Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
131	0.01426	0.3575	b0048	folA	-12.08	0.107221	135 -- 211	115 -- 187	dihydrofolate reductase	_____________134_________212\n_____________\|___________\|\n5'-UCA...UUGUU___________GUAAU...GCA-3'\n______________UUUGUUUCAUU\n______________:\|\|\|:\|\|\|\|\|:\n______________GAACGAAGUAG\n3'-UUU...UGGGG___________-5'\n_____________\|__________\|\n_____________188________115\n	56 -- 62	1 -- 7	-10.5455 kcal/mol	1.7602 kcal/mol	1.03329 kcal/mol	134 212@LB@ \| \|@LB@5'-UCA...UUGUU GUAAU...GCA-3'@LB@ UUUGUUUCAUU@LB@ :\|\|\|:\|\|\|\|\|:@LB@ GAACGAAGUAG@LB@3'-UUU...UGGGG -5'@LB@ \| \|@LB@ 188 115@LB@@LB@@LB@Energy -12.08 kcal/mol@LB@Hybridization Energy -10.5455 kcal/mol@LB@Unfolding Energy - mRNA 1.7602 kcal/mol@LB@Unfolding Energy - sRNA 1.03329 kcal/mol@LB@@LB@Position - mRNA 135 -- 211@LB@Position - sRNA 115 -- 187@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 1 -- 7@LB@
139	0.01488	0.3575	b2167	fruA	-12.05	0.108648	223 -- 242	167 -- 187	fused fructose-specific PTS enzymes: IIBcomponent/IIC components	_____________222___________________243\n_____________\|_____________________\|\n5'-CGC...UAUUG_________________G___CGCGC...AAA-3'\n______________ACGCUAAU_CUCGGUCA_GCA\n______________\|\|:\|:\|\|\|_\|\|\|:\|\|\|\|_:\|\|\n______________UGUGGUUA_GAGUCAGU_UGU\n3'-UUU...UAAAA________U________G___ACUAC...UAG-5'\n_____________\|_____________________\|\n_____________188___________________166\n	232 -- 238	171 -- 177	-25.758 kcal/mol	6.7352 kcal/mol	5.05492 kcal/mol	222 243@LB@ \| \|@LB@5'-CGC...UAUUG G CGCGC...AAA-3'@LB@ ACGCUAAU CUCGGUCA GCA@LB@ \|\|:\|:\|\|\| \|\|\|:\|\|\|\| :\|\|@LB@ UGUGGUUA GAGUCAGU UGU@LB@3'-UUU...UAAAA U G ACUAC...UAG-5'@LB@ \| \|@LB@ 188 166@LB@@LB@@LB@Energy -12.05 kcal/mol@LB@Hybridization Energy -25.758 kcal/mol@LB@Unfolding Energy - mRNA 6.7352 kcal/mol@LB@Unfolding Energy - sRNA 5.05492 kcal/mol@LB@@LB@Position - mRNA 223 -- 242@LB@Position - sRNA 167 -- 187@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 171 -- 177@LB@
24	0.001922	0.2633	b3017	ftsP	-19.79	0.002953	203 -- 291	63 -- 135	septal ring component that protects the divisome from stress; multicopy suppressor of ftsI(Ts)	_____________202__________________________________________________________________________________________292\n_____________\|____________________________________________________________________________________________\|\n5'-GAC...AAUAU_________GUCG__________A_________C__G______CACU_____CA______GUUCCCCUGAAG____________________AGCAA...CGC-3'\n______________GUCA_CUCA____GCGUCAGUUC_UUCAGGCAU_GG__GAUUG____UUGUG__GGCGCU____________GCCAGCGCAGCCGG_GCAAC\n______________\|\|\|\|_\|:\|\|____\|\|:\|\|\|\|\|:\|_\|\|\|\|:\|\|\|\|_\|\|__:\|\|:\|____\|\|\|\|\|__\|:\|\|\|\|____________:\|\|\|:\|\|\|\|:\|\|:\|_:\|\|\|\|\n______________CAGU_GGGU____CGUAGUCAGG_AAGUUCGUA_CC__UUAGC____AACAC__CUGCGA____________UGGUUGCGUUGGUC_UGUUG\n3'-UUU...AACGC____A____GA_________________________AA______________C_______AU________________________G_____AAGCG...UAG-5'\n_____________\|____________________________________________________________________________________________\|\n_____________136__________________________________________________________________________________________62\n	