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
12	2.043e-05	0.005627	b3935	priA	-14.36	0.007166	198 -- 229	1 -- 34	Primosome factor n' (replication factor Y)	_____________197________________________________230\n_____________\|__________________________________\|\n5'-GAA...AUGAU__U___________CC________C______C__UCCGC...GCG-3'\n______________GC_AUGCCCGUUGC___ACGUUGC__UUGCC_GU\n______________\|\|_\|:\|\|\|\|:\|:\|\|___\|\|\|\|\|\|\|__\|::\|\|_\|:\n______________CG_UGCGGGUAGCG___UGCAACG__AGUGG_CG\n3'-UUU...CCUCG__U___________AAC_______UA_____A__-5'\n_____________\|_________________________________\|\n_____________35________________________________1\n	214 -- 220	11 -- 17	-36.548 kcal/mol	6.92453 kcal/mol	15.2664 kcal/mol	197 230@LB@ \| \|@LB@5'-GAA...AUGAU U CC C C UCCGC...GCG-3'@LB@ GC AUGCCCGUUGC ACGUUGC UUGCC GU@LB@ \|\| \|:\|\|\|\|:\|:\|\| \|\|\|\|\|\|\| \|::\|\| \|:@LB@ CG UGCGGGUAGCG UGCAACG AGUGG CG@LB@3'-UUU...CCUCG U AAC UA A -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -14.36 kcal/mol@LB@Hybridization Energy -36.548 kcal/mol@LB@Unfolding Energy - mRNA 6.92453 kcal/mol@LB@Unfolding Energy - sRNA 15.2664 kcal/mol@LB@@LB@Position - mRNA 198 -- 229@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 11 -- 17@LB@
110	0.003505	0.1114	b4111	proP	-11.30	0.052648	186 -- 222	48 -- 93	proline/glycine betaine transporter	_____________185________________________________________________223\n_____________\|__________________________________________________\|\n5'-CAC...CCAAC_________GA_____________U________________AAAA_____AACCG...GUA-3'\n______________UC_UGCGAG__AA____GCUAUGC_________GAAAAGGA____AGUAA\n______________\|\|_\|:\|\|\|:__\|\|____\|\|\|\|\|\|\|_________:\|\|\|\|\|\|\|____\|\|\|\|\|\n______________AG_AUGCUU__UU____CGAUACG_________UUUUUCCU____UCAUU\n3'-UUU...GCCGC__C______AG__AACA_______UCAUUAAGU_________________CUGUU...ACG-5'\n_____________\|__________________________________________________\|\n_____________94_________________________________________________47\n	198 -- 204	70 -- 76	-22.6159 kcal/mol	6.45165 kcal/mol	4.87071 kcal/mol	185 223@LB@ \| \|@LB@5'-CAC...CCAAC GA U AAAA AACCG...GUA-3'@LB@ UC UGCGAG AA GCUAUGC GAAAAGGA AGUAA@LB@ \|\| \|:\|\|\|: \|\| \|\|\|\|\|\|\| :\|\|\|\|\|\|\| \|\|\|\|\|@LB@ AG AUGCUU UU CGAUACG UUUUUCCU UCAUU@LB@3'-UUU...GCCGC C AG AACA UCAUUAAGU CUGUU...ACG-5'@LB@ \| \|@LB@ 94 47@LB@@LB@@LB@Energy -11.30 kcal/mol@LB@Hybridization Energy -22.6159 kcal/mol@LB@Unfolding Energy - mRNA 6.45165 kcal/mol@LB@Unfolding Energy - sRNA 4.87071 kcal/mol@LB@@LB@Position - mRNA 186 -- 222@LB@Position - sRNA 48 -- 93@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 70 -- 76@LB@
