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
78	0.01113	0.4523	b2678	proW	-13.08	0.020853	190 -- 200	49 -- 59	glycine betaine/proline ABC transporter permease		_____________189_________201\n_____________\|___________\|\n5'-GUU...CGUGA___________AUGGC...ACG-3'\n______________GGGGGUAAAUA\n______________:\|\|\|\|\|\|\|\|:\|\n______________UCCCCAUUUGU\n3'-UUU...CUUUA___________CUGUA...UCG-5'\n_____________\|___________\|\n_____________60__________48\n	194 -- 200	49 -- 55	-15.0309 kcal/mol	1.22377 kcal/mol	0.730523 kcal/mol	189 201@LB@ \| \|@LB@5'-GUU...CGUGA AUGGC...ACG-3'@LB@ GGGGGUAAAUA@LB@ :\|\|\|\|\|\|\|\|:\|@LB@ UCCCCAUUUGU@LB@3'-UUU...CUUUA CUGUA...UCG-5'@LB@ \| \|@LB@ 60 48@LB@@LB@@LB@Energy -13.08 kcal/mol@LB@Hybridization Energy -15.0309 kcal/mol@LB@Unfolding Energy - mRNA 1.22377 kcal/mol@LB@Unfolding Energy - sRNA 0.730523 kcal/mol@LB@@LB@Position - mRNA 190 -- 200@LB@Position - sRNA 49 -- 59@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 49 -- 55@LB@
20	0.0009027	0.1482	b2696	csrA	-13.42	0.017327	268 -- 280	48 -- 60	pleiotropic regulatory protein for carbon source metabolism		_____________267___________281\n_____________\|_____________\|\n5'-CGG...AGUUU__________G__CAACC...GCG-3'\n______________UAGGGGUAAA_GG\n______________\|\|\|\|\|\|\|\|\|\|_:\|\n______________AUCCCCAUUU_UC\n3'-UUU...ACUUU__________G__UGUAA...UCG-5'\n_____________\|_____________\|\n_____________61____________47\n	271 -- 277	51 -- 57	-17.9026 kcal/mol	2.43021 kcal/mol	2.05446 kcal/mol	267 281@LB@ \| \|@LB@5'-CGG...AGUUU G CAACC...GCG-3'@LB@ UAGGGGUAAA GG@LB@ \|\|\|\|\|\|\|\|\|\| :\|@LB@ AUCCCCAUUU UC@LB@3'-UUU...ACUUU G UGUAA...UCG-5'@LB@ \| \|@LB@ 61 47@LB@@LB@@LB@Energy -13.42 kcal/mol@LB@Hybridization Energy -17.9026 kcal/mol@LB@Unfolding Energy - mRNA 2.43021 kcal/mol@LB@Unfolding Energy - sRNA 2.05446 kcal/mol@LB@@LB@Position - mRNA 268 -- 280@LB@Position - sRNA 48 -- 60@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 51 -- 57@LB@
95	0.01574	0.5059	b2714	ascG	-10.13	0.091468	184 -- 220	14 -- 55	asc operon transcriptional repressor; prpBC operon repressor		_____________183________________________________________221\n_____________\|__________________________________________\|\n5'-AAA...UGCGU_____G_____________AU_______AC____CUG_____GGCGA...AAG-3'\n______________GUAAA_GGAU_____GAAA__GAUGACG__GAUG___GAAGU\n______________\|\|\|\|\|_:\|\|:_____\|\|\|\|__:\|\|\|\|\|\|__:\|\|:___:\|\|\|\|\n______________CAUUU_UCUG_____CUUU__UUACUGC__UUAU___UUUCA\n3'-UUU...AUCCC_____G____UAAGU____AC_______CA____UUA_____AUUAC...UCG-5'\n_____________\|__________________________________________\|\n_____________56_________________________________________13\n	200 -- 206	28 -- 34	-22.7561 kcal/mol	6.30192 kcal/mol	6.32604 kcal/mol	183 221@LB@ \| \|@LB@5'-AAA...UGCGU G AU