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	Additional homologs
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@
119	0.004048	0.119	b3607	cysE	-9.06	0.179616	191 -- 204	40 -- 54	serine acetyltransferase		_____________190_____________205\n_____________\|_______________\|\n5'-CGG...CGUGU_______________CGUGU...CGA-3'\n______________GGAGUAAG_CAAUGU\n______________\|:\|\|\|\|\|\|_\|\|\|\|:\|\n______________CUUCAUUC_GUUAUA\n3'-UUU...UUUUC________U______CCUCG...ACG-5'\n_____________\|_______________\|\n_____________55______________39\n	192 -- 198	47 -- 53	-13.6491 kcal/mol	2.75521 kcal/mol	1.82942 kcal/mol	190 205@LB@ \| \|@LB@5'-CGG...CGUGU CGUGU...CGA-3'@LB@ GGAGUAAG CAAUGU@LB@ \|:\|\|\|\|\|\| \|\|\|\|:\|@LB@ CUUCAUUC GUUAUA@LB@3'-UUU...UUUUC U CCUCG...ACG-5'@LB@ \| \|@LB@ 55 39@LB@@LB@@LB@Energy -9.06 kcal/mol@LB@Hybridization Energy -13.6491 kcal/mol@LB@Unfolding Energy - mRNA 2.75521 kcal/mol@LB@Unfolding Energy - sRNA 1.82942 kcal/mol@LB@@LB@Position - mRNA 191 -- 204@LB@Position - sRNA 40 -- 54@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 47 -- 53@LB@
60	0.001013	0.05816	b2207	napD	-8.99	0.186283	27 -- 46	75 -- 92	assembly protein for periplasmic nitrate reductase		_____________26___________________47\n_____________\|____________________\|\n5'-GUU...CCUGG_____C_________AA___CGCCG...AAG-3'\n______________CGUAU_AGUCAGUUG__UGC\n______________\|\|\|\|:_\|:\|\|\|:\|\|\|__\|\|\|\n______________GCAUG_UUAGUUAAC__ACG\n3'-UUU...CCGCA_____C______________AUACG...ACG-5'\n_____________\|____________________\|\n_____________93___________________74\n	35 -- 41	78 -- 84	-16.0375 kcal/mol	4.6767 kcal/mol	2.37539 kcal/mol	26 47@LB@ \| \|@LB@5'-GUU...CCUGG C AA CGCCG...AAG-3'@LB@ CGUAU AGUCAGUUG UGC@LB@ \|\|\|\|: \|:\|\|\|:\|\|\| \|\|\|@LB@ GCAUG UUAGUUAAC ACG@LB@3'-UUU...CCGCA C AUACG...ACG-5'@LB@ \| \|@LB@ 93 74@LB@@LB@@LB@Energy -8.99 kcal/mol@LB@Hybridization Energy -16.0375 kcal/mol@LB@Unfolding Energy - mRNA 4.6767 kcal/mol@LB@Unfolding Energy - sRNA 2.37539 kcal/mol@LB@@LB@Position - mRNA 27 -- 46@LB@Position - sRNA 75 -- 92@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 78 -- 84@LB@
31	0.0001757	0.01997	b4222	ytfP	-8.86	0.198985	202 -- 224	67 -- 90	GGCT-like protein		_____________201_______________________225\n_____________\|_________________________\|\n5'-ACC...AGCAA_______AU_________CG_____UUACG...ACC-3'\n______________UGCGAAU___UUGU_CUA__GCAGU\n______________\|:\|\|\|\|\|___\|\|\|\|_\|\|\|__\|\|\|\|\|\n______________AUGCUUA___AACA_GAU__CGUCA\n3'-UUU...GCAGC_______GUU____C___A______UUAAG...ACG-5'\n_____________\|_________________________\|\n_____________91________________________66\n	202 -- 208	84 -- 90	