Input and runtime details for job 3202356 (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 3202356 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:02 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:35 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:03:47 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:03:55 CET 2018
	Job Completed		@ Sat Feb 17 02:04:28 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

Description of the job

GcvB

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_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

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
78	0.003685	0.1596	stm0423	ispA	-20.49	0.014403	269 -- 289	38 -- 58	(2E 6E)-farnesyl diphosphate synthase	_____________268____________________290\n_____________\|______________________\|\n5'-UGA...AUCGC____CU_____UU_________UCCCG...UCG-3'\n______________GCCA___GCCC__UCAGAACAC\n______________\|\|\|\|___\|\|\|\|__\|\|\|\|\|\|\|\|\|\n______________CGGU___CGGG__AGUCUUGUG\n3'-UUU...GCAUU____UUU____U__________CGUAA...UCA-5'\n_____________\|______________________\|\n_____________59_____________________37\n	281 -- 287	40 -- 46	-28.5082 kcal/mol	2.40221 kcal/mol	13.7699 kcal/mol	268 290@LB@ \| \|@LB@5'-UGA...AUCGC CU UU UCCCG...UCG-3'@LB@ GCCA GCCC UCAGAACAC@LB@ \|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ CGGU CGGG AGUCUUGUG@LB@3'-UUU...GCAUU UUU U CGUAA...UCA-5'@LB@ \| \|@LB@ 59 37@LB@@LB@@LB@Energy -20.49 kcal/mol@LB@Hybridization Energy -28.5082 kcal/mol@LB@Unfolding Energy - mRNA 2.40221 kcal/mol@LB@Unfolding Energy - sRNA 13.7699 kcal/mol@LB@@LB@Position - mRNA 269 -- 289@LB@Position - sRNA 38 -- 58@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 40 -- 46@LB@
152	0.008087	0.1845	stm0213	dapD	-12.65	0.271269	222 -- 289	49 -- 104	2 3 4 5-tetrahydropyridine-2 6-dicarboxylate N-succinyltransferase	_____________221______________________290\n_____________\|________________________\|\n5'-UUU...UUAAC_________GUU___G________UGAGA...AGG-3'\n______________AAUGCAGCA___ACA_AACGUUAU\n______________\|\|::\|\|:\|\|___\|\|\|_\|\|\|:\|:\|:\n______________UUGUGUUGU___UGU_UUGUAGUG\n3'-UUU...AACGU_______________G________UUGGC...UCA-5'\n_____________\|________________________\|\n_____________105______________________48\n	202 -- 208	79 -- 85	-17.6746 kcal/mol	3.78795 kcal/mol	5.3513 kcal/mol	221 290@LB@ \| \|@LB@5'-UUU...UUAAC GUU G UGAGA...AGG-3'@LB@ AAUGCAGCA ACA AACGUUAU@LB@ \|\|::\|\|:\|\| \|\|\| \|\|\|:\|:\|:@LB@ UUGUGUUGU UGU UUGUAGUG@LB@3'-UUU...AACGU G UUGGC...UCA-5'@LB@ \| \|@LB@ 105 48@LB@@LB@@LB@Energy -12.65 kcal/mol@LB@Hybridization Energy -17.6746 kcal/mol@LB@Unfolding Energy - mRNA 3.78795 kcal/mol@LB@Unfolding Energy - sRNA 5.3513 kcal/mol@LB@@LB@Position - mRNA 222 -- 289@LB@Position - sRNA 49 -- 104@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 79 -- 85@LB@
