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
63	0.003024	0.1596	stm3563	livH	-16.49	0.067433	27 -- 175	36 -- 184	branched-chain amino acid ABC transporter permease LivH		_____________26_____________176\n_____________\|______________\|\n5'-GAU...GAAAU______________CGAUC...ACG-3'\n______________GGGA_UGAAAAAGG\n______________\|\|:\|_\|\|\|\|\|\|\|\|\|\n______________CCUU_ACUUUUUCC\n3'-UUU...CAUGU____C_________CAUCA...UCA-5'\n_____________\|______________\|\n_____________185____________35\n	65 -- 71	128 -- 134	-14.2251 kcal/mol	3.55711 kcal/mol	3.77758 kcal/mol	26 176@LB@ \| \|@LB@5'-GAU...GAAAU CGAUC...ACG-3'@LB@ GGGA UGAAAAAGG@LB@ \|\|:\| \|\|\|\|\|\|\|\|\|@LB@ CCUU ACUUUUUCC@LB@3'-UUU...CAUGU C CAUCA...UCA-5'@LB@ \| \|@LB@ 185 35@LB@@LB@@LB@Energy -16.49 kcal/mol@LB@Hybridization Energy -14.2251 kcal/mol@LB@Unfolding Energy - mRNA 3.55711 kcal/mol@LB@Unfolding Energy - sRNA 3.77758 kcal/mol@LB@@LB@Position - mRNA 27 -- 175@LB@Position - sRNA 36 -- 184@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 128 -- 134@LB@
4	5.758e-05	0.04123	stm3564	livK	-17.90	0.039430	157 -- 215	37 -- 90	leucine ABC transporter subunit substrate-binding protein LivK		_____________156______________________216\n_____________\|________________________\|\n5'-UUU...GCAAA_____A__________________AUGGG...CGA-3'\n______________AAACA_AAC_AUAUAACAUCACGA\n______________\|\|\|\|\|_\|\|\|_\|:\|:\|\|\|\|\|\|\|\|:\|\n______________UUUGU_UUG_UGUGUUGUAGUGUU\n3'-UUU...UAACG_____G___U______________GGCAU...UCA-5'\n_____________\|________________________\|\n_____________91_______________________36\n	178 -- 184	65 -- 71	-21.8749 kcal/mol	0.694231 kcal/mol	6.38817 kcal/mol	156 216@LB@ \| \|@LB@5'-UUU...GCAAA A AUGGG...CGA-3'@LB@ AAACA AAC AUAUAACAUCACGA@LB@ \|\|\|\|\| \|\|\| \|:\|:\|\|\|\|\|\|\|\|:\|@LB@ UUUGU UUG UGUGUUGUAGUGUU@LB@3'-UUU...UAACG G U GGCAU...UCA-5'@LB@ \| \|@LB@ 91 36@LB@@LB@@LB@Energy -17.90 kcal/mol@LB@Hybridization Energy -21.8749 kcal/mol@LB@Unfolding Energy - mRNA 0.694231 kcal/mol@LB@Unfolding Energy - sRNA 6.38817 kcal/mol@LB@@LB@Position - mRNA 157 -- 215@LB@Position - sRNA 37 -- 90@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 65 -- 71@LB@
61	0.002902	0.1596	stm3567	livJ	-18.03	0.037474	150 -- 196	40 -- 87	high-affinity branched-chain amino acid transporter		_____________149_______________________197\n_____________\|_________________________\|\n5'-CGG...ACAAU_____C____________A______AGAAU...CCG-3'\n______________AACAC_ACAACACA_CGU_ACAACC\n______________\|\|\|\|\|_\|\|\|\|\|\|\|\|_\|:\|_\|\|\|\|\|\|\n______________UUGUG_UGUUGUGU_GUA_UGUUGG\n3'-UUU...AACGU_____U________U___G______CAUUC...UCA-5'\n_____________\|_________________________\|\n_____________88________________________39\n	157 -- 163	74 -- 80	-27.1738 kcal/mol	3.63117 kcal/mol	8.28637 kcal/mol	149 197@LB@ \| \|@LB@5'-CGG...ACAAU C A AGAAU...CCG-3'@LB@ AACAC ACAACACA CGU ACAACC@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\| \|:\| \|\|\|\|\|\|@LB@ UUGUG UGUUGUGU GUA UGUUGG@LB@3'-UUU...AACGU U U G CAUUC...UCA-5'@LB@ \| \|@LB@ 88 39@LB@@LB@@LB@Energy -18.03 kcal/mol@LB@Hybridization Energy -27.1738 kcal/mol@LB@Unfolding Energy - mRNA 3.63117 kcal/mol@LB@Unfolding Energy - sRNA 8.28637 kcal/mol@LB@@LB@Position - mRNA 150 -- 196@LB@Position - sRNA 40 -- 87@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 74 -- 80@LB@