149	0.005854	0.1368	b2166	psuK	-12.08	0.032688	265 -- 298	54 -- 89	pseudouridine kinase	_____________264___________________________________299\n_____________\|_____________________________________\|\n5'-UUU...UUCAC________UUAAA__________________UCC___UA-3'\n______________AUGAAUCA______UUAUGCGG__AUUCAAA___AGG\n______________\|:\|\|\|\|\|\|______:\|\|\|\|\|:\|__\|\|\|\|\|\|\|___\|\|\|\n______________UGCUUAGU______GAUACGUC__UAAGUUU___UCC\n3'-UUU...CAGCA________UAACAC________AU_______UU____UUCAU...ACG-5'\n_____________\|_____________________________________\|\n_____________90____________________________________53\n	279 -- 285	68 -- 74	-22.7366 kcal/mol	5.9989 kcal/mol	4.66068 kcal/mol	264 299@LB@ \| \|@LB@5'-UUU...UUCAC UUAAA UCC UA-3'@LB@ AUGAAUCA UUAUGCGG AUUCAAA AGG@LB@ \|:\|\|\|\|\|\| :\|\|\|\|\|:\| \|\|\|\|\|\|\| \|\|\|@LB@ UGCUUAGU GAUACGUC UAAGUUU UCC@LB@3'-UUU...CAGCA UAACAC AU UU UUCAU...ACG-5'@LB@ \| \|@LB@ 90 53@LB@@LB@@LB@Energy -12.08 kcal/mol@LB@Hybridization Energy -22.7366 kcal/mol@LB@Unfolding Energy - mRNA 5.9989 kcal/mol@LB@Unfolding Energy - sRNA 4.66068 kcal/mol@LB@@LB@Position - mRNA 265 -- 298@LB@Position - sRNA 54 -- 89@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 68 -- 74@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@
56	0.0007477	0.04704	b2777	queE	-11.99	0.034574	197 -- 232	45 -- 77	7-carboxy-7-deazaguanine synthase; queosine biosynthesis	_____________196___________________________________233\n_____________\|_____________________________________\|\n5'-AAU...GAGAA____________CC____UU__C_A__U__UCC____CCUGC...UUG-3'\n______________UGCUAUGCAGUA___CGA__AA_G_GA_GU___AGAC\n______________\|\|\|\|\|\|\|\|\|\|\|\|___\|:\|__\|\|_\|_\|\|_\|\|___\|\|\|\|\n______________ACGAUACGUCAU___GUU__UU_C_CU_CA___UCUG\n3'-UUU...UUAAC____________UAA___UU_______U__U______UUAUA...ACG-5'\n_____________\|_____________________________________\|\n_____________78____________________________________44\n	202 -- 208	66 -- 72	-23.7263 kcal/mol	6.13303 kcal/mol	5.60521 kcal/mol	196 233@LB@ \| \|@LB@5'-AAU...GAGAA CC UU C A U UCC CCUGC...UUG-3'@LB@ UGCUAUGCAGUA CGA AA G GA GU AGAC@LB@ \|\|\|\|\|\|\|\|\|\|\|\| \|:\| \|\| \| \|\| \|\| \|\|\|\|@LB@ ACGAUACGUCAU GUU UU C CU CA UCUG@LB@3'-UUU...UUAAC UAA UU U U UUAUA...ACG-5'@LB@ \| \|@LB@ 78 44@LB@@LB@@LB@Energy -11.99 kcal/mol@LB@Hybridization Energy -23.7263 kcal/mol@LB@Unfolding Energy - mRNA 6.13303 kcal/mol@LB@Unfolding Energy - sRNA 5.60521 kcal/mol@LB@@LB@Position - mRNA 197 -- 232@LB@Position - sRNA 45 -- 77@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 66 -- 72@LB@
73	0.001571	0.0758	b3746	ravA	-8.41	0.246327	240 -- 262	54 -- 75	hexameric AAA+ MoxR family ATPase putative molecular chaperone	_____________239_____________________263\n_____________\|_______________________\|\n5'-UGA...CCCGC___A_____UC___G________GCUUU...UAU-3'\n______________CUG_GCAGU__GUU_GAAAAGGG\n______________\|\|:_\|\|\|\|\|__:\|\|_:\|\|\|\|:\|\|\n______________GAU_CGUCA__UAA_UUUUUUCC\n3'-UUU...AACAC___A_____U____G________UUCAU...ACG-5'\n_____________\|_______________________\|\n_____________76______________________53\n	