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
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@
65	0.003171	0.1596	stm0830	glnH	-11.06	0.446113	180 -- 193	153 -- 165	glutamine ABC transporter substrate-binding protein GlnH	_____________179____________194\n_____________\|______________\|\n5'-AGA...GCCCC_________AA___AAAUG...CGG-3'\n______________GUGGAUAGA__AGG\n______________:\|\|\|\|:\|\|\|__\|\|\|\n______________UACCUGUCU__UCC\n3'-UUU...AGUGA_________G____CAUUU...UCA-5'\n_____________\|______________\|\n_____________166____________152\n	182 -- 188	157 -- 163	-15.2236 kcal/mol	3.11192 kcal/mol	2.82582 kcal/mol	179 194@LB@ \| \|@LB@5'-AGA...GCCCC AA AAAUG...CGG-3'@LB@ GUGGAUAGA AGG@LB@ :\|\|\|\|:\|\|\| \|\|\|@LB@ UACCUGUCU UCC@LB@3'-UUU...AGUGA G CAUUU...UCA-5'@LB@ \| \|@LB@ 166 152@LB@@LB@@LB@Energy -11.06 kcal/mol@LB@Hybridization Energy -15.2236 kcal/mol@LB@Unfolding Energy - mRNA 3.11192 kcal/mol@LB@Unfolding Energy - sRNA 2.82582 kcal/mol@LB@@LB@Position - mRNA 180 -- 193@LB@Position - sRNA 153 -- 165@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 157 -- 163@LB@
66	0.003179	0.1596	stm0264	dnaQ	-14.69	0.132400	209 -- 271	35 -- 91	DNA polymerase III epsilon subunit	_____________208__________________________________________272\n_____________\|____________________________________________\|\n5'-CGG...CGCAA______C__AAAU_______AU_______U___AUU________GAUUG...UCG-3'\n______________GUCUGA_AU____GACCGAU___GAGCAC_GCA___ACACGACA\n______________\|\|\|\|\|\|_\|\|____\|\|\|\|:\|\|___:\|:\|\|\|_:\|\|___\|\|\|\|:\|\|\|\n______________CAGACU_UA____CUGGUUA___UUUGUG_UGU___UGUGUUGU\n3'-UUU...GGCAC_________GCGU_______ACG______U______________AGUGU...UCA-5'\n_____________\|____________________________________________\|\n_____________92___________________________________________34\n	217 -- 223	71 -- 77	-33.8618 kcal/mol	8.04508 kcal/mol	13.5573 kcal/mol	208 272@LB@ \| \|@LB@5'-CGG...CGCAA C AAAU AU U AUU GAUUG...UCG-3'@LB@ GUCUGA AU GACCGAU GAGCAC GCA ACACGACA@LB@ \|\|\|\|\|\| \|\| \|\|\|\|:\|\| :\|:\|\|\| :\|\| \|\|\|\|:\|\|\|@LB@ CAGACU UA CUGGUUA UUUGUG UGU UGUGUUGU@LB@3'-UUU...GGCAC GCGU ACG U AGUGU...UCA-5'@LB@ \| \|@LB@ 92 34@LB@@LB@@LB@Energy -14.69 kcal/mol@LB@Hybridization Energy -33.8618 kcal/mol@LB@Unfolding Energy - mRNA 8.04508 kcal/mol@LB@Unfolding Energy - sRNA 13.5573 kcal/mol@LB@@LB@Position - mRNA 209 -- 271@LB@Position - sRNA 35 -- 91@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 71 -- 77@LB@
