Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
156	0.02543	0.526	b2805	fucR	-9.08	0.146396	128 -- 135	52 -- 59	l-fucose operon activator	_____________127______136\n_____________\|________\|\n5'-CAC...AAAAA________CACCG...AAA-3'\n______________AGGGGUAA\n______________\|\|\|\|\|\|\|\|\n______________UCCCCAUU\n3'-UUU...CUUUA________UGUCU...UCG-5'\n_____________\|________\|\n_____________60_______51\n	129 -- 135	52 -- 58	-12.2757 kcal/mol	3.13783 kcal/mol	0.0599826 kcal/mol	127 136@LB@ \| \|@LB@5'-CAC...AAAAA CACCG...AAA-3'@LB@ AGGGGUAA@LB@ \|\|\|\|\|\|\|\|@LB@ UCCCCAUU@LB@3'-UUU...CUUUA UGUCU...UCG-5'@LB@ \| \|@LB@ 60 51@LB@@LB@@LB@Energy -9.08 kcal/mol@LB@Hybridization Energy -12.2757 kcal/mol@LB@Unfolding Energy - mRNA 3.13783 kcal/mol@LB@Unfolding Energy - sRNA 0.0599826 kcal/mol@LB@@LB@Position - mRNA 128 -- 135@LB@Position - sRNA 52 -- 59@LB@Position Seed - mRNA 129 -- 135@LB@Position Seed - sRNA 52 -- 58@LB@
165	0.02655	0.526	b2388	glk	-7.68	0.259430	184 -- 233	1 -- 52	glucokinase	_____________183_____________________________________________________234\n_____________\|_______________________________________________________\|\n5'-CUA...ACUUU______G__GUU_____________AAA___UGCAUU_____C_______UG___GGCAC...AUU-3'\n______________AGCGGA_CA____GAA__GAAUGAC___GUA________AGU_GGUGAUG__GGC\n______________\|:\|:\|\|_\|\|____\|\|\|__\|\|\|\|\|\|\|___\|\|\|________\|\|\|_::\|\|\|\|\|__:\|\|\n______________UUGUCU_GU____CUU__CUUACUG___CAU________UCA_UUACUAC__UCG\n3'-UUU...CCCAU_________AAGU___UA_______C_____UAUUUAUU___A_______UA___-5'\n_____________\|______________________________________________________\|\n_____________53_____________________________________________________1\n	222 -- 228	6 -- 12	-28.455 kcal/mol	14.4434 kcal/mol	6.33555 kcal/mol	183 234@LB@ \| \|@LB@5'-CUA...ACUUU G GUU AAA UGCAUU C UG GGCAC...AUU-3'@LB@ AGCGGA CA GAA GAAUGAC GUA AGU GGUGAUG GGC@LB@ \|:\|:\|\| \|\| \|\|\| \|\|\|\|\|\|\| \|\|\| \|\|\| ::\|\|\|\|\| :\|\|@LB@ UUGUCU GU CUU CUUACUG CAU UCA UUACUAC UCG@LB@3'-UUU...CCCAU AAGU UA C UAUUUAUU A UA -5'@LB@ \| \|@LB@ 53 1@LB@@LB@@LB@Energy -7.68 kcal/mol@LB@Hybridization Energy -28.455 kcal/mol@LB@Unfolding Energy - mRNA 14.4434 kcal/mol@LB@Unfolding Energy - sRNA 6.33555 kcal/mol@LB@@LB@Position - mRNA 184 -- 233@LB@Position - sRNA 1 -- 52@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 6 -- 12@LB@
49	0.00563	0.3739	b2239	glpQ	-9.17	0.140723	61 -- 103	1 -- 49	periplasmic glycerophosphodiester phosphodiesterase	_____________60__________________________________________________104\n_____________\|___________________________________________________\|\n5'-CGG...ACCGU____UUC_____CUG__________CUU______U________________GGCAG...UCA-3'\n______________GGAC___UUCGG____GGAUGGCGG_______UA_GG_UAAUGAU__UGGC\n______________:\|\|\|___\|\|\|:\|____\|:\|\|\|:\|\|\|_______\|\|_:\|_\|\|\|\|\|\|\|__\|:\|\|\n______________UCUG___AAGUC____CUUACUGCC_______AU_UC_AUUACUA__AUCG\n3'-UUU...AUUUG____U_______UUUA_________AUUAUUU__U__A_______CU____-5'\n_____________\|__________________________________________________\|\n_____________50_________________________________________________1\n	