278 -- 284	71 -- 77	-82.7619 kcal/mol	32.3928 kcal/mol	37.2191 kcal/mol	202 292@LB@ \| \|@LB@5'-GAC...AAUAU GUCG A C G CACU CA GUUCCCCUGAAG AGCAA...CGC-3'@LB@ GUCA CUCA GCGUCAGUUC UUCAGGCAU GG GAUUG UUGUG GGCGCU GCCAGCGCAGCCGG GCAAC@LB@ \|\|\|\| \|:\|\| \|\|:\|\|\|\|\|:\| \|\|\|\|:\|\|\|\| \|\| :\|\|:\| \|\|\|\|\| \|:\|\|\|\| :\|\|\|:\|\|\|\|:\|\|:\| :\|\|\|\|@LB@ CAGU GGGU CGUAGUCAGG AAGUUCGUA CC UUAGC AACAC CUGCGA UGGUUGCGUUGGUC UGUUG@LB@3'-UUU...AACGC A GA AA C AU G AAGCG...UAG-5'@LB@ \| \|@LB@ 136 62@LB@@LB@@LB@Energy -19.79 kcal/mol@LB@Hybridization Energy -82.7619 kcal/mol@LB@Unfolding Energy - mRNA 32.3928 kcal/mol@LB@Unfolding Energy - sRNA 37.2191 kcal/mol@LB@@LB@Position - mRNA 203 -- 291@LB@Position - sRNA 63 -- 135@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 71 -- 77@LB@
48	0.004626	0.3205	b3462	ftsX	-13.20	0.063258	14 -- 27	192 -- 205	putative ABC transporter permease	_____________13_____________28\n_____________\|______________\|\n5'-CAA...CGGUA__________AC__ACCGA...ACG-3'\n______________CUGCUGGCGG__GA\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\n______________GACGACCGCC__CU\n3'-UUU...UAUUA__________CA__AAAAU...UAG-5'\n_____________\|______________\|\n_____________206____________191\n	17 -- 23	196 -- 202	-23.0043 kcal/mol	4.65554 kcal/mol	9.06563 kcal/mol	13 28@LB@ \| \|@LB@5'-CAA...CGGUA AC ACCGA...ACG-3'@LB@ CUGCUGGCGG GA@LB@ \|\|\|\|\|\|\|\|\|\| \|\|@LB@ GACGACCGCC CU@LB@3'-UUU...UAUUA CA AAAAU...UAG-5'@LB@ \| \|@LB@ 206 191@LB@@LB@@LB@Energy -13.20 kcal/mol@LB@Hybridization Energy -23.0043 kcal/mol@LB@Unfolding Energy - mRNA 4.65554 kcal/mol@LB@Unfolding Energy - sRNA 9.06563 kcal/mol@LB@@LB@Position - mRNA 14 -- 27@LB@Position - sRNA 192 -- 205@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 196 -- 202@LB@
121	0.01323	0.3575	b3429	glgA	-14.56	0.033318	190 -- 240	123 -- 176	glycogen synthase	_____________189__________________241\n_____________\|____________________\|\n5'-GUA...AUGCA__________GU________AGAUG...ACG-3'\n______________GGUUUUACAU__AUGUUCAG\n______________\|:\|\|\|\|\|\|\|:__\|\|::\|\|\|\|\n______________CUAAAAUGUG__UAUGAGUC\n3'-UUU...GCCCA__________GU________AGUGU...UAG-5'\n_____________\|____________________\|\n_____________177__________________122\n	219 -- 225	174 -- 180	-15.9439 kcal/mol	3.46677 kcal/mol	4.94566 kcal/mol	189 241@LB@ \| \|@LB@5'-GUA...AUGCA GU AGAUG...ACG-3'@LB@ GGUUUUACAU AUGUUCAG@LB@ \|:\|\|\|\|\|\|\|: \|\|::\|\|\|\|@LB@ CUAAAAUGUG UAUGAGUC@LB@3'-UUU...GCCCA GU AGUGU...UAG-5'@LB@ \| \|@LB@ 177 122@LB@@LB@@LB@Energy -14.56 kcal/mol@LB@Hybridization Energy -15.9439 kcal/mol@LB@Unfolding Energy - mRNA 3.46677 kcal/mol@LB@Unfolding Energy - sRNA 4.94566 kcal/mol@LB@@LB@Position - mRNA 190 -- 240@LB@Position - sRNA 123 -- 176@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 174 -- 180@LB@
