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
199	0.01101	0.197	stm3346	yhcM	-12.83	0.254909	186 -- 228	33 -- 82	cell division protein ZapE	_____________185____________________229\n_____________\|______________________\|\n5'-CAG...UUCAA_G__UA__________UAU___AAGCC...AAA-3'\n______________G_AA__ACAAUAACAU___GCA\n______________\|_\|\|__\|\|\|\|:\|\|\|\|:___:\|\|\n______________C_UU__UGUUGUUGUG___UGU\n3'-UUU...GUUAA_G__UG__________U_____AGUGU...UCA-5'\n_____________\|______________________\|\n_____________83_____________________32\n	193 -- 199	75 -- 81	-14.0954 kcal/mol	2.45302 kcal/mol	3.80671 kcal/mol	185 229@LB@ \| \|@LB@5'-CAG...UUCAA G UA UAU AAGCC...AAA-3'@LB@ G AA ACAAUAACAU GCA@LB@ \| \|\| \|\|\|\|:\|\|\|\|: :\|\|@LB@ C UU UGUUGUUGUG UGU@LB@3'-UUU...GUUAA G UG U AGUGU...UCA-5'@LB@ \| \|@LB@ 83 32@LB@@LB@@LB@Energy -12.83 kcal/mol@LB@Hybridization Energy -14.0954 kcal/mol@LB@Unfolding Energy - mRNA 2.45302 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 186 -- 228@LB@Position - sRNA 33 -- 82@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 75 -- 81@LB@
11	0.0001804	0.05681	stm0959	lrp	-12.80	0.257711	163 -- 181	139 -- 159	leucine-responsive transcriptional regulator	_____________162_______________________________________________182\n_____________\|_________________________________________________\|\n5'-UGA...AGAGU________A_____GA________UAC______ACAAUAAUAAU_____AUAGC...AGC-3'\n______________CAGGCAGG_GUAGG_____AGGAA___AGAGAG___________GGUAG\n______________\|\|\|:\|\|\|\|_\|\|\|::_____\|\|\|\|\|___\|:\|:\|\|___________\|\|\|\|\|\n______________GUCUGUCC_CAUUU_____UCCUU___UUUUUC___________CCAUC\n3'-UUU...UACCU______________ACAUG_____CAC______________________AGAGC...UCA-5'\n_____________\|_________________________________________________\|\n_____________160_______________________________________________138\n	163 -- 169	153 -- 159	-28.6161 kcal/mol	5.81197 kcal/mol	10.0349 kcal/mol	162 182@LB@ \| \|@LB@5'-UGA...AGAGU A GA UAC ACAAUAAUAAU AUAGC...AGC-3'@LB@ CAGGCAGG GUAGG AGGAA AGAGAG GGUAG@LB@ \|\|\|:\|\|\|\| \|\|\|:: \|\|\|\|\| \|:\|:\|\| \|\|\|\|\|@LB@ GUCUGUCC CAUUU UCCUU UUUUUC CCAUC@LB@3'-UUU...UACCU ACAUG CAC AGAGC...UCA-5'@LB@ \| \|@LB@ 160 138@LB@@LB@@LB@Energy -12.80 kcal/mol@LB@Hybridization Energy -28.6161 kcal/mol@LB@Unfolding Energy - mRNA 5.81197 kcal/mol@LB@Unfolding Energy - sRNA 10.0349 kcal/mol@LB@@LB@Position - mRNA 163 -- 181@LB@Position - sRNA 139 -- 159@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 153 -- 159@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@