93 -- 99	7 -- 13	-28.1898 kcal/mol	12.697 kcal/mol	6.32371 kcal/mol	60 104@LB@ \| \|@LB@5'-CGG...ACCGU UUC CUG CUU U GGCAG...UCA-3'@LB@ GGAC UUCGG GGAUGGCGG UA GG UAAUGAU UGGC@LB@ :\|\|\| \|\|\|:\| \|:\|\|\|:\|\|\| \|\| :\| \|\|\|\|\|\|\| \|:\|\|@LB@ UCUG AAGUC CUUACUGCC AU UC AUUACUA AUCG@LB@3'-UUU...AUUUG U UUUA AUUAUUU U A CU -5'@LB@ \| \|@LB@ 50 1@LB@@LB@@LB@Energy -9.17 kcal/mol@LB@Hybridization Energy -28.1898 kcal/mol@LB@Unfolding Energy - mRNA 12.697 kcal/mol@LB@Unfolding Energy - sRNA 6.32371 kcal/mol@LB@@LB@Position - mRNA 61 -- 103@LB@Position - sRNA 1 -- 49@LB@Position Seed - mRNA 93 -- 99@LB@Position Seed - sRNA 7 -- 13@LB@
195	0.03271	0.5507	b3213	gltD	-10.79	0.067022	188 -- 211	38 -- 59	glutamate synthase 4Fe-4S protein small subunit	_____________187______________________212\n_____________\|________________________\|\n5'-AGC...CAGUA_______GC____AUGAG______UGUUU...AGC-3'\n______________AGGGGUA__AACA_____UCAGAA\n______________\|\|\|\|\|\|\|__\|\|\|\|_____\|\|\|\|\|\|\n______________UCCCCAU__UUGU_____AGUCUU\n3'-UUU...CUUUA_____________CUGUA______UACUU...UCG-5'\n_____________\|________________________\|\n_____________60_______________________37\n	188 -- 194	53 -- 59	-20.1632 kcal/mol	3.12506 kcal/mol	6.25108 kcal/mol	187 212@LB@ \| \|@LB@5'-AGC...CAGUA GC AUGAG UGUUU...AGC-3'@LB@ AGGGGUA AACA UCAGAA@LB@ \|\|\|\|\|\|\| \|\|\|\| \|\|\|\|\|\|@LB@ UCCCCAU UUGU AGUCUU@LB@3'-UUU...CUUUA CUGUA UACUU...UCG-5'@LB@ \| \|@LB@ 60 37@LB@@LB@@LB@Energy -10.79 kcal/mol@LB@Hybridization Energy -20.1632 kcal/mol@LB@Unfolding Energy - mRNA 3.12506 kcal/mol@LB@Unfolding Energy - sRNA 6.25108 kcal/mol@LB@@LB@Position - mRNA 188 -- 211@LB@Position - sRNA 38 -- 59@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 53 -- 59@LB@
15	0.0006204	0.1358	b0652	gltL	-11.66	0.043639	269 -- 295	1 -- 25	glutamate/aspartate ABC transporter ATPase	_____________268_________________________296\n_____________\|___________________________\|\n5'-CUC...ACCGA______A____GCGA____________UUGCG-3'\n______________AGUGAA_AAAG____AGUGGUGGUGGU\n______________\|:\|:\|\|_\|\|\|\|____\|:\|\|:\|\|:\|:\|:\n______________UUAUUU_UUUC____UUACUACUAUCG\n3'-UUU...UGCCA______A____AA______________-5'\n_____________\|__________________________\|\n_____________26_________________________1\n	289 -- 295	1 -- 7	-17.2962 kcal/mol	5.52495 kcal/mol	0.112205 kcal/mol	268 296@LB@ \| \|@LB@5'-CUC...ACCGA A GCGA UUGCG-3'@LB@ AGUGAA AAAG AGUGGUGGUGGU@LB@ \|:\|:\|\| \|\|\|\| \|:\|\|:\|\|:\|:\|:@LB@ UUAUUU UUUC UUACUACUAUCG@LB@3'-UUU...UGCCA A AA -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -11.66 kcal/mol@LB@Hybridization Energy -17.2962 kcal/mol@LB@Unfolding Energy - mRNA 5.52495 kcal/mol@LB@Unfolding Energy - sRNA 0.112205 kcal/mol@LB@@LB@Position - mRNA 269 -- 295@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 1 -- 7@LB@
