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
184	0.01016	0.1966	stm1690	pspA	-15.34	0.103900	116 -- 183	38 -- 113	phage shock protein PspA	_____________115____________________________________________________184\n_____________\|______________________________________________________\|\n5'-GCC...UAUCA_____A____AAGU_G___C__A_______UUAAU__________G________CCGUU...UUC-3'\n______________GUGGU_UGAA____U_GCA_GC_AAUUGUA_____CAC_AUAGCA_GGCAUCGC\n______________\|\|\|\|\|_\|\|\|\|____\|_\|\|\|_:\|_\|\|\|\|\|:\|_____\|\|\|_\|:\|:\|\|_::\|\|\|\|:\|\n______________CACCA_ACUU____A_CGU_UG_UUAACGU_____GUG_UGUUGU_UUGUAGUG\n3'-UUU...GAUGG_____G_________G___C__G_______UU______U______G________UUGGC...UCA-5'\n_____________\|______________________________________________________\|\n_____________114____________________________________________________37\n	162 -- 168	67 -- 73	-39.4413 kcal/mol	11.996 kcal/mol	15.147 kcal/mol	115 184@LB@ \| \|@LB@5'-GCC...UAUCA A AAGU G C A UUAAU G CCGUU...UUC-3'@LB@ GUGGU UGAA U GCA GC AAUUGUA CAC AUAGCA GGCAUCGC@LB@ \|\|\|\|\| \|\|\|\| \| \|\|\| :\| \|\|\|\|\|:\| \|\|\| \|:\|:\|\| ::\|\|\|\|:\|@LB@ CACCA ACUU A CGU UG UUAACGU GUG UGUUGU UUGUAGUG@LB@3'-UUU...GAUGG G G C G UU U G UUGGC...UCA-5'@LB@ \| \|@LB@ 114 37@LB@@LB@@LB@Energy -15.34 kcal/mol@LB@Hybridization Energy -39.4413 kcal/mol@LB@Unfolding Energy - mRNA 11.996 kcal/mol@LB@Unfolding Energy - sRNA 15.147 kcal/mol@LB@@LB@Position - mRNA 116 -- 183@LB@Position - sRNA 38 -- 113@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 67 -- 73@LB@
100	0.00495	0.1728	stm1879	ptrB	-19.83	0.018631	144 -- 223	40 -- 120	oligopeptidase B	_____________143____________________________________________224\n_____________\|______________________________________________\|\n5'-AAG...UAUAA_________________AAGAAAAA_____A___U___________AAUCG...AGC-3'\n______________CAAAUAU__UAACGCAA________ACGAC_UGU__GCCAAAAGCC\n______________\|\|\|\|:\|:__:\|\|\|:\|\|\|________\|\|:\|\|_:\|\|__\|\|\|\|\|\|\|\|\|\|\n______________GUUUGUG__GUUGUGUU________UGUUG_GCA__CGGUUUUCGG\n3'-UUU...UUAAC_______UU________GUAG_____________UU__________GUAGU...UCA-5'\n_____________\|______________________________________________\|\n_____________121____________________________________________39\n	209 -- 215	49 -- 55	-34.4525 kcal/mol	3.62291 kcal/mol	15.2208 kcal/mol	143 224@LB@ \| \|@LB@5'-AAG...UAUAA AAGAAAAA A U AAUCG...AGC-3'@LB@ CAAAUAU UAACGCAA ACGAC UGU GCCAAAAGCC@LB@ \|\|\|\|:\|: :\|\|\|:\|\|\| \|\|:\|\| :\|\| \|\|\|\|\|\|\|\|\|\|@LB@ GUUUGUG GUUGUGUU UGUUG GCA CGGUUUUCGG@LB@3'-UUU...UUAAC UU GUAG UU GUAGU...UCA-5'@LB@ \| \|@LB@ 121 39@LB@@LB@@LB@Energy -19.83 kcal/mol@LB@Hybridization Energy -34.4525 kcal/mol@LB@Unfolding Energy - mRNA 3.62291 kcal/mol@LB@Unfolding Energy - sRNA 15.2208 kcal/mol@LB@@LB@Position - mRNA 144 -- 223@LB@Position - sRNA 40 -- 120@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 49 -- 55@LB@
