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
7	0.0005448	0.1842	b1912	pgsA	-14.68	0.031521	247 -- 274	111 -- 134	phosphatidylglycerophosphate synthetase	_____________246__________________________275\n_____________\|____________________________\|\n5'-GUC...CAUCC_________UCUU_______________UCUGC...UUG-3'\n______________UUAUCCCAU____UGUAUUGGUCUUUUA\n______________\|:\|\|\|\|\|\|:____\|\|:\|\|::\|\|\|:\|\|:\|\n______________AGUAGGGUG____ACGUAGUCAGGAAGU\n3'-UUU...ACGCC____________________________UCGUA...UAG-5'\n_____________\|____________________________\|\n_____________135__________________________110\n	268 -- 274	111 -- 117	-27.9222 kcal/mol	1.79949 kcal/mol	14.1586 kcal/mol	246 275@LB@ \| \|@LB@5'-GUC...CAUCC UCUU UCUGC...UUG-3'@LB@ UUAUCCCAU UGUAUUGGUCUUUUA@LB@ \|:\|\|\|\|\|\|: \|\|:\|\|::\|\|\|:\|\|:\|@LB@ AGUAGGGUG ACGUAGUCAGGAAGU@LB@3'-UUU...ACGCC UCGUA...UAG-5'@LB@ \| \|@LB@ 135 110@LB@@LB@@LB@Energy -14.68 kcal/mol@LB@Hybridization Energy -27.9222 kcal/mol@LB@Unfolding Energy - mRNA 1.79949 kcal/mol@LB@Unfolding Energy - sRNA 14.1586 kcal/mol@LB@@LB@Position - mRNA 247 -- 274@LB@Position - sRNA 111 -- 134@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 111 -- 117@LB@
8	0.0005643	0.1842	b2557	purL	-10.01	0.273478	129 -- 143	111 -- 124	phosphoribosylformyl-glycineamide synthetase	_____________128______________144\n_____________\|________________\|\n5'-AGG...UUGGG________AA______AAGAC...UUU-3'\n______________UACACCGA__GCUUAG\n______________\|\|\|\|\|\|:\|__:\|\|:\|\|\n______________AUGUGGUU__UGAGUC\n3'-UUU...CUAAA________A_______AGUGU...UAG-5'\n_____________\|________________\|\n_____________125______________110\n	172 -- 178	181 -- 187	-14.8421 kcal/mol	1.97129 kcal/mol	3.669 kcal/mol	128 144@LB@ \| \|@LB@5'-AGG...UUGGG AA AAGAC...UUU-3'@LB@ UACACCGA GCUUAG@LB@ \|\|\|\|\|\|:\| :\|\|:\|\|@LB@ AUGUGGUU UGAGUC@LB@3'-UUU...CUAAA A AGUGU...UAG-5'@LB@ \| \|@LB@ 125 110@LB@@LB@@LB@Energy -10.01 kcal/mol@LB@Hybridization Energy -14.8421 kcal/mol@LB@Unfolding Energy - mRNA 1.97129 kcal/mol@LB@Unfolding Energy - sRNA 3.669 kcal/mol@LB@@LB@Position - mRNA 129 -- 143@LB@Position - sRNA 111 -- 124@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 181 -- 187@LB@
9	0.0005653	0.1842	b3527	yhjJ	-12.58	0.084694	198 -- 237	133 -- 170	putative periplasmic M16 family chaperone	_____________197__________________________________________________238\n_____________\|____________________________________________________\|\n5'-CUC...GUUGA____GGGUU______CA_______CAAAAAU___________CGG_______UGCUG...GGC-3'\n______________UCAG_____CACAUG____GGGCA_______UCGACUUUUAG____GCGGUU\n______________\|\|\|\|_____\|\|\|\|\|\|____:\|\|\|\|_______\|\|:\|\|\|\|\|:\|\|____\|\|\|\|\|:\n______________AGUC_____GUGUAC____UCCGU_______AGUUGAAAGUC____CGCCAG\n3'-UUU...UUAUG____AGU________UACG_____UC________________UUAA______UAGGG...UAG-5'\n_____________\|____________________________________________________\|\n_____________171__________________________________________________132\n	