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: https://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
96	0.004303	0.1596	stm4243	yjbN	-11.74	0.363864	272 -- 280	155 -- 163	tRNA dihydrouridine(20/20a) synthase DusA	_____________271______________________________281\n_____________\|________________________________\|\n5'-UUA...UUAAU___AC_________C____A_____CCU____GGCAG...GUU-3'\n______________GGG____UGUACGG_GAAG_UGAAA___GGGG\n______________\|\|\|____\|\|\|\|\|:\|_\|\|\|\|_\|\|\|\|\|___:\|\|\|\n______________CCC____ACAUGUC_CUUC_ACUUU___UCCC\n3'-UUU...UCUGU___AUUU__________________U______AUCAG...UCA-5'\n_____________\|________________________________\|\n_____________164______________________________154\n	58 -- 64	141 -- 147	-26.0653 kcal/mol	8.12251 kcal/mol	7.07058 kcal/mol	271 281@LB@ \| \|@LB@5'-UUA...UUAAU AC C A CCU GGCAG...GUU-3'@LB@ GGG UGUACGG GAAG UGAAA GGGG@LB@ \|\|\| \|\|\|\|\|:\| \|\|\|\| \|\|\|\|\| :\|\|\|@LB@ CCC ACAUGUC CUUC ACUUU UCCC@LB@3'-UUU...UCUGU AUUU U AUCAG...UCA-5'@LB@ \| \|@LB@ 164 154@LB@@LB@@LB@Energy -11.74 kcal/mol@LB@Hybridization Energy -26.0653 kcal/mol@LB@Unfolding Energy - mRNA 8.12251 kcal/mol@LB@Unfolding Energy - sRNA 7.07058 kcal/mol@LB@@LB@Position - mRNA 272 -- 280@LB@Position - sRNA 155 -- 163@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 141 -- 147@LB@
123	0.006073	0.1758	stm4355	yjeS	-17.69	0.042665	80 -- 140	31 -- 90	putative Fe-S protein	_____________79______________________________141\n_____________\|_______________________________\|\n_______5'-CGUU______________C________________AGUGU...UUA-3'\n______________GUUGC___CAUGAC_ACACAACA_C_CAGCC\n______________:\|\|\|\|___\|\|::\|\|_\|\|\|\|\|\|\|\|_\|_\|\|:\|\|\n______________UAACG___GUGUUG_UGUGUUGU_G_GUUGG\n3'-UUU...CUGGU_____UUU______U________A_U_____CAUUC...UCA-5'\n_____________\|_______________________________\|\n_____________91______________________________30\n	18 -- 24	71 -- 77	-27.2663 kcal/mol	5.13395 kcal/mol	8.62086 kcal/mol	79 141@LB@ \| \|@LB@ 5'-CGUU C AGUGU...UUA-3'@LB@ GUUGC CAUGAC ACACAACA C CAGCC@LB@ :\|\|\|\| \|\|::\|\| \|\|\|\|\|\|\|\| \| \|\|:\|\|@LB@ UAACG GUGUUG UGUGUUGU G GUUGG@LB@3'-UUU...CUGGU UUU U A U CAUUC...UCA-5'@LB@ \| \|@LB@ 91 30@LB@@LB@@LB@Energy -17.69 kcal/mol@LB@Hybridization Energy -27.2663 kcal/mol@LB@Unfolding Energy - mRNA 5.13395 kcal/mol@LB@Unfolding Energy - sRNA 8.62086 kcal/mol@LB@@LB@Position - mRNA 80 -- 140@LB@Position - sRNA 31 -- 90@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 71 -- 77@LB@
77	0.003608	0.1596	stm4473	yjgM	-11.12	0.437983	252 -- 285	42 -- 82	GNAT family N-acetyltransferase	_____________251________________286\n_____________\|__________________\|\n5'-AUU...CGCCG________CC___C____AUGCC...ACG-3'\n______________AAUCACUA___GC_GACA\n______________\|\|\|\|\|\|\|\|___:\|_\|\|\|\|\n______________UUAGUGAU___UG_CUGU\n3'-UUU...UGUAA________ACC__U____CCCAU...UCA-5'\n_____________\|__________________\|\n_____________83_________________41\n	240 -- 246	165 -- 171	-13.0222 kcal/mol	3.39479 kcal/mol	3.49149 kcal/mol	251 286@LB@ \| \|@LB@5'-AUU...CGCCG CC C AUGCC...ACG-3'@LB@ AAUCACUA GC GACA@LB@ \|\|\|\|\|\|\|\| :\| \|\|\|\|@LB@ UUAGUGAU UG CUGU@LB@3'-UUU...UGUAA ACC U CCCAU...UCA-5'@LB@ \| \|@LB@ 83 41@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -13.0222 kcal/mol@LB@Unfolding Energy - mRNA 3.39479 kcal/mol@LB@Unfolding Energy - sRNA 3.49149 kcal/mol@LB@@LB@Position - mRNA 252 -- 285@LB@Position - sRNA 42 -- 82@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 165 -- 171@LB@
