Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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_000913 Escherichia coli str. K-12 substr. MG1655

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
127	0.01385	0.3575	b3832	rmuC	-11.83	0.120260	236 -- 246	193 -- 203	DNA recombination protein	_____________235____________________________________________________________247\n_____________\|______________________________________________________________\|\n5'-AAA...UUGUA________AUUC___UUU_____________GUU__G______AGGC_______AUU_____AUCAU...AGC-3'\n______________CAG_CACA____UAU___GUGCGGGUAAGUU___GC__UCAGG____GUUGUGG___UCUCA\n______________\|\|\|_\|\|\|\|____:\|\|___:\|\|\|:\|\|:\|\|\|\|:___:\|__\|\|\|\|:____:\|\|\|:\|\|___\|\|:\|\|\n______________GUC_GUGU____GUA___UACGUCCGUUCAG___UG__AGUCU____UAACGCC___AGGGU\n3'-UUU...UAUGA___A___________C_______________U____AA________________AGU_____GACGU...UAG-5'\n_____________\|______________________________________________________________\|\n_____________204____________________________________________________________192\n	198 -- 204	135 -- 141	-42.9883 kcal/mol	19.1075 kcal/mol	15.6146 kcal/mol	235 247@LB@ \| \|@LB@5'-AAA...UUGUA AUUC UUU GUU G AGGC AUU AUCAU...AGC-3'@LB@ CAG CACA UAU GUGCGGGUAAGUU GC UCAGG GUUGUGG UCUCA@LB@ \|\|\| \|\|\|\| :\|\| :\|\|\|:\|\|:\|\|\|\|: :\| \|\|\|\|: :\|\|\|:\|\| \|\|:\|\|@LB@ GUC GUGU GUA UACGUCCGUUCAG UG AGUCU UAACGCC AGGGU@LB@3'-UUU...UAUGA A C U AA AGU GACGU...UAG-5'@LB@ \| \|@LB@ 204 192@LB@@LB@@LB@Energy -11.83 kcal/mol@LB@Hybridization Energy -42.9883 kcal/mol@LB@Unfolding Energy - mRNA 19.1075 kcal/mol@LB@Unfolding Energy - sRNA 15.6146 kcal/mol@LB@@LB@Position - mRNA 236 -- 246@LB@Position - sRNA 193 -- 203@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 135 -- 141@LB@
2	4.964e-05	0.08352	b0475	hemH	-12.83	0.075395	238 -- 275	45 -- 93	ferrochelatase	_____________237______________________________________________________________________276\n_____________\|________________________________________________________________________\|\n5'-CGG...AGACU_______________C__________AAACCU_____________C_______C_C_______C___A____UAAAA...GCG-3'\n______________AAAACC____GGUAU___CUGCUGGC______GGGU______ACG_CCGAUGC_C___CACAC_UGA_GCGG\n______________\|\|\|\|\|\|____\|\|\|\|\|___\|\|\|\|\|\|\|\|______\|\|\|\|______\|\|:_\|\|:\|\|:\|_\|___\|\|\|\|\|_\|\|\|_\|\|:\|\n______________UUUUGG____CCAUA___GACGACCG______CCCA______UGU_GGUUAUG_G___GUGUG_ACU_CGUC\n_______3'-UUUU______UCGU_____UUA__________________CUAAAA___________A_UCA_____U___A____CGUUC...UAG-5'\n_____________\|________________________________________________________________________\|\n_____________94_______________________________________________________________________44\n	247 -- 253	178 -- 184	-50.8068 kcal/mol	15.6732 kcal/mol	22.9013 kcal/mol	237 276@LB@ \| \|@LB@5'-CGG...AGACU C AAACCU C C C C A UAAAA...GCG-3'@LB@ AAAACC GGUAU CUGCUGGC GGGU ACG CCGAUGC C CACAC UGA GCGG@LB@ \|\|\|\|\|\| \|\|\|\|\| \|\|\|\|\|\|\|\| \|\|\|\| \|\|: \|\|:\|\|:\| \| \|\|\|\|\| \|\|\| \|\|:\|@LB@ UUUUGG CCAUA GACGACCG CCCA UGU GGUUAUG G GUGUG ACU CGUC@LB@ 3'-UUUU UCGU UUA CUAAAA A UCA U A CGUUC...UAG-5'@LB@ \| \|@LB@ 94 44@LB@@LB@@LB@Energy -12.83 kcal/mol@LB@Hybridization Energy -50.8068 kcal/mol@LB@Unfolding Energy - mRNA 15.6732 kcal/mol@LB@Unfolding Energy - sRNA 22.9013 kcal/mol@LB@@LB@Position - mRNA 238 -- 275@LB@Position - sRNA 45 -- 93@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 178 -- 184@LB@
