Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
42	0.0009586	0.08031	b3747	kup	-11.44	0.134185	159 -- 185	49 -- 77	potassium transporter	_____________158___________________________186\n_____________\|_____________________________\|\n5'-AAA...GCCAA_______A________U___AUA______ACGAA...GUG-3'\n______________GGGACUA_GCACA_CA_UUC____UUUCA\n______________::\|\|\|\|\|_:\|\|\|\|_\|\|_\|\|\|____\|\|\|\|\|\n______________UUCUGAU_UGUGU_GU_AAG____AAAGU\n3'-UUU...CCCGU_______G_____C__U___CAAC_____GAGUC...GCA-5'\n_____________\|_____________________________\|\n_____________78____________________________48\n	159 -- 165	71 -- 77	-19.3471 kcal/mol	4.22429 kcal/mol	3.68465 kcal/mol	158 186@LB@ \| \|@LB@5'-AAA...GCCAA A U AUA ACGAA...GUG-3'@LB@ GGGACUA GCACA CA UUC UUUCA@LB@ ::\|\|\|\|\| :\|\|\|\| \|\| \|\|\| \|\|\|\|\|@LB@ UUCUGAU UGUGU GU AAG AAAGU@LB@3'-UUU...CCCGU G C U CAAC GAGUC...GCA-5'@LB@ \| \|@LB@ 78 48@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -19.3471 kcal/mol@LB@Unfolding Energy - mRNA 4.22429 kcal/mol@LB@Unfolding Energy - sRNA 3.68465 kcal/mol@LB@@LB@Position - mRNA 159 -- 185@LB@Position - sRNA 49 -- 77@LB@Position Seed - mRNA 159 -- 165@LB@Position Seed - sRNA 71 -- 77@LB@
143	0.006558	0.1605	b0161	degP	-10.78	0.178564	159 -- 170	58 -- 69	serine endoprotease (protease Do) membrane-associated	_____________158__________171\n_____________\|____________\|\n5'-AUU...GAAGA____________UGCGU...CGA-3'\n______________ACACAGCAAUUU\n______________\|\|\|\|\|\|\|\|\|\|\|:\n______________UGUGUCGUUAAG\n3'-UUU...UGAUG____________CAACA...GCA-5'\n_____________\|____________\|\n_____________70___________57\n	164 -- 170	58 -- 64	-16.5275 kcal/mol	2.62124 kcal/mol	3.12494 kcal/mol	158 171@LB@ \| \|@LB@5'-AUU...GAAGA UGCGU...CGA-3'@LB@ ACACAGCAAUUU@LB@ \|\|\|\|\|\|\|\|\|\|\|:@LB@ UGUGUCGUUAAG@LB@3'-UUU...UGAUG CAACA...GCA-5'@LB@ \| \|@LB@ 70 57@LB@@LB@@LB@Energy -10.78 kcal/mol@LB@Hybridization Energy -16.5275 kcal/mol@LB@Unfolding Energy - mRNA 2.62124 kcal/mol@LB@Unfolding Energy - sRNA 3.12494 kcal/mol@LB@@LB@Position - mRNA 159 -- 170@LB@Position - sRNA 58 -- 69@LB@Position Seed - mRNA 164 -- 170@LB@Position Seed - sRNA 58 -- 64@LB@
147	0.006785	0.1624	b1920	fliY	-15.06	0.020217	159 -- 198	40 -- 75	cystine transporter subunit	_____________158______________________________________199\n_____________\|________________________________________\|\n5'-CCA...ACAAU____C_____U____ACAGACAUAACAA_________U__AUAUG...UGC-3'\n______________GGCU_UACAC_GCAA_____________CAUUCGGGG_GA\n______________\|:\|\|_:\|\|\|\|_\|\|\|\|_____________\|\|:\|\|:\|\|\|_\|\|\n______________CUGA_GUGUG_CGUU_____________GUGAGUCCC_CU\n3'-UUU...CGUUU____U_____U____AAGCAACAAA_______________AAAGG...GCA-5'\n_____________\|________________________________________\|\n_____________76_______________________________________39\n	189 -- 195	42 -- 48	-27.6268 kcal/mol	7.79206 kcal/mol	4.77786 kcal/mol	158 199@LB@ \| \|@LB@5'-CCA...ACAAU C U ACAGACAUAACAA U AUAUG...UGC-3'@LB@ GGCU UACAC GCAA CAUUCGGGG GA@LB@ \|:\|\| :\|\|\|\| \|\|\|\| \|\|:\|\|:\|\|\| \|\|@LB@ CUGA GUGUG CGUU GUGAGUCCC CU@LB@3'-UUU...CGUUU U U AAGCAACAAA AAAGG...GCA-5'@LB@ \| \|@LB@ 76 39@LB@@LB@@LB@Energy -15.06 kcal/mol@LB@Hybridization Energy -27.6268 kcal/mol@LB@Unfolding Energy - mRNA 7.79206 kcal/mol@LB@Unfolding Energy - sRNA 4.77786 kcal/mol@LB@@LB@Position - mRNA 159 -- 198@LB@Position - sRNA 40 -- 75@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 42 -- 48@LB@
