Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
83	0.001966	0.08273	b1584	speG	-9.79	0.123144	169 -- 214	25 -- 77	spermidine N(1)-acetyltransferase	_____________168_____________________________________________________215\n_____________\|_______________________________________________________\|\n5'-UCU...UAACC__________________________U____G____CGUUAU___CA________CAGUG...GGU-3'\n______________UGUUAU____UGAUUUA____AGGAA_GUAA_GACA_______GC__AGCGCCCA\n______________\|\|:\|\|\|____\|:\|\|\|:\|____\|\|\|\|\|_\|\|\|\|_\|\|\|\|_______\|\|__\|:\|\|\|\|\|\|\n______________ACGAUA____AUUAAGU____UCCUU_CAUU_CUGU_______CG__UUGCGGGU\n3'-UUU...UUAAC______CGUC_______UUUU_______________UAUACCU__CG________AGCGA...ACG-5'\n_____________\|_______________________________________________________\|\n_____________78______________________________________________________24\n	208 -- 214	25 -- 31	-32.6914 kcal/mol	9.23779 kcal/mol	13.6641 kcal/mol	168 215@LB@ \| \|@LB@5'-UCU...UAACC U G CGUUAU CA CAGUG...GGU-3'@LB@ UGUUAU UGAUUUA AGGAA GUAA GACA GC AGCGCCCA@LB@ \|\|:\|\|\| \|:\|\|\|:\| \|\|\|\|\| \|\|\|\| \|\|\|\| \|\| \|:\|\|\|\|\|\|@LB@ ACGAUA AUUAAGU UCCUU CAUU CUGU CG UUGCGGGU@LB@3'-UUU...UUAAC CGUC UUUU UAUACCU CG AGCGA...ACG-5'@LB@ \| \|@LB@ 78 24@LB@@LB@@LB@Energy -9.79 kcal/mol@LB@Hybridization Energy -32.6914 kcal/mol@LB@Unfolding Energy - mRNA 9.23779 kcal/mol@LB@Unfolding Energy - sRNA 13.6641 kcal/mol@LB@@LB@Position - mRNA 169 -- 214@LB@Position - sRNA 25 -- 77@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 25 -- 31@LB@
84	0.001972	0.08273	b0968	yccX	-8.34	0.253881	183 -- 226	2 -- 49	weak acylphosphatase	_____________182_________________________________________________227\n_____________\|___________________________________________________\|\n5'-GGC...CAUUA_______GGA_____A________G_AA__C___________AA_______GGUUU...CCG-3'\n______________AGGAUAA____GAGC_GCAAUGUC_A__GU_______UGCAU__UUGCCUG\n______________\|:\|\|:\|\|____\|\|\|\|_\|\|\|\|:\|:\|_\|__\|:_______\|\|\|\|\|__\|::\|\|\|\|\n______________UUCUGUU____CUCG_CGUUGCGG_U__CG_______ACGUA__AGUGGAC\n3'-UUU...CUUCA_______AUAC_____________G_AG__AACUGCA______________G-5'\n_____________\|___________________________________________________\|\n_____________50__________________________________________________1\n	220 -- 226	2 -- 8	-35.2137 kcal/mol	10.0937 kcal/mol	16.7804 kcal/mol	182 227@LB@ \| \|@LB@5'-GGC...CAUUA GGA A G AA C AA GGUUU...CCG-3'@LB@ AGGAUAA GAGC GCAAUGUC A GU UGCAU UUGCCUG@LB@ \|:\|\|:\|\| \|\|\|\| \|\|\|\|:\|:\| \| \|: \|\|\|\|\| \|::\|\|\|\|@LB@ UUCUGUU CUCG CGUUGCGG U CG ACGUA AGUGGAC@LB@3'-UUU...CUUCA AUAC G AG AACUGCA G-5'@LB@ \| \|@LB@ 50 1@LB@@LB@@LB@Energy -8.34 kcal/mol@LB@Hybridization Energy -35.2137 kcal/mol@LB@Unfolding Energy - mRNA 10.0937 kcal/mol@LB@Unfolding Energy - sRNA 16.7804 kcal/mol@LB@@LB@Position - mRNA 183 -- 226@LB@Position - sRNA 2 -- 49@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 2 -- 8@LB@