74	0.0107	0.4523	b3385	gph	-12.85	0.023515	41 -- 77	8 -- 48	phosphoglycolate phosphatase	_____________40____________________________________________78\n_____________\|_____________________________________________\|\n5'-ACU...GCUUU_______GACU__________________C_______________ACAAC...UGU-3'\n______________GACAUUC____AGAAGUG___GACGGUGG___GUGAAG___GUGA\n______________\|\|\|\|\|\|\|____\|\|\|\|:\|\|___\|\|\|\|\|\|::___:\|:\|\|\|___:\|\|\|\n______________CUGUAAG____UCUUUAC___CUGCCAUU___UAUUUC___UACU\n3'-UUU...UUUGU__________________UUA________AUU______AAU____ACUAUCG-5'\n_____________\|_____________________________________________\|\n_____________49____________________________________________7\n	60 -- 66	24 -- 30	-29.3756 kcal/mol	10.2075 kcal/mol	6.31567 kcal/mol	40 78@LB@ \| \|@LB@5'-ACU...GCUUU GACU C ACAAC...UGU-3'@LB@ GACAUUC AGAAGUG GACGGUGG GUGAAG GUGA@LB@ \|\|\|\|\|\|\| \|\|\|\|:\|\| \|\|\|\|\|\|:: :\|:\|\|\| :\|\|\|@LB@ CUGUAAG UCUUUAC CUGCCAUU UAUUUC UACU@LB@3'-UUU...UUUGU UUA AUU AAU ACUAUCG-5'@LB@ \| \|@LB@ 49 7@LB@@LB@@LB@Energy -12.85 kcal/mol@LB@Hybridization Energy -29.3756 kcal/mol@LB@Unfolding Energy - mRNA 10.2075 kcal/mol@LB@Unfolding Energy - sRNA 6.31567 kcal/mol@LB@@LB@Position - mRNA 41 -- 77@LB@Position - sRNA 8 -- 48@LB@Position Seed - mRNA 60 -- 66@LB@Position Seed - sRNA 24 -- 30@LB@
47	0.005156	0.3601	b2614	grpE	-12.03	0.036099	152 -- 179	1 -- 26	heat shock protein	_____________151__________________________180\n_____________\|____________________________\|\n5'-GAG...CCCCA_______C________CGA_____AU__GAAAA...CUG-3'\n______________UAAUAAG_GAAGUUAG___GAUGA__GC\n______________\|\|\|\|\|\|:_:\|\|\|\|\|\|:___\|\|\|\|\|__\|\|\n______________AUUAUUU_UUUCAAUU___CUACU__CG\n3'-UUU...CUGCC_______A________A_______AU__-5'\n_____________\|___________________________\|\n_____________27__________________________1\n	161 -- 167	11 -- 17	-17.6467 kcal/mol	5.03361 kcal/mol	0.580494 kcal/mol	151 180@LB@ \| \|@LB@5'-GAG...CCCCA C CGA AU GAAAA...CUG-3'@LB@ UAAUAAG GAAGUUAG GAUGA GC@LB@ \|\|\|\|\|\|: :\|\|\|\|\|\|: \|\|\|\|\| \|\|@LB@ AUUAUUU UUUCAAUU CUACU CG@LB@3'-UUU...CUGCC A A AU -5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -12.03 kcal/mol@LB@Hybridization Energy -17.6467 kcal/mol@LB@Unfolding Energy - mRNA 5.03361 kcal/mol@LB@Unfolding Energy - sRNA 0.580494 kcal/mol@LB@@LB@Position - mRNA 152 -- 179@LB@Position - sRNA 1 -- 26@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 11 -- 17@LB@
107	0.01649	0.5059	b0830	gsiB	-12.67	0.025954	282 -- 298	1 -- 18	glutathione ABC transporter periplasmic binding protein	_____________281________________299\n_____________\|__________________\|\n5'-GGC...CUGCC____AU____________GG-3'\n______________AAAG___GUGGUGGUGGC\n______________\|\|\|\|___:\|\|:\|\|:\|:\|\|\n______________UUUC___UACUACUAUCG\n3'-UUU...AUUUA____AAU___________-5'\n_____________\|_________________\|\n_____________19________________1\n	292 -- 298	1 -- 7	-15.5562 kcal/mol	2.82856 kcal/mol	0.0611543 kcal/mol	281 299@LB@ \| \|@LB@5'-GGC...CUGCC AU GG-3'@LB@ AAAG GUGGUGGUGGC@LB@ \|\|\|\| :\|\|:\|\|:\|:\|\|@LB@ UUUC UACUACUAUCG@LB@3'-UUU...AUUUA AAU -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -12.67 kcal/mol@LB@Hybridization Energy -15.5562 kcal/mol@LB@Unfolding Energy - mRNA 2.82856 kcal/mol@LB@Unfolding Energy - sRNA 0.0611543 kcal/mol@LB@@LB@Position - mRNA 282 -- 298@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 1 -- 7@LB@