256 -- 262	54 -- 60	-19.2007 kcal/mol	7.09588 kcal/mol	3.69534 kcal/mol	239 263@LB@ \| \|@LB@5'-UGA...CCCGC A UC G GCUUU...UAU-3'@LB@ CUG GCAGU GUU GAAAAGGG@LB@ \|\|: \|\|\|\|\| :\|\| :\|\|\|\|:\|\|@LB@ GAU CGUCA UAA UUUUUUCC@LB@3'-UUU...AACAC A U G UUCAU...ACG-5'@LB@ \| \|@LB@ 76 53@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -19.2007 kcal/mol@LB@Unfolding Energy - mRNA 7.09588 kcal/mol@LB@Unfolding Energy - sRNA 3.69534 kcal/mol@LB@@LB@Position - mRNA 240 -- 262@LB@Position - sRNA 54 -- 75@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 54 -- 60@LB@
190	0.008377	0.1548	b3167	rbfA	-7.61	0.351010	14 -- 35	19 -- 38	30s ribosome binding factor	_____________13_____________________36\n_____________\|______________________\|\n5'-AUU...UCAUC___A_C______A_________AAGGU...GCA-3'\n______________GAG_U_CAACGU_CCAUUGCUU\n______________\|\|\|_:_\|\|\|\|\|:_\|\|\|\|:\|\|\|\|\n______________CUC_G_GUUGCG_GGUAGCGAA\n3'-UUU...UAUAC_____C________________CUGCA...ACG-5'\n_____________\|______________________\|\n_____________39_____________________18\n	29 -- 35	19 -- 25	-22.6036 kcal/mol	2.81921 kcal/mol	12.1801 kcal/mol	13 36@LB@ \| \|@LB@5'-AUU...UCAUC A C A AAGGU...GCA-3'@LB@ GAG U CAACGU CCAUUGCUU@LB@ \|\|\| : \|\|\|\|\|: \|\|\|\|:\|\|\|\|@LB@ CUC G GUUGCG GGUAGCGAA@LB@3'-UUU...UAUAC C CUGCA...ACG-5'@LB@ \| \|@LB@ 39 18@LB@@LB@@LB@Energy -7.61 kcal/mol@LB@Hybridization Energy -22.6036 kcal/mol@LB@Unfolding Energy - mRNA 2.81921 kcal/mol@LB@Unfolding Energy - sRNA 12.1801 kcal/mol@LB@@LB@Position - mRNA 14 -- 35@LB@Position - sRNA 19 -- 38@LB@Position Seed - mRNA 29 -- 35@LB@Position Seed - sRNA 19 -- 25@LB@
43	0.0004177	0.03347	b3652	recG	-10.52	0.082371	49 -- 71	17 -- 38	ATP-dependent DNA helicase	_____________48______________________72\n_____________\|_______________________\|\n5'-CAA...AAGCA____AA_________________AGGCG...UGC-3'\n______________GAGC__CAACGCCUGUUGUUUGA\n______________\|\|\|\|__\|\|\|\|\|\|\|::\|:\|:\|\|\|\|\n______________CUCG__GUUGCGGGUAGCGAACU\n3'-UUU...UAUAC____C__________________GCAAC...ACG-5'\n_____________\|_______________________\|\n_____________39______________________16\n	63 -- 69	19 -- 25	-31.2627 kcal/mol	8.52631 kcal/mol	12.2147 kcal/mol	48 72@LB@ \| \|@LB@5'-CAA...AAGCA AA AGGCG...UGC-3'@LB@ GAGC CAACGCCUGUUGUUUGA@LB@ \|\|\|\| \|\|\|\|\|\|\|::\|:\|:\|\|\|\|@LB@ CUCG GUUGCGGGUAGCGAACU@LB@3'-UUU...UAUAC C GCAAC...ACG-5'@LB@ \| \|@LB@ 39 16@LB@@LB@@LB@Energy -10.52 kcal/mol@LB@Hybridization Energy -31.2627 kcal/mol@LB@Unfolding Energy - mRNA 8.52631 kcal/mol@LB@Unfolding Energy - sRNA 12.2147 kcal/mol@LB@@LB@Position - mRNA 49 -- 71@LB@Position - sRNA 17 -- 38@LB@Position Seed - mRNA 63 -- 69@LB@Position Seed - sRNA 19 -- 25@LB@
