Input and runtime details for job 6793193 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation
76	0.003141	0.1452	b0187	yaeR	-8.98	0.354982	261 -- 292	48 -- 78	putative lyase	_____________260_______________________________293\n_____________\|_________________________________\|\n5'-AAA...UGAGC_______UUC___U_____AU__UUG_______GCUGCAAA-3'\n______________AAAG_CU___UAC_GCGAU__UC___GUUUCAC\n______________\|\|\|\|_\|\|___:\|\|_\|\|:\|\|__\|\|___\|\|\|\|\|\|\|\n______________UUUC_GA___GUG_CGUUA__AG___CAAAGUG\n3'-UUU...ACCCG____U__UGU___U_________CAA_______AGUCC...GCA-5'\n_____________\|_________________________________\|\n_____________79________________________________47\n	286 -- 292	48 -- 54	-17.4111 kcal/mol	4.74942 kcal/mol	3.68736 kcal/mol	260 293@LB@ \| \|@LB@5'-AAA...UGAGC UUC U AU UUG GCUGCAAA-3'@LB@ AAAG CU UAC GCGAU UC GUUUCAC@LB@ \|\|\|\| \|\| :\|\| \|\|:\|\| \|\| \|\|\|\|\|\|\|@LB@ UUUC GA GUG CGUUA AG CAAAGUG@LB@3'-UUU...ACCCG U UGU U CAA AGUCC...GCA-5'@LB@ \| \|@LB@ 79 47@LB@@LB@@LB@Energy -8.98 kcal/mol@LB@Hybridization Energy -17.4111 kcal/mol@LB@Unfolding Energy - mRNA 4.74942 kcal/mol@LB@Unfolding Energy - sRNA 3.68736 kcal/mol@LB@@LB@Position - mRNA 261 -- 292@LB@Position - sRNA 48 -- 78@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 48 -- 54@LB@
154	0.007512	0.1668	b2180	yejF	-18.70	0.001576	262 -- 293	44 -- 72	microcin C ABC transporter ATPase	_____________261______________________________294\n_____________\|________________________________\|\n5'-GAC...AACCG_____________CAA__A_________A___AUUGAGG-3'\n______________UACGUACAGUAGU___UG_UGUUUCACU_CAG\n______________\|\|\|::\|\|\|\|:\|:\|___:\|_\|\|\|\|\|\|\|\|\|_\|\|\|\n______________AUGUGUGUCGUUA___GC_ACAAAGUGA_GUC\n3'-UUU...UUCUG_____________A____A_____________CCCUA...GCA-5'\n_____________\|________________________________\|\n_____________73_______________________________43\n	283 -- 289	47 -- 53	-27.8629 kcal/mol	5.03502 kcal/mol	4.12429 kcal/mol	261 294@LB@ \| \|@LB@5'-GAC...AACCG CAA A A AUUGAGG-3'@LB@ UACGUACAGUAGU UG UGUUUCACU CAG@LB@ \|\|\|::\|\|\|\|:\|:\| :\| \|\|\|\|\|\|\|\|\| \|\|\|@LB@ AUGUGUGUCGUUA GC ACAAAGUGA GUC@LB@3'-UUU...UUCUG A A CCCUA...GCA-5'@LB@ \| \|@LB@ 73 43@LB@@LB@@LB@Energy -18.70 kcal/mol@LB@Hybridization Energy -27.8629 kcal/mol@LB@Unfolding Energy - mRNA 5.03502 kcal/mol@LB@Unfolding Energy - sRNA 4.12429 kcal/mol@LB@@LB@Position - mRNA 262 -- 293@LB@Position - sRNA 44 -- 72@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 47 -- 53@LB@
