rs1308235785	994	dbSNP
rs748123518	996	dbSNP
rs1012185265	1000	dbSNP
rs1192613059	1000	dbSNP
rs970425460	1002	dbSNP
rs1254596521	1007	dbSNP
rs1194036723	1011	dbSNP
rs563714151	1014	dbSNP
rs1375416216	1022	dbSNP
rs1250846766	1042	dbSNP
rs1053190343	1043	dbSNP
rs891974750	1043	dbSNP
rs192131755	1048	dbSNP
rs1433272658	1055	dbSNP
rs1009636365	1058	dbSNP
rs893510356	1060	dbSNP
rs933585034	1063	dbSNP
rs1306027914	1065	dbSNP
rs1390170336	1070	dbSNP
rs577092432	1078	dbSNP
rs1032986433	1079	dbSNP
rs1288155631	1094	dbSNP
rs1463129192	1096	dbSNP
rs1373063569	1098	dbSNP
rs1179951451	1103	dbSNP
rs1434907998	1104	dbSNP
rs1396668799	1105	dbSNP
rs1482592274	1115	dbSNP
rs200312469	1116	dbSNP
rs397727492	1117	dbSNP
rs558873622	1117	dbSNP
rs1178851348	1119	dbSNP

- Nature methods, 2011

Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.