9	4.743e-05	0.01855	b1204	pth	-17.38	0.004387	162 -- 190	43 -- 74	peptidyl-tRNA hydrolase	_____________161_______________________________191\n_____________\|_________________________________\|\n5'-UGG...AGUAA________________A_____ACA________ACAAA...AGC-3'\n______________ACUACGCGC__CAGUU___UGU___CACUCAGG\n______________\|\|\|\|\|:\|:\|__\|\|:\|\|___\|\|\|___\|\|\|\|\|\|\|\|\n______________UGAUGUGUG__GUUAA___ACA___GUGAGUCC\n3'-UUU...GUUUC_________UC_____GCA___AA_________CCUAA...GCA-5'\n_____________\|_________________________________\|\n_____________75________________________________42\n	184 -- 190	43 -- 49	-27.969 kcal/mol	6.24318 kcal/mol	4.35222 kcal/mol	161 191@LB@ \| \|@LB@5'-UGG...AGUAA A ACA ACAAA...AGC-3'@LB@ ACUACGCGC CAGUU UGU CACUCAGG@LB@ \|\|\|\|\|:\|:\| \|\|:\|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ UGAUGUGUG GUUAA ACA GUGAGUCC@LB@3'-UUU...GUUUC UC GCA AA CCUAA...GCA-5'@LB@ \| \|@LB@ 75 42@LB@@LB@@LB@Energy -17.38 kcal/mol@LB@Hybridization Energy -27.969 kcal/mol@LB@Unfolding Energy - mRNA 6.24318 kcal/mol@LB@Unfolding Energy - sRNA 4.35222 kcal/mol@LB@@LB@Position - mRNA 162 -- 190@LB@Position - sRNA 43 -- 74@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 43 -- 49@LB@
82	0.00343	0.1462	b4043	lexA	-10.80	0.176998	163 -- 196	40 -- 72	transcriptional repressor of SOS regulon	_____________162________________________________197\n_____________\|__________________________________\|\n5'-CGC...GUAUA___U_______UAAC___AUAUA___C_______CGGAA...AGC-3'\n______________UAC_CACAGCA____UGU_____CAC_CAGGGGG\n______________\|\|\|_\|\|\|\|\|\|\|____:\|\|_____\|\|\|_\|\|\|\|\|\|:\n______________AUG_GUGUCGU____GCA_____GUG_GUCCCCU\n3'-UUU...UUCUG___U_______UAA____ACAAA___A_______AAAGG...GCA-5'\n_____________\|__________________________________\|\n_____________73_________________________________39\n	190 -- 196	40 -- 46	-30.123 kcal/mol	14.5591 kcal/mol	4.76217 kcal/mol	162 197@LB@ \| \|@LB@5'-CGC...GUAUA U UAAC AUAUA C CGGAA...AGC-3'@LB@ UAC CACAGCA UGU CAC CAGGGGG@LB@ \|\|\| \|\|\|\|\|\|\| :\|\| \|\|\| \|\|\|\|\|\|:@LB@ AUG GUGUCGU GCA GUG GUCCCCU@LB@3'-UUU...UUCUG U UAA ACAAA A AAAGG...GCA-5'@LB@ \| \|@LB@ 73 39@LB@@LB@@LB@Energy -10.80 kcal/mol@LB@Hybridization Energy -30.123 kcal/mol@LB@Unfolding Energy - mRNA 14.5591 kcal/mol@LB@Unfolding Energy - sRNA 4.76217 kcal/mol@LB@@LB@Position - mRNA 163 -- 196@LB@Position - sRNA 40 -- 72@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 40 -- 46@LB@