168	0.009144	0.1938	stm3609	yhjE	-18.08	0.036777	202 -- 261	35 -- 91	MFS transporter		_____________201__________________________________262\n_____________\|____________________________________\|\n5'-UAA...UAGUA_______A__C_____________U_____A_____AGGAA...UUG-3'\n______________UGCAAGC_AC_GC__CACAACA_C_CGACC_UGAGC\n______________\|\|\|\|\|:\|_\|\|_:\|__\|\|\|\|\|\|\|_\|_\|:\|\|\|_\|:\|\|\|\n______________ACGUUUG_UG_UG__GUGUUGU_G_GUUGG_AUUCG\n3'-UUU...GGUUA__________U__UU_______A_U_____C_____GUUUU...UCA-5'\n_____________\|____________________________________\|\n_____________92___________________________________34\n	215 -- 221	71 -- 77	-32.2191 kcal/mol	4.27941 kcal/mol	11.5198 kcal/mol	201 262@LB@ \| \|@LB@5'-UAA...UAGUA A C U A AGGAA...UUG-3'@LB@ UGCAAGC AC GC CACAACA C CGACC UGAGC@LB@ \|\|\|\|\|:\| \|\| :\| \|\|\|\|\|\|\| \| \|:\|\|\| \|:\|\|\|@LB@ ACGUUUG UG UG GUGUUGU G GUUGG AUUCG@LB@3'-UUU...GGUUA U UU A U C GUUUU...UCA-5'@LB@ \| \|@LB@ 92 34@LB@@LB@@LB@Energy -18.08 kcal/mol@LB@Hybridization Energy -32.2191 kcal/mol@LB@Unfolding Energy - mRNA 4.27941 kcal/mol@LB@Unfolding Energy - sRNA 11.5198 kcal/mol@LB@@LB@Position - mRNA 202 -- 261@LB@Position - sRNA 35 -- 91@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 71 -- 77@LB@
159	0.008305	0.1845	stm3625	yhjV	-13.06	0.235438	203 -- 240	55 -- 86	transporter		_____________202________________________241\n_____________\|__________________________\|\n5'-UUA...UAUUU_____________CUCUA________CGACA...UCU-3'\n______________UGGGCAG__GGGG______UGCAGGA\n______________\|\|\|:\|\|\|__:\|\|\|______\|:\|\|\|\|\|\n______________ACCUGUC__UCCC______AUGUCCU\n3'-UUU...GUGAU_______UG____AUUUAC_______UCACU...UCA-5'\n_____________\|__________________________\|\n_____________87_________________________54\n	202 -- 208	139 -- 145	-24.2103 kcal/mol	7.6176 kcal/mol	3.71206 kcal/mol	202 241@LB@ \| \|@LB@5'-UUA...UAUUU CUCUA CGACA...UCU-3'@LB@ UGGGCAG GGGG UGCAGGA@LB@ \|\|\|:\|\|\| :\|\|\| \|:\|\|\|\|\|@LB@ ACCUGUC UCCC AUGUCCU@LB@3'-UUU...GUGAU UG AUUUAC UCACU...UCA-5'@LB@ \| \|@LB@ 87 54@LB@@LB@@LB@Energy -13.06 kcal/mol@LB@Hybridization Energy -24.2103 kcal/mol@LB@Unfolding Energy - mRNA 7.6176 kcal/mol@LB@Unfolding Energy - sRNA 3.71206 kcal/mol@LB@@LB@Position - mRNA 203 -- 240@LB@Position - sRNA 55 -- 86@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 139 -- 145@LB@
15	0.000269	0.06194	stm3630	dppA	-21.81	0.008578	158 -- 199	51 -- 92	ABC transporter substrate-binding protein		_____________157_____________________________________200\n_____________\|_______________________________________\|\n5'-AUU...AGCCU______AGG___A__________________________AGAAG...AUU-3'\n______________UUGCAA___GCA_AACAACAU_ACAUCACAAUUG_GAGC\n______________\|\|\|\|\|\|___:\|\|_\|\|\|\|\|\|\|:_\|\|\|\|\|\|\|\|\|::\|_:\|\|\|\n______________AACGUU___UGU_UUGUUGUG_UGUAGUGUUGGC_UUCG\n3'-UUU...UGGUU____________G________U____________A____GUUUU...UCA-5'\n_____________\|_______________________________________\|\n_____________93______________________________________50\n	183 -- 189	63 -- 69	-36.2763 kcal/mol	6.81868 kcal/mol	11.5217 kcal/mol	157 200@LB@ \| \|@LB@5'-AUU...AGCCU AGG A AGAAG...AUU-3'@LB@ UUGCAA GCA AACAACAU ACAUCACAAUUG GAGC@LB@ \|\|\|\|\|\| :\|\| \|\|\|\|\|\|\|: \|\|\|\|\|\|\|\|\|::\| :\|\|\|@LB@ AACGUU UGU UUGUUGUG UGUAGUGUUGGC UUCG@LB@3'-UUU...UGGUU G U A GUUUU...UCA-5'@LB@ \| \|@LB@ 93 50@LB@@LB@@LB@Energy -21.81 kcal/mol@LB@Hybridization Energy -36.2763 kcal/mol@LB@Unfolding Energy - mRNA 6.81868 kcal/mol@LB@Unfolding Energy - sRNA 11.5217 kcal/mol@LB@@LB@Position - mRNA 158 -- 199@LB@Position - sRNA 51 -- 92@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 63 -- 69@LB@