113	0.01268	0.3575	b2066	udk	-9.33	0.364673	240 -- 253	17 -- 31	uridine/cytidine kinase	_____________239________________254\n_____________\|__________________\|\n5'-CGC...UUCGU_________C__AA____CAGGU...GUG-3'\n______________CGCCCCCUU_CU__CAUC\n______________\|:\|\|\|\|\|\|\|_\|\|__\|\|\|\|\n______________GUGGGGGAA_GA__GUAG\n3'-UUU...ACCCC_________C__A_____-5'\n_____________\|_________________\|\n_____________32________________17\n	161 -- 167	9 -- 15	-20.5437 kcal/mol	3.26859 kcal/mol	7.16879 kcal/mol	239 254@LB@ \| \|@LB@5'-CGC...UUCGU C AA CAGGU...GUG-3'@LB@ CGCCCCCUU CU CAUC@LB@ \|:\|\|\|\|\|\|\| \|\| \|\|\|\|@LB@ GUGGGGGAA GA GUAG@LB@3'-UUU...ACCCC C A -5'@LB@ \| \|@LB@ 32 17@LB@@LB@@LB@Energy -9.33 kcal/mol@LB@Hybridization Energy -20.5437 kcal/mol@LB@Unfolding Energy - mRNA 3.26859 kcal/mol@LB@Unfolding Energy - sRNA 7.16879 kcal/mol@LB@@LB@Position - mRNA 240 -- 253@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 9 -- 15@LB@
187	0.02173	0.3833	b3679	yidK	-10.16	0.256396	240 -- 256	191 -- 205	putative transporter	_____________239________________________________________257\n_____________\|__________________________________________\|\n5'-UUU...UUACG_________GC______________U____GAA_________AAACA...AAG-3'\n______________CUGCUGGUG__GGUGAU____CACC_GGUG___GGUC_CGCA\n______________\|\|\|\|\|\|\|:\|__\|\|\|\|\|\|____\|\|\|\|_::\|:___:\|\|\|_\|:\|\|\n______________GACGACCGC__CCACUA____GUGG_UUAU___UCAG_GUGU\n3'-UUU...UAUUA_________________AAAU_________GAG____U____ACUAC...UAG-5'\n_____________\|__________________________________________\|\n_____________206________________________________________190\n	242 -- 248	197 -- 203	-39.2862 kcal/mol	16.885 kcal/mol	15.3993 kcal/mol	239 257@LB@ \| \|@LB@5'-UUU...UUACG GC U GAA AAACA...AAG-3'@LB@ CUGCUGGUG GGUGAU CACC GGUG GGUC CGCA@LB@ \|\|\|\|\|\|\|:\| \|\|\|\|\|\| \|\|\|\| ::\|: :\|\|\| \|:\|\|@LB@ GACGACCGC CCACUA GUGG UUAU UCAG GUGU@LB@3'-UUU...UAUUA AAAU GAG U ACUAC...UAG-5'@LB@ \| \|@LB@ 206 190@LB@@LB@@LB@Energy -10.16 kcal/mol@LB@Hybridization Energy -39.2862 kcal/mol@LB@Unfolding Energy - mRNA 16.885 kcal/mol@LB@Unfolding Energy - sRNA 15.3993 kcal/mol@LB@@LB@Position - mRNA 240 -- 256@LB@Position - sRNA 191 -- 205@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 197 -- 203@LB@