174	0.009594	0.1945	stm1955	fliZ	-12.61	0.274939	261 -- 282	33 -- 59	flagellar regulatory protein FliZ	_____________260________________283\n_____________\|__________________\|\n5'-GCA...GACUU__________CA______UUGCG...ACC-3'\n______________UAAACACAGC__GACGCA\n______________:\|\|\|\|\|\|\|:\|__:\|\|:\|\|\n______________GUUUGUGUUG__UUGUGU\n3'-UUU...UUAAC__________________UGUAG...UCA-5'\n_____________\|__________________\|\n_____________60_________________32\n	257 -- 263	80 -- 86	-16.495 kcal/mol	1.82497 kcal/mol	3.72065 kcal/mol	260 283@LB@ \| \|@LB@5'-GCA...GACUU CA UUGCG...ACC-3'@LB@ UAAACACAGC GACGCA@LB@ :\|\|\|\|\|\|\|:\| :\|\|:\|\|@LB@ GUUUGUGUUG UUGUGU@LB@3'-UUU...UUAAC UGUAG...UCA-5'@LB@ \| \|@LB@ 60 32@LB@@LB@@LB@Energy -12.61 kcal/mol@LB@Hybridization Energy -16.495 kcal/mol@LB@Unfolding Energy - mRNA 1.82497 kcal/mol@LB@Unfolding Energy - sRNA 3.72065 kcal/mol@LB@@LB@Position - mRNA 261 -- 282@LB@Position - sRNA 33 -- 59@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 80 -- 86@LB@
109	0.005328	0.1728	stm3082	N/A	-12.60	0.275269	106 -- 154	38 -- 90	galactonate oxidoreductase	_____________105________________________155\n_____________\|__________________________\|\n5'-AAU...ACAAC______UUUUUA_______UU_____GGCCU...CGG-3'\n______________GCAGAC______AACAACA__CAGCA\n______________\|\|\|:\|\|______\|\|\|\|\|\|\|__\|\|:\|\|\n______________CGUUUG______UUGUUGU__GUUGU\n3'-UUU...GUUAA______UG__________________AGUGU...UCA-5'\n_____________\|__________________________\|\n_____________91_________________________37\n	118 -- 124	76 -- 82	-16.9817 kcal/mol	2.50135 kcal/mol	3.80671 kcal/mol	105 155@LB@ \| \|@LB@5'-AAU...ACAAC UUUUUA UU GGCCU...CGG-3'@LB@ GCAGAC AACAACA CAGCA@LB@ \|\|\|:\|\| \|\|\|\|\|\|\| \|\|:\|\|@LB@ CGUUUG UUGUUGU GUUGU@LB@3'-UUU...GUUAA UG AGUGU...UCA-5'@LB@ \| \|@LB@ 91 37@LB@@LB@@LB@Energy -12.60 kcal/mol@LB@Hybridization Energy -16.9817 kcal/mol@LB@Unfolding Energy - mRNA 2.50135 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 106 -- 154@LB@Position - sRNA 38 -- 90@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 76 -- 82@LB@
110	0.005337	0.1728	stm1920	cheW	-12.58	0.277263	149 -- 192	51 -- 90	chemotaxis protein CheW	_____________148__________193\n_____________\|____________\|\n5'-GUC...UGAUU____________AAUAA...UCC-3'\n______________GAGUGAGAAGGG\n______________:\|\|\|\|\|:\|\|:\|\|\n______________UUCACUUUUUCC\n3'-UUU...UGUCC____________CAUCA...UCA-5'\n_____________\|____________\|\n_____________91___________50\n	188 -- 194	128 -- 134	-15.4894 kcal/mol	2.64754 kcal/mol	3.77328 kcal/mol	148 193@LB@ \| \|@LB@5'-GUC...UGAUU AAUAA...UCC-3'@LB@ GAGUGAGAAGGG@LB@ :\|\|\|\|\|:\|\|:\|\|@LB@ UUCACUUUUUCC@LB@3'-UUU...UGUCC CAUCA...UCA-5'@LB@ \| \|@LB@ 91 50@LB@@LB@@LB@Energy -12.58 kcal/mol@LB@Hybridization Energy -15.4894 kcal/mol@LB@Unfolding Energy - mRNA 2.64754 kcal/mol@LB@Unfolding Energy - sRNA 3.77328 kcal/mol@LB@@LB@Position - mRNA 149 -- 192@LB@Position - sRNA 51 -- 90@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 128 -- 134@LB@
