Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
178	0.02184	0.4127	b1466	narW	-11.23	0.066200	254 -- 267	42 -- 56	nitrate reductase 2 (NRZ) delta subunit (assembly subunit)	_____________253_____________268\n_____________\|_______________\|\n5'-AUU...CUGUU____G__________AGGAC...CGC-3'\n______________GUGG_AAUGCAA_GG\n______________\|\|\|\|_\|\|\|\|\|\|\|_\|\|\n______________CACC_UUACGUU_CC\n3'-UUU...UUAGU____G_______A__GGGUU...UUG-5'\n_____________\|_______________\|\n_____________57______________41\n	259 -- 265	45 -- 51	-17.8423 kcal/mol	3.07693 kcal/mol	3.53153 kcal/mol	253 268@LB@ \| \|@LB@5'-AUU...CUGUU G AGGAC...CGC-3'@LB@ GUGG AAUGCAA GG@LB@ \|\|\|\| \|\|\|\|\|\|\| \|\|@LB@ CACC UUACGUU CC@LB@3'-UUU...UUAGU G A GGGUU...UUG-5'@LB@ \| \|@LB@ 57 41@LB@@LB@@LB@Energy -11.23 kcal/mol@LB@Hybridization Energy -17.8423 kcal/mol@LB@Unfolding Energy - mRNA 3.07693 kcal/mol@LB@Unfolding Energy - sRNA 3.53153 kcal/mol@LB@@LB@Position - mRNA 254 -- 267@LB@Position - sRNA 42 -- 56@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 45 -- 51@LB@
200	0.0254	0.4256	b0975	hyaD	-14.05	0.013908	10 -- 31	42 -- 66	hydrogenase 1 maturation protease	_____________9_________________________32\n_____________\|_________________________\|\n5'-UUU...UCUAC____CG___________CU______ACAUU...ACC-3'\n______________UGGA_____GGUGGCAA__CAAUGG\n______________\|\|\|\|_____:\|\|\|\|\|\|\|__\|\|\|\|\|\|\n______________ACCU_____UCACCGUU__GUUACC\n3'-UUU...AUACA____UUUAG________AC______GGGUU...UUG-5'\n_____________\|_________________________\|\n_____________67________________________41\n	17 -- 23	50 -- 56	-23.7385 kcal/mol	4.08533 kcal/mol	5.59884 kcal/mol	9 32@LB@ \| \|@LB@5'-UUU...UCUAC CG CU ACAUU...ACC-3'@LB@ UGGA GGUGGCAA CAAUGG@LB@ \|\|\|\| :\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ ACCU UCACCGUU GUUACC@LB@3'-UUU...AUACA UUUAG AC GGGUU...UUG-5'@LB@ \| \|@LB@ 67 41@LB@@LB@@LB@Energy -14.05 kcal/mol@LB@Hybridization Energy -23.7385 kcal/mol@LB@Unfolding Energy - mRNA 4.08533 kcal/mol@LB@Unfolding Energy - sRNA 5.59884 kcal/mol@LB@@LB@Position - mRNA 10 -- 31@LB@Position - sRNA 42 -- 66@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 50 -- 56@LB@
105	0.009758	0.3118	b4478	dgoD	-14.76	0.009064	185 -- 203	43 -- 60	D-galactonate dehydratase	_____________184_________________204\n_____________\|___________________\|\n5'-AAA...GGCGU___G__A____________AAAAU...UGA-3'\n______________AUC_AG_GGCAGUGCAAUG\n______________\|\|\|_\|\|_\|\|\|\|:\|\|\|\|\|\|\|\n______________UAG_UC_CCGUUACGUUAC\n3'-UUU...CCUUU______A____________CGGGU...UUG-5'\n_____________\|___________________\|\n_____________61__________________42\n	197 -- 203	43 -- 49	