-18.173 kcal/mol	4.78992 kcal/mol	4.5307 kcal/mol	201 225@LB@ \| \|@LB@5'-ACC...AGCAA AU CG UUACG...ACC-3'@LB@ UGCGAAU UUGU CUA GCAGU@LB@ \|:\|\|\|\|\| \|\|\|\| \|\|\| \|\|\|\|\|@LB@ AUGCUUA AACA GAU CGUCA@LB@3'-UUU...GCAGC GUU C A UUAAG...ACG-5'@LB@ \| \|@LB@ 91 66@LB@@LB@@LB@Energy -8.86 kcal/mol@LB@Hybridization Energy -18.173 kcal/mol@LB@Unfolding Energy - mRNA 4.78992 kcal/mol@LB@Unfolding Energy - sRNA 4.5307 kcal/mol@LB@@LB@Position - mRNA 202 -- 224@LB@Position - sRNA 67 -- 90@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 84 -- 90@LB@
49	0.0005476	0.03937	b2432	yfeY	-8.84	0.200409	189 -- 199	48 -- 58	RpoE-regulated lipoprotein		_____________188_________200\n_____________\|___________\|\n5'-GCU...UAACC___________CAUGA...ACU-3'\n______________AAAGGAAGUGA\n______________\|\|\|\|\|\|\|\|\|:\|\n______________UUUCCUUCAUU\n3'-UUU...AGUUU___________CUGUU...ACG-5'\n_____________\|___________\|\n_____________59__________47\n	193 -- 199	48 -- 54	-12.8959 kcal/mol	3.31176 kcal/mol	0.745549 kcal/mol	188 200@LB@ \| \|@LB@5'-GCU...UAACC CAUGA...ACU-3'@LB@ AAAGGAAGUGA@LB@ \|\|\|\|\|\|\|\|\|:\|@LB@ UUUCCUUCAUU@LB@3'-UUU...AGUUU CUGUU...ACG-5'@LB@ \| \|@LB@ 59 47@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -12.8959 kcal/mol@LB@Unfolding Energy - mRNA 3.31176 kcal/mol@LB@Unfolding Energy - sRNA 0.745549 kcal/mol@LB@@LB@Position - mRNA 189 -- 199@LB@Position - sRNA 48 -- 58@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 48 -- 54@LB@
181	0.007702	0.1499	b3145	yraK	-8.82	0.202558	266 -- 280	35 -- 49	putative fimbrial-like adhesin protein	b0533 b0941	_____________265_____________281\n_____________\|_______________\|\n5'-CGA...UCCUC____G__________CGACA...CGA-3'\n______________AGGA_GGUGUGGAGC\n______________\|:\|\|_::\|:\|\|\|\|\|\|\n______________UUCU_UUAUACCUCG\n3'-UUU...CUUCA____G__________CGUUG...ACG-5'\n_____________\|_______________\|\n_____________50______________34\n	274 -- 280	35 -- 41	-19.5909 kcal/mol	7.00879 kcal/mol	3.74396 kcal/mol	265 281@LB@ \| \|@LB@5'-CGA...UCCUC G CGACA...CGA-3'@LB@ AGGA GGUGUGGAGC@LB@ \|:\|\| ::\|:\|\|\|\|\|\|@LB@ UUCU UUAUACCUCG@LB@3'-UUU...CUUCA G CGUUG...ACG-5'@LB@ \| \|@LB@ 50 34@LB@@LB@@LB@Energy -8.82 kcal/mol@LB@Hybridization Energy -19.5909 kcal/mol@LB@Unfolding Energy - mRNA 7.00879 kcal/mol@LB@Unfolding Energy - sRNA 3.74396 kcal/mol@LB@@LB@Position - mRNA 266 -- 280@LB@Position - sRNA 35 -- 49@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 35 -- 41@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@