48	0.001762	0.1291	stm4523	yjiW	-20.55	0.014078	157 -- 299	40 -- 186	endoribonuclease SymE	_____________156____________________________________________________________________________________________300\n_____________\|______________________________________________________________________________________________\|\n5'-GUG...AUUUU____AA___CCA__A__A_______CCAUUCU__________CG______UC__GAAGUCUCCC___________C______CUU_________UAUGC...AUU-3'\n______________AGGG__UAG___UC_UG_CUACCGU_______AUUGCAGAUC___UGCGA__CA__________CAACAA_AUAA_CGUCAC___ACCGUGAGU\n______________\|\|\|\|__\|\|\|___\|\|_:\|_\|\|\|\|\|\|\|_______\|\|:\|\|\|\|\|:\|___\|\|\|:\|__\|\|__________\|\|\|\|\|\|_\|:\|\|_\|:\|\|\|\|___\|\|\|\|\|:\|\|:\n______________UCCC__AUC___AG_GC_GAUGGCA_______UAGCGUCUGG___ACGUU__GU__________GUUGUU_UGUU_GUAGUG___UGGCAUUCG\n3'-UUU...CUUUU______________A__________CCAGACU__________UUA_____U___________________G___________U___________GUUUU...UCA-5'\n_____________\|______________________________________________________________________________________________\|\n_____________187____________________________________________________________________________________________39\n	222 -- 228	95 -- 101	-59.8396 kcal/mol	18.2388 kcal/mol	27.0823 kcal/mol	156 300@LB@ \| \|@LB@5'-GUG...AUUUU AA CCA A A CCAUUCU CG UC GAAGUCUCCC C CUU UAUGC...AUU-3'@LB@ AGGG UAG UC UG CUACCGU AUUGCAGAUC UGCGA CA CAACAA AUAA CGUCAC ACCGUGAGU@LB@ \|\|\|\| \|\|\| \|\| :\| \|\|\|\|\|\|\| \|\|:\|\|\|\|\|:\| \|\|\|:\| \|\| \|\|\|\|\|\| \|:\|\| \|:\|\|\|\| \|\|\|\|\|:\|\|:@LB@ UCCC AUC AG GC GAUGGCA UAGCGUCUGG ACGUU GU GUUGUU UGUU GUAGUG UGGCAUUCG@LB@3'-UUU...CUUUU A CCAGACU UUA U G U GUUUU...UCA-5'@LB@ \| \|@LB@ 187 39@LB@@LB@@LB@Energy -20.55 kcal/mol@LB@Hybridization Energy -59.8396 kcal/mol@LB@Unfolding Energy - mRNA 18.2388 kcal/mol@LB@Unfolding Energy - sRNA 27.0823 kcal/mol@LB@@LB@Position - mRNA 157 -- 299@LB@Position - sRNA 40 -- 186@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 95 -- 101@LB@
144	0.00736	0.182	stm4559	yjjG	-11.80	0.356804	189 -- 218	128 -- 159	putative haloacid dehalogenase-like hydrolase	_____________188_________________________________219\n_____________\|___________________________________\|\n5'-UUG...AUAAA_G_____A____U__________________CU__AUUUU...UCA-3'\n______________A_AGGCA_GGUG_AAUG_AU__GAAGUGGGA__GG\n______________\|_\|\|:\|\|_\|\|\|:_\|\|\|\|_\|:__\|\|\|\|\|\|::\|__\|\|\n______________U_UCUGU_CCAU_UUAC_UG__CUUCACUUU__CC\n3'-UUU...AUACC_G_____C_________A__UC_________UU__CAUCA...UCA-5'\n_____________\|___________________________________\|\n_____________160_________________________________127\n	208 -- 214	132 -- 138	-24.694 kcal/mol	5.33554 kcal/mol	7.83417 kcal/mol	188 219@LB@ \| \|@LB@5'-UUG...AUAAA G A U CU AUUUU...UCA-3'@LB@ A AGGCA GGUG AAUG AU GAAGUGGGA GG@LB@ \| \|\|:\|\| \|\|\|: \|\|\|\| \|: \|\|\|\|\|\|::\| \|\|@LB@ U UCUGU CCAU UUAC UG CUUCACUUU CC@LB@3'-UUU...AUACC G C A UC UU CAUCA...UCA-5'@LB@ \| \|@LB@ 160 127@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -24.694 kcal/mol@LB@Unfolding Energy - mRNA 5.33554 kcal/mol@LB@Unfolding Energy - sRNA 7.83417 kcal/mol@LB@@LB@Position - mRNA 189 -- 218@LB@Position - sRNA 128 -- 159@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 132 -- 138@LB@
