Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
12	0.0004505	0.1262	b3248	yhdE	-11.12	0.070056	184 -- 205	1 -- 21	dTTP/UTP pyrophosphatase; m(5)UTP/m(5)CTP/pseudo-UTP pyrophosphatase	_____________183_____________________206\n_____________\|_______________________\|\n5'-UUA...UUGCA______________UUC______UUCUC...AGC-3'\n______________GUG_CAAUAAAGGU___UAUGAC\n______________\|\|\|_\|\|\|\|\|\|\|\|\|:___\|\|\|:\|\|\n______________CAC_GUUAUUUCCG___AUAUUG\n3'-UUU...UUAGA___U__________U________-5'\n_____________\|______________________\|\n_____________22_____________________1\n	190 -- 196	8 -- 14	-19.9684 kcal/mol	4.43203 kcal/mol	4.41334 kcal/mol	183 206@LB@ \| \|@LB@5'-UUA...UUGCA UUC UUCUC...AGC-3'@LB@ GUG CAAUAAAGGU UAUGAC@LB@ \|\|\| \|\|\|\|\|\|\|\|\|: \|\|\|:\|\|@LB@ CAC GUUAUUUCCG AUAUUG@LB@3'-UUU...UUAGA U U -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -19.9684 kcal/mol@LB@Unfolding Energy - mRNA 4.43203 kcal/mol@LB@Unfolding Energy - sRNA 4.41334 kcal/mol@LB@@LB@Position - mRNA 184 -- 205@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 8 -- 14@LB@
176	0.02144	0.4097	b0948	rlmL	-6.91	0.434425	184 -- 201	13 -- 33	23S rRNA m(2)G2445 and m(7)G2069 methyltransferases SAM-dependent	_____________183___________________202\n_____________\|_____________________\|\n5'-GAC...CUCUU_____________________UGAAU...GUG-3'\n______________AGAGUAAAA___GUGACGAUA\n______________\|:\|:\|\|\|\|\|___\|\|\|\|\|:\|\|\|\n______________UUUUAUUUU___CACUGUUAU\n3'-UUU...UUGUC_________AGA_________UUCCG...UUG-5'\n_____________\|_____________________\|\n_____________34____________________12\n	195 -- 201	13 -- 19	-14.282 kcal/mol	2.4415 kcal/mol	4.9341 kcal/mol	183 202@LB@ \| \|@LB@5'-GAC...CUCUU UGAAU...GUG-3'@LB@ AGAGUAAAA GUGACGAUA@LB@ \|:\|:\|\|\|\|\| \|\|\|\|\|:\|\|\|@LB@ UUUUAUUUU CACUGUUAU@LB@3'-UUU...UUGUC AGA UUCCG...UUG-5'@LB@ \| \|@LB@ 34 12@LB@@LB@@LB@Energy -6.91 kcal/mol@LB@Hybridization Energy -14.282 kcal/mol@LB@Unfolding Energy - mRNA 2.4415 kcal/mol@LB@Unfolding Energy - sRNA 4.9341 kcal/mol@LB@@LB@Position - mRNA 184 -- 201@LB@Position - sRNA 13 -- 33@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 13 -- 19@LB@
82	0.006986	0.2822	b3128	garD	-14.80	0.008847	185 -- 224	15 -- 66	D-galactarate dehydrogenase	_____________184__________________________________________________225\n_____________\|____________________________________________________\|\n5'-AUA...CUGGC________AUU_____________________UC__________A_______GAAAC...UGA-3'\n______________UGGAGAAU_____GCA___CAAUGGCC_AACA______GAAAUC___GACAA\n______________\|\|\|\|:\|\|\|_____\|\|\|___\|\|\|\|\|\|\|\|_\|\|\|\|______:\|\|\|\|\|___\|\|\|\|\|\n______________ACCUUUUA_____CGU___GUUACCGG_UUGU______UUUUAG___CUGUU\n3'-UUU...AUACA________GUCAC___UAC________G____CUUUUA______ACA_____AUUUC...UUG-5'\n_____________\|____________________________________________________\|\n_____________67___________________________________________________14\n	200 -- 206	40 -- 46	-31.4715 kcal/mol	5.54782 kcal/mol	11.1209 kcal/mol	184 