-22.2033 kcal/mol	3.91427 kcal/mol	3.52557 kcal/mol	184 204@LB@ \| \|@LB@5'-AAA...GGCGU G A AAAAU...UGA-3'@LB@ AUC AG GGCAGUGCAAUG@LB@ \|\|\| \|\| \|\|\|\|:\|\|\|\|\|\|\|@LB@ UAG UC CCGUUACGUUAC@LB@3'-UUU...CCUUU A CGGGU...UUG-5'@LB@ \| \|@LB@ 61 42@LB@@LB@@LB@Energy -14.76 kcal/mol@LB@Hybridization Energy -22.2033 kcal/mol@LB@Unfolding Energy - mRNA 3.91427 kcal/mol@LB@Unfolding Energy - sRNA 3.52557 kcal/mol@LB@@LB@Position - mRNA 185 -- 203@LB@Position - sRNA 43 -- 60@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 43 -- 49@LB@
21	0.0009862	0.1579	b2572	rseA	-10.60	0.091224	9 -- 29	44 -- 65	anti-sigma factor	_____________8______________________30\n_____________\|______________________\|\n___5'-UCCCUCCC________UAC____UG_____AACCU...GGG-3'\n______________GGAAGAUU____GCA__GCAAU\n______________\|\|\|\|:\|\|:____\|\|\|__\|\|\|\|\|\n______________CCUUUUAG____CGU__CGUUA\n3'-UUU...UACAA________UCAC___UA_____CCGGG...UUG-5'\n_____________\|______________________\|\n_____________66_____________________43\n	10 -- 16	58 -- 64	-18.0609 kcal/mol	3.14057 kcal/mol	4.32401 kcal/mol	8 30@LB@ \| \|@LB@ 5'-UCCCUCCC UAC UG AACCU...GGG-3'@LB@ GGAAGAUU GCA GCAAU@LB@ \|\|\|\|:\|\|: \|\|\| \|\|\|\|\|@LB@ CCUUUUAG CGU CGUUA@LB@3'-UUU...UACAA UCAC UA CCGGG...UUG-5'@LB@ \| \|@LB@ 66 43@LB@@LB@@LB@Energy -10.60 kcal/mol@LB@Hybridization Energy -18.0609 kcal/mol@LB@Unfolding Energy - mRNA 3.14057 kcal/mol@LB@Unfolding Energy - sRNA 4.32401 kcal/mol@LB@@LB@Position - mRNA 9 -- 29@LB@Position - sRNA 44 -- 65@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 58 -- 64@LB@
118	0.01176	0.3326	b3601	mtlR	-9.20	0.175568	190 -- 199	44 -- 53	mannitol operon repressor	_____________189________200\n_____________\|__________\|\n5'-UAU...AUAAA__________AAUGG...UUG-3'\n______________GCAAUGCAAU\n______________\|\|\|\|\|\|\|\|\|\|\n______________CGUUACGUUA\n3'-UUU...GUCAC__________CCGGG...UUG-5'\n_____________\|__________\|\n_____________54_________43\n	193 -- 199	44 -- 50	-14.2394 kcal/mol	1.82821 kcal/mol	3.20822 kcal/mol	189 200@LB@ \| \|@LB@5'-UAU...AUAAA AAUGG...UUG-3'@LB@ GCAAUGCAAU@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CGUUACGUUA@LB@3'-UUU...GUCAC CCGGG...UUG-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -9.20 kcal/mol@LB@Hybridization Energy -14.2394 kcal/mol@LB@Unfolding Energy - mRNA 1.82821 kcal/mol@LB@Unfolding Energy - sRNA 3.20822 kcal/mol@LB@@LB@Position - mRNA 190 -- 199@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 44 -- 50@LB@