67	0.003193	0.1596	stm0122	ftsI	-11.87	0.349270	199 -- 241	52 -- 90	peptidoglycan glycosyltransferase FtsI	_____________198_______________________242\n_____________\|_________________________\|\n5'-GUU...CGCGA____UUG_____UG___________CUGAU...UGG-3'\n______________UGCA___GACAU__AAUGGCGCAAC\n______________\|\|\|\|___:\|\|\|:__\|\|:::\|:\|\|\|\|\n______________ACGU___UUGUG__UUGUUGUGUUG\n3'-UUU...GGUUA_________________________UAGUG...UCA-5'\n_____________\|_________________________\|\n_____________91________________________51\n	62 -- 68	72 -- 78	-17.673 kcal/mol	4.85802 kcal/mol	3.80548 kcal/mol	198 242@LB@ \| \|@LB@5'-GUU...CGCGA UUG UG CUGAU...UGG-3'@LB@ UGCA GACAU AAUGGCGCAAC@LB@ \|\|\|\| :\|\|\|: \|\|:::\|:\|\|\|\|@LB@ ACGU UUGUG UUGUUGUGUUG@LB@3'-UUU...GGUUA UAGUG...UCA-5'@LB@ \| \|@LB@ 91 51@LB@@LB@@LB@Energy -11.87 kcal/mol@LB@Hybridization Energy -17.673 kcal/mol@LB@Unfolding Energy - mRNA 4.85802 kcal/mol@LB@Unfolding Energy - sRNA 3.80548 kcal/mol@LB@@LB@Position - mRNA 199 -- 241@LB@Position - sRNA 52 -- 90@LB@Position Seed - mRNA 62 -- 68@LB@Position Seed - sRNA 72 -- 78@LB@
68	0.003225	0.1596	stm3930	yifK	-15.10	0.113746	177 -- 247	44 -- 93	amino acid permease	_____________176____________________248\n_____________\|______________________\|\n5'-CUU...GAACC_______________UG_G___UUAUG...GCG-3'\n______________GUUGCAAACACGACA__A_GAU\n______________:\|\|\|\|\|\|\|\|\|\|:\|\|\|__\|_:\|:\n______________UAACGUUUGUGUUGU__U_UUG\n3'-UUU...CUGGU_______________UG_G___UAGUG...UCA-5'\n_____________\|______________________\|\n_____________94_____________________43\n	185 -- 191	79 -- 85	-22.6062 kcal/mol	5.26496 kcal/mol	3.80917 kcal/mol	176 248@LB@ \| \|@LB@5'-CUU...GAACC UG G UUAUG...GCG-3'@LB@ GUUGCAAACACGACA A GAU@LB@ :\|\|\|\|\|\|\|\|\|\|:\|\|\| \| :\|:@LB@ UAACGUUUGUGUUGU U UUG@LB@3'-UUU...CUGGU UG G UAGUG...UCA-5'@LB@ \| \|@LB@ 94 43@LB@@LB@@LB@Energy -15.10 kcal/mol@LB@Hybridization Energy -22.6062 kcal/mol@LB@Unfolding Energy - mRNA 5.26496 kcal/mol@LB@Unfolding Energy - sRNA 3.80917 kcal/mol@LB@@LB@Position - mRNA 177 -- 247@LB@Position - sRNA 44 -- 93@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 79 -- 85@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@
70	0.003306	0.1596	stm2688	smpB	-12.25	0.308628	191 -- 230	36 -- 77	SsrA-binding protein	_____________190_________________231\n_____________\|___________________\|\n5'-AAU...GCAUA____UUCC__U________AUCGU...GUC-3'\n______________GCAA____CA_CAACAUAA\n______________\|\|\|\|____\|\|_\|\|\|\|\|:\|\|\n______________CGUU____GU_GUUGUGUU\n3'-UUU...GUUAA____UGU___U________GUAGU...UCA-5'\n_____________\|___________________\|\n_____________78__________________35\n	26 -- 32	73 -- 79	-12.551 kcal/mol	1.44298 kcal/mol	3.77104 kcal/mol	190 231@LB@ \| \|@LB@5'-AAU...GCAUA UUCC U AUCGU...GUC-3'@LB@ GCAA CA CAACAUAA@LB@ \|\|\|\| \|\| \|\|\|\|\|:\|\|@LB@ CGUU GU GUUGUGUU@LB@3'-UUU...GUUAA UGU U GUAGU...UCA-5'@LB@ \| \|@LB@ 78 35@LB@@LB@@LB@Energy -12.25 kcal/mol@LB@Hybridization Energy -12.551 kcal/mol@LB@Unfolding Energy - mRNA 1.44298 kcal/mol@LB@Unfolding Energy - sRNA 3.77104 kcal/mol@LB@@LB@Position - mRNA 191 -- 230@LB@Position - sRNA 36 -- 77@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 73 -- 79@LB@
