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	Additional homologs
77	0.01108	0.4523	b2099	yegU	-9.55	0.118747	1 -- 10	2 -- 11	ADP-ribosylglycohydrolase family protein		______________1_________11\n______________\|_________\|\n___________5'-__________AAAAG...CAC-3'\n______________GUGAUGAUGG\n______________:\|\|\|\|\|\|\|:\|\n______________UACUACUAUC\n3'-UUU...UCAAU__________G-5'\n_____________\|__________\|\n_____________12_________1\n	4 -- 10	2 -- 8	-12.4903 kcal/mol	2.91076 kcal/mol	0.0252227 kcal/mol	1 11@LB@ \| \|@LB@ 5'- AAAAG...CAC-3'@LB@ GUGAUGAUGG@LB@ :\|\|\|\|\|\|\|:\|@LB@ UACUACUAUC@LB@3'-UUU...UCAAU G-5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -9.55 kcal/mol@LB@Hybridization Energy -12.4903 kcal/mol@LB@Unfolding Energy - mRNA 2.91076 kcal/mol@LB@Unfolding Energy - sRNA 0.0252227 kcal/mol@LB@@LB@Position - mRNA 1 -- 10@LB@Position - sRNA 2 -- 11@LB@Position Seed - mRNA 4 -- 10@LB@Position Seed - sRNA 2 -- 8@LB@
114	0.01806	0.5155	b3033	yqiB	-9.53	0.119911	174 -- 206	15 -- 50	DUF1249 protein YqiB		_____________173__________________________________207\n_____________\|____________________________________\|\n5'-UGG...AUCAU__A_____AAA_____________C___________CGUUA...GCG-3'\n______________CA_GCGUU___AAAUGAGUG__GG__AUAAAUGAAG\n______________\|\|_:\|:\|\|___\|\|\|\|\|\|:\|\|__\|\|__\|\|\|\|\|\|:\|\|\|\n______________GU_UGUAA___UUUACUUAC__CC__UAUUUAUUUC\n3'-UUU...CAUUU__C_____GUC_________UG__AU__________AAUUA...UCG-5'\n_____________\|____________________________________\|\n_____________51___________________________________14\n	200 -- 206	15 -- 21	-20.8588 kcal/mol	5.00376 kcal/mol	6.32253 kcal/mol	173 207@LB@ \| \|@LB@5'-UGG...AUCAU A AAA C CGUUA...GCG-3'@LB@ CA GCGUU AAAUGAGUG GG AUAAAUGAAG@LB@ \|\| :\|:\|\| \|\|\|\|\|\|:\|\| \|\| \|\|\|\|\|\|:\|\|\|@LB@ GU UGUAA UUUACUUAC CC UAUUUAUUUC@LB@3'-UUU...CAUUU C GUC UG AU AAUUA...UCG-5'@LB@ \| \|@LB@ 51 14@LB@@LB@@LB@Energy -9.53 kcal/mol@LB@Hybridization Energy -20.8588 kcal/mol@LB@Unfolding Energy - mRNA 5.00376 kcal/mol@LB@Unfolding Energy - sRNA 6.32253 kcal/mol@LB@@LB@Position - mRNA 174 -- 206@LB@Position - sRNA 15 -- 50@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 15 -- 21@LB@
86	0.013	0.4962	b0451	amtB	-9.48	0.122870	5 -- 23	1 -- 22	ammonium transporter		_____________4______________________24\n_____________\|______________________\|\n_______5'-CCAA_______AAU____________GAUUG...CGU-3'\n______________AAGUAAA_____UGAUG_UGGC\n______________\|\|:\|\|\|\|_____\|\|\|\|\|_\|:\|\|\n______________UUUAUUU_____ACUAC_AUCG\n3'-UUU...CAUUA_______CAAUU_____U____-5'\n_____________\|_____________________\|\n_____________23____________________1\n	5 -- 11	16 -- 22	-11.4865 kcal/mol	1.90989 kcal/mol	0.0989066 kcal/mol	4 24@LB@ \| \|@LB@ 5'-CCAA AAU GAUUG...CGU-3'@LB@ AAGUAAA UGAUG UGGC@LB@ \|\|:\|\|\|\| \|\|\|\|\| \|:\|\|@LB@ UUUAUUU ACUAC AUCG@LB@3'-UUU...CAUUA CAAUU U -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -11.4865 kcal/mol@LB@Unfolding Energy - mRNA 1.90989 kcal/mol@LB@Unfolding Energy - sRNA 0.0989066 kcal/mol@LB@@LB@Position - mRNA 5 -- 23@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 16 -- 22@LB@