124	0.005471	0.1553	b1249	clsA	-8.47	0.418250	164 -- 196	34 -- 71	cardiolipin synthase 1	_____________163____________________________________197\n_____________\|______________________________________\|\n5'-GUC...CGUAA__U____A____G__C_______AAA____________AUCUA...CAG-3'\n______________AC_CAUA_CAAU_CG___UUUCA______GGAUUUCUA\n______________\|\|_\|\|:\|_\|\|\|\|_\|\|___\|\|\|\|\|______\|\|\|\|\|\|\|:\|\n______________UG_GUGU_GUUA_GC___AAAGU______CCUAAAGGU\n3'-UUU...UCUGA__U____C____A__AAC_____GAGUCC_________ACGAA...GCA-5'\n_____________\|______________________________________\|\n_____________72_____________________________________33\n	190 -- 196	34 -- 40	-20.3655 kcal/mol	7.10457 kcal/mol	4.79237 kcal/mol	163 197@LB@ \| \|@LB@5'-GUC...CGUAA U A G C AAA AUCUA...CAG-3'@LB@ AC CAUA CAAU CG UUUCA GGAUUUCUA@LB@ \|\| \|\|:\| \|\|\|\| \|\| \|\|\|\|\| \|\|\|\|\|\|\|:\|@LB@ UG GUGU GUUA GC AAAGU CCUAAAGGU@LB@3'-UUU...UCUGA U C A AAC GAGUCC ACGAA...GCA-5'@LB@ \| \|@LB@ 72 33@LB@@LB@@LB@Energy -8.47 kcal/mol@LB@Hybridization Energy -20.3655 kcal/mol@LB@Unfolding Energy - mRNA 7.10457 kcal/mol@LB@Unfolding Energy - sRNA 4.79237 kcal/mol@LB@@LB@Position - mRNA 164 -- 196@LB@Position - sRNA 34 -- 71@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 34 -- 40@LB@
105	0.004683	0.1538	b3349	slyD	-10.61	0.192215	166 -- 197	39 -- 73	FKBP-type peptidyl prolyl cis-trans isomerase (rotamase)	_____________165_________________________________198\n_____________\|___________________________________\|\n5'-UGU...ACAAU___________U____UUCCCAU________A___AUCAU...ACU-3'\n______________CUGCGC_CA_C_AUUC________GCUCAGG_GAU\n______________\|\|:\|:\|_\|\|_\|_\|\|\|\|________:\|\|\|\|\|\|_\|\|\|\n______________GAUGUG_GU_G_UAAG________UGAGUCC_CUA\n3'-UUU...UUUCU______U__C_U____CAACAAAG_______C___AAGGU...GCA-5'\n_____________\|___________________________________\|\n_____________74__________________________________38\n	187 -- 193	43 -- 49	-23.2642 kcal/mol	7.88699 kcal/mol	4.77295 kcal/mol	165 198@LB@ \| \|@LB@5'-UGU...ACAAU U UUCCCAU A AUCAU...ACU-3'@LB@ CUGCGC CA C AUUC GCUCAGG GAU@LB@ \|\|:\|:\| \|\| \| \|\|\|\| :\|\|\|\|\|\| \|\|\|@LB@ GAUGUG GU G UAAG UGAGUCC CUA@LB@3'-UUU...UUUCU U C U CAACAAAG C AAGGU...GCA-5'@LB@ \| \|@LB@ 74 38@LB@@LB@@LB@Energy -10.61 kcal/mol@LB@Hybridization Energy -23.2642 kcal/mol@LB@Unfolding Energy - mRNA 7.88699 kcal/mol@LB@Unfolding Energy - sRNA 4.77295 kcal/mol@LB@@LB@Position - mRNA 166 -- 197@LB@Position - sRNA 39 -- 73@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 43 -- 49@LB@
155	0.007577	0.1668	b4364	yjjP	-9.15	0.334468	166 -- 178	62 -- 74	DUF1212 family inner membrane protein	_____________165___________179\n_____________\|_____________\|\n5'-UCA...UCUGA__A__________CGUCU...UUU-3'\n______________AC_AUACGCAGCA\n______________\|\|_\|:\|\|:\|\|\|\|\|\n______________UG_UGUGUGUCGU\n3'-UUU...GUUUC__A__________UAAGC...GCA-5'\n_____________\|_____________\|\n_____________75____________61\n	172 -- 178	62 -- 68	-14.8746 kcal/mol	2.48219 kcal/mol	3.24359 kcal/mol	165 179@LB@ \| \|@LB@5'-UCA...UCUGA A CGUCU...UUU-3'@LB@ AC AUACGCAGCA@LB@ \|\| \|:\|\|:\|\|\|\|\|@LB@ UG UGUGUGUCGU@LB@3'-UUU...GUUUC A UAAGC...GCA-5'@LB@ \| \|@LB@ 75 61@LB@@LB@@LB@Energy -9.15 kcal/mol@LB@Hybridization Energy -14.8746 kcal/mol@LB@Unfolding Energy - mRNA 2.48219 kcal/mol@LB@Unfolding Energy - sRNA 3.24359 kcal/mol@LB@@LB@Position - mRNA 166 -- 178@LB@Position - sRNA 62 -- 74@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 62 -- 68@LB@