85	0.002164	0.08969	b0910	cmk	-11.54	0.045559	249 -- 300	1 -- 56	cytidylate kinase	_____________248________________________________________________________300\n_____________\|__________________________________________________________\|\n5'-CCG...GUGCA_____________CCUU_________G______G__GGAA________AUGG_______-3'\n______________GGGA___AAGGCA_______GUGUAA_G_CUAU_GC____GCGUUGCA____CAUCUGC\n______________:\|\|\|___\|\|\|:\|\|_______\|:\|:\|\|_\|_\|:\|\|_\|\|____:\|\|\|\|\|\|\|____\|\|:\|\|\|\|\n______________UCCU___UUCUGU_______CGCGUU_C_GGUA_CG____UGCAACGU____GUGGACG\n3'-UUU...UUUUU____UCA______UAUACCU______G_G____G__AAC_________AA_________-5'\n_____________\|__________________________________________________________\|\n_____________57_________________________________________________________1\n	294 -- 300	1 -- 7	-44.7718 kcal/mol	16.3932 kcal/mol	16.8439 kcal/mol	248 300@LB@ \| \|@LB@5'-CCG...GUGCA CCUU G G GGAA AUGG -3'@LB@ GGGA AAGGCA GUGUAA G CUAU GC GCGUUGCA CAUCUGC@LB@ :\|\|\| \|\|\|:\|\| \|:\|:\|\| \| \|:\|\| \|\| :\|\|\|\|\|\|\| \|\|:\|\|\|\|@LB@ UCCU UUCUGU CGCGUU C GGUA CG UGCAACGU GUGGACG@LB@3'-UUU...UUUUU UCA UAUACCU G G G AAC AA -5'@LB@ \| \|@LB@ 57 1@LB@@LB@@LB@Energy -11.54 kcal/mol@LB@Hybridization Energy -44.7718 kcal/mol@LB@Unfolding Energy - mRNA 16.3932 kcal/mol@LB@Unfolding Energy - sRNA 16.8439 kcal/mol@LB@@LB@Position - mRNA 249 -- 300@LB@Position - sRNA 1 -- 56@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 1 -- 7@LB@
86	0.002341	0.09591	b0144	gluQ	-7.21	0.411815	221 -- 264	26 -- 65	glutamyl-Q tRNA(Asp) synthetase	_____________220__________________________________________265\n_____________\|____________________________________________\|\n5'-AGA...UUUUU__________AU__C__ACAC_______AUU__C___UU_____CCUCU...UGA-3'\n______________GUUCAAAGAG__GA_AG____ACAGUAU___GG_CGC__CGCCC\n______________:\|\|\|\|\|\|:\|:__\|\|_\|\|____\|\|\|:\|\|\|___:\|_\|\|\|__\|\|\|\|\|\n______________UAAGUUUUUU__CU_UC____UGUUAUA___UC_GCG__GCGGG\n3'-UUU...GUCAU__________C______AUUC_______CC_______UU_____UAGCG...ACG-5'\n_____________\|____________________________________________\|\n_____________66___________________________________________25\n	242 -- 248	40 -- 46	-28.4973 kcal/mol	7.75098 kcal/mol	13.5387 kcal/mol	220 265@LB@ \| \|@LB@5'-AGA...UUUUU AU C ACAC AUU C UU CCUCU...UGA-3'@LB@ GUUCAAAGAG GA AG ACAGUAU GG CGC CGCCC@LB@ :\|\|\|\|\|\|:\|: \|\| \|\| \|\|\|:\|\|\| :\| \|\|\| \|\|\|\|\|@LB@ UAAGUUUUUU CU UC UGUUAUA UC GCG GCGGG@LB@3'-UUU...GUCAU C AUUC CC UU UAGCG...ACG-5'@LB@ \| \|@LB@ 66 25@LB@@LB@@LB@Energy -7.21 kcal/mol@LB@Hybridization Energy -28.4973 kcal/mol@LB@Unfolding Energy - mRNA 7.75098 kcal/mol@LB@Unfolding Energy - sRNA 13.5387 kcal/mol@LB@@LB@Position - mRNA 221 -- 264@LB@Position - sRNA 26 -- 65@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 40 -- 46@LB@
87	0.002406	0.09689	b3317	rplB	-11.53	0.045926	6 -- 24	68 -- 86	50S ribosomal subunit protein L2	_____________5___________________25\n_____________\|___________________\|\n______5'-GCAGA______AGC__________AAACU...UGC-3'\n______________AAUCAA___UGCUGUGCAG\n______________\|\|\|\|\|\|___\|\|\|\|:\|\|\|\|\|\n______________UUAGUU___ACGAUACGUC\n3'-UUU...CAUGC______AAC__________AUUAA...ACG-5'\n_____________\|___________________\|\n_____________87__________________67\n	18 -- 24	68 -- 74	-20.8348 kcal/mol	5.62876 kcal/mol	3.67996 kcal/mol	5 25@LB@ \| \|@LB@ 5'-GCAGA AGC AAACU...UGC-3'@LB@ AAUCAA UGCUGUGCAG@LB@ \|\|\|\|\|\| \|\|\|\|:\|\|\|\|\|@LB@ UUAGUU ACGAUACGUC@LB@3'-UUU...CAUGC AAC AUUAA...ACG-5'@LB@ \| \|@LB@ 87 67@LB@@LB@@LB@Energy -11.53 kcal/mol@LB@Hybridization Energy -20.8348 kcal/mol@LB@Unfolding Energy - mRNA 5.62876 kcal/mol@LB@Unfolding Energy - sRNA 3.67996 kcal/mol@LB@@LB@Position - mRNA 6 -- 24@LB@Position - sRNA 68 -- 86@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 68 -- 74@LB@
