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
61	0.006025	0.3261	b4330	yjiH	-10.68	0.204041	214 -- 227	80 -- 92	nucleoside recognition pore and gate family putative inner membrane transporter	_____________213______228\n_____________\|________\|\n5'-ACU...ACAAG________GUAGC...CCG-3'\n______________GGGAUGCU\n______________\|\|\|\|:\|\|\|\n______________CCCUGCGA\n3'-UUU...CAACA________AUUGG...UAG-5'\n_____________\|________\|\n_____________93_______79\n	215 -- 221	85 -- 91	-14.2816 kcal/mol	2.08889 kcal/mol	5.76908 kcal/mol	213 228@LB@ \| \|@LB@5'-ACU...ACAAG GUAGC...CCG-3'@LB@ GGGAUGCU@LB@ \|\|\|\|:\|\|\|@LB@ CCCUGCGA@LB@3'-UUU...CAACA AUUGG...UAG-5'@LB@ \| \|@LB@ 93 79@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -14.2816 kcal/mol@LB@Unfolding Energy - mRNA 2.08889 kcal/mol@LB@Unfolding Energy - sRNA 5.76908 kcal/mol@LB@@LB@Position - mRNA 214 -- 227@LB@Position - sRNA 80 -- 92@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 85 -- 91@LB@
156	0.01739	0.3749	b4332	yjiJ	-7.83	0.625728	95 -- 115	80 -- 101	DUF1228 family putative inner membrane MFS superfamily transporter	_____________94_______116\n_____________\|________\|\n5'-AAC...GGUUU________ACAUC...UUU-3'\n______________GUCGCAUA\n______________\|\|\|:\|\|:\|\n______________CAGUGUGU\n3'-UUU...UGAGU________ACUAC...UAG-5'\n_____________\|________\|\n_____________102______79\n	23 -- 29	167 -- 173	-9.78459 kcal/mol	1.62979 kcal/mol	0.409692 kcal/mol	94 116@LB@ \| \|@LB@5'-AAC...GGUUU ACAUC...UUU-3'@LB@ GUCGCAUA@LB@ \|\|\|:\|\|:\|@LB@ CAGUGUGU@LB@3'-UUU...UGAGU ACUAC...UAG-5'@LB@ \| \|@LB@ 102 79@LB@@LB@@LB@Energy -7.83 kcal/mol@LB@Hybridization Energy -9.78459 kcal/mol@LB@Unfolding Energy - mRNA 1.62979 kcal/mol@LB@Unfolding Energy - sRNA 0.409692 kcal/mol@LB@@LB@Position - mRNA 95 -- 115@LB@Position - sRNA 80 -- 101@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 167 -- 173@LB@
64	0.006252	0.3261	b3195	mlaF	-10.58	0.212925	52 -- 62	81 -- 91	ABC transporter maintaining OM lipid asymmetry ATP-binding protein	_____________51____________________________________63\n_____________\|_____________________________________\|\n5'-UUU...UUCAA___UAA___GA______________AAAA__A_____AGACG...GAG-3'\n______________GGU___AUU__GCGCC_AUGCUUAG____UC_ACGCA\n______________\|\|\|___\|\|\|__:\|:\|\|_\|\|:\|\|:\|\|____\|\|_\|\|:\|\|\n______________CCA___UAA__UGUGG_UAUGAGUC____AG_UGUGU\n3'-UUU...ACCGC___C_____AA_____U____________________ACUAC...UAG-5'\n_____________\|_____________________________________\|\n_____________92____________________________________80\n	166 -- 172	174 -- 180	-23.2269 kcal/mol	9.4943 kcal/mol	5.22711 kcal/mol	51 63@LB@ \| \|@LB@5'-UUU...UUCAA UAA GA AAAA A AGACG...GAG-3'@LB@ GGU AUU GCGCC AUGCUUAG UC