Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
140	0.01599	0.3828	b0119	yacL	-11.32	0.063485	266 -- 299	25 -- 57	UPF0231 family protein	_____________265_________________________________300\n_____________\|___________________________________\|\n5'-GGU...CAUGA______CGG___C_________GA___________G-3'\n______________AGUGGU___GCA_UGGUUUAAU__AGA_GGUGAAA\n______________\|\|\|\|\|:___\|\|\|_\|\|\|:::\|\|:__\|\|\|_::\|:\|\|\|\n______________UCACCG___CGU_ACCGGGUUG__UCU_UUAUUUU\n3'-UUU...UUUAG______UUA___U______________U_______AGACA...UUG-5'\n_____________\|___________________________________\|\n_____________58__________________________________24\n	293 -- 299	25 -- 31	-25.5028 kcal/mol	4.248 kcal/mol	9.93955 kcal/mol	265 300@LB@ \| \|@LB@5'-GGU...CAUGA CGG C GA G-3'@LB@ AGUGGU GCA UGGUUUAAU AGA GGUGAAA@LB@ \|\|\|\|\|: \|\|\| \|\|\|:::\|\|: \|\|\| ::\|:\|\|\|@LB@ UCACCG CGU ACCGGGUUG UCU UUAUUUU@LB@3'-UUU...UUUAG UUA U U AGACA...UUG-5'@LB@ \| \|@LB@ 58 24@LB@@LB@@LB@Energy -11.32 kcal/mol@LB@Hybridization Energy -25.5028 kcal/mol@LB@Unfolding Energy - mRNA 4.248 kcal/mol@LB@Unfolding Energy - sRNA 9.93955 kcal/mol@LB@@LB@Position - mRNA 266 -- 299@LB@Position - sRNA 25 -- 57@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 25 -- 31@LB@
191	0.02382	0.4194	b4567	yjjZ	-11.31	0.063816	288 -- 298	51 -- 61	uncharacterized protein	_____________287_________299\n_____________\|___________\|\n5'-CGG...CGUCA___________GA-3'\n______________GAUCAGUGGCG\n______________:\|\|\|\|\|\|\|\|\|:\n______________UUAGUCACCGU\n3'-UUU...ACCUU___________UACGU...UUG-5'\n_____________\|___________\|\n_____________62__________50\n	292 -- 298	51 -- 57	-17.6489 kcal/mol	3.61415 kcal/mol	2.72961 kcal/mol	287 299@LB@ \| \|@LB@5'-CGG...CGUCA GA-3'@LB@ GAUCAGUGGCG@LB@ :\|\|\|\|\|\|\|\|\|:@LB@ UUAGUCACCGU@LB@3'-UUU...ACCUU UACGU...UUG-5'@LB@ \| \|@LB@ 62 50@LB@@LB@@LB@Energy -11.31 kcal/mol@LB@Hybridization Energy -17.6489 kcal/mol@LB@Unfolding Energy - mRNA 3.61415 kcal/mol@LB@Unfolding Energy - sRNA 2.72961 kcal/mol@LB@@LB@Position - mRNA 288 -- 298@LB@Position - sRNA 51 -- 61@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 51 -- 57@LB@
156	0.01801	0.3828	b1942	fliJ	-11.30	0.063944	187 -- 254	7 -- 65	flagellar protein	_____________186______________________________________________________________________255\n_____________\|________________________________________________________________________\|\n5'-UUC...ACCCA_____UAACGG___A_____GAACAUG_____C____GACCCU______________GCAGA__A_______GAGGA...AGC-3'\n______________GGAGA______CAG_UGGCA_______GUGCG_UGGC______GAAA____GAUCUG_____AA_AGAGGUA\n______________\|\|\|:\|______\|\|\|_\|\|\|\|\|_______:\|\|\|:_\|\|\|\|______\|\|\|\|____:\|\|\|\|\|_____\|\|_\|:\|\|\|:\|\n______________CCUUU______GUC_ACCGU_______UACGU_ACCG______CUUU____UUAGAC_____UU_UUUCCGU\n3'-UUU...UACAA_____UA_________________________U____GGUUGU____UAUU______ACUG___A_______AUAUUG-5'\n_____________\|________________________________________________________________________\|\n_____________66_______________________________________________________________________6\n	248 -- 254	7 -- 13	-39.8056 kcal/mol	16.3505 kcal/mol	12.1538 kcal/mol	186 255@LB@ \| \|@LB@5'-UUC...ACCCA UAACGG A GAACAUG C GACCCU GCAGA A GAGGA...AGC-3'@LB@ GGAGA CAG UGGCA GUGCG UGGC GAAA GAUCUG AA AGAGGUA@LB@ \|\|\|:\| \|\|\| \|\|\|\|\| :\|\|\|: \|\|\|\| \|\|\|\| :\|\|\|\|\| \|\| \|:\|\|\|:\|@LB@ CCUUU GUC ACCGU UACGU ACCG CUUU UUAGAC UU UUUCCGU@LB@3'-UUU...UACAA UA U GGUUGU UAUU ACUG A AUAUUG-5'@LB@ \| \|@LB@ 66 6@LB@@LB@@LB@Energy -11.30 kcal/mol@LB@Hybridization Energy -39.8056 kcal/mol@LB@Unfolding Energy - mRNA 16.3505 kcal/mol@LB@Unfolding Energy - sRNA 12.1538 kcal/mol@LB@@LB@Position - mRNA 187 -- 254@LB@Position - sRNA 7 -- 65@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 7 -- 13@LB@
164	0.01912	0.392	b0585	fes	-11.27	0.064985	233 -- 253	39 -- 56	enterobactin/ferrienterobactin esterase	_____________232____________________254\n_____________\|______________________\|\n5'-CAU...AGCUG____________AACA______GGAAU...GGU-3'\n______________GUGGCAGU_CGA____UGGCCC\n______________\|\|\|\|\|\|:\|_\|:\|____\|\|\|\|\|\|\n______________CACCGUUA_GUU____ACCGGG\n3'-UUU...UUAGU________C_____________UUGUC...UUG-5'\n_____________\|______________________\|\n_____________57_____________________38\n	234 -- 240	49 -- 55	-24.6014 kcal/mol	8.56812 kcal/mol	4.76336 kcal/mol	232 254@LB@ \| \|@LB@5'-CAU...AGCUG AACA GGAAU...GGU-3'@LB@ GUGGCAGU CGA UGGCCC@LB@ \|\|\|\|\|\|:\| \|:\| \|\|\|\|\|\|@LB@ CACCGUUA GUU ACCGGG@LB@3'-UUU...UUAGU C UUGUC...UUG-5'@LB@ \| \|@LB@ 57 38@LB@@LB@@LB@Energy -11.27 kcal/mol@LB@Hybridization Energy -24.6014 kcal/mol@LB@Unfolding Energy - mRNA 8.56812 kcal/mol@LB@Unfolding Energy - sRNA 4.76336 kcal/mol@LB@@LB@Position - mRNA 233 -- 253@LB@Position - sRNA 39 -- 56@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 49 -- 55@LB@
171	0.02062	0.4033	b3192	mlaC	-11.25	0.065504	113 -- 124	47 -- 58	ABC transporter maintaining OM lipid asymmetry periplasmic binding protein	_____________112__________125\n_____________\|____________\|\n5'-GGA...AAGAA____________GCCAG...AGG-3'\n______________UAGUGGCGAUGC\n______________:\|\|\|\|\|\|:\|\|\|\|\n______________GUCACCGUUACG\n3'-UUU...UUUUA____________UUACC...UUG-5'\n_____________\|____________\|\n_____________59___________46\n	118 -- 124	47 -- 53	-20.0531 kcal/mol	5.42731 kcal/mol	3.37136 kcal/mol	112 125@LB@ \| \|@LB@5'-GGA...AAGAA GCCAG...AGG-3'@LB@ UAGUGGCGAUGC@LB@ :\|\|\|\|\|\|:\|\|\|\|@LB@ GUCACCGUUACG@LB@3'-UUU...UUUUA UUACC...UUG-5'@LB@ \| \|@LB@ 59 46@LB@@LB@@LB@Energy -11.25 kcal/mol@LB@Hybridization Energy -20.0531 kcal/mol@LB@Unfolding Energy - mRNA 5.42731 kcal/mol@LB@Unfolding Energy - sRNA 3.37136 kcal/mol@LB@@LB@Position - mRNA 113 -- 124@LB@Position - sRNA 47 -- 58@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 47 -- 53@LB@