222 -- 228	143 -- 149	-37.5898 kcal/mol	10.9006 kcal/mol	12.7286 kcal/mol	197 238@LB@ \| \|@LB@5'-CUC...GUUGA GGGUU CA CAAAAAU CGG UGCUG...GGC-3'@LB@ UCAG CACAUG GGGCA UCGACUUUUAG GCGGUU@LB@ \|\|\|\| \|\|\|\|\|\| :\|\|\|\| \|\|:\|\|\|\|\|:\|\| \|\|\|\|\|:@LB@ AGUC GUGUAC UCCGU AGUUGAAAGUC CGCCAG@LB@3'-UUU...UUAUG AGU UACG UC UUAA UAGGG...UAG-5'@LB@ \| \|@LB@ 171 132@LB@@LB@@LB@Energy -12.58 kcal/mol@LB@Hybridization Energy -37.5898 kcal/mol@LB@Unfolding Energy - mRNA 10.9006 kcal/mol@LB@Unfolding Energy - sRNA 12.7286 kcal/mol@LB@@LB@Position - mRNA 198 -- 237@LB@Position - sRNA 133 -- 170@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 143 -- 149@LB@
10	0.0006004	0.1842	b3656	yicI	-12.42	0.091283	58 -- 101	169 -- 207	putative alpha-glucosidase	_____________57_________102\n_____________\|__________\|\n5'-ACA...GAUAA__________G-3'\n______________UGAAAUGGUG\n______________\|:\|\|\|\|:\|\|\|\n______________AUUUUAUCAC\n3'-UUU...GCGCC__________GACUA...UAG-5'\n_____________\|__________\|\n_____________208________168\n	293 -- 299	40 -- 46	-9.13222 kcal/mol	0.486237 kcal/mol	4.51378 kcal/mol	57 102@LB@ \| \|@LB@5'-ACA...GAUAA G-3'@LB@ UGAAAUGGUG@LB@ \|:\|\|\|\|:\|\|\|@LB@ AUUUUAUCAC@LB@3'-UUU...GCGCC GACUA...UAG-5'@LB@ \| \|@LB@ 208 168@LB@@LB@@LB@Energy -12.42 kcal/mol@LB@Hybridization Energy -9.13222 kcal/mol@LB@Unfolding Energy - mRNA 0.486237 kcal/mol@LB@Unfolding Energy - sRNA 4.51378 kcal/mol@LB@@LB@Position - mRNA 58 -- 101@LB@Position - sRNA 169 -- 207@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 40 -- 46@LB@
11	0.0006963	0.1842	b1739	osmE	-13.14	0.065080	250 -- 260	194 -- 204	osmotically-inducible lipoprotein	_____________249_________261\n_____________\|___________\|\n5'-GAA...AACCA___________UGUAC...AGC-3'\n______________UGCUGGCGGGU\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________ACGACCGCCCA\n3'-UUU...AUUAG___________CUAAA...UAG-5'\n_____________\|___________\|\n_____________205_________193\n	254 -- 260	194 -- 200	-22.742 kcal/mol	5.67651 kcal/mol	8.00138 kcal/mol	249 261@LB@ \| \|@LB@5'-GAA...AACCA UGUAC...AGC-3'@LB@ UGCUGGCGGGU@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ ACGACCGCCCA@LB@3'-UUU...AUUAG CUAAA...UAG-5'@LB@ \| \|@LB@ 205 193@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -22.742 kcal/mol@LB@Unfolding Energy - mRNA 5.67651 kcal/mol@LB@Unfolding Energy - sRNA 8.00138 kcal/mol@LB@@LB@Position - mRNA 250 -- 260@LB@Position - sRNA 194 -- 204@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 194 -- 200@LB@