AC CUG GGCGA...AAG-3'@LB@ GUAAA GGAU GAAA GAUGACG GAUG GAAGU@LB@ \|\|\|\|\| :\|\|: \|\|\|\| :\|\|\|\|\|\| :\|\|: :\|\|\|\|@LB@ CAUUU UCUG CUUU UUACUGC UUAU UUUCA@LB@3'-UUU...AUCCC G UAAGU AC CA UUA AUUAC...UCG-5'@LB@ \| \|@LB@ 56 13@LB@@LB@@LB@Energy -10.13 kcal/mol@LB@Hybridization Energy -22.7561 kcal/mol@LB@Unfolding Energy - mRNA 6.30192 kcal/mol@LB@Unfolding Energy - sRNA 6.32604 kcal/mol@LB@@LB@Position - mRNA 184 -- 220@LB@Position - sRNA 14 -- 55@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 28 -- 34@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@
10	0.0003219	0.1057	b2727	hypB	-18.91	0.000562	181 -- 230	1 -- 53	GTP hydrolase involved in nickel liganding into hydrogenases		_____________180____________________________________________________231\n_____________\|______________________________________________________\|\n5'-GCC...GAUAG_____________________C____U___CAAC___C_____C______A___AACCU...CGG-3'\n______________AAAUAGAC___CAGGAGUGAG_GAUG_GUA____AUG_GGUUG__GGUGA_GGC\n______________\|\|\|:\|\|\|\|___\|\|\|:\|:\|\|\|:_\|\|:\|_\|\|\|____\|\|:_:\|\|\|:__\|:\|\|\|_:\|\|\n______________UUUGUCUG___GUCUUUACUU_CUGC_CAU____UAU_UCAAU__CUACU_UCG\n3'-UUU...CCCCA________UAA__________A________UAUU___U_____UA_____A___-5'\n_____________\|_____________________________________________________\|\n_____________54____________________________________________________1\n	182 -- 188	46 -- 52	-37.7845 kcal/mol	12.539 kcal/mol	6.33709 kcal/mol	180 231@LB@ \| \|@LB@5'-GCC...GAUAG C U CAAC C C A AACCU...CGG-3'@LB@ AAAUAGAC CAGGAGUGAG GAUG GUA AUG GGUUG GGUGA GGC@LB@ \|\|\|:\|\|\|\| \|\|\|:\|:\|\|\|: \|\|:\| \|\|\| \|\|: :\|\|\|: \|:\|\|\| :\|\|@LB@ UUUGUCUG GUCUUUACUU CUGC CAU UAU UCAAU CUACU UCG@LB@3'-UUU...CCCCA UAA A UAUU U UA A -5'@LB@ \| \|@LB@ 54 1@LB@@LB@@LB@Energy -18.91 kcal/mol@LB@Hybridization Energy -37.7845 kcal/mol@LB@Unfolding Energy - mRNA 12.539 kcal/mol@LB@Unfolding Energy - sRNA 6.33709 kcal/mol@LB@@LB@Position - mRNA 181 -- 230@LB@Position - sRNA 1 -- 53@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 46 -- 52@LB@
153	0.02513	0.526	b2745	truD	-9.91	0.100940	94 -- 116	1 -- 24	tRNA(Glu) pseudouridine(13) synthase		_____________93_______________________117\n_____________\|________________________\|\n5'-AAC...GCCAU________U_____C_____A___CACUA...UGG-3'\n______________AUGGAUGA_GUUAA__GUGA_AGC\n______________\|\|::\|\|:\|_\|\|\|\|\|__:\|\|\|_\|\|\|\n______________UAUUUAUU_CAAUU__UACU_UCG\n3'-UUU...GCCAU________U_____AC____A___-5'\n_____________\|_______________________\|\n_____________25______________________1\n	95 -- 101	17 -- 23	-14.0384 kcal/mol	4.01581 kcal/mol	0.108605 kcal/mol	93 117@LB@ \| \|@LB@5'-AAC...GCCAU U C A CACUA...UGG-3'@LB@ AUGGAUGA GUUAA GUGA AGC@LB@ \|\|::\|\|:\| \|\|\|\|\| :\|\|\| \|\|\|@LB@ UAUUUAUU CAAUU UACU UCG@LB@3'-UUU...GCCAU U AC A -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -9.91 kcal/mol@LB@Hybridization Energy -14.0384 kcal/mol@LB@Unfolding Energy - mRNA 4.01581 kcal/mol@LB@Unfolding Energy - sRNA 0.108605 kcal/mol@LB@@LB@Position - mRNA 94 -- 116@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 17 -- 23@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@