167	0.008121	0.1711	b2603	yfiR	-9.52	0.293133	262 -- 278	35 -- 51	putative periplasmic inhibitor of YfiN activity	_____________261_______________279\n_____________\|_________________\|\n5'-GUA...AAUAC_________A_CC____GACGU...GUA-3'\n______________UCGCUCAGG_G__UUCU\n______________\|\|:\|\|\|\|\|\|_\|__\|\|\|:\n______________AGUGAGUCC_C__AAGG\n3'-UUU...AACAA_________C_UA____UACGA...GCA-5'\n_____________\|_________________\|\n_____________52________________34\n	264 -- 270	43 -- 49	-18.1931 kcal/mol	6.80204 kcal/mol	1.87111 kcal/mol	261 279@LB@ \| \|@LB@5'-GUA...AAUAC A CC GACGU...GUA-3'@LB@ UCGCUCAGG G UUCU@LB@ \|\|:\|\|\|\|\|\| \| \|\|\|:@LB@ AGUGAGUCC C AAGG@LB@3'-UUU...AACAA C UA UACGA...GCA-5'@LB@ \| \|@LB@ 52 34@LB@@LB@@LB@Energy -9.52 kcal/mol@LB@Hybridization Energy -18.1931 kcal/mol@LB@Unfolding Energy - mRNA 6.80204 kcal/mol@LB@Unfolding Energy - sRNA 1.87111 kcal/mol@LB@@LB@Position - mRNA 262 -- 278@LB@Position - sRNA 35 -- 51@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 43 -- 49@LB@
151	0.007209	0.1668	b0968	yccX	-9.35	0.311742	266 -- 274	62 -- 70	weak acylphosphatase	_____________265_______275\n_____________\|_________\|\n5'-GGC...UACAC_________CGAAG...CCG-3'\n______________CACACAGUA\n______________\|\|\|\|\|\|\|:\|\n______________GUGUGUCGU\n3'-UUU...CUGAU_________UAAGC...GCA-5'\n_____________\|_________\|\n_____________71________61\n	268 -- 274	62 -- 68	-13.335 kcal/mol	0.836274 kcal/mol	3.14945 kcal/mol	265 275@LB@ \| \|@LB@5'-GGC...UACAC CGAAG...CCG-3'@LB@ CACACAGUA@LB@ \|\|\|\|\|\|\|:\|@LB@ GUGUGUCGU@LB@3'-UUU...CUGAU UAAGC...GCA-5'@LB@ \| \|@LB@ 71 61@LB@@LB@@LB@Energy -9.35 kcal/mol@LB@Hybridization Energy -13.335 kcal/mol@LB@Unfolding Energy - mRNA 0.836274 kcal/mol@LB@Unfolding Energy - sRNA 3.14945 kcal/mol@LB@@LB@Position - mRNA 266 -- 274@LB@Position - sRNA 62 -- 70@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 62 -- 68@LB@
39	0.0006857	0.06187	b1305	pspB	-16.08	0.010660	268 -- 296	48 -- 75	psp operon transcription co-activator	_____________267____________________________297\n_____________\|______________________________\|\n5'-AUU...GUUAU_______U______________CUGG____AGUG-3'\n______________GGCUGCA_UACAGCAAU_CGUU____UCGC\n______________\|:\|\|:\|\|_:\|\|\|\|\|\|\|\|_\|\|\|\|____\|\|:\|\n______________CUGAUGU_GUGUCGUUA_GCAA____AGUG\n3'-UUU...CGUUU_________________A____CAA_____AGUCC...GCA-5'\n_____________\|______________________________\|\n_____________76_____________________________47\n	278 -- 284	60 -- 66	-29.5086 kcal/mol	9.74074 kcal/mol	3.68696 kcal/mol	267 297@LB@ \| \|@LB@5'-AUU...GUUAU U CUGG AGUG-3'@LB@ GGCUGCA UACAGCAAU CGUU UCGC@LB@ \|:\|\|:\|\| :\|\|\|\|\|\|\|\| \|\|\|\| \|\|:\|@LB@ CUGAUGU GUGUCGUUA GCAA AGUG@LB@3'-UUU...CGUUU A CAA AGUCC...GCA-5'@LB@ \| \|@LB@ 76 47@LB@@LB@@LB@Energy -16.08 kcal/mol@LB@Hybridization Energy -29.5086 kcal/mol@LB@Unfolding Energy - mRNA 9.74074 kcal/mol@LB@Unfolding Energy - sRNA 3.68696 kcal/mol@LB@@LB@Position - mRNA 268 -- 296@LB@Position - sRNA 48 -- 75@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 60 -- 66@LB@