107	0.003422	0.1114	b0415	ribE	-10.96	0.064092	190 -- 254	4 -- 58	riboflavin synthase beta chain	_____________189_________________________________________________________________255\n_____________\|___________________________________________________________________\|\n5'-CGG...AACCC________AAAAU_A___U___U_A_________UUGCUAC____GA____C_____C__CA_____AUCGC...GUG-3'\n______________GAAGGAAG_____G_ACA_UAU_G_AGC_UAACG_______CCCG__CGCU__GCGU_GC__UCACC\n______________:\|\|\|\|\|\|\|_____\|_\|\|\|_\|\|\|_\|_\|\|\|_:\|\|\|\|_______\|\|\|:__\|\|\|\|__:\|\|\|_\|\|__\|\|\|\|\|\n______________UUUCCUUC_____C_UGU_AUA_C_UCG_GUUGC_______GGGU__GCGA__UGCA_CG__AGUGG\n3'-UUU...AGUUU________AUU_______U___C_____C________________A_____AC____A__UA_____ACG-5'\n_____________\|___________________________________________________________________\|\n_____________59__________________________________________________________________3\n	191 -- 197	51 -- 57	-41.366 kcal/mol	13.5359 kcal/mol	16.8715 kcal/mol	189 255@LB@ \| \|@LB@5'-CGG...AACCC AAAAU A U U A UUGCUAC GA C C CA AUCGC...GUG-3'@LB@ GAAGGAAG G ACA UAU G AGC UAACG CCCG CGCU GCGU GC UCACC@LB@ :\|\|\|\|\|\|\| \| \|\|\| \|\|\| \| \|\|\| :\|\|\|\| \|\|\|: \|\|\|\| :\|\|\| \|\| \|\|\|\|\|@LB@ UUUCCUUC C UGU AUA C UCG GUUGC GGGU GCGA UGCA CG AGUGG@LB@3'-UUU...AGUUU AUU U C C A AC A UA ACG-5'@LB@ \| \|@LB@ 59 3@LB@@LB@@LB@Energy -10.96 kcal/mol@LB@Hybridization Energy -41.366 kcal/mol@LB@Unfolding Energy - mRNA 13.5359 kcal/mol@LB@Unfolding Energy - sRNA 16.8715 kcal/mol@LB@@LB@Position - mRNA 190 -- 254@LB@Position - sRNA 4 -- 58@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 51 -- 57@LB@
17	4.003e-05	0.007917	b1066	rimJ	-10.62	0.078044	194 -- 220	65 -- 91	ribosomal-protein-S5-alanine N-acetyltransferase	_____________193___________________________221\n_____________\|_____________________________\|\n5'-AUU...AGUAG____A____GU__________C_______CGUGC...AUU-3'\n______________GUAU_GAAU___UUG_GCUAU_GCAGUAA\n______________\|\|\|:_\|\|\|\|___\|\|\|_\|\|\|\|\|_\|\|\|\|\|\|\|\n______________CAUG_CUUA___AAC_CGAUA_CGUCAUU\n3'-UUU...CGCAG_________GUU___A_____________AAGUU...ACG-5'\n_____________\|_____________________________\|\n_____________92____________________________64\n	214 -- 220	65 -- 71	-21.0331 kcal/mol	5.8812 kcal/mol	4.53558 kcal/mol	193 221@LB@ \| \|@LB@5'-AUU...AGUAG A GU C CGUGC...AUU-3'@LB@ GUAU GAAU UUG GCUAU GCAGUAA@LB@ \|\|\|: \|\|\|\| \|\|\| \|\|\|\|\| \|\|\|\|\|\|\|@LB@ CAUG CUUA AAC CGAUA CGUCAUU@LB@3'-UUU...CGCAG GUU A AAGUU...ACG-5'@LB@ \| \|@LB@ 92 64@LB@@LB@@LB@Energy -10.62 kcal/mol@LB@Hybridization Energy -21.0331 kcal/mol@LB@Unfolding Energy - mRNA 5.8812 kcal/mol@LB@Unfolding Energy - sRNA 4.53558 kcal/mol@LB@@LB@Position - mRNA 194 -- 220@LB@Position - sRNA 65 -- 91@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 65 -- 71@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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