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
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@
176	0.02871	0.5353	b0518	fdrA	-11.39	0.049925	288 -- 297	6 -- 15	putative NAD(P)-binding acyl-CoA synthetase	b0320	_____________287________298\n_____________\|__________\|\n5'-CGC...AAAAU__________UUU-3'\n______________GUUGAUGAUG\n______________\|\|\|:\|\|\|\|\|\|\n______________CAAUUACUAC\n3'-UUU...UAUUU__________UAUCG-5'\n_____________\|__________\|\n_____________16_________5\n	291 -- 297	6 -- 12	-11.8608 kcal/mol	0.426728 kcal/mol	0.0442104 kcal/mol	287 298@LB@ \| \|@LB@5'-CGC...AAAAU UUU-3'@LB@ GUUGAUGAUG@LB@ \|\|\|:\|\|\|\|\|\|@LB@ CAAUUACUAC@LB@3'-UUU...UAUUU UAUCG-5'@LB@ \| \|@LB@ 16 5@LB@@LB@@LB@Energy -11.39 kcal/mol@LB@Hybridization Energy -11.8608 kcal/mol@LB@Unfolding Energy - mRNA 0.426728 kcal/mol@LB@Unfolding Energy - sRNA 0.0442104 kcal/mol@LB@@LB@Position - mRNA 288 -- 297@LB@Position - sRNA 6 -- 15@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 6 -- 12@LB@
200	0.03384	0.5555	b0316	yahB	-11.86	0.039401	41 -- 57	47 -- 61	putative DNA-bindng transcriptional regulator	b0504	_____________40________________58\n_____________\|_________________\|\n5'-CUG...ACUGC__________UUU____AUAUG...CUU-3'\n______________GUGGGGGUAA___CAGA\n______________:\|:\|\|\|\|\|\|\|___\|\|\|\|\n______________UAUCCCCAUU___GUCU\n3'-UUU...AACUU__________U______GUAAG...UCG-5'\n_____________\|_________________\|\n_____________62________________46\n	44 -- 50	52 -- 58	-17.391 kcal/mol	3.44789 kcal/mol	2.08204 kcal/mol	40 58@LB@ \| \|@LB@5'-CUG...ACUGC UUU AUAUG...CUU-3'@LB@ GUGGGGGUAA CAGA@LB@ :\|:\|\|\|\|\|\|\| \|\|\|\|@LB@ UAUCCCCAUU GUCU@LB@3'-UUU...AACUU U GUAAG...UCG-5'@LB@ \| \|@LB@ 62 46@LB@@LB@@LB@Energy -11.86 kcal/mol@LB@Hybridization Energy -17.391 kcal/mol@LB@Unfolding Energy - mRNA 3.44789 kcal/mol@LB@Unfolding Energy - sRNA 2.08204 kcal/mol@LB@@LB@Position - mRNA 41 -- 57@LB@Position - sRNA 47 -- 61@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 52 -- 58@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@
120	0.01923	0.5155	b4004	zraR	-8.11	0.219313	234 -- 248	1 -- 12	fused DNA-binding response regulator in two-component regulatory system with ZraS: response regulator/sigma54 interaction protein	b2220	_____________233_____________249\n_____________\|_______________\|\n5'-GGA...UGGUG________CAU____CACUG...CGC-3'\n______________GAUGAUGA___UAGC\n______________:\|\|\|\|\|\|\|___\|\|\|\|\n______________UUACUACU___AUCG\n3'-UUU...UUCAA_______________-5'\n_____________\|______________\|\n_____________13_____________1\n	235 -- 241	5 -- 11	-11.3572 kcal/mol	3.21186 kcal/mol	0.0394463 kcal/mol	233 249@LB@ \| \|@LB@5'-GGA...UGGUG CAU CACUG...CGC-3'@LB@ GAUGAUGA UAGC@LB@ :\|\|\|\|\|\|\| \|\|\|\|@LB@ UUACUACU AUCG@LB@3'-UUU...UUCAA -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -8.11 kcal/mol@LB@Hybridization Energy -11.3572 kcal/mol@LB@Unfolding Energy - mRNA 3.21186 kcal/mol@LB@Unfolding Energy - sRNA 0.0394463 kcal/mol@LB@@LB@Position - mRNA 234 -- 248@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 5 -- 11@LB@
141	0.0236	0.526	b3339	tufA	-10.69	0.070202	69 -- 84	1 -- 19	translation elongation factor EF-Tu 1	b3980	_____________68__________________85\n_____________\|___________________\|\n5'-AAU...AUUCC___________________GCCGA...CCA-3'\n______________UGAAGU__AUGAUGA_AGC\n______________\|:\|\|\|\|__\|\|\|\|\|\|\|_\|\|\|\n______________AUUUCA__UACUACU_UCG\n3'-UUU...UAUUU______AU_______A___-5'\n_____________\|__________________\|\n_____________20_________________1\n	75 -- 81	5 -- 11	-13.5879 kcal/mol	2.83361 kcal/mol	0.0638423 kcal/mol	68 85@LB@ \| \|@LB@5'-AAU...AUUCC GCCGA...CCA-3'@LB@ UGAAGU AUGAUGA AGC@LB@ \|:\|\|\|\| \|\|\|\|\|\|\| \|\|\|@LB@ AUUUCA UACUACU UCG@LB@3'-UUU...UAUUU AU A -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -10.69 kcal/mol@LB@Hybridization Energy -13.5879 kcal/mol@LB@Unfolding Energy - mRNA 2.83361 kcal/mol@LB@Unfolding Energy - sRNA 0.0638423 kcal/mol@LB@@LB@Position - mRNA 69 -- 84@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 5 -- 11@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@