101	0.005112	0.1728	stm0113	leuA	-13.72	0.187230	187 -- 230	37 -- 84	2-isopropylmalate synthase	_____________186_____________________231\n_____________\|_______________________\|\n5'-AUA...UGGAG____G_____________G____AGCAA...UGG-3'\n______________ACAA_GAC_C_ACAUCAU_AGCC\n______________\|\|\|\|_:\|\|_\|_\|\|\|\|\|\|:_\|:\|\|\n______________UGUU_UUG_G_UGUAGUG_UUGG\n3'-UUU...GUUUG____G___U_U____________CAUUC...UCA-5'\n_____________\|_______________________\|\n_____________85______________________36\n	196 -- 202	67 -- 73	-19.8594 kcal/mol	2.76514 kcal/mol	8.15907 kcal/mol	186 231@LB@ \| \|@LB@5'-AUA...UGGAG G G AGCAA...UGG-3'@LB@ ACAA GAC C ACAUCAU AGCC@LB@ \|\|\|\| :\|\| \| \|\|\|\|\|\|: \|:\|\|@LB@ UGUU UUG G UGUAGUG UUGG@LB@3'-UUU...GUUUG G U U CAUUC...UCA-5'@LB@ \| \|@LB@ 85 36@LB@@LB@@LB@Energy -13.72 kcal/mol@LB@Hybridization Energy -19.8594 kcal/mol@LB@Unfolding Energy - mRNA 2.76514 kcal/mol@LB@Unfolding Energy - sRNA 8.15907 kcal/mol@LB@@LB@Position - mRNA 187 -- 230@LB@Position - sRNA 37 -- 84@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 67 -- 73@LB@
8	9.263e-05	0.04123	stm0369	prpC	-29.42	0.000431	202 -- 269	31 -- 91	2-methylcitrate synthase	_____________201______________________________________________________________270\n_____________\|________________________________________________________________\|\n5'-AAC...CAAUA__A_____________C_U___AA_____A__CAU____UU______AAAAA_____U______UUUCC...GUA-3'\n______________UG_CAGACACGACGAU_C_GCA__ACAAC_CG___GUCA__AAGCCU_____AUCGG__CGCGC\n______________\|\|_\|\|:\|\|\|\|:\|\|:\|:_\|_:\|\|__\|\|\|\|\|_\|\|___\|:\|\|__\|\|\|\|\|:_____\|\|\|:\|__\|:\|\|\|\n______________AC_GUUUGUGUUGUUG_G_UGU__UGUUG_GC___CGGU__UUCGGG_____UAGUC__GUGCG\n3'-UUU...GGUUA________________U_U___AG________AUU____U_________________UU_____UAAGG...UCA-5'\n_____________\|________________________________________________________________\|\n_____________92_______________________________________________________________30\n	211 -- 217	77 -- 83	-51.7305 kcal/mol	8.34164 kcal/mol	22.503 kcal/mol	201 270@LB@ \| \|@LB@5'-AAC...CAAUA A C U AA A CAU UU AAAAA U UUUCC...GUA-3'@LB@ UG CAGACACGACGAU C GCA ACAAC CG GUCA AAGCCU AUCGG CGCGC@LB@ \|\| \|\|:\|\|\|\|:\|\|:\|: \| :\|\| \|\|\|\|\| \|\| \|:\|\| \|\|\|\|\|: \|\|\|:\| \|:\|\|\|@LB@ AC GUUUGUGUUGUUG G UGU UGUUG GC CGGU UUCGGG UAGUC GUGCG@LB@3'-UUU...GGUUA U U AG AUU U UU UAAGG...UCA-5'@LB@ \| \|@LB@ 92 30@LB@@LB@@LB@Energy -29.42 kcal/mol@LB@Hybridization Energy -51.7305 kcal/mol@LB@Unfolding Energy - mRNA 8.34164 kcal/mol@LB@Unfolding Energy - sRNA 22.503 kcal/mol@LB@@LB@Position - mRNA 202 -- 269@LB@Position - sRNA 31 -- 91@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 77 -- 83@LB@
143	0.007336	0.182	stm2276	ubiG	-14.65	0.134291	225 -- 278	36 -- 81	2-octaprenyl-6-hydroxy phenol methylase	_____________224_________________279\n_____________\|___________________\|\n5'-CAC...CGGCA____________CA_____UUUGC...AAU-3'\n______________GUAGAUAUAACG__GCGAC\n______________\|:\|:\|:\|:\|\|\|:__:\|:\|\|\n______________CGUUUGUGUUGU__UGUUG\n3'-UUU...GUUAA____________UG_____UAGUG...UCA-5'\n_____________\|___________________\|\n_____________82__________________35\n	134 -- 140	80 -- 86	-18.0681 kcal/mol	5.41873 kcal/mol	3.80362 kcal/mol	224 279@LB@ \| \|@LB@5'-CAC...CGGCA CA UUUGC...AAU-3'@LB@ GUAGAUAUAACG GCGAC@LB@ \|:\|:\|:\|:\|\|\|: :\|:\|\|@LB@ CGUUUGUGUUGU UGUUG@LB@3'-UUU...GUUAA UG UAGUG...UCA-5'@LB@ \| \|@LB@ 82 35@LB@@LB@@LB@Energy -14.65 kcal/mol@LB@Hybridization Energy -18.0681 kcal/mol@LB@Unfolding Energy - mRNA 5.41873 kcal/mol@LB@Unfolding Energy - sRNA 3.80362 kcal/mol@LB@@LB@Position - mRNA 225 -- 278@LB@Position - sRNA 36 -- 81@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 80 -- 86@LB@
