Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
195	0.01134	0.1946	b0633	rlpA	-8.12	0.339483	43 -- 55	25 -- 37	septal ring protein suppressor of prc minor lipoprotein	_____________42____________56\n_____________\|_____________\|\n5'-CGG...AAUAU_________A___GGUAU...CUG-3'\n______________UGGUAUGGU_AGC\n______________\|\|\|\|\|::\|:_\|\|\|\n______________ACCAUGUCG_UCG\n3'-UUU...CAAGG_________A___UAAAA...UCG-5'\n_____________\|_____________\|\n_____________38____________24\n	45 -- 51	29 -- 35	-15.087 kcal/mol	4.33932 kcal/mol	2.62824 kcal/mol	42 56@LB@ \| \|@LB@5'-CGG...AAUAU A GGUAU...CUG-3'@LB@ UGGUAUGGU AGC@LB@ \|\|\|\|\|::\|: \|\|\|@LB@ ACCAUGUCG UCG@LB@3'-UUU...CAAGG A UAAAA...UCG-5'@LB@ \| \|@LB@ 38 24@LB@@LB@@LB@Energy -8.12 kcal/mol@LB@Hybridization Energy -15.087 kcal/mol@LB@Unfolding Energy - mRNA 4.33932 kcal/mol@LB@Unfolding Energy - sRNA 2.62824 kcal/mol@LB@@LB@Position - mRNA 43 -- 55@LB@Position - sRNA 25 -- 37@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 29 -- 35@LB@
61	0.001594	0.08781	b1905	ftnA	-13.68	0.025904	280 -- 298	27 -- 44	ferritin iron storage protein (cytoplasmic)	_____________279_________________299\n_____________\|___________________\|\n5'-CAU...GCAAA__A_CG_____________UC-3'\n______________UG_G__CCUGGUGCAGCUA\n______________\|\|_\|__\|\|\|\|\|\|:\|\|\|\|\|\|\n______________AC_C__GGACCAUGUCGAU\n3'-UUU...CCUCC____AA_____________CGUAA...UCG-5'\n_____________\|___________________\|\n_____________45__________________26\n	292 -- 298	27 -- 33	-25.294 kcal/mol	7.30746 kcal/mol	4.30747 kcal/mol	279 299@LB@ \| \|@LB@5'-CAU...GCAAA A CG UC-3'@LB@ UG G CCUGGUGCAGCUA@LB@ \|\| \| \|\|\|\|\|\|:\|\|\|\|\|\|@LB@ AC C GGACCAUGUCGAU@LB@3'-UUU...CCUCC AA CGUAA...UCG-5'@LB@ \| \|@LB@ 45 26@LB@@LB@@LB@Energy -13.68 kcal/mol@LB@Hybridization Energy -25.294 kcal/mol@LB@Unfolding Energy - mRNA 7.30746 kcal/mol@LB@Unfolding Energy - sRNA 4.30747 kcal/mol@LB@@LB@Position - mRNA 280 -- 298@LB@Position - sRNA 27 -- 44@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 27 -- 33@LB@
139	0.00635	0.1535	b0800	ybiB	-9.74	0.186276	120 -- 129	27 -- 36	putative family 3 glycosyltransferase	_____________119________130\n_____________\|__________\|\n5'-GCC...CUGAA__________AAAAG...UCA-3'\n______________GGUAUAGUUA\n______________\|\|\|\|:\|\|:\|\|\n______________CCAUGUCGAU\n3'-UUU...AAGGA__________CGUAA...UCG-5'\n_____________\|__________\|\n_____________37_________26\n	123 -- 129	27 -- 33	-12.0711 kcal/mol	1.15693 kcal/mol	1.17709 kcal/mol	119 130@LB@ \| \|@LB@5'-GCC...CUGAA AAAAG...UCA-3'@LB@ GGUAUAGUUA@LB@ \|\|\|\|:\|\|:\|\|@LB@ CCAUGUCGAU@LB@3'-UUU...AAGGA CGUAA...UCG-5'@LB@ \| \|@LB@ 37 26@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -12.0711 kcal/mol@LB@Unfolding Energy - mRNA 1.15693 kcal/mol@LB@Unfolding Energy - sRNA 1.17709 kcal/mol@LB@@LB@Position - mRNA 120 -- 129@LB@Position - sRNA 27 -- 36@LB@Position Seed - mRNA 123 -- 129@LB@Position Seed - sRNA 27 -- 33@LB@