12	0.0007005	0.1842	b1101	ptsG	-16.86	0.011310	173 -- 192	168 -- 187	fused glucose-specific PTS enzymes: IIB component/IIC component	_____________172__________________193\n_____________\|____________________\|\n5'-CAU...AAAAA_____C________GA____UCUCA...GUU-3'\n______________GCACC_AUACUCAG__GCAC\n______________:\|\|\|\|_\|\|\|\|\|\|\|\|__:\|\|\|\n______________UGUGG_UAUGAGUC__UGUG\n3'-UUU...UAAAA_____U________AG____UACUA...UAG-5'\n_____________\|____________________\|\n_____________188__________________167\n	180 -- 186	174 -- 180	-27.3381 kcal/mol	3.90127 kcal/mol	4.88067 kcal/mol	172 193@LB@ \| \|@LB@5'-CAU...AAAAA C GA UCUCA...GUU-3'@LB@ GCACC AUACUCAG GCAC@LB@ :\|\|\|\| \|\|\|\|\|\|\|\| :\|\|\|@LB@ UGUGG UAUGAGUC UGUG@LB@3'-UUU...UAAAA U AG UACUA...UAG-5'@LB@ \| \|@LB@ 188 167@LB@@LB@@LB@Energy -16.86 kcal/mol@LB@Hybridization Energy -27.3381 kcal/mol@LB@Unfolding Energy - mRNA 3.90127 kcal/mol@LB@Unfolding Energy - sRNA 4.88067 kcal/mol@LB@@LB@Position - mRNA 173 -- 192@LB@Position - sRNA 168 -- 187@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 174 -- 180@LB@
13	0.0007116	0.1842	b3052	hldE	-13.53	0.054228	111 -- 134	141 -- 169	heptose 7-phosphate kinase and heptose 1-phosphate adenyltransferase	_____________110______________135\n_____________\|________________\|\n5'-GCG...CGUGA________________CUGGC...CGC-3'\n______________AC_UGGUGCGGGCAAG\n______________\|\|_\|\|:\|\|\|:\|\|\|\|\|\|\n______________UG_ACUACGUCCGUUC\n3'-UUU...CAGUG__U_____________AGUUG...UAG-5'\n_____________\|________________\|\n_____________170______________140\n	119 -- 125	154 -- 160	-22.7709 kcal/mol	5.4675 kcal/mol	7.07904 kcal/mol	110 135@LB@ \| \|@LB@5'-GCG...CGUGA CUGGC...CGC-3'@LB@ AC UGGUGCGGGCAAG@LB@ \|\| \|\|:\|\|\|:\|\|\|\|\|\|@LB@ UG ACUACGUCCGUUC@LB@3'-UUU...CAGUG U AGUUG...UAG-5'@LB@ \| \|@LB@ 170 140@LB@@LB@@LB@Energy -13.53 kcal/mol@LB@Hybridization Energy -22.7709 kcal/mol@LB@Unfolding Energy - mRNA 5.4675 kcal/mol@LB@Unfolding Energy - sRNA 7.07904 kcal/mol@LB@@LB@Position - mRNA 111 -- 134@LB@Position - sRNA 141 -- 169@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 154 -- 160@LB@
14	0.00083	0.1886	b2721	hycE	-15.91	0.017607	169 -- 185	190 -- 205	hydrogenase 3 large subunit	_____________168_______________186\n_____________\|_________________\|\n5'-UUC...UCUCC__________C______AAAGA...UGA-3'\n______________UUGCUGGCGG_GUGAUU\n______________:\|\|\|\|\|\|\|\|\|_\|\|\|\|\|\|\n______________GACGACCGCC_CACUAA\n3'-UUU...UAUUA_________________AAUGU...UAG-5'\n_____________\|_________________\|\n_____________206_______________189\n	172 -- 178	196 -- 202	-26.9802 kcal/mol	6.4269 kcal/mol	9.06848 kcal/mol	168 186@LB@ \| \|@LB@5'-UUC...UCUCC C AAAGA...UGA-3'@LB@ UUGCUGGCGG GUGAUU@LB@ :\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GACGACCGCC CACUAA@LB@3'-UUU...UAUUA AAUGU...UAG-5'@LB@ \| \|@LB@ 206 189@LB@@LB@@LB@Energy -15.91 kcal/mol@LB@Hybridization Energy -26.9802 kcal/mol@LB@Unfolding Energy - mRNA 6.4269 kcal/mol@LB@Unfolding Energy - sRNA 9.06848 kcal/mol@LB@@LB@Position - mRNA 169 -- 185@LB@Position - sRNA 190 -- 205@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 196 -- 202@LB@