47	0.004619	0.3205	b4142	groS	-15.85	0.018169	259 -- 271	196 -- 208	Cpn10 chaperonin GroES small subunit of GroESL	_____________258_______________________________272\n_____________\|_________________________________\|\n5'-UGA...AACUA_____________CAUCGUUCUG__________UGCAG...CUA-3'\n______________AAUCUGCUGGCGG__________ACCG__GCUC\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|__________\|\|\|:__:\|\|\|\n______________UUAGACGACCGCC__________UGGU__UGAG\n3'-UUU...CCAUA_____________CACUAAAAUG____UA____UCAGU...UAG-5'\n_____________\|_________________________________\|\n_____________209_______________________________195\n	265 -- 271	196 -- 202	-33.1058 kcal/mol	10.148 kcal/mol	14.8106 kcal/mol	258 272@LB@ \| \|@LB@5'-UGA...AACUA CAUCGUUCUG UGCAG...CUA-3'@LB@ AAUCUGCUGGCGG ACCG GCUC@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|: :\|\|\|@LB@ UUAGACGACCGCC UGGU UGAG@LB@3'-UUU...CCAUA CACUAAAAUG UA UCAGU...UAG-5'@LB@ \| \|@LB@ 209 195@LB@@LB@@LB@Energy -15.85 kcal/mol@LB@Hybridization Energy -33.1058 kcal/mol@LB@Unfolding Energy - mRNA 10.148 kcal/mol@LB@Unfolding Energy - sRNA 14.8106 kcal/mol@LB@@LB@Position - mRNA 259 -- 271@LB@Position - sRNA 196 -- 208@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 196 -- 202@LB@
89	0.009985	0.3575	b0477	gsk	-9.51	0.338446	88 -- 115	123 -- 150	inosine/guanosine kinase	_____________87_____________116\n_____________\|______________\|\n5'-UUU...UCGCC_________AC___CCGUA...CUG-3'\n______________GCUCAGUUA__CAC\n______________:\|\|\|\|\|\|:\|__\|\|\|\n______________UGAGUCAGU__GUG\n3'-UUU...GGUUA______________UACUA...UAG-5'\n_____________\|______________\|\n_____________151____________122\n	175 -- 181	171 -- 177	-13.3754 kcal/mol	2.68541 kcal/mol	0.283892 kcal/mol	87 116@LB@ \| \|@LB@5'-UUU...UCGCC AC CCGUA...CUG-3'@LB@ GCUCAGUUA CAC@LB@ :\|\|\|\|\|\|:\| \|\|\|@LB@ UGAGUCAGU GUG@LB@3'-UUU...GGUUA UACUA...UAG-5'@LB@ \| \|@LB@ 151 122@LB@@LB@@LB@Energy -9.51 kcal/mol@LB@Hybridization Energy -13.3754 kcal/mol@LB@Unfolding Energy - mRNA 2.68541 kcal/mol@LB@Unfolding Energy - sRNA 0.283892 kcal/mol@LB@@LB@Position - mRNA 88 -- 115@LB@Position - sRNA 123 -- 150@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 171 -- 177@LB@
