Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
68	0.001184	0.06134	b3188	sfsB	-9.82	0.121108	186 -- 205	37 -- 57	malPQ operon transcriptional activator	_____________185___________________206\n_____________\|_____________________\|\n5'-CGG...AACUU____________AAAA_____AAGUA...UGA-3'\n______________AAGG_AGUGAGG____AUGGA\n______________\|\|\|\|_\|\|\|:\|\|:____\|\|\|\|\|\n______________UUCC_UCAUUCU____UACCU\n3'-UUU...GUUUU____U_______GUUA_____CGCGU...ACG-5'\n_____________\|_____________________\|\n_____________58____________________36\n	190 -- 196	46 -- 52	-17.294 kcal/mol	3.7439 kcal/mol	3.68958 kcal/mol	185 206@LB@ \| \|@LB@5'-CGG...AACUU AAAA AAGUA...UGA-3'@LB@ AAGG AGUGAGG AUGGA@LB@ \|\|\|\| \|\|\|:\|\|: \|\|\|\|\|@LB@ UUCC UCAUUCU UACCU@LB@3'-UUU...GUUUU U GUUA CGCGU...ACG-5'@LB@ \| \|@LB@ 58 36@LB@@LB@@LB@Energy -9.82 kcal/mol@LB@Hybridization Energy -17.294 kcal/mol@LB@Unfolding Energy - mRNA 3.7439 kcal/mol@LB@Unfolding Energy - sRNA 3.68958 kcal/mol@LB@@LB@Position - mRNA 186 -- 205@LB@Position - sRNA 37 -- 57@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 46 -- 52@LB@
191	0.008524	0.1548	b3203	hpf	-8.75	0.209451	199 -- 206	68 -- 75	ribosome hibernation promoting factor HPF; stabilizes 100S dimers	_____________198______207\n_____________\|________\|\n5'-GAU...AGACA________CUCAA...GAA-3'\n______________CUAUGCAG\n______________\|\|\|\|\|\|\|\|\n______________GAUACGUC\n3'-UUU...AACAC________AUUAA...ACG-5'\n_____________\|________\|\n_____________76_______67\n	200 -- 206	68 -- 74	-11.4515 kcal/mol	0.966058 kcal/mol	1.73443 kcal/mol	198 207@LB@ \| \|@LB@5'-GAU...AGACA CUCAA...GAA-3'@LB@ CUAUGCAG@LB@ \|\|\|\|\|\|\|\|@LB@ GAUACGUC@LB@3'-UUU...AACAC AUUAA...ACG-5'@LB@ \| \|@LB@ 76 67@LB@@LB@@LB@Energy -8.75 kcal/mol@LB@Hybridization Energy -11.4515 kcal/mol@LB@Unfolding Energy - mRNA 0.966058 kcal/mol@LB@Unfolding Energy - sRNA 1.73443 kcal/mol@LB@@LB@Position - mRNA 199 -- 206@LB@Position - sRNA 68 -- 75@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 68 -- 74@LB@
80	0.001886	0.08273	b3205	yhbJ	-9.88	0.117656	21 -- 27	1 -- 7	adaptor protein for GlmZ/GlmY sRNA decay glucosamine-6-phosphate-regulated; NTPase	_____________20______28\n_____________\|_______\|\n5'-CGG...AAACG_______AUACU...CCG-3'\n______________CACCUGC\n______________\|\|\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	21 -- 27	1 -- 7	-13.6981 kcal/mol	1.48735 kcal/mol	2.34039 kcal/mol	20 28@LB@ \| \|@LB@5'-CGG...AAACG AUACU...CCG-3'@LB@ CACCUGC@LB@ \|\|\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -13.6981 kcal/mol@LB@Unfolding Energy - mRNA 1.48735 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 21 -- 27@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 1 -- 7@LB@
184	0.008005	0.1528	b3209	elbB	-11.15	0.057587	162 -- 192	53 -- 86	isoprenoid biosynthesis protein with amidotransferase-like domain	_____________161_________________________________193\n_____________\|___________________________________\|\n5'-GCG...AAAAA_____________U______C____GC________UGAUC...GUG-3'\n______________AAUUAA_UGUGUU___CAGU_AAUU___GAAAGGA\n______________\|\|\|:\|\|_\|\|\|\|:\|___\|\|\|\|_\|\|\|\|___:\|\|\|\|\|\|\n______________UUAGUU_ACACGA___GUCA_UUAA___UUUUCCU\n3'-UUU...CAUGC______A______UAC_________GUU_______UCAUU...ACG-5'\n_____________\|___________________________________\|\n_____________87__________________________________52\n	186 -- 192	53 -- 59	-19.5143 kcal/mol	4.60736 kcal/mol	3.76074 kcal/mol	161 193@LB@ \| \|@LB@5'-GCG...AAAAA U C GC UGAUC...GUG-3'@LB@ AAUUAA UGUGUU CAGU AAUU GAAAGGA@LB@ \|\|\|:\|\| \|\|\|\|:\| \|\|\|\| \|\|\|\| :\|\|\|\|\|\|@LB@ UUAGUU ACACGA GUCA UUAA UUUUCCU@LB@3'-UUU...CAUGC A UAC GUU UCAUU...ACG-5'@LB@ \| \|@LB@ 87 52@LB@@LB@@LB@Energy -11.15 kcal/mol@LB@Hybridization Energy -19.5143 kcal/mol@LB@Unfolding Energy - mRNA 4.60736 kcal/mol@LB@Unfolding Energy - sRNA 3.76074 kcal/mol@LB@@LB@Position - mRNA 162 -- 192@LB@Position - sRNA 53 -- 86@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 53 -- 59@LB@