16	0.0008966	0.1886	b0807	rlmF	-16.29	0.014793	117 -- 160	51 -- 97	23S rRNA m(6)A1618 methyltransferase SAM-dependent	_____________116_____________________________________________161\n_____________\|_______________________________________________\|\n5'-AUU...UUAAG___U_____AA______A_______________U__A_C________UUAUG...UCC-3'\n______________GUU_UGGGG____UGAU_AACGCAGCCAG_AUA_UU_C_CUGUCGCG\n______________\|\|\|_\|\|\|\|:____\|:\|:_\|\|\|\|\|\|:\|\|\|\|_\|:\|_:\|_\|_\|\|\|\|\|\|\|\|\n______________CAA_ACCCU____AUUG_UUGCGUUGGUC_UGU_GA_G_GACAGCGC\n3'-UUU...AUUAG___C_____GCGA____G___________G___U__A_C________CAUUU...UAG-5'\n_____________\|_______________________________________________\|\n_____________98______________________________________________50\n	154 -- 160	51 -- 57	-44.7843 kcal/mol	10.0752 kcal/mol	25.3667 kcal/mol	116 161@LB@ \| \|@LB@5'-AUU...UUAAG U AA A U A C UUAUG...UCC-3'@LB@ GUU UGGGG UGAU AACGCAGCCAG AUA UU C CUGUCGCG@LB@ \|\|\| \|\|\|\|: \|:\|: \|\|\|\|\|\|:\|\|\|\| \|:\| :\| \| \|\|\|\|\|\|\|\|@LB@ CAA ACCCU AUUG UUGCGUUGGUC UGU GA G GACAGCGC@LB@3'-UUU...AUUAG C GCGA G G U A C CAUUU...UAG-5'@LB@ \| \|@LB@ 98 50@LB@@LB@@LB@Energy -16.29 kcal/mol@LB@Hybridization Energy -44.7843 kcal/mol@LB@Unfolding Energy - mRNA 10.0752 kcal/mol@LB@Unfolding Energy - sRNA 25.3667 kcal/mol@LB@@LB@Position - mRNA 117 -- 160@LB@Position - sRNA 51 -- 97@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 51 -- 57@LB@
17	0.001014	0.2007	b4032	malG	-14.09	0.041561	127 -- 139	193 -- 205	maltose transporter subunit	_____________126___________140\n_____________\|_____________\|\n5'-CGU...UCUUC_____________CGCUG...UGG-3'\n______________CUGCUGGUGGGUG\n______________\|\|\|\|\|\|\|:\|\|\|\|\|\n______________GACGACCGCCCAC\n3'-UUU...UAUUA_____________UAAAA...UAG-5'\n_____________\|_____________\|\n_____________206___________192\n	132 -- 138	194 -- 200	-26.9183 kcal/mol	7.69341 kcal/mol	9.06058 kcal/mol	126 140@LB@ \| \|@LB@5'-CGU...UCUUC CGCUG...UGG-3'@LB@ CUGCUGGUGGGUG@LB@ \|\|\|\|\|\|\|:\|\|\|\|\|@LB@ GACGACCGCCCAC@LB@3'-UUU...UAUUA UAAAA...UAG-5'@LB@ \| \|@LB@ 206 192@LB@@LB@@LB@Energy -14.09 kcal/mol@LB@Hybridization Energy -26.9183 kcal/mol@LB@Unfolding Energy - mRNA 7.69341 kcal/mol@LB@Unfolding Energy - sRNA 9.06058 kcal/mol@LB@@LB@Position - mRNA 127 -- 139@LB@Position - sRNA 193 -- 205@LB@Position Seed - mRNA 132 -- 138@LB@Position Seed - sRNA 194 -- 200@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching