Input and runtime details for job 2727377 (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 2727377 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:09 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:28 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:18:35 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:18:43 CET 2018
	Job Completed		@ Fri Feb 16 20:19:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=2727377&toolName=CopraRNA ( 30 days expiry )

Description of the job

RyhB

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
143	0.01687	0.3964	b3103	yhaH	-11.09	0.125996	208 -- 287	3 -- 67	DUF805 family inner membrane protein	_____________207_________________________________________________________________________________288\n_____________\|___________________________________________________________________________________\|\n5'-AUU...GGACU____U_____A_____CUAAAAAAUU___________C____G__G_G_____CGCAAAGAGUACU__AU____A________AACAU...UUA-3'\n______________GGUA___CUG_AAGUA__________AUGUCG_GUUU_CGGG_UC_U_CGCGG_____________GG__GUUU_UUCUGGUC\n______________:\|\|\|___\|\|\|_\|\|\|:\|__________\|\|\|\|\|\|_\|:\|\|_\|:\|\|_\|\|_\|_\|\|\|\|:_____________\|\|__\|\|:\|_\|:\|\|\|:\|\|\n______________UCAU___GAC_UUCGU__________UACAGC_CGAA_GUCC_AG_A_GCGCU_____________CC__CAGA_AGGACUAG\n3'-UUU...CCGAU____UAU___C_____UACACUCGU_______A____A____A____G___________________________________CG-5'\n_____________\|___________________________________________________________________________________\|\n_____________68__________________________________________________________________________________2\n	281 -- 287	3 -- 9	-42.8726 kcal/mol	17.657 kcal/mol	14.1245 kcal/mol	207 288@LB@ \| \|@LB@5'-AUU...GGACU U A CUAAAAAAUU C G G G CGCAAAGAGUACU AU A AACAU...UUA-3'@LB@ GGUA CUG AAGUA AUGUCG GUUU CGGG UC U CGCGG GG GUUU UUCUGGUC@LB@ :\|\|\| \|\|\| \|\|\|:\| \|\|\|\|\|\| \|:\|\| \|:\|\| \|\| \| \|\|\|\|: \|\| \|\|:\| \|:\|\|\|:\|\|@LB@ UCAU GAC UUCGU UACAGC CGAA GUCC AG A GCGCU CC CAGA AGGACUAG@LB@3'-UUU...CCGAU UAU C UACACUCGU A A A G CG-5'@LB@ \| \|@LB@ 68 2@LB@@LB@@LB@Energy -11.09 kcal/mol@LB@Hybridization Energy -42.8726 kcal/mol@LB@Unfolding Energy - mRNA 17.657 kcal/mol@LB@Unfolding Energy - sRNA 14.1245 kcal/mol@LB@@LB@Position - mRNA 208 -- 287@LB@Position - sRNA 3 -- 67@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 3 -- 9@LB@
188	0.02302	0.4113	b3105	yhaJ	-12.66	0.069284	224 -- 245	40 -- 61	LysR family putative transcriptional regulator	_____________223____________________246\n_____________\|______________________\|\n5'-CGG...UUAAC__________CUAC____U___GAUGC...GCG-3'\n______________GCUGGAAGCA____GGGU_AUG\n______________:\|\|\|\|\|\|\|\|\|____\|:\|:_\|\|\|\n______________UGACCUUCGU____CUCG_UAC\n3'-UUU...CAUUA__________UACA____U___AGCAC...GCG-5'\n_____________\|______________________\|\n_____________62_____________________39\n	227 -- 233	52 -- 58	-21.8067 kcal/mol	5.84576 kcal/mol	3.30075 kcal/mol	223 246@LB@ \| \|@LB@5'-CGG...UUAAC CUAC U GAUGC...GCG-3'@LB@ GCUGGAAGCA GGGU AUG@LB@ :\|\|\|\|\|\|\|\|\| \|:\|: \|\|\|@LB@ UGACCUUCGU CUCG UAC@LB@3'-UUU...CAUUA UACA U AGCAC...GCG-5'@LB@ \| \|@LB@ 62 39@LB@@LB@@LB@Energy -12.66 kcal/mol@LB@Hybridization Energy -21.8067 kcal/mol@LB@Unfolding Energy - mRNA 5.84576 kcal/mol@LB@Unfolding Energy - sRNA 3.30075 kcal/mol@LB@@LB@Position - mRNA 224 -- 245@LB@Position - sRNA 40 -- 61@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 52 -- 58@LB@