139	0.007115	0.182	stm0826	ybiN	-18.61	0.029895	232 -- 282	36 -- 90	23S rRNA (adenine(1618)-N(6))-methyltransferase	_____________231___________________283\n_____________\|_____________________\|\n5'-CUC...GAGCC_____AACGAGCG________AAUUC...UUC-3'\n______________GAUCA________AGGCAGGG\n______________:\|\|\|\|________\|\|:\|\|\|\|\|\n______________UUAGU________UCUGUCCC\n3'-UUU...UGUAA_____GAUACCUG________AUUUA...UCA-5'\n_____________\|_____________________\|\n_____________91____________________35\n	124 -- 130	152 -- 158	-17.5433 kcal/mol	4.82059 kcal/mol	3.53427 kcal/mol	231 283@LB@ \| \|@LB@5'-CUC...GAGCC AACGAGCG AAUUC...UUC-3'@LB@ GAUCA AGGCAGGG@LB@ :\|\|\|\| \|\|:\|\|\|\|\|@LB@ UUAGU UCUGUCCC@LB@3'-UUU...UGUAA GAUACCUG AUUUA...UCA-5'@LB@ \| \|@LB@ 91 35@LB@@LB@@LB@Energy -18.61 kcal/mol@LB@Hybridization Energy -17.5433 kcal/mol@LB@Unfolding Energy - mRNA 4.82059 kcal/mol@LB@Unfolding Energy - sRNA 3.53427 kcal/mol@LB@@LB@Position - mRNA 232 -- 282@LB@Position - sRNA 36 -- 90@LB@Position Seed - mRNA 124 -- 130@LB@Position Seed - sRNA 152 -- 158@LB@
89	0.004143	0.1596	stm2957	ygcA	-15.40	0.101796	159 -- 208	35 -- 82	23S rRNA (uracil(1939)-C(5))-methyltransferase	_____________158____________________________________________209\n_____________\|______________________________________________\|\n5'-AUA...UACUC_____AACG____GU_________UCAG___________UA_____AAUGA...GUC-3'\n______________UGCAA____GCGC__GACGACGCG____AUCAUAACCGU__AAGUC\n______________\|\|\|\|\|____:\|:\|__:\|\|:\|\|:\|:____\|\|\|\|:\|\|\|\|\|\|__\|\|\|:\|\n______________ACGUU____UGUG__UUGUUGUGU____UAGUGUUGGCA__UUCGG\n3'-UUU...GGUUA________________________UG____________________UUUUC...UCA-5'\n_____________\|______________________________________________\|\n_____________83_____________________________________________34\n	250 -- 256	61 -- 67	-36.475 kcal/mol	14.3441 kcal/mol	11.8308 kcal/mol	158 209@LB@ \| \|@LB@5'-AUA...UACUC AACG GU UCAG UA AAUGA...GUC-3'@LB@ UGCAA GCGC GACGACGCG AUCAUAACCGU AAGUC@LB@ \|\|\|\|\| :\|:\| :\|\|:\|\|:\|: \|\|\|\|:\|\|\|\|\|\| \|\|\|:\|@LB@ ACGUU UGUG UUGUUGUGU UAGUGUUGGCA UUCGG@LB@3'-UUU...GGUUA UG UUUUC...UCA-5'@LB@ \| \|@LB@ 83 34@LB@@LB@@LB@Energy -15.40 kcal/mol@LB@Hybridization Energy -36.475 kcal/mol@LB@Unfolding Energy - mRNA 14.3441 kcal/mol@LB@Unfolding Energy - sRNA 11.8308 kcal/mol@LB@@LB@Position - mRNA 159 -- 208@LB@Position - sRNA 35 -- 82@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 61 -- 67@LB@
116	0.005629	0.1728	stm2662	rluD	-17.46	0.046576	204 -- 257	36 -- 86	23S rRNA pseudouridine(1911/1915/1917) synthase	_____________203____________________258\n_____________\|______________________\|\n5'-UGA...UAUAU__________G___________CGCAA...GUU-3'\n______________GGCACAACGA_UACAAC_UCAC\n______________::\|\|\|\|\|\|:\|_:\|\|\|\|\|_\|\|\|\|\n______________UUGUGUUGUU_GUGUUG_AGUG\n3'-UUU...AACGU_________________U____UUGGC...UCA-5'\n_____________\|______________________\|\n_____________87_____________________35\n	206 -- 212	78 -- 84	-22.2469 kcal/mol	4.97176 kcal/mol	5.3513 kcal/mol	203 258@LB@ \| \|@LB@5'-UGA...UAUAU G CGCAA...GUU-3'@LB@ GGCACAACGA UACAAC UCAC@LB@ ::\|\|\|\|\|\|:\| :\|\|\|\|\| \|\|\|\|@LB@ UUGUGUUGUU GUGUUG AGUG@LB@3'-UUU...AACGU U UUGGC...UCA-5'@LB@ \| \|@LB@ 87 35@LB@@LB@@LB@Energy -17.46 kcal/mol@LB@Hybridization Energy -22.2469 kcal/mol@LB@Unfolding Energy - mRNA 4.97176 kcal/mol@LB@Unfolding Energy - sRNA 5.3513 kcal/mol@LB@@LB@Position - mRNA 204 -- 257@LB@Position - sRNA 36 -- 86@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 78 -- 84@LB@