139	0.00529	0.1336	b3211	yhcC	-9.14	0.172713	199 -- 227	39 -- 75	putative Fe-S oxidoreductase Radical SAM superfamily protein	_____________198___________________________________228\n_____________\|_____________________________________\|\n5'-UGC...UCAGA_________UA________UU________U_______UUUGG...GCC-3'\n______________UUAUGCAGU____CAGAAA________AG_CAAUAUG\n______________:\|\|\|\|\|\|\|\|____\|\|:\|\|\|________\|\|_\|\|\|\|\|\|\|\n______________GAUACGUCA____GUUUUU________UC_GUUAUAC\n3'-UUU...AACAC_________UUAA______UCCUUCAU__U_______CUCGC...ACG-5'\n_____________\|_____________________________________\|\n_____________76____________________________________38\n	221 -- 227	39 -- 45	-19.1659 kcal/mol	3.3824 kcal/mol	6.6377 kcal/mol	198 228@LB@ \| \|@LB@5'-UGC...UCAGA UA UU U UUUGG...GCC-3'@LB@ UUAUGCAGU CAGAAA AG CAAUAUG@LB@ :\|\|\|\|\|\|\|\| \|\|:\|\|\| \|\| \|\|\|\|\|\|\|@LB@ GAUACGUCA GUUUUU UC GUUAUAC@LB@3'-UUU...AACAC UUAA UCCUUCAU U CUCGC...ACG-5'@LB@ \| \|@LB@ 76 38@LB@@LB@@LB@Energy -9.14 kcal/mol@LB@Hybridization Energy -19.1659 kcal/mol@LB@Unfolding Energy - mRNA 3.3824 kcal/mol@LB@Unfolding Energy - sRNA 6.6377 kcal/mol@LB@@LB@Position - mRNA 199 -- 227@LB@Position - sRNA 39 -- 75@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 39 -- 45@LB@
24	0.0001125	0.01591	b3212	gltB	-12.14	0.031409	27 -- 43	59 -- 75	glutamate synthase large subunit	_____________26________________44\n_____________\|_________________\|\n5'-CUG...CAUAU_____________G___UCCCC...UAC-3'\n______________UUAUGCAGUAAUU_AGA\n______________:\|\|\|\|\|\|\|\|\|\|\|\|_\|:\|\n______________GAUACGUCAUUAA_UUU\n3'-UUU...AACAC_____________G___UUUCC...ACG-5'\n_____________\|_________________\|\n_____________76________________58\n	33 -- 39	63 -- 69	-17.8824 kcal/mol	2.24537 kcal/mol	3.49177 kcal/mol	26 44@LB@ \| \|@LB@5'-CUG...CAUAU G UCCCC...UAC-3'@LB@ UUAUGCAGUAAUU AGA@LB@ :\|\|\|\|\|\|\|\|\|\|\|\| \|:\|@LB@ GAUACGUCAUUAA UUU@LB@3'-UUU...AACAC G UUUCC...ACG-5'@LB@ \| \|@LB@ 76 58@LB@@LB@@LB@Energy -12.14 kcal/mol@LB@Hybridization Energy -17.8824 kcal/mol@LB@Unfolding Energy - mRNA 2.24537 kcal/mol@LB@Unfolding Energy - sRNA 3.49177 kcal/mol@LB@@LB@Position - mRNA 27 -- 43@LB@Position - sRNA 59 -- 75@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 63 -- 69@LB@
179	0.007631	0.1495	b3229	sspA	-8.36	0.252415	276 -- 298	54 -- 83	stringent starvation protein A phage P1 late gene activator RNAP-associated acid-resistance protein inactive glutathione S-transferase homolog	_____________275_____________________________299\n_____________\|_______________________________\|\n5'-CCA...AGGUC__C____________________________UG-3'\n______________CG_AUUGUGCUG_GC_______UGAGAAAGG\n______________\|:_\|\|\|\|\|\|\|\|:_\|\|_______::\|:\|\|\|\|\|\n______________GU_UAACACGAU_CG_______GUUUUUUCC\n3'-UUU...GCUUA____________A__UCAUUAA_________UUCAU...ACG-5'\n_____________\|_______________________________\|\n_____________84______________________________53\n	292 -- 298	54 -- 60	-18.0489 kcal/mol	5.94535 kcal/mol	3.74667 kcal/mol	275 299@LB@ \| \|@LB@5'-CCA...AGGUC C UG-3'@LB@ CG AUUGUGCUG GC UGAGAAAGG@LB@ \|: \|\|\|\|\|\|\|\|: \|\| ::\|:\|\|\|\|\|@LB@ GU UAACACGAU CG GUUUUUUCC@LB@3'-UUU...GCUUA A UCAUUAA UUCAU...ACG-5'@LB@ \| \|@LB@ 84 53@LB@@LB@@LB@Energy -8.36 kcal/mol@LB@Hybridization Energy -18.0489 kcal/mol@LB@Unfolding Energy - mRNA 5.94535 kcal/mol@LB@Unfolding Energy - sRNA 3.74667 kcal/mol@LB@@LB@Position - mRNA 276 -- 298@LB@Position - sRNA 54 -- 83@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 54 -- 60@LB@
