Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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	Additional homologs
122	0.006658	0.1913	b0600	ybdL	-10.23	0.125775	275 -- 297	68 -- 86	methionine aminotransferase PLP-dependent		_____________274_____________________298\n_____________\|_______________________\|\n5'-UCA...AGCGC___G____AG__________C__UUA-3'\n______________GCU_GCGC__CAACACCAGG_GA\n______________:\|\|_\|\|\|\|__\|\|\|\|\|\|\|\|\|\|_\|\|\n______________UGA_CGCG__GUUGUGGUCC_CU\n3'-UUU...GCUUA_______________________UUAGA...GUG-5'\n_____________\|_______________________\|\n_____________87______________________67\n	288 -- 294	70 -- 76	-27.7616 kcal/mol	10.1544 kcal/mol	7.37523 kcal/mol	274 298@LB@ \| \|@LB@5'-UCA...AGCGC G AG C UUA-3'@LB@ GCU GCGC CAACACCAGG GA@LB@ :\|\| \|\|\|\| \|\|\|\|\|\|\|\|\|\| \|\|@LB@ UGA CGCG GUUGUGGUCC CU@LB@3'-UUU...GCUUA UUAGA...GUG-5'@LB@ \| \|@LB@ 87 67@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -27.7616 kcal/mol@LB@Unfolding Energy - mRNA 10.1544 kcal/mol@LB@Unfolding Energy - sRNA 7.37523 kcal/mol@LB@@LB@Position - mRNA 275 -- 297@LB@Position - sRNA 68 -- 86@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 70 -- 76@LB@
102	0.005508	0.1855	b0659	ybeY	-7.73	0.351978	30 -- 54	64 -- 89	ssRNA-specific endoribonuclease; 16S rRNA 3' end maturation and quality control co-endoribonuclease working with RNase R; rRNA transcription antitermination factor		_____________29_________________________55\n_____________\|__________________________\|\n5'-ACU...AUCGA__________________AA______AGCUU...CGC-3'\n______________AGUGCUG_GCCGAUGUCG__GAGAUC\n______________\|:\|:\|\|\|_\|\|\|:\|:::\|:__\|\|:\|\|\|\n______________UUAUGAC_CGGUUGUGGU__CUUUAG\n3'-UUU...CGCGC_______G__________CC______AACCG...GUG-5'\n_____________\|__________________________\|\n_____________90_________________________63\n	30 -- 36	83 -- 89	-23.8058 kcal/mol	8.19456 kcal/mol	7.88317 kcal/mol	29 55@LB@ \| \|@LB@5'-ACU...AUCGA AA AGCUU...CGC-3'@LB@ AGUGCUG GCCGAUGUCG GAGAUC@LB@ \|:\|:\|\|\| \|\|\|:\|:::\|: \|\|:\|\|\|@LB@ UUAUGAC CGGUUGUGGU CUUUAG@LB@3'-UUU...CGCGC G CC AACCG...GUG-5'@LB@ \| \|@LB@ 90 63@LB@@LB@@LB@Energy -7.73 kcal/mol@LB@Hybridization Energy -23.8058 kcal/mol@LB@Unfolding Energy - mRNA 8.19456 kcal/mol@LB@Unfolding Energy - sRNA 7.88317 kcal/mol@LB@@LB@Position - mRNA 30 -- 54@LB@Position - sRNA 64 -- 89@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 83 -- 89@LB@
5	5.466e-05	0.03849	b0713	ybgL	-10.83	0.096857	234 -- 242	53 -- 61	UPF0271 family protein		_____________233_______243\n_____________\|_________\|\n5'-GCC...GCGAA_________AGCGA...AUG-3'\n______________GGCUGCGCC\n______________\|\|\|\|\|\|\|\|\|\n______________CCGACGCGG\n3'-UUU...UAGAA_________CAUUU...GUG-5'\n_____________\|_________\|\n_____________62________52\n	236 -- 242	53 -- 59	-22.2033 kcal/mol	6.50503 kcal/mol	4.87107 kcal/mol	233 243@LB@ \| \|@LB@5'-GCC...GCGAA AGCGA...AUG-3'@LB@ GGCUGCGCC@LB@ \|\|\|\|\|\|\|\|\|@LB@ CCGACGCGG@LB@3'-UUU...UAGAA CAUUU...GUG-5'@LB@ \| \|@LB@ 62 52@LB@@LB@@LB@Energy -10.83 kcal/mol@LB@Hybridization Energy -22.2033 kcal/mol@LB@Unfolding Energy - mRNA 6.50503 kcal/mol@LB@Unfolding Energy - sRNA 4.87107 kcal/mol@LB@@LB@Position - mRNA 234 -- 242@LB@Position - sRNA 53 -- 61@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 53 -- 59@LB@
22	0.001393	0.1727	b0794	ybhF	-14.07	0.022426	148 -- 164	67 -- 84	putative ABC transporter ATPase		_____________147________________165\n_____________\|__________________\|\n5'-UAC...GAUGA__________________UGCCA...GUU-3'\n______________UGCGUU_ACGCCAGGGAA\n______________\|\|\|\|::_\|\|:\|\|\|\|\|\|\|\|\n______________ACGCGG_UGUGGUCCCUU\n3'-UUU...UUAUG______U___________UAGAA...GUG-5'\n_____________\|__________________\|\n_____________85_________________66\n	158 -- 164	67 -- 73	-27.705 kcal/mol	6.27905 kcal/mol	7.35473 kcal/mol	147 165@LB@ \| \|@LB@5'-UAC...GAUGA UGCCA...GUU-3'@LB@ UGCGUU ACGCCAGGGAA@LB@ \|\|\|\|:: \|\|:\|\|\|\|\|\|\|\|@LB@ ACGCGG UGUGGUCCCUU@LB@3'-UUU...UUAUG U UAGAA...GUG-5'@LB@ \| \|@LB@ 85 66@LB@@LB@@LB@Energy -14.07 kcal/mol@LB@Hybridization Energy -27.705 kcal/mol@LB@Unfolding Energy - mRNA 6.27905 kcal/mol@LB@Unfolding Energy - sRNA 7.35473 kcal/mol@LB@@LB@Position - mRNA 148 -- 164@LB@Position - sRNA 67 -- 84@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 67 -- 73@LB@
187	0.01114	0.2089	b0801	ybiC	-12.72	0.041489	266 -- 279	27 -- 40	putative dehydrogenase	b0517	_____________265____________280\n_____________\|______________\|\n5'-GCU...CGUCA_______A______AACAA...UUG-3'\n______________GAUGGGU_GCGAGG\n______________\|\|\|\|:\|\|_:\|:\|\|\|\n______________CUACUCA_UGUUCC\n3'-UUU...UAAUA_______A______CGUGU...GUG-5'\n_____________\|______________\|\n_____________41_____________26\n	266 -- 272	34 -- 40	-18.8068 kcal/mol	3.48138 kcal/mol	2.60767 kcal/mol	265 280@LB@ \| \|@LB@5'-GCU...CGUCA A AACAA...UUG-3'@LB@ GAUGGGU GCGAGG@LB@ \|\|\|\|:\|\| :\|:\|\|\|@LB@ CUACUCA UGUUCC@LB@3'-UUU...UAAUA A CGUGU...GUG-5'@LB@ \| \|@LB@ 41 26@LB@@LB@@LB@Energy -12.72 kcal/mol@LB@Hybridization Energy -18.8068 kcal/mol@LB@Unfolding Energy - mRNA 3.48138 kcal/mol@LB@Unfolding Energy - sRNA 2.60767 kcal/mol@LB@@LB@Position - mRNA 266 -- 279@LB@Position - sRNA 27 -- 40@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 34 -- 40@LB@
26	0.001553	0.1727	b0853	ybjN	-8.94	0.217650	161 -- 169	52 -- 60	negative regulator of motility; multicopy suppressor of coaA(Ts)		_____________160_______170\n_____________\|_________\|\n5'-CGC...CGUAA_________GUCUU...AUC-3'\n______________GCUGUGCCG\n______________\|\|\|\|:\|\|\|\|\n______________CGACGCGGC\n3'-UUU...AGAAC_________AUUUA...GUG-5'\n_____________\|_________\|\n_____________61________51\n	163 -- 169	52 -- 58	-18.9448 kcal/mol	5.13325 kcal/mol	4.86882 kcal/mol	160 170@LB@ \| \|@LB@5'-CGC...CGUAA GUCUU...AUC-3'@LB@ GCUGUGCCG@LB@ \|\|\|\|:\|\|\|\|@LB@ CGACGCGGC@LB@3'-UUU...AGAAC AUUUA...GUG-5'@LB@ \| \|@LB@ 61 51@LB@@LB@@LB@Energy -8.94 kcal/mol@LB@Hybridization Energy -18.9448 kcal/mol@LB@Unfolding Energy - mRNA 5.13325 kcal/mol@LB@Unfolding Energy - sRNA 4.86882 kcal/mol@LB@@LB@Position - mRNA 161 -- 169@LB@Position - sRNA 52 -- 60@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 52 -- 58@LB@
183	0.011	0.2089	b0906	ycaP	-11.77	0.063722	48 -- 74	48 -- 75	UPF0702 family putative inner membrane protein		_____________47___________________________75\n_____________\|____________________________\|\n5'-AGU...UCUUU________UAAA___U_______A____AAUCA...UCU-3'\n______________GCCGGGGA_____UG_UUGCGUC_UGAA\n______________:\|\|:\|\|\|\|_____\|\|_:\|\|\|\|:\|_\|:\|\|\n______________UGGUCCCU_____AC_GACGCGG_AUUU\n3'-UUU...GGUUG________UUAGA__C_______C____AAUAA...GUG-5'\n_____________\|____________________________\|\n_____________76___________________________47\n	63 -- 69	53 -- 59	-25.8143 kcal/mol	5.22968 kcal/mol	8.81811 kcal/mol	47 75@LB@ \| \|@LB@5'-AGU...UCUUU UAAA U A AAUCA...UCU-3'@LB@ GCCGGGGA UG UUGCGUC UGAA@LB@ :\|\|:\|\|\|\| \|\| :\|\|\|\|:\| \|:\|\|@LB@ UGGUCCCU AC GACGCGG AUUU@LB@3'-UUU...GGUUG UUAGA C C AAUAA...GUG-5'@LB@ \| \|@LB@ 76 47@LB@@LB@@LB@Energy -11.77 kcal/mol@LB@Hybridization Energy -25.8143 kcal/mol@LB@Unfolding Energy - mRNA 5.22968 kcal/mol@LB@Unfolding Energy - sRNA 8.81811 kcal/mol@LB@@LB@Position - mRNA 48 -- 74@LB@Position - sRNA 48 -- 75@LB@Position Seed - mRNA 63 -- 69@LB@Position Seed - sRNA 53 -- 59@LB@
9	0.0003241	0.1198	b1110	ycfJ	-9.50	0.172514	224 -- 251	52 -- 76	uncharacterized protein		_____________223__________________________252\n_____________\|____________________________\|\n5'-ACU...GCGGG_______AUU__U___GCA_________GGCGU...AAU-3'\n______________UAUCGGG___GG_GUC___GCUGCGCUG\n______________:\|:\|:\|\|___\|:_:\|\|___\|\|\|\|\|\|\|:\|\n______________GUGGUCC___CU_UAG___CGACGCGGC\n3'-UUU...CGGUU____________U___AAC_________AUUUA...GUG-5'\n_____________\|____________________________\|\n_____________77___________________________51\n	245 -- 251	52 -- 58	-26.6822 kcal/mol	7.91875 kcal/mol	9.26585 kcal/mol	223 252@LB@ \| \|@LB@5'-ACU...GCGGG AUU U GCA GGCGU...AAU-3'@LB@ UAUCGGG GG GUC GCUGCGCUG@LB@ :\|:\|:\|\| \|: :\|\| \|\|\|\|\|\|\|:\|@LB@ GUGGUCC CU UAG CGACGCGGC@LB@3'-UUU...CGGUU U AAC AUUUA...GUG-5'@LB@ \| \|@LB@ 77 51@LB@@LB@@LB@Energy -9.50 kcal/mol@LB@Hybridization Energy -26.6822 kcal/mol@LB@Unfolding Energy - mRNA 7.91875 kcal/mol@LB@Unfolding Energy - sRNA 9.26585 kcal/mol@LB@@LB@Position - mRNA 224 -- 251@LB@Position - sRNA 52 -- 76@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 52 -- 58@LB@