128	0.0201	0.5155	b2782	mazF	-10.78	0.067406	32 -- 50	1 -- 23	mRNA interferase toxin antitoxin is MazE	b4225	_____________31______________________51\n_____________\|_______________________\|\n5'-AUC...CAAUC_______________________GAAGA...UCC-3'\n______________UGAAUA___UUGAUGAUGA_AGU\n______________\|:\|\|\|\|___\|\|:\|\|\|\|\|\|\|_\|\|:\n______________AUUUAU___AAUUACUACU_UCG\n3'-UUU...CCAUU______UUC__________A___-5'\n_____________\|______________________\|\n_____________24_____________________1\n	41 -- 47	5 -- 11	-13.6359 kcal/mol	2.75565 kcal/mol	0.105066 kcal/mol	31 51@LB@ \| \|@LB@5'-AUC...CAAUC GAAGA...UCC-3'@LB@ UGAAUA UUGAUGAUGA AGU@LB@ \|:\|\|\|\| \|\|:\|\|\|\|\|\|\| \|\|:@LB@ AUUUAU AAUUACUACU UCG@LB@3'-UUU...CCAUU UUC A -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -10.78 kcal/mol@LB@Hybridization Energy -13.6359 kcal/mol@LB@Unfolding Energy - mRNA 2.75565 kcal/mol@LB@Unfolding Energy - sRNA 0.105066 kcal/mol@LB@@LB@Position - mRNA 32 -- 50@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 5 -- 11@LB@
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@
179	0.02973	0.5424	b2812	tcdA	-11.60	0.044907	209 -- 228	1 -- 28	tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA		_____________208___________________________229\n_____________\|_____________________________\|\n5'-GUG...UCUGU_______________________C_____GUCAG...UUU-3'\n______________GGUAAU_________UAGUGAUG_AUGGC\n______________\|\|\|\|\|\|_________\|\|:\|\|\|\|\|_\|\|:\|\|\n______________CCAUUA_________AUUACUAC_UAUCG\n3'-UUU...UACUG______UUUAUUUCA______________-5'\n_____________\|____________________________\|\n_____________29___________________________1\n	216 -- 222	6 -- 12	-16.3639 kcal/mol	3.995 kcal/mol	0.766821 kcal/mol	208 229@LB@ \| \|@LB@5'-GUG...UCUGU C GUCAG...UUU-3'@LB@ GGUAAU UAGUGAUG AUGGC@LB@ \|\|\|\|\|\| \|\|:\|\|\|\|\| \|\|:\|\|@LB@ CCAUUA AUUACUAC UAUCG@LB@3'-UUU...UACUG UUUAUUUCA -5'@LB@ \| \|@LB@ 29 1@LB@@LB@@LB@Energy -11.60 kcal/mol@LB@Hybridization Energy -16.3639 kcal/mol@LB@Unfolding Energy - mRNA 3.995 kcal/mol@LB@Unfolding Energy - sRNA 0.766821 kcal/mol@LB@@LB@Position - mRNA 209 -- 228@LB@Position - sRNA 1 -- 28@LB@Position Seed - mRNA 216 -- 222@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)

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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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