18	0.0001516	0.02826	b2817	amiC	-14.62	0.026197	167 -- 204	31 -- 70	N-acetylmuramoyl-L-alanine amidase	_____________166______________________________________205\n_____________\|________________________________________\|\n5'-AGU...CUUGU________UUAGAUUUC___________A__GG_______CAGGA...UCA-3'\n______________UACACAGC_________UUUUGCUCGGG_GA____CAUGU\n______________:\|\|\|\|\|\|\|_________\|\|\|::\|\|\|:\|\|_\|\|____\|\|\|\|:\n______________GUGUGUCG_________AAAGUGAGUCC_CU____GUACG\n3'-UUU...CUGAU________UUAAGCAAC___________C__AAAG_____AAUAU...GCA-5'\n_____________\|________________________________________\|\n_____________71_______________________________________30\n	188 -- 194	43 -- 49	-32.0387 kcal/mol	10.1821 kcal/mol	7.23824 kcal/mol	166 205@LB@ \| \|@LB@5'-AGU...CUUGU UUAGAUUUC A GG CAGGA...UCA-3'@LB@ UACACAGC UUUUGCUCGGG GA CAUGU@LB@ :\|\|\|\|\|\|\| \|\|\|::\|\|\|:\|\| \|\| \|\|\|\|:@LB@ GUGUGUCG AAAGUGAGUCC CU GUACG@LB@3'-UUU...CUGAU UUAAGCAAC C AAAG AAUAU...GCA-5'@LB@ \| \|@LB@ 71 30@LB@@LB@@LB@Energy -14.62 kcal/mol@LB@Hybridization Energy -32.0387 kcal/mol@LB@Unfolding Energy - mRNA 10.1821 kcal/mol@LB@Unfolding Energy - sRNA 7.23824 kcal/mol@LB@@LB@Position - mRNA 167 -- 204@LB@Position - sRNA 31 -- 70@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 43 -- 49@LB@
7	1.819e-05	0.009142	b1849	purT	-22.68	0.000026	168 -- 199	33 -- 74	phosphoribosylglycinamide formyltransferase 2	_____________167________________________________________200\n_____________\|__________________________________________\|\n5'-UUU...UUUAU________________AA__________________A_____UAUGA...GUC-3'\n______________ACUGCGCGCGG_AAUU___________UCAGGGGAU_UUCGU\n______________\|\|\|:\|:\|:\|:\|_\|\|\|\|___________\|\|\|\|\|\|\|\|\|_\|:\|:\|\n______________UGAUGUGUGUC_UUAA___________AGUCCCCUA_AGGUA\n3'-UUU...GUUUC___________G____GCAACAAAGUG_________A_____CGAAU...GCA-5'\n_____________\|__________________________________________\|\n_____________75_________________________________________32\n	187 -- 193	39 -- 45	-34.2979 kcal/mol	6.80622 kcal/mol	4.81602 kcal/mol	167 200@LB@ \| \|@LB@5'-UUU...UUUAU AA A UAUGA...GUC-3'@LB@ ACUGCGCGCGG AAUU UCAGGGGAU UUCGU@LB@ \|\|\|:\|:\|:\|:\| \|\|\|\| \|\|\|\|\|\|\|\|\| \|:\|:\|@LB@ UGAUGUGUGUC UUAA AGUCCCCUA AGGUA@LB@3'-UUU...GUUUC G GCAACAAAGUG A CGAAU...GCA-5'@LB@ \| \|@LB@ 75 32@LB@@LB@@LB@Energy -22.68 kcal/mol@LB@Hybridization Energy -34.2979 kcal/mol@LB@Unfolding Energy - mRNA 6.80622 kcal/mol@LB@Unfolding Energy - sRNA 4.81602 kcal/mol@LB@@LB@Position - mRNA 168 -- 199@LB@Position - sRNA 33 -- 74@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 39 -- 45@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