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
91	0.01018	0.3575	b1660	ydhC	-16.12	0.016020	223 -- 255	172 -- 209	putative arabinose efflux transporter	_____________222_____________________________________256\n_____________\|_______________________________________\|\n5'-GAA...AUUUU______G_________________A______________UUCUG...AGG-3'\n______________UAGUCU_GCUGGCGGGU____UUG_GC__GUACUCGGUU\n______________\|\|:\|\|\|_\|\|\|\|\|\|\|\|\|\|____\|\|:_:\|__:\|\|\|\|\|:\|\|:\n______________AUUAGA_CGACCGCCCA____AAU_UG__UAUGAGUCAG\n3'-UUU...UCCAU_________________CUAA___G__GU__________UGUGU...UAG-5'\n_____________\|_______________________________________\|\n_____________210_____________________________________171\n	249 -- 255	172 -- 178	-38.0361 kcal/mol	10.2504 kcal/mol	15.0669 kcal/mol	222 256@LB@ \| \|@LB@5'-GAA...AUUUU G A UUCUG...AGG-3'@LB@ UAGUCU GCUGGCGGGU UUG GC GUACUCGGUU@LB@ \|\|:\|\|\| \|\|\|\|\|\|\|\|\|\| \|\|: :\| :\|\|\|\|\|:\|\|:@LB@ AUUAGA CGACCGCCCA AAU UG UAUGAGUCAG@LB@3'-UUU...UCCAU CUAA G GU UGUGU...UAG-5'@LB@ \| \|@LB@ 210 171@LB@@LB@@LB@Energy -16.12 kcal/mol@LB@Hybridization Energy -38.0361 kcal/mol@LB@Unfolding Energy - mRNA 10.2504 kcal/mol@LB@Unfolding Energy - sRNA 15.0669 kcal/mol@LB@@LB@Position - mRNA 223 -- 255@LB@Position - sRNA 172 -- 209@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 172 -- 178@LB@
81	0.008673	0.3575	b1683	sufB	-9.84	0.294156	211 -- 257	124 -- 171	component of SufBCD Fe-S cluster assembly scaffold	_____________210_______________258\n_____________\|_________________\|\n5'-GUU...AAUCA________AAUU_____ACCCU...AGC-3'\n______________GAUAUUCA____UCACA\n______________:\|\|\|:\|\|\|____\|\|\|\|\|\n______________UUAUGAGU____AGUGU\n3'-UUU...UGUGG________C________GUACU...UAG-5'\n_____________\|_________________\|\n_____________172_______________123\n	127 -- 133	175 -- 181	-8.93573 kcal/mol	1.46068 kcal/mol	0.409577 kcal/mol	210 258@LB@ \| \|@LB@5'-GUU...AAUCA AAUU ACCCU...AGC-3'@LB@ GAUAUUCA UCACA@LB@ :\|\|\|:\|\|\| \|\|\|\|\|@LB@ UUAUGAGU AGUGU@LB@3'-UUU...UGUGG C GUACU...UAG-5'@LB@ \| \|@LB@ 172 123@LB@@LB@@LB@Energy -9.84 kcal/mol@LB@Hybridization Energy -8.93573 kcal/mol@LB@Unfolding Energy - mRNA 1.46068 kcal/mol@LB@Unfolding Energy - sRNA 0.409577 kcal/mol@LB@@LB@Position - mRNA 211 -- 257@LB@Position - sRNA 124 -- 171@LB@Position Seed - mRNA 127 -- 133@LB@Position Seed - sRNA 175 -- 181@LB@
177	0.02028	0.3833	b1732	katE	-12.45	0.090323	227 -- 246	168 -- 187	catalase HPII heme d-containing	_____________226___________________247\n_____________\|_____________________\|\n5'-UGG...AACCC_______C__________C__UACAC...ACG-3'\n______________ACAUCAG_AC_CAGUCAC_AC\n______________\|\|\|:\|\|:_\|\|_\|\|\|\|\|\|\|_\|\|\n______________UGUGGUU_UG_GUCAGUG_UG\n3'-UUU...UAAAA_______A__A__________UACUA...UAG-5'\n_____________\|_____________________\|\n_____________188___________________167\n	237 -- 243	170 -- 176	-19.9766 kcal/mol	1.23864 kcal/mol	4.88067 kcal/mol	226 247@LB@ \| \|@LB@5'-UGG...AACCC C C UACAC...ACG-3'@LB@ ACAUCAG AC CAGUCAC AC@LB@ \|\|\|:\|\|: \|\| \|\|\|\|\|\|\| \|\|@LB@ UGUGGUU UG GUCAGUG UG@LB@3'-UUU...UAAAA A A UACUA...UAG-5'@LB@ \| \|@LB@ 188 167@LB@@LB@@LB@Energy -12.45 kcal/mol@LB@Hybridization Energy -19.9766 kcal/mol@LB@Unfolding Energy - mRNA 1.23864 kcal/mol@LB@Unfolding Energy - sRNA 4.88067 kcal/mol@LB@@LB@Position - mRNA 227 -- 246@LB@Position - sRNA 168 -- 187@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 170 -- 176@LB@