175	0.009595	0.1945	stm0268	N/A	-12.50	0.284574	64 -- 117	80 -- 130	type VI secretion protein	_____________63__________________________________________________________118\n_____________\|___________________________________________________________\|\n5'-GUU...CCGGC__________AUAACA______A__________AU________A______U________CGUAU...GAC-3'\n______________AGGGUAG_CU______CGCUAC____GUUUGAA__UCGCGGAC_AAUU_C_GACGCAGC\n______________\|\|\|\|\|\|\|_\|\|______\|\|\|\|\|\|____\|\|:\|\|\|\|__\|\|\|\|:\|\|\|_\|\|\|\|_\|_:\|\|:\|\|:\|\n______________UCCCAUC_GA______GCGAUG____CAGACUU__AGCGUCUG_UUAA_G_UUGUGUUG\n3'-UUU...CUUUU_______A______________GCAC_________________G____C_U________UUGUG...UCA-5'\n_____________\|___________________________________________________________\|\n_____________131_________________________________________________________79\n	111 -- 117	80 -- 86	-48.3519 kcal/mol	16.091 kcal/mol	19.1381 kcal/mol	63 118@LB@ \| \|@LB@5'-GUU...CCGGC AUAACA A AU A U CGUAU...GAC-3'@LB@ AGGGUAG CU CGCUAC GUUUGAA UCGCGGAC AAUU C GACGCAGC@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\|\|\| \|\|:\|\|\|\| \|\|\|\|:\|\|\| \|\|\|\| \| :\|\|:\|\|:\|@LB@ UCCCAUC GA GCGAUG CAGACUU AGCGUCUG UUAA G UUGUGUUG@LB@3'-UUU...CUUUU A GCAC G C U UUGUG...UCA-5'@LB@ \| \|@LB@ 131 79@LB@@LB@@LB@Energy -12.50 kcal/mol@LB@Hybridization Energy -48.3519 kcal/mol@LB@Unfolding Energy - mRNA 16.091 kcal/mol@LB@Unfolding Energy - sRNA 19.1381 kcal/mol@LB@@LB@Position - mRNA 64 -- 117@LB@Position - sRNA 80 -- 130@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 80 -- 86@LB@
171	0.009384	0.1945	stm1741	N/A	-12.47	0.287408	104 -- 168	71 -- 131	transporter	_____________103_________________________________________________________________________169\n_____________\|___________________________________________________________________________\|\n5'-GAG...CGACC____CU__________U______CA______UUC___CCUUAAA_______C___A___U_____G_________AUUCG...UGU-3'\n______________GGUG__GGAAGGG_AG_UUUCGC__UGCCGU___CUG_______GUAGACC_GUU_UAA_CGCAA_GGC_UGACA\n______________:\|\|\|__::\|\|\|\|\|_\|\|_\|:\|\|\|\|__\|:\|\|\|\|___\|\|\|_______\|:\|\|\|\|\|_:\|\|_:\|\|_\|:\|\|\|_::\|_::\|\|\|\n______________UCAC__UUUUCCC_UC_AGAGCG__AUGGCA___GAC_______CGUCUGG_UAA_GUU_GUGUU_UUG_GUUGU\n3'-UUU...GUCCU____U________A_________________CCA___UUAG__________U___C___U_____G___U_____AGUGU...UCA-5'\n_____________\|___________________________________________________________________________\|\n_____________132_________________________________________________________________________70\n	139 -- 145	95 -- 101	-55.0636 kcal/mol	20.4542 kcal/mol	20.5091 kcal/mol	103 169@LB@ \| \|@LB@5'-GAG...CGACC CU U CA UUC CCUUAAA C A U