89	0.002455	0.09689	b0466	ybaM	-10.99	0.063193	248 -- 263	68 -- 82	DUF2496 family protein	_____________247______________264\n_____________\|________________\|\n5'-GCA...GAUUU__________C__G__GAAAA...CGC-3'\n______________GAUUGUGCUG_UG_AG\n______________:\|\|\|\|\|\|\|\|:_\|\|_\|\|\n______________UUAACACGAU_AC_UC\n3'-UUU...CUUAG_____________G__AUUAA...ACG-5'\n_____________\|________________\|\n_____________83_______________67\n	251 -- 257	73 -- 79	-16.1643 kcal/mol	2.45269 kcal/mol	2.72435 kcal/mol	247 264@LB@ \| \|@LB@5'-GCA...GAUUU C G GAAAA...CGC-3'@LB@ GAUUGUGCUG UG AG@LB@ :\|\|\|\|\|\|\|\|: \|\| \|\|@LB@ UUAACACGAU AC UC@LB@3'-UUU...CUUAG G AUUAA...ACG-5'@LB@ \| \|@LB@ 83 67@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -16.1643 kcal/mol@LB@Unfolding Energy - mRNA 2.45269 kcal/mol@LB@Unfolding Energy - sRNA 2.72435 kcal/mol@LB@@LB@Position - mRNA 248 -- 263@LB@Position - sRNA 68 -- 82@LB@Position Seed - mRNA 251 -- 257@LB@Position Seed - sRNA 73 -- 79@LB@
90	0.002477	0.09689	b4020	yjbB	-17.01	0.000941	168 -- 222	1 -- 56	putative Na+/Pi-cotransporter	_____________167________________________________________________________223\n_____________\|__________________________________________________________\|\n5'-UCC...GCUUC_____CA__UA______A____AACC___AA______GUUA___C_____________UUUCU...UGC-3'\n______________AGGAA__UA__ACGAUA_GGAG_____UG__C_UCGU____ACG_UGC_UUCACCUGC\n______________\|\|\|\|\|__\|\|__\|\|:\|\|\|_\|\|\|\|_____:\|__\|_\|\|\|:____\|\|\|_\|\|\|_\|\|\|\|\|\|\|\|\|\n______________UCCUU__AU__UGUUAU_CCUC_____GC__G_AGCG____UGC_ACG_AAGUGGACG\n3'-UUU...UUUUU_____C___UC______A____GCGUU__GG_U____AAC____A___U_________-5'\n_____________\|_________________________________________________________\|\n_____________57________________________________________________________1\n	216 -- 222	1 -- 7	-44.3986 kcal/mol	10.5518 kcal/mol	16.8439 kcal/mol	167 223@LB@ \| \|@LB@5'-UCC...GCUUC CA UA A AACC AA GUUA C UUUCU...UGC-3'@LB@ AGGAA UA ACGAUA GGAG UG C UCGU ACG UGC UUCACCUGC@LB@ \|\|\|\|\| \|\| \|\|:\|\|\| \|\|\|\| :\| \| \|\|\|: \|\|\| \|\|\| \|\|\|\|\|\|\|\|\|@LB@ UCCUU AU UGUUAU CCUC GC G AGCG UGC ACG AAGUGGACG@LB@3'-UUU...UUUUU C UC A GCGUU GG U AAC A U -5'@LB@ \| \|@LB@ 57 1@LB@@LB@@LB@Energy -17.01 kcal/mol@LB@Hybridization Energy -44.3986 kcal/mol@LB@Unfolding Energy - mRNA 10.5518 kcal/mol@LB@Unfolding Energy - sRNA 16.8439 kcal/mol@LB@@LB@Position - mRNA 168 -- 222@LB@Position - sRNA 1 -- 56@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 1 -- 7@LB@
91	0.002503	0.09689	b1062	pyrC	-7.37	0.386343	231 -- 263	1 -- 35	dihydro-orotase	_____________230_______________________________________264\n_____________\|_________________________________________\|\n5'-GCG...AGAUC_____________________ACUG___CC_______CC__GAUGG...CCA-3'\n______________CGC__CGCCCA______GACG____GCA__UUCACCU__GC\n______________\|\|\|__\|\|\|\|\|\|______\|\|\|\|____\|\|\|__\|\|\|\|\|\|\|__\|\|\n______________GCG__GCGGGU______CUGC____CGU__AAGUGGA__CG\n3'-UUU...ACCUC___UU______AGCGAA____AA__________________-5'\n_____________\|________________________________________\|\n_____________36_______________________________________1\n	253 -- 259	3 -- 9	-30.041 kcal/mol	7.38685 