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
191	0.01055	0.1967	stm0634	ybeF	-18.83	0.027435	210 -- 262	35 -- 82	putative LysR family transcriptional regulator		_____________209____________________________________________________________263\n_____________\|______________________________________________________________\|\n5'-GCU...CGUGA____UA_____C_G____AAAG_______________UCAACA____________AAC____AAUUU...UGU-3'\n______________GUGA__AUAAU_A_GCAG____ACAACCG___GCCGA______CCUA_CAGGACA___CGCA\n______________\|::\|__\|:\|\|:_\|_:\|\|:____\|\|\|\|\|\|\|___\|\|\|:\|______\|\|:\|_\|\|\|:\|\|\|___\|\|\|\|\n______________CGUU__UGUUG_U_UGUU____UGUUGGC___CGGUU______GGGU_GUCUUGU___GCGU\n3'-UUU...GUUAA____UG_____U_G____GUAG_______AUU_____UUC_______A______________AAGGC...UCA-5'\n_____________\|______________________________________________________________\|\n_____________83_____________________________________________________________34\n	227 -- 233	62 -- 68	-42.1612 kcal/mol	9.04443 kcal/mol	22.5095 kcal/mol	209 263@LB@ \| \|@LB@5'-GCU...CGUGA UA C G AAAG UCAACA AAC AAUUU...UGU-3'@LB@ GUGA AUAAU A GCAG ACAACCG GCCGA CCUA CAGGACA CGCA@LB@ \|::\| \|:\|\|: \| :\|\|: \|\|\|\|\|\|\| \|\|\|:\| \|\|:\| \|\|\|:\|\|\| \|\|\|\|@LB@ CGUU UGUUG U UGUU UGUUGGC CGGUU GGGU GUCUUGU GCGU@LB@3'-UUU...GUUAA UG U G GUAG AUU UUC A AAGGC...UCA-5'@LB@ \| \|@LB@ 83 34@LB@@LB@@LB@Energy -18.83 kcal/mol@LB@Hybridization Energy -42.1612 kcal/mol@LB@Unfolding Energy - mRNA 9.04443 kcal/mol@LB@Unfolding Energy - sRNA 22.5095 kcal/mol@LB@@LB@Position - mRNA 210 -- 262@LB@Position - sRNA 35 -- 82@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 62 -- 68@LB@
92	0.004229	0.1596	stm0669	phoL	-19.39	0.022083	221 -- 286	36 -- 89	putative phosphate starvation-inducible protein ATP-binding		_____________220__________________________________________________________________287\n_____________\|____________________________________________________________________\|\n5'-AAA...CGAUA_________G__GAACAGUUUGAAUAUA____C______AAUUAC___UU____________CA____CCGUC...GCC-3'\n______________CAGACACAA_AG________________GACA_UCGCGA_______CC__GAGCCCG_CAGA__ACGC\n______________\|\|:\|\|\|\|\|\|_\|:________________:\|\|\|_\|\|:\|:\|_______\|\|__:\|\|\|\|\|:_\|\|\|\|__\|\|\|\|\n______________GUUUGUGUU_UU________________UUGU_AGUGUU_______GG__UUCGGGU_GUCU__UGCG\n3'-UUU...UUAAC_________G__GUG________________________GGCAUUC__UU_______A____UG____UAAGG...UCA-5'\n_____________\|____________________________________________________________________\|\n_____________90___________________________________________________________________35\n	270 -- 276	47 -- 53	-43.5648 kcal/mol	9.30805 kcal/mol	22.4875 kcal/mol	220 287@LB@ \| \|@LB@5'-AAA...CGAUA G GAACAGUUUGAAUAUA C AAUUAC UU CA CCGUC...GCC-3'@LB@ CAGACACAA AG GACA UCGCGA CC GAGCCCG CAGA ACGC@LB@ \|\|:\|\|\|\|\|\| \|: :\|\|\| \|\|:\|:\| \|\| :\|\|\|\|\|: \|\|\|\| \|\|\|\|@LB@ GUUUGUGUU UU UUGU AGUGUU GG UUCGGGU GUCU UGCG@LB@3'-UUU...UUAAC G GUG GGCAUUC UU A UG UAAGG...UCA-5'@LB@ \| \|@LB@ 90 35@LB@@LB@@LB@Energy -19.39 kcal/mol@LB@Hybridization Energy -43.5648 kcal/mol@LB@Unfolding Energy - mRNA 9.30805 kcal/mol@LB@Unfolding Energy - sRNA 22.4875 kcal/mol@LB@@LB@Position - mRNA 221 -- 286@LB@Position - sRNA 36 -- 89@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 47 -- 53@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@