151	0.008943	0.2059	b1284	yciT	-9.40	0.179701	94 -- 109	63 -- 77	global regulator of transcription; DeoR family		_____________93_______________110\n_____________\|________________\|\n5'-GCA...CGAAG______U_________AACAA...CCA-3'\n______________GCACCG_GGGAGAUUU\n______________:\|\|\|\|:_\|\|\|\|:\|\|:\|\n______________UGUGGU_CCCUUUAGA\n3'-UUU...GCGGU________________ACCGA...GUG-5'\n_____________\|________________\|\n_____________78_______________62\n	103 -- 109	63 -- 69	-19.5221 kcal/mol	5.38652 kcal/mol	4.72953 kcal/mol	93 110@LB@ \| \|@LB@5'-GCA...CGAAG U AACAA...CCA-3'@LB@ GCACCG GGGAGAUUU@LB@ :\|\|\|\|: \|\|\|\|:\|\|:\|@LB@ UGUGGU CCCUUUAGA@LB@3'-UUU...GCGGU ACCGA...GUG-5'@LB@ \| \|@LB@ 78 62@LB@@LB@@LB@Energy -9.40 kcal/mol@LB@Hybridization Energy -19.5221 kcal/mol@LB@Unfolding Energy - mRNA 5.38652 kcal/mol@LB@Unfolding Energy - sRNA 4.72953 kcal/mol@LB@@LB@Position - mRNA 94 -- 109@LB@Position - sRNA 63 -- 77@LB@Position Seed - mRNA 103 -- 109@LB@Position Seed - sRNA 63 -- 69@LB@
179	0.01058	0.208	b1325	ycjG	-11.81	0.062523	258 -- 297	32 -- 77	L-Ala-D/L-Glu epimerase		_____________257_______________________________________________298\n_____________\|_________________________________________________\|\n5'-AAG...UGAUU______________GCA__GAA____G______________________AAC-3'\n______________GC_CCGGGGAAGUC___GU___GCGC_CGUG_______GUGGUG_GUUG\n______________:\|_\|\|:\|\|\|\|\|:\|\|___\|:___\|\|\|\|_\|\|\|:_______:\|\|:\|\|_\|\|\|:\n______________UG_GGUCCCUUUAG___CG___CGCG_GCAU_______UACUAC_CAAU\n3'-UUU...GCGGU__U___________AAC__A___________UUAAUAA______U____GUUCC...GUG-5'\n_____________\|_________________________________________________\|\n_____________78________________________________________________31\n	264 -- 270	64 -- 70	-38.4326 kcal/mol	17.2613 kcal/mol	9.36253 kcal/mol	257 298@LB@ \| \|@LB@5'-AAG...UGAUU GCA GAA G AAC-3'@LB@ GC CCGGGGAAGUC GU GCGC CGUG GUGGUG GUUG@LB@ :\| \|\|:\|\|\|\|\|:\|\| \|: \|\|\|\| \|\|\|: :\|\|:\|\| \|\|\|:@LB@ UG GGUCCCUUUAG CG CGCG GCAU UACUAC CAAU@LB@3'-UUU...GCGGU U AAC A UUAAUAA U GUUCC...GUG-5'@LB@ \| \|@LB@ 78 31@LB@@LB@@LB@Energy -11.81 kcal/mol@LB@Hybridization Energy -38.4326 kcal/mol@LB@Unfolding Energy - mRNA 17.2613 kcal/mol@LB@Unfolding Energy - sRNA 9.36253 kcal/mol@LB@@LB@Position - mRNA 258 -- 297@LB@Position - sRNA 32 -- 77@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 64 -- 70@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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