Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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	Additional homologs
42	0.0004615	0.03766	b3341	rpsG	-11.13	0.020425	227 -- 249	53 -- 76	30S ribosomal subunit protein S7		_____________226______________________250\n_____________\|________________________\|\n5'-CGG...GGUCA__GU________U___________AGUUC...AUG-3'\n______________GC__AAA_AUUC_GCCGGAUCCGA\n______________\|\|__\|\|\|_\|\|\|\|_\|\|\|::\|\|\|\|\|\|\n______________CG__UUU_UAAG_CGGUUUAGGCU\n3'-AUU...CCCGC__AU___A____U___________AAUGC...AUG-5'\n_____________\|________________________\|\n_____________77_______________________52\n	243 -- 249	53 -- 59	-23.8099 kcal/mol	6.33566 kcal/mol	6.36489 kcal/mol	226 250@LB@ \| \|@LB@5'-CGG...GGUCA GU U AGUUC...AUG-3'@LB@ GC AAA AUUC GCCGGAUCCGA@LB@ \|\| \|\|\| \|\|\|\| \|\|\|::\|\|\|\|\|\|@LB@ CG UUU UAAG CGGUUUAGGCU@LB@3'-AUU...CCCGC AU A U AAUGC...AUG-5'@LB@ \| \|@LB@ 77 52@LB@@LB@@LB@Energy -11.13 kcal/mol@LB@Hybridization Energy -23.8099 kcal/mol@LB@Unfolding Energy - mRNA 6.33566 kcal/mol@LB@Unfolding Energy - sRNA 6.36489 kcal/mol@LB@@LB@Position - mRNA 227 -- 249@LB@Position - sRNA 53 -- 76@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 53 -- 59@LB@
47	0.0005047	0.03778	b1888	cheA	-10.26	0.037926	179 -- 191	53 -- 66	fused chemotactic sensory histidine kinase in two-component regulatory system with CheB and CheY: sensory histidine kinase/signal sensing protein		_____________178____________192\n_____________\|______________\|\n5'-GAU...UGCCA______________GGUGA...AAG-3'\n______________UCAGCCGAA_CCGA\n______________\|\|\|\|\|\|:\|\|_\|\|\|\|\n______________AGUCGGUUU_GGCU\n3'-AUU...UUAUA_________A____AAUGC...AUG-5'\n_____________\|______________\|\n_____________67_____________52\n	181 -- 187	58 -- 64	-19.401 kcal/mol	2.99348 kcal/mol	6.16775 kcal/mol	178 192@LB@ \| \|@LB@5'-GAU...UGCCA GGUGA...AAG-3'@LB@ UCAGCCGAA CCGA@LB@ \|\|\|\|\|\|:\|\| \|\|\|\|@LB@ AGUCGGUUU GGCU@LB@3'-AUU...UUAUA A AAUGC...AUG-5'@LB@ \| \|@LB@ 67 52@LB@@LB@@LB@Energy -10.26 kcal/mol@LB@Hybridization Energy -19.401 kcal/mol@LB@Unfolding Energy - mRNA 2.99348 kcal/mol@LB@Unfolding Energy - sRNA 6.16775 kcal/mol@LB@@LB@Position - mRNA 179 -- 191@LB@Position - sRNA 53 -- 66@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 58 -- 64@LB@