103	0.005167	0.1728	stm2670	aroF	-17.31	0.049328	173 -- 242	25 -- 90	3-deoxy-7-phosphoheptulonate synthase	_____________172______________________________________________________________________243\n_____________\|________________________________________________________________________\|\n5'-CUU...CUAUC_______AGAA__G____G_____C___AU____A_____A_G____U___UAACG_______CA_______ACAGG...AGG-3'\n______________GCAAACA____AA_ACAG_AUCGC_AUC____GC_AAAAG_C_CG_C_GAA_____UACGUAU__CCGAUGA\n______________\|\|\|\|\|\|\|____\|\|_\|\|\|:_\|\|\|:\|_\|:\|____\|\|_\|\|\|\|\|_\|_\|:_\|_\|\|\|_____:\|\|\|:\|\|__\|\|\|\|\|:\|\n______________CGUUUGU____UU_UGUU_UAGUG_UGG____CG_UUUUC_G_GU_G_CUU_____GUGCGUA__GGCUAUU\n3'-UUU...GUUAA_______GUUG__G____G_____U___CAUU__G_______G__A_U_______________A________UUGAA...UCA-5'\n_____________\|________________________________________________________________________\|\n_____________91_______________________________________________________________________24\n	226 -- 232	34 -- 40	-46.7665 kcal/mol	10.372 kcal/mol	24.1795 kcal/mol	172 243@LB@ \| \|@LB@5'-CUU...CUAUC AGAA G G C AU A A G U UAACG CA ACAGG...AGG-3'@LB@ GCAAACA AA ACAG AUCGC AUC GC AAAAG C CG C GAA UACGUAU CCGAUGA@LB@ \|\|\|\|\|\|\| \|\| \|\|\|: \|\|\|:\| \|:\| \|\| \|\|\|\|\| \| \|: \| \|\|\| :\|\|\|:\|\| \|\|\|\|\|:\|@LB@ CGUUUGU UU UGUU UAGUG UGG CG UUUUC G GU G CUU GUGCGUA GGCUAUU@LB@3'-UUU...GUUAA GUUG G G U CAUU G G A U A UUGAA...UCA-5'@LB@ \| \|@LB@ 91 24@LB@@LB@@LB@Energy -17.31 kcal/mol@LB@Hybridization Energy -46.7665 kcal/mol@LB@Unfolding Energy - mRNA 10.372 kcal/mol@LB@Unfolding Energy - sRNA 24.1795 kcal/mol@LB@@LB@Position - mRNA 173 -- 242@LB@Position - sRNA 25 -- 90@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 34 -- 40@LB@
18	0.0003131	0.06194	stm0112	leuB	-16.29	0.072835	153 -- 217	44 -- 93	3-isopropylmalate dehydrogenase	_____________152___________218\n_____________\|_____________\|\n5'-AAA...AAAGA_____________AGCUC...GUU-3'\n______________AUUGC_AACGCAA\n______________\|\|\|\|\|_\|\|\|:\|\|\|\n______________UAACG_UUGUGUU\n3'-UUU...CUGGU_____U_______GUUGU...UCA-5'\n_____________\|_____________\|\n_____________94____________43\n	158 -- 164	81 -- 87	-11.6192 kcal/mol	1.90811 kcal/mol	3.57619 kcal/mol	152 218@LB@ \| \|@LB@5'-AAA...AAAGA AGCUC...GUU-3'@LB@ AUUGC AACGCAA@LB@ \|\|\|\|\| \|\|\|:\|\|\|@LB@ UAACG UUGUGUU@LB@3'-UUU...CUGGU U GUUGU...UCA-5'@LB@ \| \|@LB@ 94 43@LB@@LB@@LB@Energy -16.29 kcal/mol@LB@Hybridization Energy -11.6192 kcal/mol@LB@Unfolding Energy - mRNA 1.90811 kcal/mol@LB@Unfolding Energy - sRNA 3.57619 kcal/mol@LB@@LB@Position - mRNA 153 -- 217@LB@Position - sRNA 44 -- 93@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 81 -- 87@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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