31	0.0004964	0.05552	b2325	yfcL	-14.31	0.031288	272 -- 297	32 -- 57	uncharacterized protein	_____________271__________________________298\n_____________\|____________________________\|\n5'-AAC...GAUGA______________U___U____G____GCC-3'\n______________GUUGUUU_GC_CAG_GGG_AUUU_CGUG\n______________\|\|\|\|\|\|\|_:\|_\|\|\|_\|\|\|_\|\|\|\|_\|:\|\|\n______________CAACAAA_UG_GUC_CCC_UAAA_GUAC\n3'-UUU...UUAAG_______G__A____________G____GAAUA...GCA-5'\n_____________\|____________________________\|\n_____________58___________________________31\n	272 -- 278	51 -- 57	-23.7407 kcal/mol	4.96676 kcal/mol	4.4642 kcal/mol	271 298@LB@ \| \|@LB@5'-AAC...GAUGA U U G GCC-3'@LB@ GUUGUUU GC CAG GGG AUUU CGUG@LB@ \|\|\|\|\|\|\| :\| \|\|\| \|\|\| \|\|\|\| \|:\|\|@LB@ CAACAAA UG GUC CCC UAAA GUAC@LB@3'-UUU...UUAAG G A G GAAUA...GCA-5'@LB@ \| \|@LB@ 58 31@LB@@LB@@LB@Energy -14.31 kcal/mol@LB@Hybridization Energy -23.7407 kcal/mol@LB@Unfolding Energy - mRNA 4.96676 kcal/mol@LB@Unfolding Energy - sRNA 4.4642 kcal/mol@LB@@LB@Position - mRNA 272 -- 297@LB@Position - sRNA 32 -- 57@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 51 -- 57@LB@
132	0.005915	0.1577	b3356	yhfA	-11.83	0.112173	273 -- 293	39 -- 71	OsmC family protein	_____________272_______________________________294\n_____________\|_________________________________\|\n5'-CUG...UUUUA___G_________________________C___AAAGCAC-3'\n______________AUG_ACGGCA____________ACUCAGG_GAU\n______________\|::_\|\|:\|\|\|____________\|\|\|\|\|\|\|_\|\|\|\n______________UGU_UGUCGU____________UGAGUCC_CUA\n3'-UUU...UCUGA___G______UAAGCAACAAAG_______C___AAGGU...GCA-5'\n_____________\|_________________________________\|\n_____________72________________________________38\n	283 -- 289	43 -- 49	-20.9729 kcal/mol	4.393 kcal/mol	4.74947 kcal/mol	272 294@LB@ \| \|@LB@5'-CUG...UUUUA G C AAAGCAC-3'@LB@ AUG ACGGCA ACUCAGG GAU@LB@ \|:: \|\|:\|\|\| \|\|\|\|\|\|\| \|\|\|@LB@ UGU UGUCGU UGAGUCC CUA@LB@3'-UUU...UCUGA G UAAGCAACAAAG C AAGGU...GCA-5'@LB@ \| \|@LB@ 72 38@LB@@LB@@LB@Energy -11.83 kcal/mol@LB@Hybridization Energy -20.9729 kcal/mol@LB@Unfolding Energy - mRNA 4.393 kcal/mol@LB@Unfolding Energy - sRNA 4.74947 kcal/mol@LB@@LB@Position - mRNA 273 -- 293@LB@Position - sRNA 39 -- 71@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 43 -- 49@LB@