90	0.004161	0.1596	stm1124	putA	-17.89	0.039481	159 -- 201	125 -- 168	trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase	_____________158______________________________________________202\n_____________\|________________________________________________\|\n5'-UAA...CGCUA____U___UUA________A_C____A_____________________UGGGA...UAA-3'\n______________ACUA_UGG___GCAGAUAG_G_GAAU__ACAGG_AGU___AGAGGGUA\n______________\|\|\|\|_\|\|\|___:\|\|\|\|:\|\|_\|_:\|\|\|__\|\|\|\|\|_\|\|\|___\|:\|\|\|\|\|\|\n______________UGAU_ACC___UGUCUGUC_C_UUUA__UGUCC_UCA___UUUCCCAU\n3'-UUU...AUUAG___________________C_A____CA_____U___CUU________CAGAG...UCA-5'\n_____________\|________________________________________________\|\n_____________169______________________________________________124\n	195 -- 201	125 -- 131	-33.9858 kcal/mol	7.26317 kcal/mol	8.4265 kcal/mol	158 202@LB@ \| \|@LB@5'-UAA...CGCUA U UUA A C A UGGGA...UAA-3'@LB@ ACUA UGG GCAGAUAG G GAAU ACAGG AGU AGAGGGUA@LB@ \|\|\|\| \|\|\| :\|\|\|\|:\|\| \| :\|\|\| \|\|\|\|\| \|\|\| \|:\|\|\|\|\|\|@LB@ UGAU ACC UGUCUGUC C UUUA UGUCC UCA UUUCCCAU@LB@3'-UUU...AUUAG C A CA U CUU CAGAG...UCA-5'@LB@ \| \|@LB@ 169 124@LB@@LB@@LB@Energy -17.89 kcal/mol@LB@Hybridization Energy -33.9858 kcal/mol@LB@Unfolding Energy - mRNA 7.26317 kcal/mol@LB@Unfolding Energy - sRNA 8.4265 kcal/mol@LB@@LB@Position - mRNA 159 -- 201@LB@Position - sRNA 125 -- 168@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 125 -- 131@LB@
16	0.0002876	0.06194	stm1378	pykF	-16.63	0.064116	5 -- 66	31 -- 91	pyruvate kinase	_____________4____________________________________________________________________67\n_____________\|____________________________________________________________________\|\n_______5'-GGAC___A____U_______UA__AU____CCCUUC___U__________C______________A______UCUGC...UGA-3'\n______________UGU_AAAC_CAACGAC__AA__UAUC______CCG_UGGGCUGAAA_GC______GAGCAC_CAUUCC\n______________\|\|:_\|\|\|\|_\|\|\|\|:\|\|__\|\|__:\|\|\|______\|\|\|_\|::\|\|::\|\|\|_\|\|______\|\|:\|\|\|_\|\|\|\|\|\|\n______________ACG_UUUG_GUUGUUG__UU__GUAG______GGC_AUUCGGUUUU_CG______CUUGUG_GUAAGG\n3'-UUU...GGUUA________U_______UG________UGUU___________________GGUAGU______C______CUAUU...UCA-5'\n_____________\|____________________________________________________________________\|\n_____________92___________________________________________________________________30\n	14 -- 20	77 -- 83	-44.7981 kcal/mol	9.74365 kcal/mol	24.1415 kcal/mol	4 67@LB@ \| \|@LB@ 5'-GGAC A U UA AU CCCUUC U C A UCUGC...UGA-3'@LB@ UGU AAAC CAACGAC AA UAUC CCG UGGGCUGAAA GC GAGCAC CAUUCC@LB@ \|\|: \|\|\|\| \|\|\|\|:\|\| \|\| :\|\|\| \|\|\| \|::\|\|::\|\|\| \|\| \|\|:\|\|\| \|\|\|\|\|\|@LB@ ACG UUUG GUUGUUG UU GUAG GGC AUUCGGUUUU CG CUUGUG GUAAGG@LB@3'-UUU...GGUUA U UG UGUU GGUAGU C CUAUU...UCA-5'@LB@ \| \|@LB@ 92 30@LB@@LB@@LB@Energy -16.63 kcal/mol@LB@Hybridization Energy -44.7981 kcal/mol@LB@Unfolding Energy - mRNA 9.74365 kcal/mol@LB@Unfolding Energy - sRNA 24.1415 kcal/mol@LB@@LB@Position - mRNA 5 -- 66@LB@Position - sRNA 31 -- 91@LB@Position Seed - mRNA 14 -- 20@LB@Position Seed - sRNA 77 -- 83@LB@
179	0.009806	0.1951	stm3912	rep	-13.00	0.240883	219 -- 287	22 -- 83	ATP-dependent DNA helicase Rep	_____________218__________________________288\n_____________\|____________________________\|\n5'-AGU...UCCCA____UUUAAAUCCC______________CUGUC...CCA-3'\n______________UGCG__________GGC_CAACAACACG\n______________\|\|\|:__________::\|_\|\|\|\|\|\|\|\|\|:\n______________ACGU__________UUG_GUUGUUGUGU\n3'-UUU...GGUUA_________________U__________UGUAG...UCA-5'\n_____________\|____________________________\|\n_____________84___________________________21\n	222 -- 228	74 -- 80	-15.5311 kcal/mol	3.54327 kcal/mol	3.73631 kcal/mol	218 288@LB@ \| \|@LB@5'-AGU...UCCCA UUUAAAUCCC CUGUC...CCA-3'@LB@ UGCG GGC CAACAACACG@LB@ \|\|\|: ::\| \|\|\|\|\|\|\|\|\|:@LB@ ACGU UUG GUUGUUGUGU@LB@3'-UUU...GGUUA U UGUAG...UCA-5'@LB@ \| \|@LB@ 84 21@LB@@LB@@LB@Energy -13.00 kcal/mol@LB@Hybridization Energy -15.5311 kcal/mol@LB@Unfolding Energy - mRNA 3.54327 kcal/mol@LB@Unfolding Energy - sRNA 3.73631 kcal/mol@LB@@LB@Position - mRNA 219 -- 287@LB@Position - sRNA 22 -- 83@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 74 -- 80@LB@
56	0.002144	0.1363	pslt006	repA	-15.36	0.103288	219 -- 279	36 -- 87	DNA replication	_____________218_____________________280\n_____________\|_______________________\|\n5'-ACU...ACACC_______UGUU____U_______CGACA...CCC-3'\n______________CGAACAC_____CAC__CAUUAC\n______________\|:\|\|\|\|\|_____\|\|\|__\|\|\|:\|\|\n______________GUUUGUG_____GUG__GUAGUG\n3'-UUU...UUAAC_______UUGUU___UU______UUGGC...UCA-5'\n_____________\|_______________________\|\n_____________88______________________35\n	225 -- 231	83 -- 89	-15.7114 kcal/mol	3.78124 kcal/mol	5.66809 kcal/mol	218 280@LB@ \| \|@LB@5'-ACU...ACACC UGUU U CGACA...CCC-3'@LB@ CGAACAC CAC CAUUAC@LB@ \|:\|\|\|\|\| \|\|\| \|\|\|:\|\|@LB@ GUUUGUG GUG GUAGUG@LB@3'-UUU...UUAAC UUGUU UU UUGGC...UCA-5'@LB@ \| \|@LB@ 88 35@LB@@LB@@LB@Energy -15.36 kcal/mol@LB@Hybridization Energy -15.7114 kcal/mol@LB@Unfolding Energy - mRNA 3.78124 kcal/mol@LB@Unfolding Energy - sRNA 5.66809 kcal/mol@LB@@LB@Position - mRNA 219 -- 279@LB@Position - sRNA 36 -- 87@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 83 -- 89@LB@
187	0.01045	0.1967	stm4558	rimI	-18.19	0.035171	194 -- 252	42 -- 91	ribosomal-protein-alanine N-acetyltransferase	_____________193______________________________________253\n_____________\|________________________________________\|\n5'-GAC...AAAUC_________G__________UUCUAUCCUCAG________AUCUC...UCG-3'\n______________UGCGAACAU___AACACGAU____________CACGACCG\n______________\|\|\|:\|\|\|\|:___\|\|\|\|\|:\|:____________\|\|\|:\|\|\|\|\n______________ACGUUUGUG___UUGUGUUG____________GUGUUGGC\n3'-UUU...GGUUA_________UUG________UA__________________AUUCG...UCA-5'\n_____________\|________________________________________\|\n_____________92_______________________________________41\n	