183	0.02285	0.4143	b3262	yhdJ	-12.72	0.029953	3 -- 23	44 -- 69	DNA adenine methyltransferase SAM-dependent	_____________2__________________________24\n_____________\|__________________________\|\n_________5'-CC__________________________ACACC...GUG-3'\n______________UGUUGGA____CA_UGGUGAUGCAAU\n______________\|\|\|\|\|\|\|____\|\|_\|\|\|::\|\|\|\|\|\|\|\n______________ACAACCU____GU_ACCGUUACGUUA\n3'-UUU...AAUAU_______UUUA__C____________CCGGG...UUG-5'\n_____________\|__________________________\|\n_____________70_________________________43\n	17 -- 23	44 -- 50	-23.8856 kcal/mol	6.69358 kcal/mol	4.47358 kcal/mol	2 24@LB@ \| \|@LB@ 5'-CC ACACC...GUG-3'@LB@ UGUUGGA CA UGGUGAUGCAAU@LB@ \|\|\|\|\|\|\| \|\| \|\|\|::\|\|\|\|\|\|\|@LB@ ACAACCU GU ACCGUUACGUUA@LB@3'-UUU...AAUAU UUUA C CCGGG...UUG-5'@LB@ \| \|@LB@ 70 43@LB@@LB@@LB@Energy -12.72 kcal/mol@LB@Hybridization Energy -23.8856 kcal/mol@LB@Unfolding Energy - mRNA 6.69358 kcal/mol@LB@Unfolding Energy - sRNA 4.47358 kcal/mol@LB@@LB@Position - mRNA 3 -- 23@LB@Position - sRNA 44 -- 69@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 44 -- 50@LB@
53	0.003903	0.237	b0946	zapC	-7.74	0.322468	177 -- 206	45 -- 76	FtsZ stabilizer	_____________176_________________________________207\n_____________\|___________________________________\|\n5'-AUU...UGCGG_______GG__AG______________A_______AUUAA...GUU-3'\n______________UUUUAUA__GU__GGGAGA_____GGC_GAUGCGA\n______________\|\|\|\|\|\|\|__\|\|__\|\|:\|:\|_____\|\|\|_:\|\|\|\|:\|\n______________AAAAUAU__CA__CCUUUU_____CCG_UUACGUU\n3'-UUU...ACAGA_______A___A_______AGUCA___________ACCGG...UUG-5'\n_____________\|___________________________________\|\n_____________77__________________________________44\n	200 -- 206	45 -- 51	-19.1898 kcal/mol	6.23804 kcal/mol	5.21532 kcal/mol	176 207@LB@ \| \|@LB@5'-AUU...UGCGG GG AG A AUUAA...GUU-3'@LB@ UUUUAUA GU GGGAGA GGC GAUGCGA@LB@ \|\|\|\|\|\|\| \|\| \|\|:\|:\| \|\|\| :\|\|\|\|:\|@LB@ AAAAUAU CA CCUUUU CCG UUACGUU@LB@3'-UUU...ACAGA A A AGUCA ACCGG...UUG-5'@LB@ \| \|@LB@ 77 44@LB@@LB@@LB@Energy -7.74 kcal/mol@LB@Hybridization Energy -19.1898 kcal/mol@LB@Unfolding Energy - mRNA 6.23804 kcal/mol@LB@Unfolding Energy - sRNA 5.21532 kcal/mol@LB@@LB@Position - mRNA 177 -- 206@LB@Position - sRNA 45 -- 76@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 45 -- 51@LB@
67	0.005347	0.2645	b4278	insG	-9.22	0.173962	151 -- 164	45 -- 58	IS4 transposase	_____________150____________165\n_____________\|______________\|\n5'-GUU...CGAUC_______U______GAAUC...CUC-3'\n______________CAGUGGC_GUGUAA\n______________\|\|\|\|\|\|\|_:\|\|:\|\|\n______________GUCACCG_UACGUU\n3'-UUU...UUUUA_______U______ACCGG...UUG-5'\n_____________\|______________\|\n_____________59_____________44\n	151 -- 157	52 -- 58	-18.8848 kcal/mol	6.17717 kcal/mol	3.48403 kcal/mol	150 165@LB@ \| \|@LB@5'-GUU...CGAUC U