ACGCA@LB@ \|\|\| \|\|\| :\|:\|\| \|\|:\|\|:\|\| \|\| \|\|:\|\|@LB@ CCA UAA UGUGG UAUGAGUC AG UGUGU@LB@3'-UUU...ACCGC C AA U ACUAC...UAG-5'@LB@ \| \|@LB@ 92 80@LB@@LB@@LB@Energy -10.58 kcal/mol@LB@Hybridization Energy -23.2269 kcal/mol@LB@Unfolding Energy - mRNA 9.4943 kcal/mol@LB@Unfolding Energy - sRNA 5.22711 kcal/mol@LB@@LB@Position - mRNA 52 -- 62@LB@Position - sRNA 81 -- 91@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 174 -- 180@LB@
114	0.01268	0.3575	b0888	trxB	-13.24	0.061992	5 -- 14	83 -- 92	thioredoxin reductase FAD/NAD(P)-binding	_____________4__________15\n_____________\|__________\|\n_______5'-AACA__________UUCAU...UGC-3'\n______________GGGGCGUUUA\n______________\|\|\|:\|\|:\|\|\|\n______________CCCUGCGAAU\n3'-UUU...CAACA__________UGGUU...UAG-5'\n_____________\|__________\|\n_____________93_________82\n	7 -- 13	84 -- 90	-15.9307 kcal/mol	0.512019 kcal/mol	6.69187 kcal/mol	4 15@LB@ \| \|@LB@ 5'-AACA UUCAU...UGC-3'@LB@ GGGGCGUUUA@LB@ \|\|\|:\|\|:\|\|\|@LB@ CCCUGCGAAU@LB@3'-UUU...CAACA UGGUU...UAG-5'@LB@ \| \|@LB@ 93 82@LB@@LB@@LB@Energy -13.24 kcal/mol@LB@Hybridization Energy -15.9307 kcal/mol@LB@Unfolding Energy - mRNA 0.512019 kcal/mol@LB@Unfolding Energy - sRNA 6.69187 kcal/mol@LB@@LB@Position - mRNA 5 -- 14@LB@Position - sRNA 83 -- 92@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 84 -- 90@LB@
143	0.01531	0.3575	b1641	slyB	-10.83	0.190300	158 -- 167	83 -- 92	outer membrane lipoprotein	_____________157____________________________168\n_____________\|______________________________\|\n5'-CCG...UCACA_______U______UGAC____AGG_____UUGCG...AAG-3'\n______________UAUGCCA_AUACUU____CAUG___GAUGC\n______________\|\|::\|\|\|_\|\|\|\|\|:____\|\|::___\|\|\|\|\|\n______________AUGUGGU_UAUGAG____GUGU___CUACG\n3'-UUU...CUAAA______________UCA_____GUA_____UCCGU...UAG-5'\n_____________\|______________________________\|\n_____________93_____________________________82\n	135 -- 141	182 -- 188	-20.8318 kcal/mol	7.22081 kcal/mol	7.72227 kcal/mol	157 168@LB@ \| \|@LB@5'-CCG...UCACA U UGAC AGG UUGCG...AAG-3'@LB@ UAUGCCA AUACUU CAUG GAUGC@LB@ \|\|::\|\|\| \|\|\|\|\|: \|\|:: \|\|\|\|\|@LB@ AUGUGGU UAUGAG GUGU CUACG@LB@3'-UUU...CUAAA UCA GUA UCCGU...UAG-5'@LB@ \| \|@LB@ 93 82@LB@@LB@@LB@Energy -10.83 kcal/mol@LB@Hybridization Energy -20.8318 kcal/mol@LB@Unfolding Energy - mRNA 7.22081 kcal/mol@LB@Unfolding Energy - sRNA 7.72227 kcal/mol@LB@@LB@Position - mRNA 158 -- 167@LB@Position - sRNA 83 -- 92@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 182 -- 188@LB@