225 -- 231	62 -- 68	-28.9909 kcal/mol	5.96366 kcal/mol	8.62907 kcal/mol	193 253@LB@ \| \|@LB@5'-GAC...AAAUC G UUCUAUCCUCAG AUCUC...UCG-3'@LB@ UGCGAACAU AACACGAU CACGACCG@LB@ \|\|\|:\|\|\|\|: \|\|\|\|\|:\|: \|\|\|:\|\|\|\|@LB@ ACGUUUGUG UUGUGUUG GUGUUGGC@LB@3'-UUU...GGUUA UUG UA AUUCG...UCA-5'@LB@ \| \|@LB@ 92 41@LB@@LB@@LB@Energy -18.19 kcal/mol@LB@Hybridization Energy -28.9909 kcal/mol@LB@Unfolding Energy - mRNA 5.96366 kcal/mol@LB@Unfolding Energy - sRNA 8.62907 kcal/mol@LB@@LB@Position - mRNA 194 -- 252@LB@Position - sRNA 42 -- 91@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 62 -- 68@LB@
116	0.005629	0.1728	stm2662	rluD	-17.46	0.046576	204 -- 257	36 -- 86	23S rRNA pseudouridine(1911/1915/1917) synthase	_____________203____________________258\n_____________\|______________________\|\n5'-UGA...UAUAU__________G___________CGCAA...GUU-3'\n______________GGCACAACGA_UACAAC_UCAC\n______________::\|\|\|\|\|\|:\|_:\|\|\|\|\|_\|\|\|\|\n______________UUGUGUUGUU_GUGUUG_AGUG\n3'-UUU...AACGU_________________U____UUGGC...UCA-5'\n_____________\|______________________\|\n_____________87_____________________35\n	206 -- 212	78 -- 84	-22.2469 kcal/mol	4.97176 kcal/mol	5.3513 kcal/mol	203 258@LB@ \| \|@LB@5'-UGA...UAUAU G CGCAA...GUU-3'@LB@ GGCACAACGA UACAAC UCAC@LB@ ::\|\|\|\|\|\|:\| :\|\|\|\|\| \|\|\|\|@LB@ UUGUGUUGUU GUGUUG AGUG@LB@3'-UUU...AACGU U UUGGC...UCA-5'@LB@ \| \|@LB@ 87 35@LB@@LB@@LB@Energy -17.46 kcal/mol@LB@Hybridization Energy -22.2469 kcal/mol@LB@Unfolding Energy - mRNA 4.97176 kcal/mol@LB@Unfolding Energy - sRNA 5.3513 kcal/mol@LB@@LB@Position - mRNA 204 -- 257@LB@Position - sRNA 36 -- 86@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 78 -- 84@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@
167	0.009062	0.1932	stm2673	rplS	-14.99	0.118272	119 -- 180	38 -- 88	50S ribosomal protein L19	_____________118_________________181\n_____________\|___________________\|\n5'-GAU...GUUCA_____G____C________GCAGC...UUG-3'\n______________AAACA_AACA_GCACAACA\n______________\|\|\|\|\|_\|\|\|\|_:\|\|\|\|\|\|\|\n______________UUUGU_UUGU_UGUGUUGU\n3'-UUU...UAACG_____G_____________AGUGU...UCA-5'\n_____________\|___________________\|\n_____________89__________________37\n	126 -- 132	71 -- 77	-18.964 kcal/mol	3.18358 kcal/mol	3.68874 kcal/mol	118 181@LB@ \| \|@LB@5'-GAU...GUUCA G C GCAGC...UUG-3'@LB@ AAACA AACA GCACAACA@LB@ \|\|\|\|\| \|\|\|\| :\|\|\|\|\|\|\|@LB@ UUUGU UUGU UGUGUUGU@LB@3'-UUU...UAACG G AGUGU...UCA-5'@LB@ \| \|@LB@ 89 37@LB@@LB@@LB@Energy -14.99 kcal/mol@LB@Hybridization Energy -18.964 kcal/mol@LB@Unfolding Energy - mRNA 3.18358 kcal/mol@LB@Unfolding Energy - sRNA 3.68874 kcal/mol@LB@@LB@Position - mRNA 119 -- 180@LB@Position - sRNA 38 -- 88@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 71 -- 77@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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