Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
143	0.008308	0.2033	b2049	cpsB	-11.81	0.062535	184 -- 242	25 -- 78	mannose-1-phosphate guanyltransferase	_____________183_______________________________________________________________243\n_____________\|_________________________________________________________________\|\n5'-ACA...UAAAU____U_______U____A_______A________CUCUAUCCA__________________U___UCCGG...GCC-3'\n______________GAUA_UCGGGGA_AAUU_UGGC_GC_GUCG_AAA_________GUUGUGAUG____GCAGG_GGC\n______________:\|:\|_:\|:\|\|\|\|_\|\|\|:_\|\|\|\|_\|\|_\|:\|\|_\|\|\|_________:\|\|:\|\|\|\|\|____:\|\|:\|_\|\|\|\n______________UUGU_GGUCCCU_UUAG_ACCG_CG_CGGC_UUU_________UAAUACUAC____UGUUC_CCG\n3'-UUU...CGCGG_________________A____A_______A___AA________________UCAA_________UGUCG...GUG-5'\n_____________\|_________________________________________________________________\|\n_____________79________________________________________________________________24\n	227 -- 233	37 -- 43	-41.0645 kcal/mol	15.3492 kcal/mol	13.8987 kcal/mol	183 243@LB@ \| \|@LB@5'-ACA...UAAAU U U A A CUCUAUCCA U UCCGG...GCC-3'@LB@ GAUA UCGGGGA AAUU UGGC GC GUCG AAA GUUGUGAUG GCAGG GGC@LB@ :\|:\| :\|:\|\|\|\| \|\|\|: \|\|\|\| \|\| \|:\|\| \|\|\| :\|\|:\|\|\|\|\| :\|\|:\| \|\|\|@LB@ UUGU GGUCCCU UUAG ACCG CG CGGC UUU UAAUACUAC UGUUC CCG@LB@3'-UUU...CGCGG A A A AA UCAA UGUCG...GUG-5'@LB@ \| \|@LB@ 79 24@LB@@LB@@LB@Energy -11.81 kcal/mol@LB@Hybridization Energy -41.0645 kcal/mol@LB@Unfolding Energy - mRNA 15.3492 kcal/mol@LB@Unfolding Energy - sRNA 13.8987 kcal/mol@LB@@LB@Position - mRNA 184 -- 242@LB@Position - sRNA 25 -- 78@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 37 -- 43@LB@
153	0.009069	0.2059	b3529	yhjK	-8.15	0.299018	186 -- 212	47 -- 74	cyclic-di-GMP phosphodiesterase	_____________185__________________________213\n_____________\|____________________________\|\n5'-AGC...GAUUU_________GACAAU_____________CGCUC...AUC-3'\n______________CCGGGGGGA______UUGCG_CGUAAGU\n______________\|\|:\|\|\|::\|______:\|\|\|\|_\|\|\|\|\|:\|\n______________GGUCCCUUU______GACGC_GCAUUUA\n3'-UUU...GUUGU_________AGAACC_____G_______AUAAU...GUG-5'\n_____________\|____________________________\|\n_____________75___________________________46\n	187 -- 193	67 -- 73	-27.1977 kcal/mol	10.2409 kcal/mol	8.80319 kcal/mol	185 213@LB@ \| \|@LB@5'-AGC...GAUUU GACAAU CGCUC...AUC-3'@LB@ CCGGGGGGA UUGCG CGUAAGU@LB@ \|\|:\|\|\|::\| :\|\|\|\| \|\|\|\|\|:\|@LB@ GGUCCCUUU GACGC GCAUUUA@LB@3'-UUU...GUUGU AGAACC G AUAAU...GUG-5'@LB@ \| \|@LB@ 75 46@LB@@LB@@LB@Energy -8.15 kcal/mol@LB@Hybridization Energy -27.1977 kcal/mol@LB@Unfolding Energy - mRNA 10.2409 kcal/mol@LB@Unfolding Energy - sRNA 8.80319 kcal/mol@LB@@LB@Position - mRNA 186 -- 212@LB@Position - sRNA 47 -- 74@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 67 -- 73@LB@