10	2.916e-05	0.0098	b1890	motA	-14.10	0.019983	224 -- 242	28 -- 46	proton conductor component of flagella motor	_____________223_________________243\n_____________\|___________________\|\n5'-GAC...UACCU___U_____C_________UUCGG...AAC-3'\n______________GGU_GUUCU_GGUACAGUU\n______________\|\|\|_\|\|\|\|:_\|\|\|\|\|\|\|:\|\n______________CCA_CAAGG_CCAUGUCGA\n3'-UUU...UUCCU___C_____A_________UCGUA...UCG-5'\n_____________\|___________________\|\n_____________47__________________27\n	236 -- 242	28 -- 34	-23.9025 kcal/mol	5.49413 kcal/mol	4.3041 kcal/mol	223 243@LB@ \| \|@LB@5'-GAC...UACCU U C UUCGG...AAC-3'@LB@ GGU GUUCU GGUACAGUU@LB@ \|\|\| \|\|\|\|: \|\|\|\|\|\|\|:\|@LB@ CCA CAAGG CCAUGUCGA@LB@3'-UUU...UUCCU C A UCGUA...UCG-5'@LB@ \| \|@LB@ 47 27@LB@@LB@@LB@Energy -14.10 kcal/mol@LB@Hybridization Energy -23.9025 kcal/mol@LB@Unfolding Energy - mRNA 5.49413 kcal/mol@LB@Unfolding Energy - sRNA 4.3041 kcal/mol@LB@@LB@Position - mRNA 224 -- 242@LB@Position - sRNA 28 -- 46@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 28 -- 34@LB@
200	0.01185	0.1975	b0025	ribF	-6.09	0.598433	35 -- 41	28 -- 34	bifunctional riboflavin kinase/FAD synthetase	_____________34______42\n_____________\|_______\|\n5'-UGG...GUGAA_______UUUCC...GCG-3'\n______________UACAGCU\n______________\|\|\|\|\|\|\|\n______________AUGUCGA\n3'-UUU...GGACC_______UCGUA...UCG-5'\n_____________\|_______\|\n_____________35______27\n	35 -- 41	28 -- 34	-8.9914 kcal/mol	1.72675 kcal/mol	1.17027 kcal/mol	34 42@LB@ \| \|@LB@5'-UGG...GUGAA UUUCC...GCG-3'@LB@ UACAGCU@LB@ \|\|\|\|\|\|\|@LB@ AUGUCGA@LB@3'-UUU...GGACC UCGUA...UCG-5'@LB@ \| \|@LB@ 35 27@LB@@LB@@LB@Energy -6.09 kcal/mol@LB@Hybridization Energy -8.9914 kcal/mol@LB@Unfolding Energy - mRNA 1.72675 kcal/mol@LB@Unfolding Energy - sRNA 1.17027 kcal/mol@LB@@LB@Position - mRNA 35 -- 41@LB@Position - sRNA 28 -- 34@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 28 -- 34@LB@
8	1.749e-05	0.007346	b3294	rplQ	-17.07	0.002316	5 -- 20	29 -- 46	50S ribosomal subunit protein L17	_____________4__________________21\n_____________\|__________________\|\n_______5'-UAUC____A_____________GUACC...UCA-3'\n______________GGUG___UCUGGUACAGC\n______________\|\|\|\|___:\|\|\|\|\|\|\|\|\|\|\n______________CCAC___GGACCAUGUCG\n3'-UUU...UUCCU____CAA___________AUCGU...UCG-5'\n_____________\|__________________\|\n_____________47_________________28\n	14 -- 20	29 -- 35	-24.8218 kcal/mol	3.44934 kcal/mol	4.30059 kcal/mol	4 21@LB@ \| \|@LB@ 5'-UAUC A GUACC...UCA-3'@LB@ GGUG UCUGGUACAGC@LB@ \|\|\|\| :\|\|\|\|\|\|\|\|\|\|@LB@ CCAC GGACCAUGUCG@LB@3'-UUU...UUCCU CAA AUCGU...UCG-5'@LB@ \| \|@LB@ 47 28@LB@@LB@@LB@Energy -17.07 kcal/mol@LB@Hybridization Energy -24.8218 kcal/mol@LB@Unfolding Energy - mRNA 3.44934 kcal/mol@LB@Unfolding Energy - sRNA 4.30059 kcal/mol@LB@@LB@Position - mRNA 5 -- 20@LB@Position - sRNA 29 -- 46@LB@Position Seed - mRNA 14 -- 20@LB@Position Seed - sRNA 29 -- 35@LB@
92	0.00311	0.1126	b1042	csgA	-13.02	0.037954	257 -- 281	29 -- 49	curlin subunit amyloid curli fibers cryptic	_____________256_______________________282\n_____________\|_________________________\|\n5'-CAA...GCUCU__C_____UU______CA_______GGCGG...GUG-3'\n______________GG_AGGUG__GUUCCU__GUACGGC\n______________\|\|_\|\|\|\|\|__\|\|\|\|\|\|__\|\|\|\|:\|\|\n______________CC_UCCAC__CAAGGA__CAUGUCG\n3'-UUU...CGAUU________________C________AUCGU...UCG-5'\n_____________\|_________________________\|\n_____________50________________________28\n	275 -- 281	29 -- 35	-27.0821 kcal/mol	9.75964 kcal/mol	4.30143 kcal/mol	256 282@LB@ \| \|@LB@5'-CAA...GCUCU C UU CA GGCGG...GUG-3'@LB@ GG AGGUG GUUCCU GUACGGC@LB@ \|\| \|\|\|\|\| \|\|\|\|\|\| \|\|\|\|:\|\|@LB@ CC UCCAC CAAGGA CAUGUCG@LB@3'-UUU...CGAUU C AUCGU...UCG-5'@LB@ \| \|@LB@ 50 28@LB@@LB@@LB@Energy -13.02 kcal/mol@LB@Hybridization Energy -27.0821 kcal/mol@LB@Unfolding Energy - mRNA 9.75964 kcal/mol@LB@Unfolding Energy - sRNA 4.30143 kcal/mol@LB@@LB@Position - mRNA 257 -- 281@LB@Position - sRNA 29 -- 49@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 29 -- 35@LB@