178	0.02184	0.4127	b1466	narW	-11.23	0.066200	254 -- 267	42 -- 56	nitrate reductase 2 (NRZ) delta subunit (assembly subunit)	_____________253_____________268\n_____________\|_______________\|\n5'-AUU...CUGUU____G__________AGGAC...CGC-3'\n______________GUGG_AAUGCAA_GG\n______________\|\|\|\|_\|\|\|\|\|\|\|_\|\|\n______________CACC_UUACGUU_CC\n3'-UUU...UUAGU____G_______A__GGGUU...UUG-5'\n_____________\|_______________\|\n_____________57______________41\n	259 -- 265	45 -- 51	-17.8423 kcal/mol	3.07693 kcal/mol	3.53153 kcal/mol	253 268@LB@ \| \|@LB@5'-AUU...CUGUU G AGGAC...CGC-3'@LB@ GUGG AAUGCAA GG@LB@ \|\|\|\| \|\|\|\|\|\|\| \|\|@LB@ CACC UUACGUU CC@LB@3'-UUU...UUAGU G A GGGUU...UUG-5'@LB@ \| \|@LB@ 57 41@LB@@LB@@LB@Energy -11.23 kcal/mol@LB@Hybridization Energy -17.8423 kcal/mol@LB@Unfolding Energy - mRNA 3.07693 kcal/mol@LB@Unfolding Energy - sRNA 3.53153 kcal/mol@LB@@LB@Position - mRNA 254 -- 267@LB@Position - sRNA 42 -- 56@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 45 -- 51@LB@
151	0.01786	0.3828	b0412	yajI	-11.20	0.067280	41 -- 55	41 -- 54	putative lipoprotein	_____________40______________56\n_____________\|_______________\|\n5'-CGA...GAAUG_________UAC___GUCCU...UCA-3'\n______________GGCAAUGCA___GGC\n______________\|\|\|\|\|\|\|\|\|___\|\|\|\n______________CCGUUACGU___CCG\n3'-UUU...AGUCA_________UA____GGUUG...UUG-5'\n_____________\|_______________\|\n_____________55______________40\n	43 -- 49	46 -- 52	-19.8433 kcal/mol	4.75092 kcal/mol	3.89026 kcal/mol	40 56@LB@ \| \|@LB@5'-CGA...GAAUG UAC GUCCU...UCA-3'@LB@ GGCAAUGCA GGC@LB@ \|\|\|\|\|\|\|\|\| \|\|\|@LB@ CCGUUACGU CCG@LB@3'-UUU...AGUCA UA GGUUG...UUG-5'@LB@ \| \|@LB@ 55 40@LB@@LB@@LB@Energy -11.20 kcal/mol@LB@Hybridization Energy -19.8433 kcal/mol@LB@Unfolding Energy - mRNA 4.75092 kcal/mol@LB@Unfolding Energy - sRNA 3.89026 kcal/mol@LB@@LB@Position - mRNA 41 -- 55@LB@Position - sRNA 41 -- 54@LB@Position Seed - mRNA 43 -- 49@LB@Position Seed - sRNA 46 -- 52@LB@
95	0.008588	0.304	b4551	yheV	-11.20	0.067476	257 -- 273	47 -- 65	DUF2387 family putative metal-binding protein	_____________256_________________274\n_____________\|___________________\|\n5'-AUC...GCGCA___U_____A_________GGCGC...UUG-3'\n______________GGA___UCA_UGGCGAUGU\n______________\|\|\|___\|\|\|_\|\|\|\|:\|\|\|:\n______________CCU___AGU_ACCGUUACG\n3'-UUU...UACAA___UUU___C_________UUACC...UUG-5'\n_____________\|___________________\|\n_____________66__________________46\n	267 -- 273	47 -- 53	-19.3348 kcal/mol	4.06987 