164	0.009677	0.2068	b1956	yedQ	-11.74	0.064514	187 -- 209	18 -- 41	putative membrane-anchored diguanylate cyclase	_____________186______________________210\n_____________\|________________________\|\n5'-GAG...CAGGU________CGUC____________GAGAC...UAU-3'\n______________UGG_GAGU____AGGGUGCAGCAC\n______________\|\|:_\|\|\|\|____\|\|\|\|::\|\|\|\|\|\|\n______________ACU_CUCA____UCCCGUGUCGUG\n3'-UUU...AUAAU___A____AUGU____________ACAAA...GUG-5'\n_____________\|________________________\|\n_____________42_______________________17\n	203 -- 209	18 -- 24	-27.1151 kcal/mol	6.50018 kcal/mol	8.87585 kcal/mol	186 210@LB@ \| \|@LB@5'-GAG...CAGGU CGUC GAGAC...UAU-3'@LB@ UGG GAGU AGGGUGCAGCAC@LB@ \|\|: \|\|\|\| \|\|\|\|::\|\|\|\|\|\|@LB@ ACU CUCA UCCCGUGUCGUG@LB@3'-UUU...AUAAU A AUGU ACAAA...GUG-5'@LB@ \| \|@LB@ 42 17@LB@@LB@@LB@Energy -11.74 kcal/mol@LB@Hybridization Energy -27.1151 kcal/mol@LB@Unfolding Energy - mRNA 6.50018 kcal/mol@LB@Unfolding Energy - sRNA 8.87585 kcal/mol@LB@@LB@Position - mRNA 187 -- 209@LB@Position - sRNA 18 -- 41@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 18 -- 24@LB@
198	0.01217	0.2164	b1236	galU	-11.62	0.068156	187 -- 208	56 -- 74	glucose-1-phosphate uridylyltransferase	_____________186____________________209\n_____________\|______________________\|\n5'-CAA...ACAGU_____A______AAA_______CAUUA...UGC-3'\n______________CCAGG_GAAUUU___UGGCUGC\n______________\|\|\|\|\|_:\|\|\|:\|___\|\|\|\|\|\|\|\n______________GGUCC_UUUAGA___ACCGACG\n3'-UUU...GUUGU_____C________________CGGCA...GUG-5'\n_____________\|______________________\|\n_____________75_____________________55\n	202 -- 208	56 -- 62	-24.2568 kcal/mol	4.50323 kcal/mol	8.13729 kcal/mol	186 209@LB@ \| \|@LB@5'-CAA...ACAGU A AAA CAUUA...UGC-3'@LB@ CCAGG GAAUUU UGGCUGC@LB@ \|\|\|\|\| :\|\|\|:\| \|\|\|\|\|\|\|@LB@ GGUCC UUUAGA ACCGACG@LB@3'-UUU...GUUGU C CGGCA...GUG-5'@LB@ \| \|@LB@ 75 55@LB@@LB@@LB@Energy -11.62 kcal/mol@LB@Hybridization Energy -24.2568 kcal/mol@LB@Unfolding Energy - mRNA 4.50323 kcal/mol@LB@Unfolding Energy - sRNA 8.13729 kcal/mol@LB@@LB@Position - mRNA 187 -- 208@LB@Position - sRNA 56 -- 74@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 56 -- 62@LB@
171	0.01011	0.2071	b4086	alsC	-10.38	0.118114	189 -- 207	53 -- 70	D-allose ABC transporter permease	_____________188_________________208\n_____________\|___________________\|\n5'-CGC...GAAGA_______A____A__G___UUACC...CGA-3'\n______________GGAGAUU_UGGC_UG_GCU\n______________\|\|\|:\|\|:_\|\|\|\|_\|\|_\|\|:\n______________CCUUUAG_ACCG_AC_CGG\n3'-UUU...UGGUC_______A_______G___CAUUU...GUG-5'\n_____________\|___________________\|\n_____________71__________________52\n	189 -- 195	64 -- 70	-21.9341 kcal/mol	4.72392 kcal/mol	6.83419 kcal/mol	188 208@LB@ \| \|@LB@5'-CGC...GAAGA A A G UUACC...CGA-3'@LB@ GGAGAUU UGGC UG GCU@LB@ \|\|\|:\|\|: \|\|\|\| \|\| \|\|:@LB@ CCUUUAG ACCG AC CGG@LB@3'-UUU...UGGUC A G CAUUU...GUG-5'@LB@ \| \|@LB@ 71 52@LB@@LB@@LB@Energy -10.38 kcal/mol@LB@Hybridization Energy -21.9341 kcal/mol@LB@Unfolding Energy - mRNA 4.72392 kcal/mol@LB@Unfolding Energy - sRNA 6.83419 kcal/mol@LB@@LB@Position - mRNA 189 -- 207@LB@Position - sRNA 53 -- 70@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 64 -- 70@LB@