G AUUCG...UGU-3'@LB@ GGUG GGAAGGG AG UUUCGC UGCCGU CUG GUAGACC GUU UAA CGCAA GGC UGACA@LB@ :\|\|\| ::\|\|\|\|\| \|\| \|:\|\|\|\| \|:\|\|\|\| \|\|\| \|:\|\|\|\|\| :\|\| :\|\| \|:\|\|\| ::\| ::\|\|\|@LB@ UCAC UUUUCCC UC AGAGCG AUGGCA GAC CGUCUGG UAA GUU GUGUU UUG GUUGU@LB@3'-UUU...GUCCU U A CCA UUAG U C U G U AGUGU...UCA-5'@LB@ \| \|@LB@ 132 70@LB@@LB@@LB@Energy -12.47 kcal/mol@LB@Hybridization Energy -55.0636 kcal/mol@LB@Unfolding Energy - mRNA 20.4542 kcal/mol@LB@Unfolding Energy - sRNA 20.5091 kcal/mol@LB@@LB@Position - mRNA 104 -- 168@LB@Position - sRNA 71 -- 131@LB@Position Seed - mRNA 139 -- 145@LB@Position Seed - sRNA 95 -- 101@LB@
127	0.006343	0.1774	stm1751	hns	-12.42	0.292757	1 -- 14	147 -- 162	transcriptional regulator	______________1_______________15\n______________\|_______________\|\n___________5'-________________AUCCC...UAG-3'\n______________GACAGAC__GGUGAGU\n______________\|\|\|\|\|\|\|__\|\|\|:\|:\|\n______________CUGUCUG__CCAUUUA\n3'-UUU...GAUAC_______UC_______CAUGU...UCA-5'\n_____________\|________________\|\n_____________163______________146\n	8 -- 14	147 -- 153	-17.2475 kcal/mol	3.56352 kcal/mol	3.32093 kcal/mol	1 15@LB@ \| \|@LB@ 5'- AUCCC...UAG-3'@LB@ GACAGAC GGUGAGU@LB@ \|\|\|\|\|\|\| \|\|\|:\|:\|@LB@ CUGUCUG CCAUUUA@LB@3'-UUU...GAUAC UC CAUGU...UCA-5'@LB@ \| \|@LB@ 163 146@LB@@LB@@LB@Energy -12.42 kcal/mol@LB@Hybridization Energy -17.2475 kcal/mol@LB@Unfolding Energy - mRNA 3.56352 kcal/mol@LB@Unfolding Energy - sRNA 3.32093 kcal/mol@LB@@LB@Position - mRNA 1 -- 14@LB@Position - sRNA 147 -- 162@LB@Position Seed - mRNA 8 -- 14@LB@Position Seed - sRNA 147 -- 153@LB@
125	0.006333	0.1774	stm3094	yggJ	-12.37	0.297521	35 -- 55	69 -- 89	putative cytoplasmic protein	_____________34____________________56\n_____________\|_____________________\|\n5'-GCG...GCCAA__________UUUU_______UGGGA...AGA-3'\n______________CAAACGCAGC____UAACGUC\n______________\|\|\|\|\|:\|\|:\|____:\|\|\|:\|\|\n______________GUUUGUGUUG____GUUGUAG\n3'-UUU...UUAAC__________UUGU_______UGUUG...UCA-5'\n_____________\|_____________________\|\n_____________90____________________68\n	49 -- 55	69 -- 75	-19.7914 kcal/mol	1.34113 kcal/mol	4.32311 kcal/mol	34 56@LB@ \| \|@LB@5'-GCG...GCCAA UUUU UGGGA...AGA-3'@LB@ CAAACGCAGC UAACGUC@LB@ \|\|\|\|\|:\|\|:\| :\|\|\|:\|\|@LB@ GUUUGUGUUG GUUGUAG@LB@3'-UUU...UUAAC UUGU UGUUG...UCA-5'@LB@ \| \|@LB@ 90 68@LB@@LB@@LB@Energy -12.37 kcal/mol@LB@Hybridization Energy -19.7914 kcal/mol@LB@Unfolding Energy - mRNA 1.34113 kcal/mol@LB@Unfolding Energy - sRNA 4.32311 kcal/mol@LB@@LB@Position - mRNA 35 -- 55@LB@Position - sRNA 69 -- 89@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 69 -- 75@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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