115	0.004814	0.1404	b2743	pcm	-10.63	0.126788	157 -- 183	29 -- 48	L-isoaspartate protein carboxylmethyltransferase type II	_____________156_________________________184\n_____________\|___________________________\|\n5'-AUC...CGCAA__U_______CAGA_____UAA_____GUGGG...AAA-3'\n______________GA_GUGGUUU____CUGGU___ACAGC\n______________\|\|_\|\|\|\|\|\|:____\|\|\|\|\|___\|\|\|\|\|\n______________CU_CACCAAG____GACCA___UGUCG\n3'-UUU...GAUUC__C________________________AUCGU...UCG-5'\n_____________\|___________________________\|\n_____________49__________________________28\n	160 -- 166	39 -- 45	-22.1612 kcal/mol	7.2267 kcal/mol	4.30129 kcal/mol	156 184@LB@ \| \|@LB@5'-AUC...CGCAA U CAGA UAA GUGGG...AAA-3'@LB@ GA GUGGUUU CUGGU ACAGC@LB@ \|\| \|\|\|\|\|\|: \|\|\|\|\| \|\|\|\|\|@LB@ CU CACCAAG GACCA UGUCG@LB@3'-UUU...GAUUC C AUCGU...UCG-5'@LB@ \| \|@LB@ 49 28@LB@@LB@@LB@Energy -10.63 kcal/mol@LB@Hybridization Energy -22.1612 kcal/mol@LB@Unfolding Energy - mRNA 7.2267 kcal/mol@LB@Unfolding Energy - sRNA 4.30129 kcal/mol@LB@@LB@Position - mRNA 157 -- 183@LB@Position - sRNA 29 -- 48@LB@Position Seed - mRNA 160 -- 166@LB@Position Seed - sRNA 39 -- 45@LB@
142	0.006672	0.1579	b3168	infB	-12.04	0.064271	249 -- 267	29 -- 45	translation initiation factor IF-2	_____________248_________________268\n_____________\|___________________\|\n5'-AAG...CCUCC____AACG___________AAUUU...CUG-3'\n______________GUGG____CCUGGUACAGC\n______________\|\|\|\|____\|\|\|\|\|\|\|\|\|\|\|\n______________CACC____GGACCAUGUCG\n3'-UUU...UCCUC____AA_____________AUCGU...UCG-5'\n_____________\|___________________\|\n_____________46__________________28\n	261 -- 267	29 -- 35	-27.2517 kcal/mol	10.9083 kcal/mol	4.30037 kcal/mol	248 268@LB@ \| \|@LB@5'-AAG...CCUCC AACG AAUUU...CUG-3'@LB@ GUGG CCUGGUACAGC@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|\|\|@LB@ CACC GGACCAUGUCG@LB@3'-UUU...UCCUC AA AUCGU...UCG-5'@LB@ \| \|@LB@ 46 28@LB@@LB@@LB@Energy -12.04 kcal/mol@LB@Hybridization Energy -27.2517 kcal/mol@LB@Unfolding Energy - mRNA 10.9083 kcal/mol@LB@Unfolding Energy - sRNA 4.30037 kcal/mol@LB@@LB@Position - mRNA 249 -- 267@LB@Position - sRNA 29 -- 45@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 29 -- 35@LB@
154	0.007726	0.1686	b4203	rplI	-9.34	0.218324	285 -- 297	29 -- 41	50S ribosomal subunit protein L9	_____________284___________298\n_____________\|_____________\|\n5'-AAA...GUAAC__________C__AGG-3'\n______________UUCCUGGUAC_GC\n______________\|\|\|\|\|\|\|\|\|\|_\|\|\n______________AAGGACCAUG_CG\n3'-UUU...CCACC__________U__AUCGU...UCG-5'\n_____________\|_____________\|\n_____________42____________28\n	288 -- 294	32 -- 38	-19.8737 kcal/mol	6.23655 kcal/mol	4.29727 kcal/mol	284 298@LB@ \| \|@LB@5'-AAA...GUAAC C AGG-3'@LB@ UUCCUGGUAC GC@LB@ \|\|\|\|\|\|\|\|\|\| \|\|@LB@ AAGGACCAUG CG@LB@3'-UUU...CCACC U AUCGU...UCG-5'@LB@ \| \|@LB@ 42 28@LB@@LB@@LB@Energy -9.34 kcal/mol@LB@Hybridization Energy -19.8737 kcal/mol@LB@Unfolding Energy - mRNA 6.23655 kcal/mol@LB@Unfolding Energy - sRNA 4.29727 kcal/mol@LB@@LB@Position - mRNA 285 -- 297@LB@Position - sRNA 29 -- 41@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 32 -- 38@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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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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