kcal/mol	4.06844 kcal/mol	256 274@LB@ \| \|@LB@5'-AUC...GCGCA U A GGCGC...UUG-3'@LB@ GGA UCA UGGCGAUGU@LB@ \|\|\| \|\|\| \|\|\|\|:\|\|\|:@LB@ CCU AGU ACCGUUACG@LB@3'-UUU...UACAA UUU C UUACC...UUG-5'@LB@ \| \|@LB@ 66 46@LB@@LB@@LB@Energy -11.20 kcal/mol@LB@Hybridization Energy -19.3348 kcal/mol@LB@Unfolding Energy - mRNA 4.06987 kcal/mol@LB@Unfolding Energy - sRNA 4.06844 kcal/mol@LB@@LB@Position - mRNA 257 -- 273@LB@Position - sRNA 47 -- 65@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 47 -- 53@LB@
36	0.002273	0.2088	b4138	dcuA	-11.14	0.069498	259 -- 284	41 -- 65	C4-dicarboxylate antiporter	_____________258__________________________285\n_____________\|____________________________\|\n5'-AAC...AUUGG_______A___AUU___UU_________GGAUU...UGG-3'\n______________GGGGAAU_GGU___GGU__UGCA__GGC\n______________\|\|::\|\|\|_:\|\|___\|\|:__\|\|\|\|__\|\|\|\n______________CCUUUUA_UCA___CCG__ACGU__CCG\n3'-UUU...UACAA_______G_________UU____UA___GGUUG...UUG-5'\n_____________\|____________________________\|\n_____________66___________________________40\n	259 -- 265	59 -- 65	-20.3442 kcal/mol	3.39574 kcal/mol	5.80973 kcal/mol	258 285@LB@ \| \|@LB@5'-AAC...AUUGG A AUU UU GGAUU...UGG-3'@LB@ GGGGAAU GGU GGU UGCA GGC@LB@ \|\|::\|\|\| :\|\| \|\|: \|\|\|\| \|\|\|@LB@ CCUUUUA UCA CCG ACGU CCG@LB@3'-UUU...UACAA G UU UA GGUUG...UUG-5'@LB@ \| \|@LB@ 66 40@LB@@LB@@LB@Energy -11.14 kcal/mol@LB@Hybridization Energy -20.3442 kcal/mol@LB@Unfolding Energy - mRNA 3.39574 kcal/mol@LB@Unfolding Energy - sRNA 5.80973 kcal/mol@LB@@LB@Position - mRNA 259 -- 284@LB@Position - sRNA 41 -- 65@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 59 -- 65@LB@
12	0.0004505	0.1262	b3248	yhdE	-11.12	0.070056	184 -- 205	1 -- 21	dTTP/UTP pyrophosphatase; m(5)UTP/m(5)CTP/pseudo-UTP pyrophosphatase	_____________183_____________________206\n_____________\|_______________________\|\n5'-UUA...UUGCA______________UUC______UUCUC...AGC-3'\n______________GUG_CAAUAAAGGU___UAUGAC\n______________\|\|\|_\|\|\|\|\|\|\|\|\|:___\|\|\|:\|\|\n______________CAC_GUUAUUUCCG___AUAUUG\n3'-UUU...UUAGA___U__________U________-5'\n_____________\|______________________\|\n_____________22_____________________1\n	190 -- 196	8 -- 14	-19.9684 kcal/mol	4.43203 kcal/mol	4.41334 kcal/mol	183 206@LB@ \| \|@LB@5'-UUA...UUGCA UUC UUCUC...AGC-3'@LB@ GUG CAAUAAAGGU UAUGAC@LB@ \|\|\| \|\|\|\|\|\|\|\|\|: \|\|\|:\|\|@LB@ CAC GUUAUUUCCG AUAUUG@LB@3'-UUU...UUAGA U U -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -19.9684 kcal/mol@LB@Unfolding Energy - mRNA 4.43203 kcal/mol@LB@Unfolding Energy - sRNA 4.41334 kcal/mol@LB@@LB@Position - mRNA 184 -- 205@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 8 -- 14@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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