GAAUC...CUC-3'@LB@ CAGUGGC GUGUAA@LB@ \|\|\|\|\|\|\| :\|\|:\|\|@LB@ GUCACCG UACGUU@LB@3'-UUU...UUUUA U ACCGG...UUG-5'@LB@ \| \|@LB@ 59 44@LB@@LB@@LB@Energy -9.22 kcal/mol@LB@Hybridization Energy -18.8848 kcal/mol@LB@Unfolding Energy - mRNA 6.17717 kcal/mol@LB@Unfolding Energy - sRNA 3.48403 kcal/mol@LB@@LB@Position - mRNA 151 -- 164@LB@Position - sRNA 45 -- 58@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 52 -- 58@LB@
129	0.01395	0.3636	b2314	dedD	-15.05	0.007607	192 -- 211	45 -- 65	membrane-anchored periplasmic protein involved in septation	_____________191___________________212\n_____________\|_____________________\|\n5'-UUG...CGCGA______G______________GUUUC...AUU-3'\n______________GGAGAA_CGGUGGCAA_GUAA\n______________\|\|\|:\|\|_\|:\|\|\|\|\|\|\|_\|:\|\|\n______________CCUUUU_GUCACCGUU_CGUU\n3'-UUU...UACAA______A_________A____ACCGG...UUG-5'\n_____________\|_____________________\|\n_____________66____________________44\n	201 -- 207	50 -- 56	-23.8601 kcal/mol	4.54883 kcal/mol	4.26469 kcal/mol	191 212@LB@ \| \|@LB@5'-UUG...CGCGA G GUUUC...AUU-3'@LB@ GGAGAA CGGUGGCAA GUAA@LB@ \|\|\|:\|\| \|:\|\|\|\|\|\|\| \|:\|\|@LB@ CCUUUU GUCACCGUU CGUU@LB@3'-UUU...UACAA A A ACCGG...UUG-5'@LB@ \| \|@LB@ 66 44@LB@@LB@@LB@Energy -15.05 kcal/mol@LB@Hybridization Energy -23.8601 kcal/mol@LB@Unfolding Energy - mRNA 4.54883 kcal/mol@LB@Unfolding Energy - sRNA 4.26469 kcal/mol@LB@@LB@Position - mRNA 192 -- 211@LB@Position - sRNA 45 -- 65@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 50 -- 56@LB@
174	0.02096	0.4033	b3929	rraA	-13.95	0.014802	2 -- 21	45 -- 66	ribonuclease E (RNase E) inhibitor protein	_____________1______________________22\n_____________\|______________________\|\n__________5'-A____CC________________CCAAU...GCG-3'\n______________UGGA____CGGUGGCGAUGCGA\n______________\|\|\|\|____\|:\|\|\|\|\|:\|\|\|\|:\|\n______________ACCU____GUCACCGUUACGUU\n3'-UUU...AUACA____UUUA______________ACCGG...UUG-5'\n_____________\|______________________\|\n_____________67_____________________44\n	15 -- 21	45 -- 51	-26.5083 kcal/mol	8.28748 kcal/mol	4.27166 kcal/mol	1 22@LB@ \| \|@LB@ 5'-A CC CCAAU...GCG-3'@LB@ UGGA CGGUGGCGAUGCGA@LB@ \|\|\|\| \|:\|\|\|\|\|:\|\|\|\|:\|@LB@ ACCU GUCACCGUUACGUU@LB@3'-UUU...AUACA UUUA ACCGG...UUG-5'@LB@ \| \|@LB@ 67 44@LB@@LB@@LB@Energy -13.95 kcal/mol@LB@Hybridization Energy -26.5083 kcal/mol@LB@Unfolding Energy - mRNA 8.28748 kcal/mol@LB@Unfolding Energy - sRNA 4.27166 kcal/mol@LB@@LB@Position - mRNA 2 -- 21@LB@Position - sRNA 45 -- 66@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 45 -- 51@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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