74	0.001758	0.08273	b4012	yjaB	-8.69	0.215298	234 -- 243	51 -- 60	GNAT-family putative N-acetyltransferase; acetyl coenzyme A-binding protein		_____________233________244\n_____________\|__________\|\n5'-AAG...AUGAG__________AACUC...CAG-3'\n______________GAAGGGGAGG\n______________:\|\|::\|\|\|:\|\n______________UUUUUCCUUC\n3'-UUU...UAAGU__________AUUCU...ACG-5'\n_____________\|__________\|\n_____________61_________50\n	237 -- 243	51 -- 57	-10.2171 kcal/mol	0.810771 kcal/mol	0.715621 kcal/mol	233 244@LB@ \| \|@LB@5'-AAG...AUGAG AACUC...CAG-3'@LB@ GAAGGGGAGG@LB@ :\|\|::\|\|\|:\|@LB@ UUUUUCCUUC@LB@3'-UUU...UAAGU AUUCU...ACG-5'@LB@ \| \|@LB@ 61 50@LB@@LB@@LB@Energy -8.69 kcal/mol@LB@Hybridization Energy -10.2171 kcal/mol@LB@Unfolding Energy - mRNA 0.810771 kcal/mol@LB@Unfolding Energy - sRNA 0.715621 kcal/mol@LB@@LB@Position - mRNA 234 -- 243@LB@Position - sRNA 51 -- 60@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 51 -- 57@LB@
127	0.004567	0.1258	b2320	pdxB	-8.62	0.223386	291 -- 299	20 -- 28	erythronate-4-phosphate dehydrogenase		_____________290_______300\n_____________\|_________\|\n5'-ACG...CAAUC_________C-3'\n______________CCCGUCGCU\n______________\|\|\|:\|\|\|\|\|\n______________GGGUAGCGA\n3'-UUU...GUUGC_________ACUGC...ACG-5'\n_____________\|_________\|\n_____________29________19\n	293 -- 299	20 -- 26	-15.7186 kcal/mol	1.54056 kcal/mol	5.56153 kcal/mol	290 300@LB@ \| \|@LB@5'-ACG...CAAUC C-3'@LB@ CCCGUCGCU@LB@ \|\|\|:\|\|\|\|\|@LB@ GGGUAGCGA@LB@3'-UUU...GUUGC ACUGC...ACG-5'@LB@ \| \|@LB@ 29 19@LB@@LB@@LB@Energy -8.62 kcal/mol@LB@Hybridization Energy -15.7186 kcal/mol@LB@Unfolding Energy - mRNA 1.54056 kcal/mol@LB@Unfolding Energy - sRNA 5.56153 kcal/mol@LB@@LB@Position - mRNA 291 -- 299@LB@Position - sRNA 20 -- 28@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 20 -- 26@LB@
187	0.008226	0.1545	b1446	ydcY	-8.50	0.236240	3 -- 9	2 -- 8	DUF2526 family protein		_____________2_______10\n_____________\|_______\|\n_________5'-UA_______GUUUC...ACG-3'\n______________UCACCUG\n______________\|\|\|\|\|\|\|\n______________AGUGGAC\n3'-UUU...ACGUA_______G-5'\n_____________\|_______\|\n_____________9_______1\n	3 -- 9	2 -- 8	-11.529 kcal/mol	0.673638 kcal/mol	2.36182 kcal/mol	2 10@LB@ \| \|@LB@ 5'-UA GUUUC...ACG-3'@LB@ UCACCUG@LB@ \|\|\|\|\|\|\|@LB@ AGUGGAC@LB@3'-UUU...ACGUA G-5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -8.50 kcal/mol@LB@Hybridization Energy -11.529 kcal/mol@LB@Unfolding Energy - mRNA 0.673638 kcal/mol@LB@Unfolding Energy - sRNA 2.36182 kcal/mol@LB@@LB@Position - mRNA 3 -- 9@LB@Position - sRNA 2 -- 8@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 2 -- 8@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

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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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