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@
46	0.001637	0.1267	stm2313	elaC	-17.21	0.051329	250 -- 300	51 -- 90	ribonuclease Z	stm1109	_____________249_____________________________________________301\n_____________\|_______________________________________________\|\n5'-UCG...CUCAC____UGUA________UUUAUUACAUCU________CAAC_______GGAG-3'\n______________GCAA____ACGGCAAU____________GCAACAUC____GCAGCCG\n______________\|\|\|\|____\|\|::\|\|\|:____________:\|\|\|\|\|\|\|____:\|\|:\|\|\|\n______________CGUU____UGUUGUUG____________UGUUGUAG____UGUUGGC\n3'-UUU...GUUAA____UG_________________________________________AUUCG...UCA-5'\n_____________\|_______________________________________________\|\n_____________91______________________________________________50\n	290 -- 296	62 -- 68	-28.5454 kcal/mol	7.10881 kcal/mol	8.62576 kcal/mol	249 301@LB@ \| \|@LB@5'-UCG...CUCAC UGUA UUUAUUACAUCU CAAC GGAG-3'@LB@ GCAA ACGGCAAU GCAACAUC GCAGCCG@LB@ \|\|\|\| \|\|::\|\|\|: :\|\|\|\|\|\|\| :\|\|:\|\|\|@LB@ CGUU UGUUGUUG UGUUGUAG UGUUGGC@LB@3'-UUU...GUUAA UG AUUCG...UCA-5'@LB@ \| \|@LB@ 91 50@LB@@LB@@LB@Energy -17.21 kcal/mol@LB@Hybridization Energy -28.5454 kcal/mol@LB@Unfolding Energy - mRNA 7.10881 kcal/mol@LB@Unfolding Energy - sRNA 8.62576 kcal/mol@LB@@LB@Position - mRNA 250 -- 300@LB@Position - sRNA 51 -- 90@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 62 -- 68@LB@
161	0.008343	0.1845	stm3321	yhbH	-14.15	0.160801	194 -- 246	48 -- 88	ribosomal subunit interface protein		_____________193______________________247\n_____________\|________________________\|\n5'-GAU...AAGGA______UAU_____U_________CGGAC...GGA-3'\n______________AGACAC___GCAGC_CAAUAUCAC\n______________\|:\|\|\|\|___:\|\|:\|_\|\|\|:\|\|\|\|\|\n______________UUUGUG___UGUUG_GUUGUAGUG\n3'-UUU...UAACG______U_______U_________UUGGC...UCA-5'\n_____________\|________________________\|\n_____________89_______________________47\n	211 -- 217	67 -- 73	-22.4132 kcal/mol	2.65406 kcal/mol	5.48747 kcal/mol	193 247@LB@ \| \|@LB@5'-GAU...AAGGA UAU U CGGAC...GGA-3'@LB@ AGACAC GCAGC CAAUAUCAC@LB@ \|:\|\|\|\| :\|\|:\| \|\|\|:\|\|\|\|\|@LB@ UUUGUG UGUUG GUUGUAGUG@LB@3'-UUU...UAACG U U UUGGC...UCA-5'@LB@ \| \|@LB@ 89 47@LB@@LB@@LB@Energy -14.15 kcal/mol@LB@Hybridization Energy -22.4132 kcal/mol@LB@Unfolding Energy - mRNA 2.65406 kcal/mol@LB@Unfolding Energy - sRNA 5.48747 kcal/mol@LB@@LB@Position - mRNA 194 -- 246@LB@Position - sRNA 48 -- 88@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 67 -- 73@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@