105	0.005236	0.1728	stm4566	yjjI	-12.28	0.305832	96 -- 137	40 -- 77	YjjI family glycine radical enzyme	_____________95________________138\n_____________\|_________________\|\n5'-ACA...UUUUC____________U____CCGGC...UGG-3'\n______________UACAAUAGCGCA_CGUC\n______________:\|\|\|\|:\|:\|:\|\|_\|:\|\|\n______________GUGUUGUUGUGU_GUAG\n3'-UUU...CGUUU____________U____UGUUG...UCA-5'\n_____________\|_________________\|\n_____________78________________39\n	167 -- 173	74 -- 80	-18.3997 kcal/mol	3.44142 kcal/mol	3.92987 kcal/mol	95 138@LB@ \| \|@LB@5'-ACA...UUUUC U CCGGC...UGG-3'@LB@ UACAAUAGCGCA CGUC@LB@ :\|\|\|\|:\|:\|:\|\| \|:\|\|@LB@ GUGUUGUUGUGU GUAG@LB@3'-UUU...CGUUU U UGUUG...UCA-5'@LB@ \| \|@LB@ 78 39@LB@@LB@@LB@Energy -12.28 kcal/mol@LB@Hybridization Energy -18.3997 kcal/mol@LB@Unfolding Energy - mRNA 3.44142 kcal/mol@LB@Unfolding Energy - sRNA 3.92987 kcal/mol@LB@@LB@Position - mRNA 96 -- 137@LB@Position - sRNA 40 -- 77@LB@Position Seed - mRNA 167 -- 173@LB@Position Seed - sRNA 74 -- 80@LB@
72	0.003348	0.1596	stm0849	yliB	-19.23	0.023527	175 -- 193	139 -- 162	glutathione ABC transporter substrate-binding protein GsiB	_____________174______________________194\n_____________\|________________________\|\n5'-GUU...AUUCA____________UU__________GAACA...CGG-3'\n______________GACAGGCAGGGU_______CAGGA\n______________\|\|\|\|\|:\|\|\|\|\|\|_______\|\|\|\|\|\n______________CUGUCUGUCCCA_______GUCCU\n3'-UUU...GAUAC____________UUUACAU_____UCACU...UCA-5'\n_____________\|________________________\|\n_____________163______________________138\n	180 -- 186	151 -- 157	-27.2027 kcal/mol	3.52422 kcal/mol	3.69132 kcal/mol	174 194@LB@ \| \|@LB@5'-GUU...AUUCA UU GAACA...CGG-3'@LB@ GACAGGCAGGGU CAGGA@LB@ \|\|\|\|\|:\|\|\|\|\|\| \|\|\|\|\|@LB@ CUGUCUGUCCCA GUCCU@LB@3'-UUU...GAUAC UUUACAU UCACU...UCA-5'@LB@ \| \|@LB@ 163 138@LB@@LB@@LB@Energy -19.23 kcal/mol@LB@Hybridization Energy -27.2027 kcal/mol@LB@Unfolding Energy - mRNA 3.52422 kcal/mol@LB@Unfolding Energy - sRNA 3.69132 kcal/mol@LB@@LB@Position - mRNA 175 -- 193@LB@Position - sRNA 139 -- 162@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 151 -- 157@LB@
145	0.007435	0.1826	stm1822	yoaB	-15.17	0.110813	243 -- 269	162 -- 185	similar to E. coli orf hypothetical protein (AAC74879.1); Blastp hit to AAC74879.1 (130 aa) 92% identity in aa 17 - 130	_____________242______________________270\n_____________\|________________________\|\n5'-GUG...AUUUG___AG_____UAU_U_________AAGGC...CCG-3'\n______________CAC___GGAU___G_CAGGGUAGA\n______________\|\|\|___\|\|\|:___\|_\|\|\|\|\|\|\|:\|\n______________GUG___CCUG___C_GUCCCAUUU\n3'-UUU...AAUUA___AUA____U___U_________ACAUG...UCA-5'\n_____________\|________________________\|\n_____________186______________________161\n	106 -- 112	148 -- 154	-19.875 kcal/mol	5.9246 kcal/mol	4.20228 kcal/mol	242 270@LB@ \| \|@LB@5'-GUG...AUUUG AG UAU U AAGGC...CCG-3'@LB@ CAC GGAU G CAGGGUAGA@LB@ \|\|\| \|\|\|: \| \|\|\|\|\|\|\|:\|@LB@ GUG CCUG C GUCCCAUUU@LB@3'-UUU...AAUUA AUA U U ACAUG...UCA-5'@LB@ \| \|@LB@ 186 161@LB@@LB@@LB@Energy -15.17 kcal/mol@LB@Hybridization Energy -19.875 kcal/mol@LB@Unfolding Energy - mRNA 5.9246 kcal/mol@LB@Unfolding Energy - sRNA 4.20228 kcal/mol@LB@@LB@Position - mRNA 243 -- 269@LB@Position - sRNA 162 -- 185@LB@Position Seed - mRNA 106 -- 112@LB@Position Seed - sRNA 148 -- 154@LB@