71	0.003339	0.1596	stm0105	yabI	-14.10	0.163814	151 -- 168	141 -- 162	similar to E. coli orf hypothetical protein (AAC73176.1); Blastp hit to AAC73176.1 (254 aa) 89% identity in aa 1 - 253	_____________150____________________169\n_____________\|______________________\|\n5'-UGA...ACGAA__G___________________AAUCC...GGU-3'\n______________GG_GGACGGGGUAA____GCAG\n______________\|:_:\|\|\|:\|\|\|\|\|\|____:\|\|\|\n______________CU_UCUGUCCCAUU____UGUC\n3'-UUU...GAUAC__G___________UACA____CUUCA...UCA-5'\n_____________\|______________________\|\n_____________163____________________140\n	158 -- 164	149 -- 155	-23.8591 kcal/mol	5.26969 kcal/mol	3.68511 kcal/mol	150 169@LB@ \| \|@LB@5'-UGA...ACGAA G AAUCC...GGU-3'@LB@ GG GGACGGGGUAA GCAG@LB@ \|: :\|\|\|:\|\|\|\|\|\| :\|\|\|@LB@ CU UCUGUCCCAUU UGUC@LB@3'-UUU...GAUAC G UACA CUUCA...UCA-5'@LB@ \| \|@LB@ 163 140@LB@@LB@@LB@Energy -14.10 kcal/mol@LB@Hybridization Energy -23.8591 kcal/mol@LB@Unfolding Energy - mRNA 5.26969 kcal/mol@LB@Unfolding Energy - sRNA 3.68511 kcal/mol@LB@@LB@Position - mRNA 151 -- 168@LB@Position - sRNA 141 -- 162@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 149 -- 155@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@
73	0.003444	0.1596	stm1437	ydhM	-18.33	0.033340	6 -- 47	35 -- 81	TetR family transcriptional regulator	_____________5_______________________48\n_____________\|_______________________\|\n5'-CGG...CAAAC___________CC___G______UGCUG...AGU-3'\n______________CGAACACGAUA__CGC_AACAUC\n______________\|:\|\|\|\|\|:\|:\|__\|:\|_\|\|\|\|\|\|\n______________GUUUGUGUUGU__GUG_UUGUAG\n3'-UUU...UUAAC___________U___________UGUUG...UCA-5'\n_____________\|_______________________\|\n_____________82______________________34\n	219 -- 225	79 -- 85	-19.8292 kcal/mol	2.08213 kcal/mol	4.32311 kcal/mol	5 48@LB@ \| \|@LB@5'-CGG...CAAAC CC G UGCUG...AGU-3'@LB@ CGAACACGAUA CGC AACAUC@LB@ \|:\|\|\|\|\|:\|:\| \|:\| \|\|\|\|\|\|@LB@ GUUUGUGUUGU GUG UUGUAG@LB@3'-UUU...UUAAC U UGUUG...UCA-5'@LB@ \| \|@LB@ 82 34@LB@@LB@@LB@Energy -18.33 kcal/mol@LB@Hybridization Energy -19.8292 kcal/mol@LB@Unfolding Energy - mRNA 2.08213 kcal/mol@LB@Unfolding Energy - sRNA 4.32311 kcal/mol@LB@@LB@Position - mRNA 6 -- 47@LB@Position - sRNA 35 -- 81@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 79 -- 85@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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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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