69	0.003278	0.1596	stm3675	sgbH	-16.55	0.065932	154 -- 200	33 -- 93	3-keto-L-gulonate-6-phosphate decarboxylase		_____________153_______________________201\n_____________\|_________________________\|\n5'-UUC...CAGUC__G_____GCC______________CCUGC...AGG-3'\n______________UG_AAGCA___CAACGCGAUGUCGC\n______________\|\|_\|\|:\|\|___\|\|\|\|:\|:\|::\|\|:\|\n______________AC_UUUGU___GUUGUGUUGUAGUG\n3'-UUU...GGUUA__G_____GUU______________UUGGC...UCA-5'\n_____________\|_________________________\|\n_____________94________________________32\n	258 -- 264	71 -- 77	-24.2274 kcal/mol	7.7572 kcal/mol	5.6854 kcal/mol	153 201@LB@ \| \|@LB@5'-UUC...CAGUC G GCC CCUGC...AGG-3'@LB@ UG AAGCA CAACGCGAUGUCGC@LB@ \|\| \|\|:\|\| \|\|\|\|:\|:\|::\|\|:\|@LB@ AC UUUGU GUUGUGUUGUAGUG@LB@3'-UUU...GGUUA G GUU UUGGC...UCA-5'@LB@ \| \|@LB@ 94 32@LB@@LB@@LB@Energy -16.55 kcal/mol@LB@Hybridization Energy -24.2274 kcal/mol@LB@Unfolding Energy - mRNA 7.7572 kcal/mol@LB@Unfolding Energy - sRNA 5.6854 kcal/mol@LB@@LB@Position - mRNA 154 -- 200@LB@Position - sRNA 33 -- 93@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 71 -- 77@LB@
41	0.001426	0.1215	stm3718	rfaI	-15.09	0.114319	193 -- 209	157 -- 173	lipopolysaccharide 1 3-galactosyltransferase	stm3717	_____________192_______________210\n_____________\|_________________\|\n5'-AUG...AAAAG___________A_____AAAUA...GGA-3'\n______________UGAUCACUAUG_GCAGA\n______________\|:\|\|\|\|\|\|\|\|\|_:\|\|\|\|\n______________AUUAGUGAUAC_UGUCU\n3'-UUU...AUGUA___________C_____GUCCC...UCA-5'\n_____________\|_________________\|\n_____________174_______________156\n	197 -- 203	163 -- 169	-20.9664 kcal/mol	2.81615 kcal/mol	3.98136 kcal/mol	192 210@LB@ \| \|@LB@5'-AUG...AAAAG A AAAUA...GGA-3'@LB@ UGAUCACUAUG GCAGA@LB@ \|:\|\|\|\|\|\|\|\|\| :\|\|\|\|@LB@ AUUAGUGAUAC UGUCU@LB@3'-UUU...AUGUA C GUCCC...UCA-5'@LB@ \| \|@LB@ 174 156@LB@@LB@@LB@Energy -15.09 kcal/mol@LB@Hybridization Energy -20.9664 kcal/mol@LB@Unfolding Energy - mRNA 2.81615 kcal/mol@LB@Unfolding Energy - sRNA 3.98136 kcal/mol@LB@@LB@Position - mRNA 193 -- 209@LB@Position - sRNA 157 -- 173@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 163 -- 169@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@
154	0.008185	0.1845	stm3738	yigC	-11.16	0.433331	228 -- 246	55 -- 74	similar to E. coli orf hypothetical protein (AAC76670.1); Blastp hit to AAC76670.1 (223 aa) 94% identity in aa 19 - 223		_____________227__________________247\n_____________\|____________________\|\n5'-UAA...ACCUC_____________AC_____AAAUG...UUA-3'\n______________GCA__UACAAUAA__CACAA\n______________\|\|\|__:\|\|\|\|:\|\|__\|\|\|\|\|\n______________CGU__GUGUUGUU__GUGUU\n3'-UUU...GUUAA___UU_______________GUAGU...UCA-5'\n_____________\|____________________\|\n_____________75___________________54\n	27 -- 33	78 -- 84	-12.6647 kcal/mol	0.985902 kcal/mol	3.77104 kcal/mol	227 247@LB@ \| \|@LB@5'-UAA...ACCUC AC AAAUG...UUA-3'@LB@ GCA UACAAUAA CACAA@LB@ \|\|\| :\|\|\|\|:\|\| \|\|\|\|\|@LB@ CGU GUGUUGUU GUGUU@LB@3'-UUU...GUUAA UU GUAGU...UCA-5'@LB@ \| \|@LB@ 75 54@LB@@LB@@LB@Energy -11.16 kcal/mol@LB@Hybridization Energy -12.6647 kcal/mol@LB@Unfolding Energy - mRNA 0.985902 kcal/mol@LB@Unfolding Energy - sRNA 3.77104 kcal/mol@LB@@LB@Position - mRNA 228 -- 246@LB@Position - sRNA 55 -- 74@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 78 -- 84@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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