131	0.004841	0.1302	b3242	aaeX	-9.57	0.138370	170 -- 176	1 -- 7	DUF1656 family putative inner membrane efflux pump associated protein	_____________169_____177\n_____________\|_______\|\n5'-GCG...AAUAA_______UCUCU...GGG-3'\n______________CGCCUGC\n______________\|:\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	170 -- 176	1 -- 7	-12.9142 kcal/mol	1.00865 kcal/mol	2.34039 kcal/mol	169 177@LB@ \| \|@LB@5'-GCG...AAUAA UCUCU...GGG-3'@LB@ CGCCUGC@LB@ \|:\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.57 kcal/mol@LB@Hybridization Energy -12.9142 kcal/mol@LB@Unfolding Energy - mRNA 1.00865 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 170 -- 176@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 1 -- 7@LB@
151	0.005924	0.1368	b3248	yhdE	-13.35	0.014399	2 -- 41	1 -- 42	dTTP/UTP pyrophosphatase; m(5)UTP/m(5)CTP/pseudo-UTP pyrophosphatase	_____________1___________________________________________42\n_____________\|___________________________________________\|\n__________5'-U_____C___A_______G_____C_________U______G__GGUGG...AGC-3'\n______________UAUGG_AGC__GGCGCU_GUCGU___AUGUUGC_UUCGCU_GU\n______________\|\|\|\|\|_\|\|\|__::\|\|\|:_:\|\|\|:___\|:\|\|\|\|\|_\|\|\|:\|:_\|:\n______________AUACC_UCG__UUGCGG_UAGCG___UGCAACG_AAGUGG_CG\n3'-UUU...CUGUU_________CG______G_____AAC_______U______A__-5'\n_____________\|__________________________________________\|\n_____________43_________________________________________1\n	25 -- 31	11 -- 17	-43.9582 kcal/mol	15.3205 kcal/mol	15.293 kcal/mol	1 42@LB@ \| \|@LB@ 5'-U C A G C U G GGUGG...AGC-3'@LB@ UAUGG AGC GGCGCU GUCGU AUGUUGC UUCGCU GU@LB@ \|\|\|\|\| \|\|\| ::\|\|\|: :\|\|\|: \|:\|\|\|\|\| \|\|\|:\|: \|:@LB@ AUACC UCG UUGCGG UAGCG UGCAACG AAGUGG CG@LB@3'-UUU...CUGUU CG G AAC U A -5'@LB@ \| \|@LB@ 43 1@LB@@LB@@LB@Energy -13.35 kcal/mol@LB@Hybridization Energy -43.9582 kcal/mol@LB@Unfolding Energy - mRNA 15.3205 kcal/mol@LB@Unfolding Energy - sRNA 15.293 kcal/mol@LB@@LB@Position - mRNA 2 -- 41@LB@Position - sRNA 1 -- 42@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 11 -- 17@LB@
141	0.005411	0.1351	b3260	dusB	-10.20	0.098848	236 -- 254	20 -- 38	tRNA-dihydrouridine synthase B	_____________235_________________255\n_____________\|___________________\|\n5'-ACU...CGCCU__U____________G___GGCAU...GAG-3'\n______________GA_CGCAGCGCCCAU_GCU\n______________\|\|_\|\|\|\|:\|\|\|\|\|\|\|_\|\|\|\n______________CU_GCGUUGCGGGUA_CGA\n3'-UUU...UAUAC__C____________G___ACUGC...ACG-5'\n_____________\|___________________\|\n_____________39__________________19\n	244 -- 250	24 -- 30	-30.8965 kcal/mol	8.5282 kcal/mol	12.1733 kcal/mol	235 255@LB@ \| \|@LB@5'-ACU...CGCCU U G GGCAU...GAG-3'@LB@ GA CGCAGCGCCCAU GCU@LB@ \|\| \|\|\|\|:\|\|\|\|\|\|\| \|\|\|@LB@ CU GCGUUGCGGGUA CGA@LB@3'-UUU...UAUAC C G ACUGC...ACG-5'@LB@ \| \|@LB@ 39 19@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -30.8965 kcal/mol@LB@Unfolding Energy - mRNA 8.5282 kcal/mol@LB@Unfolding Energy - sRNA 12.1733 kcal/mol@LB@@LB@Position - mRNA 236 -- 254@LB@Position - sRNA 20 -- 38@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 24 -- 30@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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