20	0.001715	0.2633	b3453	ugpB	-12.22	0.100645	241 -- 257	18 -- 32	sn-glycerol-3-phosphate ABC transporter periplasmic binding protein	_____________240______________258\n_____________\|________________\|\n5'-UUC...AAUUC_____U__________AAGAG...UGG-3'\n______________GCGCA_UCGGUACAAC\n______________:\|\|\|\|_:\|:\|:\|\|\|\|\|\n______________UGCGU_GGUCGUGUUG\n3'-UUU...UUGGU_____U__________AAGCG...UAG-5'\n_____________\|________________\|\n_____________33_______________17\n	180 -- 186	63 -- 69	-22.0099 kcal/mol	5.49331 kcal/mol	9.84719 kcal/mol	240 258@LB@ \| \|@LB@5'-UUC...AAUUC U AAGAG...UGG-3'@LB@ GCGCA UCGGUACAAC@LB@ :\|\|\|\| :\|:\|:\|\|\|\|\|@LB@ UGCGU GGUCGUGUUG@LB@3'-UUU...UUGGU U AAGCG...UAG-5'@LB@ \| \|@LB@ 33 17@LB@@LB@@LB@Energy -12.22 kcal/mol@LB@Hybridization Energy -22.0099 kcal/mol@LB@Unfolding Energy - mRNA 5.49331 kcal/mol@LB@Unfolding Energy - sRNA 9.84719 kcal/mol@LB@@LB@Position - mRNA 241 -- 257@LB@Position - sRNA 18 -- 32@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 63 -- 69@LB@
36	0.002935	0.2744	b3152	yraR	-13.11	0.066158	241 -- 255	123 -- 138	putative nucleoside-diphosphate-sugar epimerase	_____________240______________256\n_____________\|________________\|\n5'-ACU...GGUGG________________GGAUG...CGA-3'\n______________GCGGUCA_CCUGCUGC\n______________\|\|\|\|\|\|\|_\|\|::\|\|\|\|\n______________CGCCAGU_GGGUGACG\n3'-UUU...CUUAA_______A________UAGUC...UAG-5'\n_____________\|________________\|\n_____________139______________122\n	241 -- 247	132 -- 138	-26.7154 kcal/mol	6.55898 kcal/mol	13.7588 kcal/mol	240 256@LB@ \| \|@LB@5'-ACU...GGUGG GGAUG...CGA-3'@LB@ GCGGUCA CCUGCUGC@LB@ \|\|\|\|\|\|\| \|\|::\|\|\|\|@LB@ CGCCAGU GGGUGACG@LB@3'-UUU...CUUAA A UAGUC...UAG-5'@LB@ \| \|@LB@ 139 122@LB@@LB@@LB@Energy -13.11 kcal/mol@LB@Hybridization Energy -26.7154 kcal/mol@LB@Unfolding Energy - mRNA 6.55898 kcal/mol@LB@Unfolding Energy - sRNA 13.7588 kcal/mol@LB@@LB@Position - mRNA 241 -- 255@LB@Position - sRNA 123 -- 138@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 132 -- 138@LB@
49	0.004667	0.3205	b1277	ribA	-9.86	0.291903	241 -- 249	16 -- 24	GTP cyclohydrolase II	_____________240________250\n_____________\|__________\|\n5'-CCA...AAUAC__________UUAUC...UCG-3'\n______________AGAACCAGCA\n______________\|:\|\|\|\|\|\|\|\|\n______________UUUUGGUCGU\n_______3'-UUUU__________CCAUA...UAG-5'\n_____________\|__________\|\n_____________25_________15\n	178 -- 184	214 -- 220	-13.9783 kcal/mol	2.87719 kcal/mol	5.75438 kcal/mol	240 250@LB@ \| \|@LB@5'-CCA...AAUAC UUAUC...UCG-3'@LB@ AGAACCAGCA@LB@ \|:\|\|\|\|\|\|\|\|@LB@ UUUUGGUCGU@LB@ 3'-UUUU CCAUA...UAG-5'@LB@ \| \|@LB@ 25 15@LB@@LB@@LB@Energy -9.86 kcal/mol@LB@Hybridization Energy -13.9783 kcal/mol@LB@Unfolding Energy - mRNA 2.87719 kcal/mol@LB@Unfolding Energy - sRNA 5.75438 kcal/mol@LB@@LB@Position - mRNA 241 -- 249@LB@Position - sRNA 16 -- 24@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 214 -- 220@LB@
157	0.01768	0.3749	b1216	chaA	-11.60	0.134178	242 -- 292	18 -- 65	calcium/sodium:proton antiporter	_____________241_______________293\n_____________\|_________________\|\n5'-AUU...AAUGU_________C___A___UUUCU...GCC-3'\n______________UACCGAUAU_CAG_CAC\n______________:\|\|\|:\|\|\|:_\|\|\|_\|\|\|\n______________GUGGUUAUG_GUC_GUG\n3'-UUU...AAAAU_________A___A___UGUAC...UAG-5'\n_____________\|_________________\|\n_____________66________________17\n	120 -- 126	178 -- 184	-16.2011 kcal/mol	3.68451 kcal/mol	4.86651 kcal/mol	241 293@LB@ \| \|@LB@5'-AUU...AAUGU C A UUUCU...GCC-3'@LB@ UACCGAUAU CAG CAC@LB@ :\|\|\|:\|\|\|: \|\|\| \|\|\|@LB@ GUGGUUAUG GUC GUG@LB@3'-UUU...AAAAU A A UGUAC...UAG-5'@LB@ \| \|@LB@ 66 17@LB@@LB@@LB@Energy -11.60 kcal/mol@LB@Hybridization Energy -16.2011 kcal/mol@LB@Unfolding Energy - mRNA 3.68451 kcal/mol@LB@Unfolding Energy - sRNA 4.86651 kcal/mol@LB@@LB@Position - mRNA 242 -- 292@LB@Position - sRNA 18 -- 65@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 178 -- 184@LB@
7	0.0005448	0.1842	b1912	pgsA	-14.68	0.031521	247 -- 274	111 -- 134	phosphatidylglycerophosphate synthetase	_____________246__________________________275\n_____________\|____________________________\|\n5'-GUC...CAUCC_________UCUU_______________UCUGC...UUG-3'\n______________UUAUCCCAU____UGUAUUGGUCUUUUA\n______________\|:\|\|\|\|\|\|:____\|\|:\|\|::\|\|\|:\|\|:\|\n______________AGUAGGGUG____ACGUAGUCAGGAAGU\n3'-UUU...ACGCC____________________________UCGUA...UAG-5'\n_____________\|____________________________\|\n_____________135__________________________110\n	268 -- 274	111 -- 117	-27.9222 kcal/mol	1.79949 kcal/mol	14.1586 kcal/mol	246 275@LB@ \| \|@LB@5'-GUC...CAUCC UCUU UCUGC...UUG-3'@LB@ UUAUCCCAU UGUAUUGGUCUUUUA@LB@ \|:\|\|\|\|\|\|: \|\|:\|\|::\|\|\|:\|\|:\|@LB@ AGUAGGGUG ACGUAGUCAGGAAGU@LB@3'-UUU...ACGCC UCGUA...UAG-5'@LB@ \| \|@LB@ 135 110@LB@@LB@@LB@Energy -14.68 kcal/mol@LB@Hybridization Energy -27.9222 kcal/mol@LB@Unfolding Energy - mRNA 1.79949 kcal/mol@LB@Unfolding Energy - sRNA 14.1586 kcal/mol@LB@@LB@Position - mRNA 247 -- 274@LB@Position - sRNA 111 -- 134@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 111 -- 117@LB@
116	0.01276	0.3575	b2989	yghU	-14.25	0.038539	247 -- 281	170 -- 208	putative S-transferase	_____________246______________________________________282\n_____________\|________________________________________\|\n5'-UUA...GGAUA____C________C_C_UU________________A____CCGGU...CGC-3'\n______________AAUC_GCUGGCGG_G_G______CGCCAAUA_UCA_UCGC\n______________\|\|\|\|_\|\|\|\|\|\|\|\|_\|_\|______\|:\|\|\|\|\|\|_\|\|\|_\|\|:\|\n______________UUAG_CGACCGCC_C_C______GUGGUUAU_AGU_AGUG\n3'-UUU...CCAUA____A__________A_UAAAAU________G___C____UGUAC...UAG-5'\n_____________\|________________________________________\|\n_____________209______________________________________169\n	267 -- 273	179 -- 185	-35.9489 kcal/mol	9.63265 kcal/mol	15.256 kcal/mol	246 282@LB@ \| \|@LB@5'-UUA...GGAUA C C C UU A CCGGU...CGC-3'@LB@ AAUC GCUGGCGG G G CGCCAAUA UCA UCGC@LB@ \|\|\|\| \|\|\|\|\|\|\|\| \| \| \|:\|\|\|\|\|\| \|\|\| \|\|:\|@LB@ UUAG CGACCGCC C C GUGGUUAU AGU AGUG@LB@3'-UUU...CCAUA A A UAAAAU G C UGUAC...UAG-5'@LB@ \| \|@LB@ 209 169@LB@@LB@@LB@Energy -14.25 kcal/mol@LB@Hybridization Energy -35.9489 kcal/mol@LB@Unfolding Energy - mRNA 9.63265 kcal/mol@LB@Unfolding Energy - sRNA 15.256 kcal/mol@LB@@LB@Position - mRNA 247 -- 281@LB@Position - sRNA 170 -- 208@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 179 -- 185@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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