196	0.0235	0.3833	b3105	yhaJ	-11.17	0.163135	292 -- 299	86 -- 93	LysR family putative transcriptional regulator	_____________291______300\n_____________\|________\|\n5'-CGG...UGAGC________G-3'\n______________UGGGACGC\n______________\|\|\|\|\|\|\|\|\n______________ACCCUGCG\n3'-UUU...GCAAC________AAUUG...UAG-5'\n_____________\|________\|\n_____________94_______85\n	293 -- 299	86 -- 92	-14.7688 kcal/mol	2.10679 kcal/mol	4.21973 kcal/mol	291 300@LB@ \| \|@LB@5'-CGG...UGAGC G-3'@LB@ UGGGACGC@LB@ \|\|\|\|\|\|\|\|@LB@ ACCCUGCG@LB@3'-UUU...GCAAC AAUUG...UAG-5'@LB@ \| \|@LB@ 94 85@LB@@LB@@LB@Energy -11.17 kcal/mol@LB@Hybridization Energy -14.7688 kcal/mol@LB@Unfolding Energy - mRNA 2.10679 kcal/mol@LB@Unfolding Energy - sRNA 4.21973 kcal/mol@LB@@LB@Position - mRNA 292 -- 299@LB@Position - sRNA 86 -- 93@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 86 -- 92@LB@
197	0.02355	0.3833	b2764	cysJ	-10.17	0.255883	3 -- 30	98 -- 123	sulfite reductase alpha subunit flavoprotein	_____________2________31\n_____________\|________\|\n5'-UUC...AACAG________ACUGG...UUG-3'\n______________CUUUGCUU\n______________\|:\|\|\|\|\|\|\n______________GGAACGAA\n3'-UUU...GUGGG________GUAG-5'\n_____________\|________\|\n_____________124______97\n	176 -- 182	5 -- 11	-8.59037 kcal/mol	0.881795 kcal/mol	1.04254 kcal/mol	2 31@LB@ \| \|@LB@5'-UUC...AACAG ACUGG...UUG-3'@LB@ CUUUGCUU@LB@ \|:\|\|\|\|\|\|@LB@ GGAACGAA@LB@3'-UUU...GUGGG GUAG-5'@LB@ \| \|@LB@ 124 97@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -8.59037 kcal/mol@LB@Unfolding Energy - mRNA 0.881795 kcal/mol@LB@Unfolding Energy - sRNA 1.04254 kcal/mol@LB@@LB@Position - mRNA 3 -- 30@LB@Position - sRNA 98 -- 123@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 5 -- 11@LB@
38	0.003319	0.2912	b3073	patA	-6.81	0.814367	213 -- 222	107 -- 116	putrescine:2-oxoglutaric acid aminotransferase PLP-dependent	_____________212________223\n_____________\|__________\|\n5'-CAU...GGUUA__________CAUCG...CAC-3'\n______________CCUUCGAGCG\n______________\|\|\|\|\|:\|\|\|:\n______________GGAAGUUCGU\n3'-UUU...AGUCA__________ACCAA...UAG-5'\n_____________\|__________\|\n_____________117________106\n	216 -- 222	107 -- 113	-14.0153 kcal/mol	3.04157 kcal/mol	5.58351 kcal/mol	212 223@LB@ \| \|@LB@5'-CAU...GGUUA CAUCG...CAC-3'@LB@ CCUUCGAGCG@LB@ \|\|\|\|\|:\|\|\|:@LB@ GGAAGUUCGU@LB@3'-UUU...AGUCA ACCAA...UAG-5'@LB@ \| \|@LB@ 117 106@LB@@LB@@LB@Energy -6.81 kcal/mol@LB@Hybridization Energy -14.0153 kcal/mol@LB@Unfolding Energy - mRNA 3.04157 kcal/mol@LB@Unfolding Energy - sRNA 5.58351 kcal/mol@LB@@LB@Position - mRNA 213 -- 222@LB@Position - sRNA 107 -- 116@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 107 -- 113@LB@