25	0.001541	0.1727	b1948	fliP	-12.25	0.051366	190 -- 216	44 -- 71	flagellar biosynthesis protein	_____________189__________________________217\n_____________\|____________________________\|\n5'-AUU...GUAGC________C__A_________UU_____CUGUC...GCG-3'\n______________GGGAGAUC_UG__UGCGUCGU__AUUGU\n______________\|\|\|\|:\|\|\|_\|\|__\|\|\|\|:\|\|\|__\|\|\|:\|\n______________CCCUUUAG_AC__ACGCGGCA__UAAUA\n3'-UUU...GUGGU________A__CG________UU_____AUACU...GUG-5'\n_____________\|____________________________\|\n_____________72___________________________43\n	203 -- 209	51 -- 57	-29.2591 kcal/mol	10.1171 kcal/mol	6.89657 kcal/mol	189 217@LB@ \| \|@LB@5'-AUU...GUAGC C A UU CUGUC...GCG-3'@LB@ GGGAGAUC UG UGCGUCGU AUUGU@LB@ \|\|\|\|:\|\|\| \|\| \|\|\|\|:\|\|\| \|\|\|:\|@LB@ CCCUUUAG AC ACGCGGCA UAAUA@LB@3'-UUU...GUGGU A CG UU AUACU...GUG-5'@LB@ \| \|@LB@ 72 43@LB@@LB@@LB@Energy -12.25 kcal/mol@LB@Hybridization Energy -29.2591 kcal/mol@LB@Unfolding Energy - mRNA 10.1171 kcal/mol@LB@Unfolding Energy - sRNA 6.89657 kcal/mol@LB@@LB@Position - mRNA 190 -- 216@LB@Position - sRNA 44 -- 71@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 51 -- 57@LB@
133	0.007533	0.1993	b2194	ccmH	-11.64	0.067570	191 -- 199	1 -- 9	heme lyase CcmH subunit	_____________190_______200\n_____________\|_________\|\n5'-CUG...UAAGG_________AAUGA...AGU-3'\n______________AGGCCGCAC\n______________\|\|\|\|\|\|\|\|\|\n______________UCCGGCGUG\n3'-UUU...AAAAG_________-5'\n_____________\|________\|\n_____________10_______1\n	193 -- 199	1 -- 7	-19.8862 kcal/mol	2.96679 kcal/mol	5.10726 kcal/mol	190 200@LB@ \| \|@LB@5'-CUG...UAAGG AAUGA...AGU-3'@LB@ AGGCCGCAC@LB@ \|\|\|\|\|\|\|\|\|@LB@ UCCGGCGUG@LB@3'-UUU...AAAAG -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -11.64 kcal/mol@LB@Hybridization Energy -19.8862 kcal/mol@LB@Unfolding Energy - mRNA 2.96679 kcal/mol@LB@Unfolding Energy - sRNA 5.10726 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 1 -- 7@LB@
80	0.004451	0.1855	b3578	yiaN	-12.19	0.052777	198 -- 212	52 -- 66	2 3-diketo-L-gulonate TRAP transporter large permease protein	_____________197_____________213\n_____________\|_______________\|\n5'-GGC...GCUUA___A___________AUUUU...UCU-3'\n______________AUC_UGGCUGUGCUG\n______________\|\|\|_\|\|\|\|\|\|:\|\|:\|\n______________UAG_ACCGACGCGGC\n3'-UUU...CCCUU___A___________AUUUA...GUG-5'\n_____________\|_______________\|\n_____________67______________51\n	206 -- 212	52 -- 58	-22.6247 kcal/mol	3.67694 kcal/mol	6.76246 kcal/mol	197 213@LB@ \| \|@LB@5'-GGC...GCUUA A AUUUU...UCU-3'@LB@ AUC UGGCUGUGCUG@LB@ \|\|\| \|\|\|\|\|\|:\|\|:\|@LB@ UAG ACCGACGCGGC@LB@3'-UUU...CCCUU A AUUUA...GUG-5'@LB@ \| \|@LB@ 67 51@LB@@LB@@LB@Energy -12.19 kcal/mol@LB@Hybridization Energy -22.6247 kcal/mol@LB@Unfolding Energy - mRNA 3.67694 kcal/mol@LB@Unfolding Energy - sRNA 6.76246 kcal/mol@LB@@LB@Position - mRNA 198 -- 212@LB@Position - sRNA 52 -- 66@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 52 -- 58@LB@