112	0.003594	0.1129	b3866	yihI	-3.87	0.795256	171 -- 194	53 -- 75	activator of Der GTPase		_____________170______________________195\n_____________\|________________________\|\n5'-GAA...CUAUA_____UAAAA________AGA___ACCAU...GUC-3'\n______________CUGAA_____CGGCUAAA___CGA\n______________\|\|:\|\|_____\|:\|\|:\|\|\|___\|\|\|\n______________GAUUU_____GUCGGUUU___GCU\n3'-AUU...CCGCC_____UAUAA________AG____AAUGC...AUG-5'\n_____________\|________________________\|\n_____________76_______________________52\n	181 -- 187	59 -- 65	-14.4152 kcal/mol	4.20142 kcal/mol	6.36326 kcal/mol	170 195@LB@ \| \|@LB@5'-GAA...CUAUA UAAAA AGA ACCAU...GUC-3'@LB@ CUGAA CGGCUAAA CGA@LB@ \|\|:\|\| \|:\|\|:\|\|\| \|\|\|@LB@ GAUUU GUCGGUUU GCU@LB@3'-AUU...CCGCC UAUAA AG AAUGC...AUG-5'@LB@ \| \|@LB@ 76 52@LB@@LB@@LB@Energy -3.87 kcal/mol@LB@Hybridization Energy -14.4152 kcal/mol@LB@Unfolding Energy - mRNA 4.20142 kcal/mol@LB@Unfolding Energy - sRNA 6.36326 kcal/mol@LB@@LB@Position - mRNA 171 -- 194@LB@Position - sRNA 53 -- 75@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 59 -- 65@LB@
193	0.008653	0.1558	b1677	lpp	-9.16	0.078007	273 -- 298	53 -- 76	murein lipoprotein		_____________272________________________299\n_____________\|__________________________\|\n5'-UCA...GCAAC________CGA______GUCU_____CG-3'\n______________GCUAAAAU___UCAGCU____UCUGA\n______________\|\|\|\|\|\|\|\|___\|\|\|\|\|:____\|\|:\|\|\n______________CGAUUUUA___AGUCGG____AGGCU\n3'-AUU...CCCGC________UA_______UUU______AAUGC...AUG-5'\n_____________\|__________________________\|\n_____________77_________________________52\n	273 -- 279	70 -- 76	-19.09 kcal/mol	3.58418 kcal/mol	6.36489 kcal/mol	272 299@LB@ \| \|@LB@5'-UCA...GCAAC CGA GUCU CG-3'@LB@ GCUAAAAU UCAGCU UCUGA@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|: \|\|:\|\|@LB@ CGAUUUUA AGUCGG AGGCU@LB@3'-AUU...CCCGC UA UUU AAUGC...AUG-5'@LB@ \| \|@LB@ 77 52@LB@@LB@@LB@Energy -9.16 kcal/mol@LB@Hybridization Energy -19.09 kcal/mol@LB@Unfolding Energy - mRNA 3.58418 kcal/mol@LB@Unfolding Energy - sRNA 6.36489 kcal/mol@LB@@LB@Position - mRNA 273 -- 298@LB@Position - sRNA 53 -- 76@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 70 -- 76@LB@
2	0	0	b0796	ybiH	-7.52	0.201543	119 -- 140	54 -- 76	DUF1956 domain-containing tetR family putative transcriptional regulator	b1013	_____________118_____________________141\n_____________\|_______________________\|\n5'-CGG...GCGUU________UC_______UA____GACAA...CCA-3'\n______________GCUAAAAU__UUAGCCA___CUG\n______________\|\|\|\|\|\|\|\|__\|:\|\|\|\|\|___\|:\|\n______________CGAUUUUA__AGUCGGU___GGC\n3'-AUU...CCCGC________UA_______UUA___UAAUG...AUG-5'\n_____________\|_______________________\|\n_____________77______________________53\n	129 -- 135	60 -- 66	-19.7488 kcal/mol	5.88928 kcal/mol	6.3634 kcal/mol	118 141@LB@ \| \|@LB@5'-CGG...GCGUU UC UA GACAA...CCA-3'@LB@ GCUAAAAU UUAGCCA CUG@LB@ \|\|\|\|\|\|\|\| \|:\|\|\|\|\| \|:\|@LB@ CGAUUUUA AGUCGGU GGC@LB@3'-AUU...CCCGC UA UUA UAAUG...AUG-5'@LB@ \| \|@LB@ 77 53@LB@@LB@@LB@Energy -7.52 kcal/mol@LB@Hybridization Energy -19.7488 kcal/mol@LB@Unfolding Energy - mRNA 5.88928 kcal/mol@LB@Unfolding Energy - sRNA 6.3634 kcal/mol@LB@@LB@Position - mRNA 119 -- 140@LB@Position - sRNA 54 -- 76@LB@Position Seed - mRNA 129 -- 135@LB@Position Seed - sRNA 60 -- 66@LB@