kcal/mol	15.286 kcal/mol	230 264@LB@ \| \|@LB@5'-GCG...AGAUC ACUG CC CC GAUGG...CCA-3'@LB@ CGC CGCCCA GACG GCA UUCACCU GC@LB@ \|\|\| \|\|\|\|\|\| \|\|\|\| \|\|\| \|\|\|\|\|\|\| \|\|@LB@ GCG GCGGGU CUGC CGU AAGUGGA CG@LB@3'-UUU...ACCUC UU AGCGAA AA -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -7.37 kcal/mol@LB@Hybridization Energy -30.041 kcal/mol@LB@Unfolding Energy - mRNA 7.38685 kcal/mol@LB@Unfolding Energy - sRNA 15.286 kcal/mol@LB@@LB@Position - mRNA 231 -- 263@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 3 -- 9@LB@
92	0.002723	0.1042	b1413	hrpA	-14.20	0.008055	24 -- 69	1 -- 41	putative ATP-dependent helicase	_____________23_______________________________________________70\n_____________\|________________________________________________\|\n5'-GGU...UUUGA________AU____________UGU____ACUU______CAAU_____CACAG...GCG-3'\n______________AUGG_GCG__GC_CCCGUUGCU___UGAC____UAUUCA____CCUGC\n______________\|\|\|\|_\|\|\|__:\|_\|\|\|:\|:\|\|\|___\|\|\|\|____:\|\|\|\|\|____\|\|\|\|\|\n______________UACC_CGC__UG_GGGUAGCGA___ACUG____GUAAGU____GGACG\n3'-UUU...UGUUA____U___GU__C________________CAAC_______________-5'\n_____________\|_______________________________________________\|\n_____________42______________________________________________1\n	37 -- 43	20 -- 26	-41.3168 kcal/mol	11.8333 kcal/mol	15.2922 kcal/mol	23 70@LB@ \| \|@LB@5'-GGU...UUUGA AU UGU ACUU CAAU CACAG...GCG-3'@LB@ AUGG GCG GC CCCGUUGCU UGAC UAUUCA CCUGC@LB@ \|\|\|\| \|\|\| :\| \|\|\|:\|:\|\|\| \|\|\|\| :\|\|\|\|\| \|\|\|\|\|@LB@ UACC CGC UG GGGUAGCGA ACUG GUAAGU GGACG@LB@3'-UUU...UGUUA U GU C CAAC -5'@LB@ \| \|@LB@ 42 1@LB@@LB@@LB@Energy -14.20 kcal/mol@LB@Hybridization Energy -41.3168 kcal/mol@LB@Unfolding Energy - mRNA 11.8333 kcal/mol@LB@Unfolding Energy - sRNA 15.2922 kcal/mol@LB@@LB@Position - mRNA 24 -- 69@LB@Position - sRNA 1 -- 41@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 20 -- 26@LB@
93	0.002751	0.1042	b3407	yhgF	-15.01	0.004479	248 -- 282	1 -- 31	putative transcriptional accessory protein	_____________247_________________________________283\n_____________\|___________________________________\|\n5'-CCC...CAGGC_______GAACA_G______C__C___________UUGAC...CCG-3'\n______________GCGCCCG_____G_UUGACG_UG_CGUUCGCCUGC\n______________:\|\|\|\|\|:_____\|_\|\|\|\|\|\|_\|\|_\|:\|\|\|:\|\|\|\|\|\n______________UGCGGGU_____C_AACUGC_AC_GUAAGUGGACG\n3'-UUU...CGCGU_______AG____G______A______________-5'\n_____________\|__________________________________\|\n_____________32_________________________________1\n	276 -- 282	1 -- 7	-43.3047 kcal/mol	13.2535 kcal/mol	15.0438 kcal/mol	247 283@LB@ \| \|@LB@5'-CCC...CAGGC GAACA G C C UUGAC...CCG-3'@LB@ GCGCCCG G UUGACG UG CGUUCGCCUGC@LB@ :\|\|\|\|\|: \| \|\|\|\|\|\| \|\| \|:\|\|\|:\|\|\|\|\|@LB@ UGCGGGU C AACUGC AC GUAAGUGGACG@LB@3'-UUU...CGCGU AG G A -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -15.01 kcal/mol@LB@Hybridization Energy -43.3047 kcal/mol@LB@Unfolding Energy - mRNA 13.2535 kcal/mol@LB@Unfolding Energy - sRNA 15.0438 kcal/mol@LB@@LB@Position - mRNA 248 -- 282@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 1 -- 7@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

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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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