176	0.01044	0.208	b0933	ssuB	-9.69	0.158756	203 -- 226	69 -- 90	aliphatic sulfonate ABC transporter ATPase	_____________202______________________227\n_____________\|________________________\|\n5'-AUU...GGUAU_________UC___UGA_______CACGC...AUA-3'\n______________GAAUACUGC__GUC___ACCAGGG\n______________\|\|\|\|\|\|\|\|\|__\|:\|___\|\|\|\|\|\|\|\n______________CUUAUGACG__CGG___UGGUCCC\n3'-UUU...ACGCG______________UUG_______UUUAG...GUG-5'\n_____________\|________________________\|\n_____________91_______________________68\n	220 -- 226	69 -- 75	-28.101 kcal/mol	8.24441 kcal/mol	10.1628 kcal/mol	202 227@LB@ \| \|@LB@5'-AUU...GGUAU UC UGA CACGC...AUA-3'@LB@ GAAUACUGC GUC ACCAGGG@LB@ \|\|\|\|\|\|\|\|\| \|:\| \|\|\|\|\|\|\|@LB@ CUUAUGACG CGG UGGUCCC@LB@3'-UUU...ACGCG UUG UUUAG...GUG-5'@LB@ \| \|@LB@ 91 68@LB@@LB@@LB@Energy -9.69 kcal/mol@LB@Hybridization Energy -28.101 kcal/mol@LB@Unfolding Energy - mRNA 8.24441 kcal/mol@LB@Unfolding Energy - sRNA 10.1628 kcal/mol@LB@@LB@Position - mRNA 203 -- 226@LB@Position - sRNA 69 -- 90@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 69 -- 75@LB@
34	0.001871	0.1727	b4485	ytfR	-15.36	0.012458	204 -- 227	64 -- 86	putative sugar ABC transporter ATPase	_____________203_______________________228\n_____________\|_________________________\|\n5'-CCU...CCAUG__GAC__A_________________CUCCG...GCC-3'\n______________AC___CG_CCAACACCA_GGAGAUC\n______________\|\|___\|\|_\|\|\|\|\|\|\|\|\|_\|\|\|:\|\|\|\n______________UG___GC_GGUUGUGGU_CCUUUAG\n3'-UUU...GCUUA__AC_____________C_______AACCG...GUG-5'\n_____________\|_________________________\|\n_____________87________________________63\n	221 -- 227	64 -- 70	-26.9267 kcal/mol	4.18191 kcal/mol	7.38435 kcal/mol	203 228@LB@ \| \|@LB@5'-CCU...CCAUG GAC A CUCCG...GCC-3'@LB@ AC CG CCAACACCA GGAGAUC@LB@ \|\| \|\| \|\|\|\|\|\|\|\|\| \|\|\|:\|\|\|@LB@ UG GC GGUUGUGGU CCUUUAG@LB@3'-UUU...GCUUA AC C AACCG...GUG-5'@LB@ \| \|@LB@ 87 63@LB@@LB@@LB@Energy -15.36 kcal/mol@LB@Hybridization Energy -26.9267 kcal/mol@LB@Unfolding Energy - mRNA 4.18191 kcal/mol@LB@Unfolding Energy - sRNA 7.38435 kcal/mol@LB@@LB@Position - mRNA 204 -- 227@LB@Position - sRNA 64 -- 86@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 64 -- 70@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)

Job resubmission

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service.

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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