81	0.008086	0.3318	b3114	tdcE	-10.99	0.130865	237 -- 290	38 -- 86	pyruvate formate-lyase 4/2-ketobutyrate formate-lyase	_____________236_____________________________________________________291\n_____________\|_______________________________________________________\|\n5'-AGA...UGUAC____A___A____U_____UUAA_____CGG_______AAACGAAAU________CGCGA...UUA-3'\n______________GCCG_CGC_UGGC_UGGCU____AGGUA___ACUGGAA__________UAAUGUC\n______________\|\|\|:_\|:\|_:\|\|\|_\|\|\|\|\|____\|:\|\|\|___\|\|\|\|\|\|\|__________:\|\|\|\|\|\|\n______________CGGU_GUG_GCCG_ACCGA____UUCAU___UGACCUU__________GUUACAG\n_______3'-UUUU____C___G___________________UA________CGUUACACUC_______CACGA...GCG-5'\n_____________\|_______________________________________________________\|\n_____________87______________________________________________________37\n	284 -- 290	38 -- 44	-39.8415 kcal/mol	13.9412 kcal/mol	14.9106 kcal/mol	236 291@LB@ \| \|@LB@5'-AGA...UGUAC A A U UUAA CGG AAACGAAAU CGCGA...UUA-3'@LB@ GCCG CGC UGGC UGGCU AGGUA ACUGGAA UAAUGUC@LB@ \|\|\|: \|:\| :\|\|\| \|\|\|\|\| \|:\|\|\| \|\|\|\|\|\|\| :\|\|\|\|\|\|@LB@ CGGU GUG GCCG ACCGA UUCAU UGACCUU GUUACAG@LB@ 3'-UUUU C G UA CGUUACACUC CACGA...GCG-5'@LB@ \| \|@LB@ 87 37@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -39.8415 kcal/mol@LB@Unfolding Energy - mRNA 13.9412 kcal/mol@LB@Unfolding Energy - sRNA 14.9106 kcal/mol@LB@@LB@Position - mRNA 237 -- 290@LB@Position - sRNA 38 -- 86@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 38 -- 44@LB@
102	0.01034	0.3393	b3128	garD	-8.06	0.364232	93 -- 113	5 -- 25	D-galactarate dehydrogenase	_____________92____________________114\n_____________\|_____________________\|\n5'-AUA...UCACA________UUUAAAC______CAUUC...UGA-3'\n______________UUUCUGCG_______UCCUGA\n______________\|:\|\|:\|\|\|_______\|\|\|\|\|\|\n______________AGAGGCGC_______AGGACU\n3'-UUU...GUCCA________UCCCAGA______AGCG-5'\n_____________\|_____________________\|\n_____________26____________________4\n	94 -- 100	18 -- 24	-19.1191 kcal/mol	3.34271 kcal/mol	7.71155 kcal/mol	92 114@LB@ \| \|@LB@5'-AUA...UCACA UUUAAAC CAUUC...UGA-3'@LB@ UUUCUGCG UCCUGA@LB@ \|:\|\|:\|\|\| \|\|\|\|\|\|@LB@ AGAGGCGC AGGACU@LB@3'-UUU...GUCCA UCCCAGA AGCG-5'@LB@ \| \|@LB@ 26 4@LB@@LB@@LB@Energy -8.06 kcal/mol@LB@Hybridization Energy -19.1191 kcal/mol@LB@Unfolding Energy - mRNA 3.34271 kcal/mol@LB@Unfolding Energy - sRNA 7.71155 kcal/mol@LB@@LB@Position - mRNA 93 -- 113@LB@Position - sRNA 5 -- 25@LB@Position Seed - mRNA 94 -- 100@LB@Position Seed - sRNA 18 -- 24@LB@
25	0.002073	0.2692	b3163	nlpI	-16.34	0.016289	1 -- 45	38 -- 89	lipoprotein involved in osmotic sensitivity and filamentation	______________1____________________________________________________46\n______________\|____________________________________________________\|\n___________5'-______________U___A__AUUAAA_____________C_________C__AACCU...CAU-3'\n______________AGGGCC_GUAUCCG_CUG_GC____________GAAGCGA__UGAGCAGU_UC\n______________\|::\|\|\|_\|:\|:\|\|\|_\|\|\|_\|\|____________\|\|\|\|\|:\|__\|\|\|\|\|\|:\|_\|\|\n______________UUUCGG_CGUGGGC_GAC_CG____________CUUCGUU__ACUCGUUA_AG\n__________3'-U______U_______C______AUUCAUUAUGAC_______AC________C__CACGA...GCG-5'\n_____________\|_____________________________________________________\|\n_____________90____________________________________________________37\n	