187	0.03165	0.5492	b2717	hycI	-9.48	0.123006	243 -- 251	1 -- 9	protease involved in processing C-terminal end of HycE		_____________242_______252\n_____________\|_________\|\n5'-AGC...UGGGC_________GCAGG...ACU-3'\n______________GAUGAUGGC\n______________\|\|\|\|\|\|:\|\|\n______________CUACUAUCG\n3'-UUU...AAUUA_________-5'\n_____________\|________\|\n_____________10_______1\n	245 -- 251	1 -- 7	-13.2104 kcal/mol	3.71514 kcal/mol	0.0200155 kcal/mol	242 252@LB@ \| \|@LB@5'-AGC...UGGGC GCAGG...ACU-3'@LB@ GAUGAUGGC@LB@ \|\|\|\|\|\|:\|\|@LB@ CUACUAUCG@LB@3'-UUU...AAUUA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -13.2104 kcal/mol@LB@Unfolding Energy - mRNA 3.71514 kcal/mol@LB@Unfolding Energy - sRNA 0.0200155 kcal/mol@LB@@LB@Position - mRNA 243 -- 251@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 1 -- 7@LB@
59	0.008416	0.4523	b0566	envY	-9.46	0.123665	249 -- 263	50 -- 64	porin thermoregulatory transcriptional activator	b1499 b0564 b3515 b4116 b3516	_____________248_____________264\n_____________\|_______________\|\n5'-GGC...AAAAA_______A_______GUCAA...ACU-3'\n______________GAGGUAG_GGUAAGC\n______________\|\|::\|\|\|_\|\|\|\|\|:\|\n______________CUUUAUC_CCAUUUG\n3'-UUU...GCCAA_______C_______UCUGU...UCG-5'\n_____________\|_______________\|\n_____________65______________49\n	257 -- 263	50 -- 56	-15.2892 kcal/mol	5.08919 kcal/mol	0.736811 kcal/mol	248 264@LB@ \| \|@LB@5'-GGC...AAAAA A GUCAA...ACU-3'@LB@ GAGGUAG GGUAAGC@LB@ \|\|::\|\|\| \|\|\|\|\|:\|@LB@ CUUUAUC CCAUUUG@LB@3'-UUU...GCCAA C UCUGU...UCG-5'@LB@ \| \|@LB@ 65 49@LB@@LB@@LB@Energy -9.46 kcal/mol@LB@Hybridization Energy -15.2892 kcal/mol@LB@Unfolding Energy - mRNA 5.08919 kcal/mol@LB@Unfolding Energy - sRNA 0.736811 kcal/mol@LB@@LB@Position - mRNA 249 -- 263@LB@Position - sRNA 50 -- 64@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 50 -- 56@LB@
111	0.01748	0.5155	b4012	yjaB	-9.42	0.126217	155 -- 212	1 -- 59	GNAT-family putative N-acetyltransferase; acetyl coenzyme A-binding protein		