106	0.01145	0.3575	b2350	gtrA	-11.86	0.119007	4 -- 25	148 -- 167	CPS-53 (KpLE1) prophage; bactoprenol-linked glucose translocase/flippase	_____________3_____________26\n_____________\|_____________\|\n5'-GAA...UGUAU__AU_________ACAAACC-3'\n______________CU__GUCGCGCAU\n______________\|\|__\|\|\|:\|:\|\|\|\n______________GA__CAGUGUGUA\n3'-UUU...GUUAU__GU_________CUACG...UAG-5'\n_____________\|_____________\|\n_____________168___________147\n	287 -- 293	166 -- 172	-13.6011 kcal/mol	2.0532 kcal/mol	0.604639 kcal/mol	3 26@LB@ \| \|@LB@5'-GAA...UGUAU AU ACAAACC-3'@LB@ CU GUCGCGCAU@LB@ \|\| \|\|\|:\|:\|\|\|@LB@ GA CAGUGUGUA@LB@3'-UUU...GUUAU GU CUACG...UAG-5'@LB@ \| \|@LB@ 168 147@LB@@LB@@LB@Energy -11.86 kcal/mol@LB@Hybridization Energy -13.6011 kcal/mol@LB@Unfolding Energy - mRNA 2.0532 kcal/mol@LB@Unfolding Energy - sRNA 0.604639 kcal/mol@LB@@LB@Position - mRNA 4 -- 25@LB@Position - sRNA 148 -- 167@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 166 -- 172@LB@
99	0.01084	0.3575	b0872	hcr	-12.58	0.084706	106 -- 121	192 -- 205	HCP oxidoreductase NADH-dependent	_____________105______________122\n_____________\|________________\|\n5'-UCC...CAGAC__________U_C___ACGAG...AUU-3'\n______________CUGCUGGCGG_G_UGA\n______________\|\|\|\|\|\|\|\|\|\|_\|_\|\|\|\n______________GACGACCGCC_C_ACU\n3'-UUU...UAUUA________________AAAAU...UAG-5'\n_____________\|________________\|\n_____________206______________191\n	109 -- 115	196 -- 202	-24.2797 kcal/mol	6.55023 kcal/mol	9.06563 kcal/mol	105 122@LB@ \| \|@LB@5'-UCC...CAGAC U C ACGAG...AUU-3'@LB@ CUGCUGGCGG G UGA@LB@ \|\|\|\|\|\|\|\|\|\| \| \|\|\|@LB@ GACGACCGCC C ACU@LB@3'-UUU...UAUUA AAAAU...UAG-5'@LB@ \| \|@LB@ 206 191@LB@@LB@@LB@Energy -12.58 kcal/mol@LB@Hybridization Energy -24.2797 kcal/mol@LB@Unfolding Energy - mRNA 6.55023 kcal/mol@LB@Unfolding Energy - sRNA 9.06563 kcal/mol@LB@@LB@Position - mRNA 106 -- 121@LB@Position - sRNA 192 -- 205@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 196 -- 202@LB@
136	0.01456	0.3575	b0369	hemB	-9.31	0.367566	203 -- 221	75 -- 90	5-aminolevulinate dehydratase (porphobilinogen synthase)	_____________202________________222\n_____________\|__________________\|\n5'-CCA...UAAAA_______ACCC_______GGUAU...UGC-3'\n______________CAUCCCU____UGCUUCA\n______________\|\|:\|\|\|:____\|\|\|\|\|\|\|\n______________GUGGGGG____ACGAAGU\n3'-UUU...ACCCC_______A__________AG-5'\n_____________\|__________________\|\n_____________91_________________74\n	153 -- 159	3 -- 9	-17.8942 kcal/mol	1.92924 kcal/mol	7.09151 kcal/mol	202 222@LB@ \| \|@LB@5'-CCA...UAAAA ACCC GGUAU...UGC-3'@LB@ CAUCCCU UGCUUCA@LB@ \|\|:\|\|\|: \|\|\|\|\|\|\|@LB@ GUGGGGG ACGAAGU@LB@3'-UUU...ACCCC A AG-5'@LB@ \| \|@LB@ 91 74@LB@@LB@@LB@Energy -9.31 kcal/mol@LB@Hybridization Energy -17.8942 kcal/mol@LB@Unfolding Energy - mRNA 1.92924 kcal/mol@LB@Unfolding Energy - sRNA 7.09151 kcal/mol@LB@@LB@Position - mRNA 203 -- 221@LB@Position - sRNA 75 -- 90@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 3 -- 9@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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