197	0.01093	0.197	stm2924	rpoS	-16.80	0.060020	191 -- 216	36 -- 60	RNA polymerase sigma factor RpoS		_____________190________________________________217\n_____________\|__________________________________\|\n___5'-CGGGAACA_________U____C___GCAAAAAA________AUGGG...AGG-3'\n______________ACAGGAAGU_AAGG_GGG________UCGCUACU\n______________\|\|\|\|\|\|\|\|\|_\|\|::_\|\|\|________\|\|\|\|\|\|\|:\n______________UGUCCUUCA_UUUU_CCC________AGCGAUGG\n3'-UUU...UUACA_________C____U___AUCAG___________CACCA...UCA-5'\n_____________\|__________________________________\|\n_____________61_________________________________35\n	36 -- 42	114 -- 120	-31.3768 kcal/mol	8.74888 kcal/mol	8.99738 kcal/mol	190 217@LB@ \| \|@LB@ 5'-CGGGAACA U C GCAAAAAA AUGGG...AGG-3'@LB@ ACAGGAAGU AAGG GGG UCGCUACU@LB@ \|\|\|\|\|\|\|\|\| \|\|:: \|\|\| \|\|\|\|\|\|\|:@LB@ UGUCCUUCA UUUU CCC AGCGAUGG@LB@3'-UUU...UUACA C U AUCAG CACCA...UCA-5'@LB@ \| \|@LB@ 61 35@LB@@LB@@LB@Energy -16.80 kcal/mol@LB@Hybridization Energy -31.3768 kcal/mol@LB@Unfolding Energy - mRNA 8.74888 kcal/mol@LB@Unfolding Energy - sRNA 8.99738 kcal/mol@LB@@LB@Position - mRNA 191 -- 216@LB@Position - sRNA 36 -- 60@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 114 -- 120@LB@
172	0.009395	0.1945	stm3373	mreC	-15.91	0.084075	179 -- 229	45 -- 87	rod shape-determining protein MreC		_____________178____________230\n_____________\|______________\|\n5'-UGA...UGUUA_____AG_______CAUUC...GGA-3'\n______________AUGGA__AGACGGG\n______________\|\|\|\|\|__\|\|\|\|:\|\|\n______________UACCU__UCUGUCC\n3'-UUU...AGUGA_____G________CAUUU...UCA-5'\n_____________\|______________\|\n_____________88_____________44\n	21 -- 27	153 -- 159	-16.2478 kcal/mol	4.60826 kcal/mol	2.82582 kcal/mol	178 230@LB@ \| \|@LB@5'-UGA...UGUUA AG CAUUC...GGA-3'@LB@ AUGGA AGACGGG@LB@ \|\|\|\|\| \|\|\|\|:\|\|@LB@ UACCU UCUGUCC@LB@3'-UUU...AGUGA G CAUUU...UCA-5'@LB@ \| \|@LB@ 88 44@LB@@LB@@LB@Energy -15.91 kcal/mol@LB@Hybridization Energy -16.2478 kcal/mol@LB@Unfolding Energy - mRNA 4.60826 kcal/mol@LB@Unfolding Energy - sRNA 2.82582 kcal/mol@LB@@LB@Position - mRNA 179 -- 229@LB@Position - sRNA 45 -- 87@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 153 -- 159@LB@
102	0.005164	0.1728	stm0668	ybeY	-18.23	0.034693	146 -- 193	37 -- 81	rRNA maturation RNase YbeY		_____________145__________________________________________194\n_____________\|____________________________________________\|\n5'-UCC...AAAAC____________UUG____________G_______GU_______AGGAG...CGC-3'\n______________GCAAA_GCGGCG___GCGGCA____GA_CGUAAGC__GAAGCCC\n______________\|\|\|\|\|_:\|::\|:___:\|::\|\|____:\|_\|\|\|\|\|\|\|__:\|\|\|\|\|\|\n______________CGUUU_UGUUGU___UGUUGU____UU_GCAUUCG__UUUCGGG\n3'-UUU...GUUAA_____G______UG_______AGUG__G_______GU_______UAGUC...UCA-5'\n_____________\|____________________________________________\|\n_____________82___________________________________________36\n	178 -- 184	48 -- 54	-38.2699 kcal/mol	15.4401 kcal/mol	16.4278 kcal/mol	145 194@LB@ \| \|@LB@5'-UCC...AAAAC UUG G GU AGGAG...CGC-3'@LB@ GCAAA GCGGCG GCGGCA GA CGUAAGC GAAGCCC@LB@ \|\|\|\|\| :\|::\|: :\|::\|\| :\| \|\|\|\|\|\|\| :\|\|\|\|\|\|@LB@ CGUUU UGUUGU UGUUGU UU GCAUUCG UUUCGGG@LB@3'-UUU...GUUAA G UG AGUG G GU UAGUC...UCA-5'@LB@ \| \|@LB@ 82 36@LB@@LB@@LB@Energy -18.23 kcal/mol@LB@Hybridization Energy -38.2699 kcal/mol@LB@Unfolding Energy - mRNA 15.4401 kcal/mol@LB@Unfolding Energy - sRNA 16.4278 kcal/mol@LB@@LB@Position - mRNA 146 -- 193@LB@Position - sRNA 37 -- 81@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 48 -- 54@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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