_____________154_____________________________________________________________213\n_____________\|_______________________________________________________________\|\n5'-AAG...UUUCA___AAA____U___________UAUAA____________A________AA______UAU____AUUCG...CAG-3'\n______________AGG___AGAC__ACG_UUAGAA_____GAAUGAC__UAA_AGG_AGAG__AAUGGU___UAGU\n______________\|\|\|___\|:\|\|__\|\|:_\|:\|\|\|\|_____\|\|\|\|\|\|\|__\|\|\|_\|::_\|:\|\|__\|\|\|\|:\|___\|\|\|:\n______________UCC___UUUG__UGU_AGUCUU_____CUUACUG__AUU_UUU_UUUC__UUACUA___AUCG\n3'-UUU...CUUUA___CCA____UC___A______UA__________CC___A___A____AA______CU_____-5'\n_____________\|______________________________________________________________\|\n_____________60_____________________________________________________________1\n	180 -- 186	29 -- 35	-23.4815 kcal/mol	7.7268 kcal/mol	6.33764 kcal/mol	154 213@LB@ \| \|@LB@5'-AAG...UUUCA AAA U UAUAA A AA UAU AUUCG...CAG-3'@LB@ AGG AGAC ACG UUAGAA GAAUGAC UAA AGG AGAG AAUGGU UAGU@LB@ \|\|\| \|:\|\| \|\|: \|:\|\|\|\| \|\|\|\|\|\|\| \|\|\| \|:: \|:\|\| \|\|\|\|:\| \|\|\|:@LB@ UCC UUUG UGU AGUCUU CUUACUG AUU UUU UUUC UUACUA AUCG@LB@3'-UUU...CUUUA CCA UC A UA CC A A AA CU -5'@LB@ \| \|@LB@ 60 1@LB@@LB@@LB@Energy -9.42 kcal/mol@LB@Hybridization Energy -23.4815 kcal/mol@LB@Unfolding Energy - mRNA 7.7268 kcal/mol@LB@Unfolding Energy - sRNA 6.33764 kcal/mol@LB@@LB@Position - mRNA 155 -- 212@LB@Position - sRNA 1 -- 59@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 29 -- 35@LB@
51	0.006039	0.3887	b3822	recQ	-9.34	0.130811	192 -- 200	50 -- 58	ATP-dependent DNA helicase		_____________191_______201\n_____________\|_________\|\n5'-CGC...CAAUC_________GUGGC...UUA-3'\n______________GGGGUGAAU\n______________\|\|\|\|\|:\|\|:\n______________CCCCAUUUG\n3'-UUU...UUUAU_________UCUGU...UCG-5'\n_____________\|_________\|\n_____________59________49\n	194 -- 200	50 -- 56	-13.8974 kcal/mol	3.8337 kcal/mol	0.72763 kcal/mol	191 201@LB@ \| \|@LB@5'-CGC...CAAUC GUGGC...UUA-3'@LB@ GGGGUGAAU@LB@ \|\|\|\|\|:\|\|:@LB@ CCCCAUUUG@LB@3'-UUU...UUUAU UCUGU...UCG-5'@LB@ \| \|@LB@ 59 49@LB@@LB@@LB@Energy -9.34 kcal/mol@LB@Hybridization Energy -13.8974 kcal/mol@LB@Unfolding Energy - mRNA 3.8337 kcal/mol@LB@Unfolding Energy - sRNA 0.72763 kcal/mol@LB@@LB@Position - mRNA 192 -- 200@LB@Position - sRNA 50 -- 58@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 50 -- 56@LB@
171	0.02792	0.531	b2754	ygbF	-9.28	0.134010	284 -- 290	53 -- 59	CRISPR adaptation ssRNA endonuclease		_____________283_____291\n_____________\|_______\|\n5'-UGG...CGUGC_______UAUGU...GUG-3'\n______________AGGGGUA\n______________\|\|\|\|\|\|\|\n______________UCCCCAU\n3'-UUU...CUUUA_______UUGUC...UCG-5'\n_____________\|_______\|\n_____________60______52\n	284 -- 290	53 -- 59	-11.8962 kcal/mol	2.55869 kcal/mol	0.0564539 kcal/mol	283 291@LB@ \| \|@LB@5'-UGG...CGUGC UAUGU...GUG-3'@LB@ AGGGGUA@LB@ \|\|\|\|\|\|\|@LB@ UCCCCAU@LB@3'-UUU...CUUUA UUGUC...UCG-5'@LB@ \| \|@LB@ 60 52@LB@@LB@@LB@Energy -9.28 kcal/mol@LB@Hybridization Energy -11.8962 kcal/mol@LB@Unfolding Energy - mRNA 2.55869 kcal/mol@LB@Unfolding Energy - sRNA 0.0564539 kcal/mol@LB@@LB@Position - mRNA 284 -- 290@LB@Position - sRNA 53 -- 59@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 53 -- 59@LB@