119	0.013	0.3575	b0801	ybiC	-16.26	0.015008	158 -- 253	108 -- 187	putative dehydrogenase	_____________157____________________________________________________________________________________________254\n_____________\|______________________________________________________________________________________________\|\n5'-GCU...AUAAA_____AA__AA______ACAUAAA_____________CAU_____A__________G_UUUGAUGCUCAGAC_____________UA_______UGUAU...UUG-3'\n______________AAUAC__CA__CACAUA_______CAGG__AGUUAAC____GGAA__GUGGUCAUC_C______________GCUGCA_CAGUUU__UUCAGGC\n______________\|\|\|\|\|__\|\|__\|\|\|\|:\|_______\|\|\|\|__\|\|\|:\|\|\|____:\|\|\|__\|:\|\|\|\|\|\|\|_\|______________:\|\|\|\|\|_\|\|\|\|::__\|\|\|\|:\|\|\n______________UUAUG__GU__GUGUGU_______GUCC__UCAGUUG____UCUU__CGCCAGUAG_G______________UGACGU_GUCAGG__AAGUUCG\n3'-UUU...UGUGG_____A___CA______ACUAC______GU_______AAAG____AA_________G_____________________A_______________UACCA...UAG-5'\n_____________\|______________________________________________________________________________________________\|\n_____________188____________________________________________________________________________________________107\n	247 -- 253	108 -- 114	-56.5044 kcal/mol	18.8914 kcal/mol	26.5178 kcal/mol	157 254@LB@ \| \|@LB@5'-GCU...AUAAA AA AA ACAUAAA CAU A G UUUGAUGCUCAGAC UA UGUAU...UUG-3'@LB@ AAUAC CA CACAUA CAGG AGUUAAC GGAA GUGGUCAUC C GCUGCA CAGUUU UUCAGGC@LB@ \|\|\|\|\| \|\| \|\|\|\|:\| \|\|\|\| \|\|\|:\|\|\| :\|\|\| \|:\|\|\|\|\|\|\| \| :\|\|\|\|\| \|\|\|\|:: \|\|\|\|:\|\|@LB@ UUAUG GU GUGUGU GUCC UCAGUUG UCUU CGCCAGUAG G UGACGU GUCAGG AAGUUCG@LB@3'-UUU...UGUGG A CA ACUAC GU AAAG AA G A UACCA...UAG-5'@LB@ \| \|@LB@ 188 107@LB@@LB@@LB@Energy -16.26 kcal/mol@LB@Hybridization Energy -56.5044 kcal/mol@LB@Unfolding Energy - mRNA 18.8914 kcal/mol@LB@Unfolding Energy - sRNA 26.5178 kcal/mol@LB@@LB@Position - mRNA 158 -- 253@LB@Position - sRNA 108 -- 187@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 108 -- 114@LB@
167	0.01932	0.3812	b2912	fau	-13.57	0.053124	153 -- 189	109 -- 152	5-formyltetrahydrofolate cyclo-ligase family protein	_____________152__________190\n_____________\|____________\|\n5'-GAA...UGAGC____________GUCCG...UGG-3'\n______________AUGCUCGGUC_C\n______________\|\|:\|\|\|:\|\|\|_\|\n______________UAUGAGUCAG_G\n3'-UUU...GUGGU__________U_UGUAC...UAG-5'\n_____________\|____________\|\n_____________153__________108\n	31 -- 37	172 -- 178	-13.9133 kcal/mol	3.57919 kcal/mol	0.28482 kcal/mol	152 190@LB@ \| \|@LB@5'-GAA...UGAGC GUCCG...UGG-3'@LB@ AUGCUCGGUC C@LB@ \|\|:\|\|\|:\|\|\| \|@LB@ UAUGAGUCAG G@LB@3'-UUU...GUGGU U UGUAC...UAG-5'@LB@ \| \|@LB@ 153 108@LB@@LB@@LB@Energy -13.57 kcal/mol@LB@Hybridization Energy -13.9133 kcal/mol@LB@Unfolding Energy - mRNA 3.57919 kcal/mol@LB@Unfolding Energy - sRNA 0.28482 kcal/mol@LB@@LB@Position - mRNA 153 -- 189@LB@Position - sRNA 109 -- 152@LB@Position Seed - mRNA 31 -- 37@LB@Position Seed - sRNA 172 -- 178@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