79	0.001698	0.07533	b2890	lysS	-8.16	0.142186	53 -- 64	54 -- 65	lysine tRNA synthetase constitutive	b4129	_____________52___________65\n_____________\|____________\|\n5'-AAA...UGGGG____________UUCUU...GGA-3'\n______________CAGCCAGAUUCG\n______________\|\|\|\|\|\|:\|\|:\|\|\n______________GUCGGUUUAGGC\n3'-AUU...UAUAA____________UAAUG...AUG-5'\n_____________\|____________\|\n_____________66___________53\n	58 -- 64	54 -- 60	-18.439 kcal/mol	4.14677 kcal/mol	6.15795 kcal/mol	52 65@LB@ \| \|@LB@5'-AAA...UGGGG UUCUU...GGA-3'@LB@ CAGCCAGAUUCG@LB@ \|\|\|\|\|\|:\|\|:\|\|@LB@ GUCGGUUUAGGC@LB@3'-AUU...UAUAA UAAUG...AUG-5'@LB@ \| \|@LB@ 66 53@LB@@LB@@LB@Energy -8.16 kcal/mol@LB@Hybridization Energy -18.439 kcal/mol@LB@Unfolding Energy - mRNA 4.14677 kcal/mol@LB@Unfolding Energy - sRNA 6.15795 kcal/mol@LB@@LB@Position - mRNA 53 -- 64@LB@Position - sRNA 54 -- 65@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 54 -- 60@LB@
173	0.007216	0.1466	b3650	spoT	-5.39	0.520602	11 -- 17	54 -- 60	bifunctional (p)ppGpp synthetase II/ guanosine-3' 5'-bis pyrophosphate 3'-pyrophosphohydrolase		_____________10______18\n_____________\|_______\|\n5'-UAG...GGAAA_______CUGGU...CUC-3'\n______________GGAUCCG\n______________::\|\|\|\|\|\n______________UUUAGGC\n3'-AUU...GUCGG_______UAAUG...AUG-5'\n_____________\|_______\|\n_____________61______53\n	11 -- 17	54 -- 60	-6.87427 kcal/mol	1.21245 kcal/mol	0.286889 kcal/mol	10 18@LB@ \| \|@LB@5'-UAG...GGAAA CUGGU...CUC-3'@LB@ GGAUCCG@LB@ ::\|\|\|\|\|@LB@ UUUAGGC@LB@3'-AUU...GUCGG UAAUG...AUG-5'@LB@ \| \|@LB@ 61 53@LB@@LB@@LB@Energy -5.39 kcal/mol@LB@Hybridization Energy -6.87427 kcal/mol@LB@Unfolding Energy - mRNA 1.21245 kcal/mol@LB@Unfolding Energy - sRNA 0.286889 kcal/mol@LB@@LB@Position - mRNA 11 -- 17@LB@Position - sRNA 54 -- 60@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 54 -- 60@LB@
8	1.842e-05	0.007771	b2797	sdaB	-15.07	0.000654	133 -- 147	55 -- 69	L-serine dehydratase 2		_____________132_____________148\n_____________\|_______________\|\n5'-CGA...CUCUC_______________UUUCG...UGA-3'\n______________UGUUCAGCUAAGUCC\n______________\|:\|\|\|\|\|\|:\|\|:\|\|\|\n______________AUAAGUCGGUUUAGG\n3'-AUU...AUUUU_______________CUAAU...AUG-5'\n_____________\|_______________\|\n_____________70______________54\n	141 -- 147	55 -- 61	-22.3059 kcal/mol	1.18067 kcal/mol	6.0797 kcal/mol	132 