161	0.02632	0.526	b3670	ilvN	-9.27	0.134814	179 -- 196	49 -- 65	acetolactate synthase 1 small subunit		_____________178________________197\n_____________\|__________________\|\n5'-UCA...AAUAC________U___GG____AGCCA...CUU-3'\n______________UGAAAUGG_GGG__AAUA\n______________\|\|\|\|\|\|:\|_\|\|\|__\|\|:\|\n______________ACUUUAUC_CCC__UUGU\n3'-UUU...GGCCA____________AU____CUGUA...UCG-5'\n_____________\|__________________\|\n_____________66_________________48\n	180 -- 186	58 -- 64	-15.3061 kcal/mol	4.40463 kcal/mol	1.63404 kcal/mol	178 197@LB@ \| \|@LB@5'-UCA...AAUAC U GG AGCCA...CUU-3'@LB@ UGAAAUGG GGG AAUA@LB@ \|\|\|\|\|\|:\| \|\|\| \|\|:\|@LB@ ACUUUAUC CCC UUGU@LB@3'-UUU...GGCCA AU CUGUA...UCG-5'@LB@ \| \|@LB@ 66 48@LB@@LB@@LB@Energy -9.27 kcal/mol@LB@Hybridization Energy -15.3061 kcal/mol@LB@Unfolding Energy - mRNA 4.40463 kcal/mol@LB@Unfolding Energy - sRNA 1.63404 kcal/mol@LB@@LB@Position - mRNA 179 -- 196@LB@Position - sRNA 49 -- 65@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 58 -- 64@LB@
150	0.02489	0.526	b2088	insE1	-9.25	0.136086	235 -- 276	1 -- 55	IS3 transposase A	b0298 b0373 b0540 b1027	_____________234_____________________________________________________277\n_____________\|_______________________________________________________\|\n5'-ACC...ACCCC_______________CC_______UU__C____________CCC___________UUGCU...CUG-3'\n______________GUAAACAG_CAUUCG____UGAAU__CG______AGUGAAG____UGA____AGC\n______________\|\|\|\|\|\|\|\|_\|\|\|\|\|:____\|\|\|\|\|__\|\|______\|:\|:\|\|\|____\|\|\|____\|\|\|\n______________CAUUUGUC_GUAAGU____ACUUA__GC______UUAUUUC____ACU____UCG\n3'-UUU...AUCCC________U______CUUU_____CU__CAUUAU_______AAUU___ACUA___-5'\n_____________\|______________________________________________________\|\n_____________56_____________________________________________________1\n	261 -- 267	15 -- 21	-23.7484 kcal/mol	8.16492 kcal/mol	6.33758 kcal/mol	234 277@LB@ \| \|@LB@5'-ACC...ACCCC CC UU C CCC UUGCU...CUG-3'@LB@ GUAAACAG CAUUCG UGAAU CG AGUGAAG UGA AGC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|: \|\|\|\|\| \|\| \|:\|:\|\|\| \|\|\| \|\|\|@LB@ CAUUUGUC GUAAGU ACUUA GC UUAUUUC ACU UCG@LB@3'-UUU...AUCCC U CUUU CU CAUUAU AAUU ACUA -5'@LB@ \| \|@LB@ 56 1@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -23.7484 kcal/mol@LB@Unfolding Energy - mRNA 8.16492 kcal/mol@LB@Unfolding Energy - sRNA 6.33758 kcal/mol@LB@@LB@Position - mRNA 235 -- 276@LB@Position - sRNA 1 -- 55@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 15 -- 21@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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