91	0.01489	0.5059	b3805	hemC	-12.98	0.021909	168 -- 195	24 -- 52	hydroxymethylbilane synthase	_____________167___________________________196\n_____________\|_____________________________\|\n5'-AAA...GUUAG_______CA_____UGAU___________CAAGC...GCC-3'\n______________GAUGGAC___CGGA____AAUGACGGUAA\n______________:\|::\|\|\|___\|:\|\|____\|\|\|\|\|\|\|\|\|\|\|\n______________UUGUCUG___GUCU____UUACUGCCAUU\n3'-UUU...CCCAU_______UAA____UUAC___________AUUUA...UCG-5'\n_____________\|_____________________________\|\n_____________53____________________________23\n	189 -- 195	24 -- 30	-23.6136 kcal/mol	4.33145 kcal/mol	6.2974 kcal/mol	167 196@LB@ \| \|@LB@5'-AAA...GUUAG CA UGAU CAAGC...GCC-3'@LB@ GAUGGAC CGGA AAUGACGGUAA@LB@ :\|::\|\|\| \|:\|\| \|\|\|\|\|\|\|\|\|\|\|@LB@ UUGUCUG GUCU UUACUGCCAUU@LB@3'-UUU...CCCAU UAA UUAC AUUUA...UCG-5'@LB@ \| \|@LB@ 53 23@LB@@LB@@LB@Energy -12.98 kcal/mol@LB@Hybridization Energy -23.6136 kcal/mol@LB@Unfolding Energy - mRNA 4.33145 kcal/mol@LB@Unfolding Energy - sRNA 6.2974 kcal/mol@LB@@LB@Position - mRNA 168 -- 195@LB@Position - sRNA 24 -- 52@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 24 -- 30@LB@
27	0.001735	0.211	b3052	hldE	-15.91	0.004078	227 -- 261	1 -- 47	heptose 7-phosphate kinase and heptose 1-phosphate adenyltransferase	_____________226______________________________________________262\n_____________\|________________________________________________\|\n5'-GCG...UUUGA____G_____________________________________UGAU__UGGAU...CGC-3'\n______________ACGU_CAG____GAGUGAUGGU_________GGUUGGUGAUG____GC\n______________\|\|:\|_\|\|\|____\|\|:\|\|\|:\|\|\|_________:\|\|\|::\|\|\|\|\|____\|\|\n______________UGUA_GUC____CUUACUGCCA_________UCAAUUACUAC____CG\n3'-UUU...UUGUC____A___UUUA__________UUAUUUAUU___________UAU___-5'\n_____________\|_______________________________________________\|\n_____________48______________________________________________1\n	249 -- 255	6 -- 12	-30.7414 kcal/mol	8.50852 kcal/mol	6.32011 kcal/mol	226 262@LB@ \| \|@LB@5'-GCG...UUUGA G UGAU UGGAU...CGC-3'@LB@ ACGU CAG GAGUGAUGGU GGUUGGUGAUG GC@LB@ \|\|:\| \|\|\| \|\|:\|\|\|:\|\|\| :\|\|\|::\|\|\|\|\| \|\|@LB@ UGUA GUC CUUACUGCCA UCAAUUACUAC CG@LB@3'-UUU...UUGUC A UUUA UUAUUUAUU UAU -5'@LB@ \| \|@LB@ 48 1@LB@@LB@@LB@Energy -15.91 kcal/mol@LB@Hybridization Energy -30.7414 kcal/mol@LB@Unfolding Energy - mRNA 8.50852 kcal/mol@LB@Unfolding Energy - sRNA 6.32011 kcal/mol@LB@@LB@Position - mRNA 227 -- 261@LB@Position - sRNA 1 -- 47@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 6 -- 12@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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usability assessment

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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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