77	0.007981	0.3458	b1738	chbB	-9.80	0.299184	58 -- 71	174 -- 187	N N'-diacetylchitobiose-specific enzyme IIB component of PTS	_____________57_______________________________72\n_____________\|________________________________\|\n5'-AAU...UAUAA___CAAAGAA______U_______G__U____CGUAU...CGG-3'\n______________GGU_______AUACUA_UGCUCAG_UC_AUAC\n______________\|\|\|_______\|:\|\|:\|_\|:\|\|\|\|\|_\|\|_\|:\|\|\n______________CCA_______UGUGGU_AUGAGUC_AG_UGUG\n3'-UUU...ACCGC___CUAAAA_______U_______________UACUA...UAG-5'\n_____________\|________________________________\|\n_____________188______________________________173\n	65 -- 71	174 -- 180	-20.4225 kcal/mol	4.13376 kcal/mol	5.03959 kcal/mol	57 72@LB@ \| \|@LB@5'-AAU...UAUAA CAAAGAA U G U CGUAU...CGG-3'@LB@ GGU AUACUA UGCUCAG UC AUAC@LB@ \|\|\| \|:\|\|:\| \|:\|\|\|\|\| \|\| \|:\|\|@LB@ CCA UGUGGU AUGAGUC AG UGUG@LB@3'-UUU...ACCGC CUAAAA U UACUA...UAG-5'@LB@ \| \|@LB@ 188 173@LB@@LB@@LB@Energy -9.80 kcal/mol@LB@Hybridization Energy -20.4225 kcal/mol@LB@Unfolding Energy - mRNA 4.13376 kcal/mol@LB@Unfolding Energy - sRNA 5.03959 kcal/mol@LB@@LB@Position - mRNA 58 -- 71@LB@Position - sRNA 174 -- 187@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 174 -- 180@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@
134	0.01437	0.3575	b1798	leuE	-11.20	0.161096	19 -- 44	168 -- 191	leucine efflux protein	_____________18_________________________45\n_____________\|__________________________\|\n5'-UGC...AGAAU________________UGCCGA____UACCC...AAA-3'\n______________UUUUACGCCAGUAUUU______GCAC\n______________\|\|\|\|\|\|:\|\|\|:\|\|:\|:______:\|\|\|\n______________AAAAUGUGGUUAUGAG______UGUG\n3'-UUU...CCACU________________UCAG______UACUA...UAG-5'\n_____________\|__________________________\|\n_____________192________________________167\n	26 -- 32	178 -- 184	-22.4094 kcal/mol	4.02149 kcal/mol	4.92826 kcal/mol	18 45@LB@ \| \|@LB@5'-UGC...AGAAU UGCCGA UACCC...AAA-3'@LB@ UUUUACGCCAGUAUUU GCAC@LB@ \|\|\|\|\|\|:\|\|\|:\|\|:\|: :\|\|\|@LB@ AAAAUGUGGUUAUGAG UGUG@LB@3'-UUU...CCACU UCAG UACUA...UAG-5'@LB@ \| \|@LB@ 192 167@LB@@LB@@LB@Energy -11.20 kcal/mol@LB@Hybridization Energy -22.4094 kcal/mol@LB@Unfolding Energy - mRNA 4.02149 kcal/mol@LB@Unfolding Energy - sRNA 4.92826 kcal/mol@LB@@LB@Position - mRNA 19 -- 44@LB@Position - sRNA 168 -- 191@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 178 -- 184@LB@
111	0.0122	0.3575	b1813	nudL	-9.44	0.347588	99 -- 131	174 -- 206	putative CoA pyrophosphohydrolase weak 3-phosphohydroxypyruvate phosphatase	_____________98________________________________132\n_____________\|_________________________________\|\n5'-CCU...UCUGC_____G_____UG__A__GU________GC___GAAGA...CUG-3'\n______________UCUGC_GGCGG__GA_UU__CGCCGAUA__CAG\n______________\|\|\|\|\|_\|\|\|\|\|__\|\|_\|\|__\|:\|\|:\|\|\|__\|\|\|\n______________AGACG_CCGCC__CU_AA__GUGGUUAU__GUC\n3'-UUU...AUAUU_____A_____CA__A__AU________GA___AGUGU...UAG-5'\n_____________\|_________________________________\|\n_____________207_______________________________173\n	120 -- 126	179 -- 185	-36.2385 kcal/mol	15.3331 kcal/mol	14.8345 kcal/mol	98 132@LB@ \| \|@LB@5'-CCU...UCUGC G UG A GU GC GAAGA...CUG-3'@LB@ UCUGC GGCGG GA UU CGCCGAUA CAG@LB@ \|\|\|\|\| \|\|\|\|\| \|\| \|\| \|:\|\|:\|\|\| \|\|\|@LB@ AGACG CCGCC CU AA GUGGUUAU GUC@LB@3'-UUU...AUAUU A CA A AU GA AGUGU...UAG-5'@LB@ \| \|@LB@ 207 173@LB@@LB@@LB@Energy -9.44 kcal/mol@LB@Hybridization Energy -36.2385 kcal/mol@LB@Unfolding Energy - mRNA 15.3331 kcal/mol@LB@Unfolding Energy - sRNA 14.8345 kcal/mol@LB@@LB@Position - mRNA 99 -- 131@LB@Position - sRNA 174 -- 206@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 179 -- 185@LB@