225@LB@ \| \|@LB@5'-AUA...CUGGC AUU UC A GAAAC...UGA-3'@LB@ UGGAGAAU GCA CAAUGGCC AACA GAAAUC GACAA@LB@ \|\|\|\|:\|\|\| \|\|\| \|\|\|\|\|\|\|\| \|\|\|\| :\|\|\|\|\| \|\|\|\|\|@LB@ ACCUUUUA CGU GUUACCGG UUGU UUUUAG CUGUU@LB@3'-UUU...AUACA GUCAC UAC G CUUUUA ACA AUUUC...UUG-5'@LB@ \| \|@LB@ 67 14@LB@@LB@@LB@Energy -14.80 kcal/mol@LB@Hybridization Energy -31.4715 kcal/mol@LB@Unfolding Energy - mRNA 5.54782 kcal/mol@LB@Unfolding Energy - sRNA 11.1209 kcal/mol@LB@@LB@Position - mRNA 185 -- 224@LB@Position - sRNA 15 -- 66@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 40 -- 46@LB@
105	0.009758	0.3118	b4478	dgoD	-14.76	0.009064	185 -- 203	43 -- 60	D-galactonate dehydratase	_____________184_________________204\n_____________\|___________________\|\n5'-AAA...GGCGU___G__A____________AAAAU...UGA-3'\n______________AUC_AG_GGCAGUGCAAUG\n______________\|\|\|_\|\|_\|\|\|\|:\|\|\|\|\|\|\|\n______________UAG_UC_CCGUUACGUUAC\n3'-UUU...CCUUU______A____________CGGGU...UUG-5'\n_____________\|___________________\|\n_____________61__________________42\n	197 -- 203	43 -- 49	-22.2033 kcal/mol	3.91427 kcal/mol	3.52557 kcal/mol	184 204@LB@ \| \|@LB@5'-AAA...GGCGU G A AAAAU...UGA-3'@LB@ AUC AG GGCAGUGCAAUG@LB@ \|\|\| \|\| \|\|\|\|:\|\|\|\|\|\|\|@LB@ UAG UC CCGUUACGUUAC@LB@3'-UUU...CCUUU A CGGGU...UUG-5'@LB@ \| \|@LB@ 61 42@LB@@LB@@LB@Energy -14.76 kcal/mol@LB@Hybridization Energy -22.2033 kcal/mol@LB@Unfolding Energy - mRNA 3.91427 kcal/mol@LB@Unfolding Energy - sRNA 3.52557 kcal/mol@LB@@LB@Position - mRNA 185 -- 203@LB@Position - sRNA 43 -- 60@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 43 -- 49@LB@
18	0.0007704	0.1438	b4526	ydaE	-7.35	0.372707	186 -- 222	21 -- 54	conserved protein Rac prophage	_____________185___________________________________223\n_____________\|_____________________________________\|\n5'-ACU...GUAAA_____A__C_____GA____UA____________G__CUUAC...UAU-3'\n______________GGCGG_GU_AUGGU__UGAC__AGAAAAUAAAAU_UG\n______________\|\|\|::_\|:_\|\|\|\|:__::\|\|__\|\|\|\|\|\|\|\|\|\|\|\|_\|\|\n______________CCGUU_CG_UACCG__GUUG__UCUUUUAUUUUA_AC\n3'-UUU...AGUCA_____A__U_____G___________________G__ACUGU...UUG-5'\n_____________\|_____________________________________\|\n_____________55____________________________________20\n	212 -- 218	25 -- 31	-28.7009 kcal/mol	12.2907 kcal/mol	9.06413 kcal/mol	185 223@LB@ \| \|@LB@5'-ACU...GUAAA A C GA UA G CUUAC...UAU-3'@LB@ GGCGG GU AUGGU UGAC AGAAAAUAAAAU UG@LB@ \|\|\|:: \|: \|\|\|\|: ::\|\| \|\|\|\|\|\|\|\|\|\|\|\| \|\|@LB@ CCGUU CG UACCG GUUG UCUUUUAUUUUA AC@LB@3'-UUU...AGUCA A U G G ACUGU...UUG-5'@LB@ \| \|@LB@ 55 20@LB@@LB@@LB@Energy -7.35 kcal/mol@LB@Hybridization Energy -28.7009 kcal/mol@LB@Unfolding Energy - mRNA 12.2907 kcal/mol@LB@Unfolding Energy - sRNA 9.06413 kcal/mol@LB@@LB@Position - mRNA 186 -- 222@LB@Position - sRNA 21 -- 54@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 25 -- 31@LB@