100	0.01591	0.5059	b0531	sfmC	-11.86	0.039421	211 -- 227	6 -- 22	putative periplasmic pilus chaperone	b4316	_____________210_______________228\n_____________\|_________________\|\n5'-AAU...GACUA___________U_____CUCAU...GUA-3'\n______________AAAUAAAGUUA_UGAUG\n______________\|\|\|\|\|\|\|\|\|\|\|_\|\|\|\|\|\n______________UUUAUUUCAAU_ACUAC\n3'-UUU...CAUUA___________U_____UAUCG-5'\n_____________\|_________________\|\n_____________23________________5\n	215 -- 221	12 -- 18	-15.888 kcal/mol	3.9302 kcal/mol	0.0976382 kcal/mol	210 228@LB@ \| \|@LB@5'-AAU...GACUA U CUCAU...GUA-3'@LB@ AAAUAAAGUUA UGAUG@LB@ \|\|\|\|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ UUUAUUUCAAU ACUAC@LB@3'-UUU...CAUUA U UAUCG-5'@LB@ \| \|@LB@ 23 5@LB@@LB@@LB@Energy -11.86 kcal/mol@LB@Hybridization Energy -15.888 kcal/mol@LB@Unfolding Energy - mRNA 3.9302 kcal/mol@LB@Unfolding Energy - sRNA 0.0976382 kcal/mol@LB@@LB@Position - mRNA 211 -- 227@LB@Position - sRNA 6 -- 22@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 12 -- 18@LB@
152	0.02492	0.526	b3665	adeD	-5.38	0.553104	121 -- 181	3 -- 52	cryptic adenine deaminase	b4328	_____________120____________________________________________________________182\n_____________\|______________________________________________________________\|\n5'-ACG...ACAUU___________UUU_______CUCGC____UUUCUUUA__________UAAUCAAAU_____AAAUC...UUA-3'\n______________AAUGGAUAUUC___AAU_AAU_____GACG________UGAUAAAUAA_________UGAUA\n______________\|\|::\|\|:\|\|\|\|___\|\|\|_\|\|\|_____\|\|\|\|________\|:\|\|\|\|\|\|\|\|_________\|\|\|\|\|\n______________UUGUCUGUAAG___UUA_UUA_____CUGC________AUUAUUUAUU_________ACUAU\n3'-UUU...CCCAU___________UCU___C____________C_________________UCAAUUACU_____CG-5'\n_____________\|______________________________________________________________\|\n_____________53_____________________________________________________________2\n	161 -- 167	17 -- 23	-19.4771 kcal/mol	7.76071 kcal/mol	6.33547 kcal/mol	120 182@LB@ \| \|@LB@5'-ACG...ACAUU UUU CUCGC UUUCUUUA UAAUCAAAU AAAUC...UUA-3'@LB@ AAUGGAUAUUC AAU AAU GACG UGAUAAAUAA UGAUA@LB@ \|\|::\|\|:\|\|\|\| \|\|\| \|\|\| \|\|\|\| \|:\|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ UUGUCUGUAAG UUA UUA CUGC AUUAUUUAUU ACUAU@LB@3'-UUU...CCCAU UCU C C UCAAUUACU CG-5'@LB@ \| \|@LB@ 53 2@LB@@LB@@LB@Energy -5.38 kcal/mol@LB@Hybridization Energy -19.4771 kcal/mol@LB@Unfolding Energy - mRNA 7.76071 kcal/mol@LB@Unfolding Energy - sRNA 6.33547 kcal/mol@LB@@LB@Position - mRNA 121 -- 181@LB@Position - sRNA 3 -- 52@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 17 -- 23@LB@
1	2.411e-07	0.0007914	b0889	lrp	-21.69	0.000065	168 -- 212	1 -- 64	leucine-responsive global transcriptional regulator		_____________167_______________________________________________________________213\n_____________\|_________________________________________________________________\|\n5'-GUG...AGACA_________AA_______AUA_____________________________________A______AAGAA...AGC-3'\n______________GGAGUAGGG______GGA____CAGAGA_____GAC_______AAUAA___UAAUGGU_GAUAGC\n______________\|:\|:\|\|\|\|\|______:\|\|____\|\|\|\|:\|_____\|\|\|_______\|\|\|\|\|___\|\|\|\|\|:\|_\|\|\|\|\|\|\n______________CUUUAUCCC______UCU____GUCUUU_____CUG_______UUAUU___AUUACUA_CUAUCG\n3'-UUU...GCCAA_________CAUUUG___GUAA______ACUUA___CCAUUAU_____UCA______________-5'\n_____________\|________________________________________________________________\|\n_____________65_______________________________________________________________1\n	199 -- 205	7 -- 13	-30.6118 kcal/mol	2.57614 kcal/mol	6.344 kcal/mol	167 213@LB@ \| \|@LB@5'-GUG...AGACA AA AUA A AAGAA...AGC-3'@LB@ GGAGUAGGG GGA CAGAGA GAC AAUAA UAAUGGU GAUAGC@LB@ \|:\|:\|\|\|\|\| :\|\| \|\|\|\|:\| \|\|\| \|\|\|\|\| \|\|\|\|\|:\| \|\|\|\|\|\|@LB@ CUUUAUCCC UCU GUCUUU CUG UUAUU AUUACUA CUAUCG@LB@3'-UUU...GCCAA CAUUUG GUAA ACUUA CCAUUAU UCA -5'@LB@ \| \|@LB@ 65 1@LB@@LB@@LB@Energy -21.69 kcal/mol@LB@Hybridization Energy -30.6118 kcal/mol@LB@Unfolding Energy - mRNA 2.57614 kcal/mol@LB@Unfolding Energy - sRNA 6.344 kcal/mol@LB@@LB@Position - mRNA 168 -- 212@LB@Position - sRNA 1 -- 64@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 7 -- 13@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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