118	0.005761	0.1738	stm1840	yobG	-17.14	0.052758	234 -- 267	153 -- 188	PhoP regulon feedback inhibition protein MgrB	_____________233____________________________________________________________________________________268\n_____________\|______________________________________________________________________________________\|\n5'-ACA...AGAGU___________AUUUCGAU____C_U_____GC________GGUA______U___U_____UGU________GUGUU_________GUGCG...AAU-3'\n______________GGAGUGAAAAA________GGGU_G_UCUCG__AUCGUGGU_______GUA_GCC_GUUGC___GGGCGCAG_____UAAUAUCAU\n______________\|:\|\|\|\|\|\|\|\|\|________\|\|\|\|_\|_\|\|\|\|\|__\|:\|\|\|\|\|\|_______\|:\|_:\|\|_:\|\|\|\|___:::\|:\|\|:_____:\|\|:\|\|\|\|:\n______________CUUCACUUUUU________CCCA_C_AGAGC__UGGCACCA_______CGU_UGG_UAACG___UUUGUGUU_____GUUGUAGUG\n3'-UUU...AUGUC_______________________U_______GA________GACUUAG___C___U________________GUUGU_________UUGGC...UCA-5'\n_____________\|______________________________________________________________________________________\|\n_____________189____________________________________________________________________________________152\n	274 -- 280	67 -- 73	-62.0847 kcal/mol	28.922 kcal/mol	22.0106 kcal/mol	233 268@LB@ \| \|@LB@5'-ACA...AGAGU AUUUCGAU C U GC GGUA U U UGU GUGUU GUGCG...AAU-3'@LB@ GGAGUGAAAAA GGGU G UCUCG AUCGUGGU GUA GCC GUUGC GGGCGCAG UAAUAUCAU@LB@ \|:\|\|\|\|\|\|\|\|\| \|\|\|\| \| \|\|\|\|\| \|:\|\|\|\|\|\| \|:\| :\|\| :\|\|\|\| :::\|:\|\|: :\|\|:\|\|\|\|:@LB@ CUUCACUUUUU CCCA C AGAGC UGGCACCA CGU UGG UAACG UUUGUGUU GUUGUAGUG@LB@3'-UUU...AUGUC U GA GACUUAG C U GUUGU UUGGC...UCA-5'@LB@ \| \|@LB@ 189 152@LB@@LB@@LB@Energy -17.14 kcal/mol@LB@Hybridization Energy -62.0847 kcal/mol@LB@Unfolding Energy - mRNA 28.922 kcal/mol@LB@Unfolding Energy - sRNA 22.0106 kcal/mol@LB@@LB@Position - mRNA 234 -- 267@LB@Position - sRNA 153 -- 188@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 67 -- 73@LB@
29	0.0007392	0.08814	stm3096	yqgE	-16.45	0.068552	198 -- 251	37 -- 84	DUF179 domain-containing protein	_____________197___________252\n_____________\|_____________\|\n5'-UGG...UAUAU_____________CAGGA...GCG-3'\n______________UUGCGAGCACAAC\n______________\|\|\|\|:\|:\|\|\|\|\|\|\n______________AACGUUUGUGUUG\n3'-UUU...UGGUU_____________UUGUG...UCA-5'\n_____________\|_____________\|\n_____________85____________36\n	284 -- 290	80 -- 86	-18.5161 kcal/mol	2.82597 kcal/mol	3.5889 kcal/mol	197 252@LB@ \| \|@LB@5'-UGG...UAUAU CAGGA...GCG-3'@LB@ UUGCGAGCACAAC@LB@ \|\|\|\|:\|:\|\|\|\|\|\|@LB@ AACGUUUGUGUUG@LB@3'-UUU...UGGUU UUGUG...UCA-5'@LB@ \| \|@LB@ 85 36@LB@@LB@@LB@Energy -16.45 kcal/mol@LB@Hybridization Energy -18.5161 kcal/mol@LB@Unfolding Energy - mRNA 2.82597 kcal/mol@LB@Unfolding Energy - sRNA 3.5889 kcal/mol@LB@@LB@Position - mRNA 198 -- 251@LB@Position - sRNA 37 -- 84@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 80 -- 86@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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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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