49	0.003464	0.237	b4260	pepA	-9.32	0.166975	186 -- 204	42 -- 59	multifunctional aminopeptidase A: a cyteinylglycinase transcription regulator and site-specific recombination factor	_____________185__________________205\n_____________\|____________________\|\n5'-UUA...AAGAU____GA_C____________AGUUU...AAC-3'\n______________UCAG__G_GUAGUGCA_UGG\n______________\|\|\|\|__\|_\|:\|:\|\|\|\|_\|\|\|\n______________AGUC__C_CGUUACGU_ACC\n3'-UUU...CUUUU____A___________U___GGGUU...UUG-5'\n_____________\|____________________\|\n_____________60___________________41\n	195 -- 201	46 -- 52	-17.4947 kcal/mol	4.48384 kcal/mol	3.69565 kcal/mol	185 205@LB@ \| \|@LB@5'-UUA...AAGAU GA C AGUUU...AAC-3'@LB@ UCAG G GUAGUGCA UGG@LB@ \|\|\|\| \| \|:\|:\|\|\|\| \|\|\|@LB@ AGUC C CGUUACGU ACC@LB@3'-UUU...CUUUU A U GGGUU...UUG-5'@LB@ \| \|@LB@ 60 41@LB@@LB@@LB@Energy -9.32 kcal/mol@LB@Hybridization Energy -17.4947 kcal/mol@LB@Unfolding Energy - mRNA 4.48384 kcal/mol@LB@Unfolding Energy - sRNA 3.69565 kcal/mol@LB@@LB@Position - mRNA 186 -- 204@LB@Position - sRNA 42 -- 59@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 46 -- 52@LB@
89	0.007733	0.2889	b3426	glpD	-8.48	0.239884	186 -- 234	7 -- 64	sn-glycerol-3-phosphate dehydrogenase aerobic FAD/NAD(P)-binding	_____________185__________________________________________________________235\n_____________\|____________________________________________________________\|\n5'-AAC...CGAAA_U____G________________AAA________UCU_______________________GCAUC...AGG-3'\n______________G_GAAU_AG_GGCA__GC_AUGG___CCAA_AGA______GA_UUGUGAUAG__GGGGCG\n______________\|_:\|\|\|_\|\|_\|\|\|\|__\|\|_\|\|\|\|___\|\|\|\|_\|\|\|______:\|_:\|\|\|\|\|:\|:__::\|\|\|:\n______________C_UUUA_UC_CCGU__CG_UACC___GGUU_UCU______UU_GACACUGUU__UUCCGU\n3'-UUU...ACAAC_U____G__A____UA__U____G______G___UUUAUU__A_________AU______AUAUUG-5'\n_____________\|____________________________________________________________\|\n_____________65___________________________________________________________6\n	222 -- 228	15 -- 21	-34.508 kcal/mol	13.8761 kcal/mol	12.1536 kcal/mol	185 235@LB@ \| \|@LB@5'-AAC...CGAAA U G AAA UCU GCAUC...AGG-3'@LB@ G GAAU AG GGCA GC AUGG CCAA AGA GA UUGUGAUAG GGGGCG@LB@ \| :\|\|\| \|\| \|\|\|\| \|\| \|\|\|\| \|\|\|\| \|\|\| :\| :\|\|\|\|\|:\|: ::\|\|\|:@LB@ C UUUA UC CCGU CG UACC GGUU UCU UU GACACUGUU UUCCGU@LB@3'-UUU...ACAAC U G A UA U G G UUUAUU A AU AUAUUG-5'@LB@ \| \|@LB@ 65 6@LB@@LB@@LB@Energy -8.48 kcal/mol@LB@Hybridization Energy -34.508 kcal/mol@LB@Unfolding Energy - mRNA 13.8761 kcal/mol@LB@Unfolding Energy - sRNA 12.1536 kcal/mol@LB@@LB@Position - mRNA 186 -- 234@LB@Position - sRNA 7 -- 64@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 15 -- 21@LB@
