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	Additional homologs
166	0.009028	0.1932	stm1173	flgA	-14.00	0.169768	53 -- 102	33 -- 85	flagella basal body P-ring formation protein FlgA		_____________52__________________103\n_____________\|___________________\|\n5'-GCU...CCCUG___________GG______ACGCC...CCC-3'\n______________ACAAUGGCGCA__ACAUCA\n______________\|\|\|\|:::\|:\|\|__\|\|\|\|\|\|\n______________UGUUGUUGUGU__UGUAGU\n3'-UUU...GUUUG___________________GUUGG...UCA-5'\n_____________\|___________________\|\n_____________86__________________32\n	259 -- 265	74 -- 80	-16.6955 kcal/mol	2.54166 kcal/mol	4.84988 kcal/mol	52 103@LB@ \| \|@LB@5'-GCU...CCCUG GG ACGCC...CCC-3'@LB@ ACAAUGGCGCA ACAUCA@LB@ \|\|\|\|:::\|:\|\| \|\|\|\|\|\|@LB@ UGUUGUUGUGU UGUAGU@LB@3'-UUU...GUUUG GUUGG...UCA-5'@LB@ \| \|@LB@ 86 32@LB@@LB@@LB@Energy -14.00 kcal/mol@LB@Hybridization Energy -16.6955 kcal/mol@LB@Unfolding Energy - mRNA 2.54166 kcal/mol@LB@Unfolding Energy - sRNA 4.84988 kcal/mol@LB@@LB@Position - mRNA 53 -- 102@LB@Position - sRNA 33 -- 85@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 74 -- 80@LB@
173	0.009489	0.1945	stm3985	yigZ	-14.68	0.132642	77 -- 135	33 -- 90	YigZ family protein		_____________76___________________136\n_____________\|____________________\|\n5'-CGA...GUUCA________UU__________GAAAA...ACG-3'\n______________GCAAGCAC__CAAC_UGGCA\n______________\|\|\|\|:\|\|\|__\|\|\|\|_:::\|\|\n______________CGUUUGUG__GUUG_GUUGU\n3'-UUU...GUUAA________UU____U_____AGUGU...UCA-5'\n_____________\|____________________\|\n_____________91___________________32\n	78 -- 84	83 -- 89	-19.4869 kcal/mol	6.86655 kcal/mol	3.80671 kcal/mol	76 136@LB@ \| \|@LB@5'-CGA...GUUCA UU GAAAA...ACG-3'@LB@ GCAAGCAC CAAC UGGCA@LB@ \|\|\|\|:\|\|\| \|\|\|\| :::\|\|@LB@ CGUUUGUG GUUG GUUGU@LB@3'-UUU...GUUAA UU U AGUGU...UCA-5'@LB@ \| \|@LB@ 91 32@LB@@LB@@LB@Energy -14.68 kcal/mol@LB@Hybridization Energy -19.4869 kcal/mol@LB@Unfolding Energy - mRNA 6.86655 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 77 -- 135@LB@Position - sRNA 33 -- 90@LB@Position Seed - mRNA 78 -- 84@LB@Position Seed - sRNA 83 -- 89@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@
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@
2	2.663e-05	0.04123	stm2355	argT	-17.69	0.042680	144 -- 202	34 -- 91	histidine ABC transporter substrate-binding protein HisJ		_____________143____________________203\n_____________\|______________________\|\n5'-UUA...AAGUC_________________C____AAAAC...AUA-3'\n______________UGCAAACAC_ACAACGC_ACGU\n______________\|\|\|\|\|\|\|\|\|_\|\|\|\|\|:\|_\|\|:\|\n______________ACGUUUGUG_UGUUGUG_UGUA\n3'-UUU...GGUUA_________U_______U____GUGUU...UCA-5'\n_____________\|______________________\|\n_____________92_____________________33\n	153 -- 159	75 -- 81	-25.653 kcal/mol	2.98604 kcal/mol	4.21448 kcal/mol	143 203@LB@ \| \|@LB@5'-UUA...AAGUC C AAAAC...AUA-3'@LB@ UGCAAACAC