148@LB@ \| \|@LB@5'-CGA...CUCUC UUUCG...UGA-3'@LB@ UGUUCAGCUAAGUCC@LB@ \|:\|\|\|\|\|\|:\|\|:\|\|\|@LB@ AUAAGUCGGUUUAGG@LB@3'-AUU...AUUUU CUAAU...AUG-5'@LB@ \| \|@LB@ 70 54@LB@@LB@@LB@Energy -15.07 kcal/mol@LB@Hybridization Energy -22.3059 kcal/mol@LB@Unfolding Energy - mRNA 1.18067 kcal/mol@LB@Unfolding Energy - sRNA 6.0797 kcal/mol@LB@@LB@Position - mRNA 133 -- 147@LB@Position - sRNA 55 -- 69@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 55 -- 61@LB@
40	0.0004513	0.03766	b3291	mscL	-6.99	0.263134	48 -- 58	55 -- 65	mechanosensitive channel protein high conductance		_____________47__________59\n_____________\|___________\|\n5'-UGU...UCUUC________C__UUUCU...UCU-3'\n______________CAGCCAAG_CC\n______________\|\|\|\|\|\|\|:_\|\|\n______________GUCGGUUU_GG\n3'-AUU...UAUAA________A__CUAAU...AUG-5'\n_____________\|___________\|\n_____________66__________54\n	49 -- 55	58 -- 64	-14.9389 kcal/mol	1.90813 kcal/mol	6.05961 kcal/mol	47 59@LB@ \| \|@LB@5'-UGU...UCUUC C UUUCU...UCU-3'@LB@ CAGCCAAG CC@LB@ \|\|\|\|\|\|\|: \|\|@LB@ GUCGGUUU GG@LB@3'-AUU...UAUAA A CUAAU...AUG-5'@LB@ \| \|@LB@ 66 54@LB@@LB@@LB@Energy -6.99 kcal/mol@LB@Hybridization Energy -14.9389 kcal/mol@LB@Unfolding Energy - mRNA 1.90813 kcal/mol@LB@Unfolding Energy - sRNA 6.05961 kcal/mol@LB@@LB@Position - mRNA 48 -- 58@LB@Position - sRNA 55 -- 65@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 58 -- 64@LB@
147	0.005606	0.1342	b3085	ygjP	-7.80	0.173342	13 -- 33	55 -- 72	putative metal dependent hydrolase		_____________12____________________34\n_____________\|_____________________\|\n5'-AAC...GCAGC_________UCC____CU___CACGC...AAC-3'\n______________AAAUAUUCA___GCCG__UCC\n______________\|\|\|\|\|\|\|\|\|___\|\|\|:__\|\|\|\n______________UUUAUAAGU___CGGU__AGG\n3'-AUU...CCGAU________________UU___CUAAU...AUG-5'\n_____________\|_____________________\|\n_____________73____________________54\n	14 -- 20	65 -- 71	-15.2572 kcal/mol	1.39359 kcal/mol	6.08601 kcal/mol	12 34@LB@ \| \|@LB@5'-AAC...GCAGC UCC CU CACGC...AAC-3'@LB@ AAAUAUUCA GCCG UCC@LB@ \|\|\|\|\|\|\|\|\| \|\|\|: \|\|\|@LB@ UUUAUAAGU CGGU AGG@LB@3'-AUU...CCGAU UU CUAAU...AUG-5'@LB@ \| \|@LB@ 73 54@LB@@LB@@LB@Energy -7.80 kcal/mol@LB@Hybridization Energy -15.2572 kcal/mol@LB@Unfolding Energy - mRNA 1.39359 kcal/mol@LB@Unfolding Energy - sRNA 6.08601 kcal/mol@LB@@LB@Position - mRNA 13 -- 33@LB@Position - sRNA 55 -- 72@LB@Position Seed - mRNA 14 -- 20@LB@Position Seed - sRNA 65 -- 71@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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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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