134	0.01498	0.3759	b3388	damX	-9.22	0.174550	186 -- 204	42 -- 59	cell division protein that binds to the septal ring	_____________185__________________205\n_____________\|____________________\|\n5'-GGG...ACCUU_____________UA_____AUGAA...AAC-3'\n______________UUAGUGG_GGUGU__AAUGG\n______________\|:\|\|\|\|\|_::\|\|:__\|\|\|\|\|\n______________AGUCACC_UUACG__UUACC\n3'-UUU...CUUUU_______G____________GGGUU...UUG-5'\n_____________\|____________________\|\n_____________60___________________41\n	186 -- 192	53 -- 59	-16.4488 kcal/mol	3.53707 kcal/mol	3.69565 kcal/mol	185 205@LB@ \| \|@LB@5'-GGG...ACCUU UA AUGAA...AAC-3'@LB@ UUAGUGG GGUGU AAUGG@LB@ \|:\|\|\|\|\| ::\|\|: \|\|\|\|\|@LB@ AGUCACC UUACG UUACC@LB@3'-UUU...CUUUU G GGGUU...UUG-5'@LB@ \| \|@LB@ 60 41@LB@@LB@@LB@Energy -9.22 kcal/mol@LB@Hybridization Energy -16.4488 kcal/mol@LB@Unfolding Energy - mRNA 3.53707 kcal/mol@LB@Unfolding Energy - sRNA 3.69565 kcal/mol@LB@@LB@Position - mRNA 186 -- 204@LB@Position - sRNA 42 -- 59@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 53 -- 59@LB@
145	0.01667	0.3828	b1835	rsmF	-17.85	0.001164	186 -- 211	35 -- 58	16S rRNA m(5)C1407 methyltransferase SAM-dependent	_____________185________________________212\n_____________\|__________________________\|\n5'-CGC...UUUGC________C____UC___________CACCG...GUC-3'\n______________CAGUGGUA_AUGC__GUGGCCCAACA\n______________\|\|\|\|\|\|:\|_\|\|\|\|__:\|\|\|\|\|\|\|\|\|\|\n______________GUCACCGU_UACG__UACCGGGUUGU\n3'-UUU...UUUUA_____________U____________CUUUU...UUG-5'\n_____________\|__________________________\|\n_____________59_________________________34\n	205 -- 211	35 -- 41	-37.9392 kcal/mol	9.33395 kcal/mol	10.7541 kcal/mol	185 212@LB@ \| \|@LB@5'-CGC...UUUGC C UC CACCG...GUC-3'@LB@ CAGUGGUA AUGC GUGGCCCAACA@LB@ \|\|\|\|\|\|:\| \|\|\|\| :\|\|\|\|\|\|\|\|\|\|@LB@ GUCACCGU UACG UACCGGGUUGU@LB@3'-UUU...UUUUA U CUUUU...UUG-5'@LB@ \| \|@LB@ 59 34@LB@@LB@@LB@Energy -17.85 kcal/mol@LB@Hybridization Energy -37.9392 kcal/mol@LB@Unfolding Energy - mRNA 9.33395 kcal/mol@LB@Unfolding Energy - sRNA 10.7541 kcal/mol@LB@@LB@Position - mRNA 186 -- 211@LB@Position - sRNA 35 -- 58@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 35 -- 41@LB@
188	0.02326	0.4145	b2501	ppk	-10.84	0.080977	186 -- 203	48 -- 65	polyphosphate kinase component of RNA degradosome	_____________185________________204\n_____________\|__________________\|\n5'-CGC...AAAAC____UAAA__________GGUCA...UUG-3'\n______________GGAG____AGUGGUAAUG\n______________\|\|\|:____\|\|\|\|\|:\|\|\|\|\n______________CCUU____UCACCGUUAC\n3'-UUU...UACAA____UUAG__________GUUAC...UUG-5'\n_____________\|__________________\|\n_____________66_________________47\n	197 -- 203	48 -- 54	-18.775 kcal/mol	3.93073 kcal/mol	4.00814 kcal/mol	185 204@LB@ \| \|@LB@5'-CGC...AAAAC UAAA GGUCA...UUG-3'@LB@ GGAG AGUGGUAAUG@LB@ \|\|\|: \|\|\|\|\|:\|\|\|\|@LB@ CCUU UCACCGUUAC@LB@3'-UUU...UACAA UUAG GUUAC...UUG-5'@LB@ \| \|@LB@ 66 47@LB@@LB@@LB@Energy -10.84 kcal/mol@LB@Hybridization Energy -18.775 kcal/mol@LB@Unfolding Energy - mRNA 3.93073 kcal/mol@LB@Unfolding Energy - sRNA 4.00814 kcal/mol@LB@@LB@Position - mRNA 186 -- 203@LB@Position - sRNA 48 -- 65@LB@Position Seed - mRNA 197 -- 203@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

Use the following button if you want to resubmit the job with altered input or parameterization:

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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