ACAACGC ACGU@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|\|:\| \|\|:\|@LB@ ACGUUUGUG UGUUGUG UGUA@LB@3'-UUU...GGUUA U U GUGUU...UCA-5'@LB@ \| \|@LB@ 92 33@LB@@LB@@LB@Energy -17.69 kcal/mol@LB@Hybridization Energy -25.653 kcal/mol@LB@Unfolding Energy - mRNA 2.98604 kcal/mol@LB@Unfolding Energy - sRNA 4.21448 kcal/mol@LB@@LB@Position - mRNA 144 -- 202@LB@Position - sRNA 34 -- 91@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 75 -- 81@LB@
49	0.001802	0.1291	stm1787	N/A	-18.29	0.033902	137 -- 202	34 -- 90	[Ni/Fe] hydrogenase large subunit		_____________136__________________203\n_____________\|____________________\|\n5'-GGC...CCAAC________C___________GUUAG...GCG-3'\n______________GUAAACGC_ACAA_ACAACA\n______________\|:\|\|\|\|:\|_\|\|\|\|_\|\|\|\|\|\|\n______________CGUUUGUG_UGUU_UGUUGU\n3'-UUU...GUUAA________U____G______AGUGU...UCA-5'\n_____________\|____________________\|\n_____________91___________________33\n	138 -- 144	83 -- 89	-18.7581 kcal/mol	1.39906 kcal/mol	3.80671 kcal/mol	136 203@LB@ \| \|@LB@5'-GGC...CCAAC C GUUAG...GCG-3'@LB@ GUAAACGC ACAA ACAACA@LB@ \|:\|\|\|\|:\| \|\|\|\| \|\|\|\|\|\|@LB@ CGUUUGUG UGUU UGUUGU@LB@3'-UUU...GUUAA U G AGUGU...UCA-5'@LB@ \| \|@LB@ 91 33@LB@@LB@@LB@Energy -18.29 kcal/mol@LB@Hybridization Energy -18.7581 kcal/mol@LB@Unfolding Energy - mRNA 1.39906 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 137 -- 202@LB@Position - sRNA 34 -- 90@LB@Position Seed - mRNA 138 -- 144@LB@Position Seed - sRNA 83 -- 89@LB@
64	0.003108	0.1596	stm4162	thiF	-13.53	0.200092	247 -- 294	34 -- 76	molybdopterin/thiamine biosynthesis adenylyltransferase		_____________246___________________295\n_____________\|_____________________\|\n5'-GCA...GCUCG_______________A_____AGCAA...UUG-3'\n______________GCGAUAUCGCGAUUG_AGGCC\n______________:\|:\|:\|\|\|:\|:\|::\|_\|:\|\|\|\n______________UGUUGUAGUGUUGGC_UUCGG\n3'-UUU...UGUUG_______________A_____UUUUC...UCA-5'\n_____________\|_____________________\|\n_____________77____________________33\n	248 -- 254	69 -- 75	-25.2172 kcal/mol	7.66984 kcal/mol	8.92374 kcal/mol	246 295@LB@ \| \|@LB@5'-GCA...GCUCG A AGCAA...UUG-3'@LB@ GCGAUAUCGCGAUUG AGGCC@LB@ :\|:\|:\|\|\|:\|:\|::\| \|:\|\|\|@LB@ UGUUGUAGUGUUGGC UUCGG@LB@3'-UUU...UGUUG A UUUUC...UCA-5'@LB@ \| \|@LB@ 77 33@LB@@LB@@LB@Energy -13.53 kcal/mol@LB@Hybridization Energy -25.2172 kcal/mol@LB@Unfolding Energy - mRNA 7.66984 kcal/mol@LB@Unfolding Energy - sRNA 8.92374 kcal/mol@LB@@LB@Position - mRNA 247 -- 294@LB@Position - sRNA 34 -- 76@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 69 -- 75@LB@