148	0.01584	0.3602	b1822	rlmA	-10.68	0.203557	148 -- 239	111 -- 186	23S rRNA m(1)G745 methyltransferase SAM-dependent	_____________147___________240\n_____________\|_____________\|\n5'-AAG...GCGUG_____C_______UUGCG...GGU-3'\n______________AUUCG_GUUACAC\n______________\|:\|\|:_\|\|:\|\|\|\|\n______________UGAGU_CAGUGUG\n3'-UUU...GGUUA_____________UACUA...UAG-5'\n_____________\|_____________\|\n_____________187___________110\n	163 -- 169	168 -- 174	-12.5288 kcal/mol	1.89227 kcal/mol	0.283892 kcal/mol	147 240@LB@ \| \|@LB@5'-AAG...GCGUG C UUGCG...GGU-3'@LB@ AUUCG GUUACAC@LB@ \|:\|\|: \|\|:\|\|\|\|@LB@ UGAGU CAGUGUG@LB@3'-UUU...GGUUA UACUA...UAG-5'@LB@ \| \|@LB@ 187 110@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -12.5288 kcal/mol@LB@Unfolding Energy - mRNA 1.89227 kcal/mol@LB@Unfolding Energy - sRNA 0.283892 kcal/mol@LB@@LB@Position - mRNA 148 -- 239@LB@Position - sRNA 111 -- 186@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 168 -- 174@LB@
126	0.01383	0.3575	b1843	yobB	-8.48	0.503741	101 -- 118	168 -- 185	C-N hydrolase family protein	_____________100____________119\n_____________\|______________\|\n5'-CCU...AACUU____AG________UUUCU...CCA-3'\n______________AUAC__AGUUACAC\n______________\|\|\|\|__\|\|\|:\|\|\|\|\n______________UAUG__UCAGUGUG\n3'-UUU...GUGGU____AG________UACUA...UAG-5'\n_____________\|______________\|\n_____________186____________167\n	112 -- 118	168 -- 174	-13.9608 kcal/mol	3.09724 kcal/mol	0.286881 kcal/mol	100 119@LB@ \| \|@LB@5'-CCU...AACUU AG UUUCU...CCA-3'@LB@ AUAC AGUUACAC@LB@ \|\|\|\| \|\|\|:\|\|\|\|@LB@ UAUG UCAGUGUG@LB@3'-UUU...GUGGU AG UACUA...UAG-5'@LB@ \| \|@LB@ 186 167@LB@@LB@@LB@Energy -8.48 kcal/mol@LB@Hybridization Energy -13.9608 kcal/mol@LB@Unfolding Energy - mRNA 3.09724 kcal/mol@LB@Unfolding Energy - sRNA 0.286881 kcal/mol@LB@@LB@Position - mRNA 101 -- 118@LB@Position - sRNA 168 -- 185@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 168 -- 174@LB@
58	0.005664	0.3247	b1878	flhE	-13.77	0.048330	266 -- 286	140 -- 162	proton seal during flagellar secretion	_____________265_____________________287\n_____________\|_______________________\|\n5'-CGU...AUGUG__________AGUGUA_______UACGC...AUC-3'\n______________GCAGGCAAGU________GGAAU\n______________\|\|\|\|\|\|\|\|\|\|________:\|\|\|\|\n______________CGUCCGUUCA________UCUUA\n3'-UUU...UACUA__________GUUGAAAG_____ACGCC...UAG-5'\n_____________\|_______________________\|\n_____________163_____________________139\n	269 -- 275	153 -- 159	-20.7539 kcal/mol	2.26514 kcal/mol	7.696 kcal/mol	265 287@LB@ \| \|@LB@5'-CGU...AUGUG AGUGUA UACGC...AUC-3'@LB@ GCAGGCAAGU GGAAU@LB@ \|\|\|\|\|\|\|\|\|\| :\|\|\|\|@LB@ CGUCCGUUCA UCUUA@LB@3'-UUU...UACUA GUUGAAAG ACGCC...UAG-5'@LB@ \| \|@LB@ 163 139@LB@@LB@@LB@Energy -13.77 kcal/mol@LB@Hybridization Energy -20.7539 kcal/mol@LB@Unfolding Energy - mRNA 2.26514 kcal/mol@LB@Unfolding Energy - sRNA 7.696 kcal/mol@LB@@LB@Position - mRNA 266 -- 286@LB@Position - sRNA 140 -- 162@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 153 -- 159@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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