40	0.0008945	0.07693	b0525	ppiB	-7.31	0.578113	284 -- 298	61 -- 76	peptidyl-prolyl cis-trans isomerase B (rotamase B)	_____________283______________299\n_____________\|________________\|\n5'-UGU...UUCCU___________C____AG-3'\n______________GGACUAC_UGC_GCGA\n______________:\|\|\|\|\|\|_::\|_\|\|:\|\n______________UCUGAUG_GUG_CGUU\n3'-UUU...CCGUU_______U___U____AAGCA...GCA-5'\n_____________\|________________\|\n_____________77_______________60\n	284 -- 290	70 -- 76	-14.2171 kcal/mol	3.65067 kcal/mol	3.25604 kcal/mol	283 299@LB@ \| \|@LB@5'-UGU...UUCCU C AG-3'@LB@ GGACUAC UGC GCGA@LB@ :\|\|\|\|\|\| ::\| \|\|:\|@LB@ UCUGAUG GUG CGUU@LB@3'-UUU...CCGUU U U AAGCA...GCA-5'@LB@ \| \|@LB@ 77 60@LB@@LB@@LB@Energy -7.31 kcal/mol@LB@Hybridization Energy -14.2171 kcal/mol@LB@Unfolding Energy - mRNA 3.65067 kcal/mol@LB@Unfolding Energy - sRNA 3.25604 kcal/mol@LB@@LB@Position - mRNA 284 -- 298@LB@Position - sRNA 61 -- 76@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 70 -- 76@LB@
165	0.007934	0.1692	b3355	prkB	-7.13	0.603515	287 -- 294	63 -- 70	putative phosphoribulokinase	_____________286______295\n_____________\|________\|\n5'-GGC...AUAUU________UAAAUC-3'\n______________CGCGCAGU\n______________\|:\|:\|\|\|:\n______________GUGUGUCG\n3'-UUU...CUGAU________UUAAG...GCA-5'\n_____________\|________\|\n_____________71_______62\n	288 -- 294	63 -- 69	-11.0055 kcal/mol	0.741841 kcal/mol	3.13161 kcal/mol	286 295@LB@ \| \|@LB@5'-GGC...AUAUU UAAAUC-3'@LB@ CGCGCAGU@LB@ \|:\|:\|\|\|:@LB@ GUGUGUCG@LB@3'-UUU...CUGAU UUAAG...GCA-5'@LB@ \| \|@LB@ 71 62@LB@@LB@@LB@Energy -7.13 kcal/mol@LB@Hybridization Energy -11.0055 kcal/mol@LB@Unfolding Energy - mRNA 0.741841 kcal/mol@LB@Unfolding Energy - sRNA 3.13161 kcal/mol@LB@@LB@Position - mRNA 287 -- 294@LB@Position - sRNA 63 -- 70@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 63 -- 69@LB@
121	0.005439	0.1553	b1640	anmK	-7.89	0.496680	290 -- 297	63 -- 70	anhydro-N-acetylmuramic acid kinase	_____________289______298\n_____________\|________\|\n5'-CCA...CGGGU________UGG-3'\n______________CGCACAGC\n______________\|:\|\|\|\|\|\|\n______________GUGUGUCG\n3'-UUU...CUGAU________UUAAG...GCA-5'\n_____________\|________\|\n_____________71_______62\n	291 -- 297	63 -- 69	-13.0848 kcal/mol	2.06561 kcal/mol	3.13161 kcal/mol	289 298@LB@ \| \|@LB@5'-CCA...CGGGU UGG-3'@LB@ CGCACAGC@LB@ \|:\|\|\|\|\|\|@LB@ GUGUGUCG@LB@3'-UUU...CUGAU UUAAG...GCA-5'@LB@ \| \|@LB@ 71 62@LB@@LB@@LB@Energy -7.89 kcal/mol@LB@Hybridization Energy -13.0848 kcal/mol@LB@Unfolding Energy - mRNA 2.06561 kcal/mol@LB@Unfolding Energy - sRNA 3.13161 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 63 -- 70@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 63 -- 69@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

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When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

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