83	0.003855	0.1596	stm1680	ycjI	-14.22	0.156552	151 -- 200	34 -- 86	murein peptide amidase A		_____________150_________201\n_____________\|___________\|\n5'-GAA...CUGAA___________UUCGC...CGG-3'\n______________CAUUAUGGACG\n______________\|\|:\|\|\|\|\|\|\|:\n______________GUGAUACCUGU\n3'-UUU...AAUUA___________CUGUC...UCA-5'\n_____________\|___________\|\n_____________87__________33\n	259 -- 265	159 -- 165	-14.9153 kcal/mol	1.6295 kcal/mol	3.40995 kcal/mol	150 201@LB@ \| \|@LB@5'-GAA...CUGAA UUCGC...CGG-3'@LB@ CAUUAUGGACG@LB@ \|\|:\|\|\|\|\|\|\|:@LB@ GUGAUACCUGU@LB@3'-UUU...AAUUA CUGUC...UCA-5'@LB@ \| \|@LB@ 87 33@LB@@LB@@LB@Energy -14.22 kcal/mol@LB@Hybridization Energy -14.9153 kcal/mol@LB@Unfolding Energy - mRNA 1.6295 kcal/mol@LB@Unfolding Energy - sRNA 3.40995 kcal/mol@LB@@LB@Position - mRNA 151 -- 200@LB@Position - sRNA 34 -- 86@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 159 -- 165@LB@
95	0.004301	0.1596	stm4114	pflD	-11.77	0.360092	46 -- 100	34 -- 88	formate C-acetyltransferase	stm0843	_____________45_____________________101\n_____________\|______________________\|\n5'-UUU...CGGUA_______C______________GAACA...AGA-3'\n______________AAACGCG_CGACGC__CAUUAU\n______________\|\|\|\|:\|:_\|:\|\|:\|__\|\|\|:\|:\n______________UUUGUGU_GUUGUG__GUAGUG\n3'-UUU...UAACG_______U______UU______UUGGC...UCA-5'\n_____________\|______________________\|\n_____________89_____________________33\n	46 -- 52	82 -- 88	-16.7675 kcal/mol	5.49067 kcal/mol	5.48747 kcal/mol	45 101@LB@ \| \|@LB@5'-UUU...CGGUA C GAACA...AGA-3'@LB@ AAACGCG CGACGC CAUUAU@LB@ \|\|\|\|:\|: \|:\|\|:\| \|\|\|:\|:@LB@ UUUGUGU GUUGUG GUAGUG@LB@3'-UUU...UAACG U UU UUGGC...UCA-5'@LB@ \| \|@LB@ 89 33@LB@@LB@@LB@Energy -11.77 kcal/mol@LB@Hybridization Energy -16.7675 kcal/mol@LB@Unfolding Energy - mRNA 5.49067 kcal/mol@LB@Unfolding Energy - sRNA 5.48747 kcal/mol@LB@@LB@Position - mRNA 46 -- 100@LB@Position - sRNA 34 -- 88@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 82 -- 88@LB@
193	0.01075	0.197	stm3734	rph	-15.48	0.098722	165 -- 206	34 -- 78	ribonuclease PH		_____________164____________________________207\n_____________\|______________________________\|\n5'-GCG...AUAAU_____________U___UUU__________AUCUC...GAG-3'\n______________GCGCAGC__CACA_UCG___UAAGCCGGAG\n______________:\|:\|\|:\|__\|\|\|\|_:\|\|___\|\|\|\|\|\|::\|:\n______________UGUGUUG__GUGU_GGC___AUUCGGUUUU\n3'-UUU...GUUGU_______UA____U________________CGGGU...UCA-5'\n_____________\|______________________________\|\n_____________79_____________________________33\n	183 -- 189	55 -- 61	-24.9708 kcal/mol	4.11178 kcal/mol	11.3295 kcal/mol	164 207@LB@ \| \|@LB@5'-GCG...AUAAU U UUU AUCUC...GAG-3'@LB@ GCGCAGC CACA UCG UAAGCCGGAG@LB@ :\|:\|\|:\| \|\|\|\| :\|\| \|\|\|\|\|\|::\|:@LB@ UGUGUUG GUGU GGC AUUCGGUUUU@LB@3'-UUU...GUUGU UA U CGGGU...UCA-5'@LB@ \| \|@LB@ 79 33@LB@@LB@@LB@Energy -15.48 kcal/mol@LB@Hybridization Energy -24.9708 kcal/mol@LB@Unfolding Energy - mRNA 4.11178 kcal/mol@LB@Unfolding Energy - sRNA 11.3295 kcal/mol@LB@@LB@Position - mRNA 165 -- 206@LB@Position - sRNA 34 -- 78@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 55 -- 61@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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