36 -- 42	41 -- 47	-40.4977 kcal/mol	9.24688 kcal/mol	14.9106 kcal/mol	1 46@LB@ \| \|@LB@ 5'- U A AUUAAA C C AACCU...CAU-3'@LB@ AGGGCC GUAUCCG CUG GC GAAGCGA UGAGCAGU UC@LB@ \|::\|\|\| \|:\|:\|\|\| \|\|\| \|\| \|\|\|\|\|:\| \|\|\|\|\|\|:\| \|\|@LB@ UUUCGG CGUGGGC GAC CG CUUCGUU ACUCGUUA AG@LB@ 3'-U U C AUUCAUUAUGAC AC C CACGA...GCG-5'@LB@ \| \|@LB@ 90 37@LB@@LB@@LB@Energy -16.34 kcal/mol@LB@Hybridization Energy -40.4977 kcal/mol@LB@Unfolding Energy - mRNA 9.24688 kcal/mol@LB@Unfolding Energy - sRNA 14.9106 kcal/mol@LB@@LB@Position - mRNA 1 -- 45@LB@Position - sRNA 38 -- 89@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 41 -- 47@LB@
49	0.004671	0.2905	b3184	yhbE	-14.90	0.028775	284 -- 299	49 -- 64	EamA family inner membrane putative transporter	_____________283______________300\n_____________\|________________\|\n5'-AAG...AAGCA________________G-3'\n______________GGUGCUGGAGGUGAUG\n______________::\|:\|\|\|\|\|:\|::\|\|\|\n______________UUAUGACCUUCGUUAC\n3'-UUU...AUUCA________________ACUCG...GCG-5'\n_____________\|________________\|\n_____________65_______________48\n	293 -- 299	49 -- 55	-22.6177 kcal/mol	4.70237 kcal/mol	3.01036 kcal/mol	283 300@LB@ \| \|@LB@5'-AAG...AAGCA G-3'@LB@ GGUGCUGGAGGUGAUG@LB@ ::\|:\|\|\|\|\|:\|::\|\|\|@LB@ UUAUGACCUUCGUUAC@LB@3'-UUU...AUUCA ACUCG...GCG-5'@LB@ \| \|@LB@ 65 48@LB@@LB@@LB@Energy -14.90 kcal/mol@LB@Hybridization Energy -22.6177 kcal/mol@LB@Unfolding Energy - mRNA 4.70237 kcal/mol@LB@Unfolding Energy - sRNA 3.01036 kcal/mol@LB@@LB@Position - mRNA 284 -- 299@LB@Position - sRNA 49 -- 64@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 49 -- 55@LB@
142	0.01677	0.3964	b3208	mtgA	-9.50	0.224857	30 -- 43	54 -- 67	biosynthetic peptidoglycan transglycosylase	_____________29_____________44\n_____________\|______________\|\n5'-UUG...ACCGC__A___________AGAUG...UGU-3'\n______________AG_AGUGCUGGAAG\n______________\|\|_\|:\|:\|\|\|\|\|\|\|\n______________UC_UUAUGACCUUC\n3'-UUU...CCGAU__A___________GUUAC...GCG-5'\n_____________\|______________\|\n_____________68_____________53\n	37 -- 43	54 -- 60	-16.1342 kcal/mol	3.92242 kcal/mol	2.71077 kcal/mol	29 44@LB@ \| \|@LB@5'-UUG...ACCGC A AGAUG...UGU-3'@LB@ AG AGUGCUGGAAG@LB@ \|\| \|:\|:\|\|\|\|\|\|\|@LB@ UC UUAUGACCUUC@LB@3'-UUU...CCGAU A GUUAC...GCG-5'@LB@ \| \|@LB@ 68 53@LB@@LB@@LB@Energy -9.50 kcal/mol@LB@Hybridization Energy -16.1342 kcal/mol@LB@Unfolding Energy - mRNA 3.92242 kcal/mol@LB@Unfolding Energy - sRNA 2.71077 kcal/mol@LB@@LB@Position - mRNA 30 -- 43@LB@Position - sRNA 54 -- 67@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 54 -- 60@LB@
28	0.002335	0.2776	b3248	yhdE	-16.83	0.013392	101 -- 153	6 -- 68	dTTP/UTP pyrophosphatase; m(5)UTP/m(5)CTP/pseudo-UTP pyrophosphatase	_____________100______________________________________________________________154\n_____________\|________________________________________________________________\|\n5'-UUA...ACCGG_____U__________________U_____GG_____CU______________A__________CUGAU...AGC-3'\n______________AAGUG_U_CUGG_AGUAGUGU_AG_CAAUG__GUGCU____GG____CCGUGG___UUUUCUUG\n______________\|\|\|\|:_\|_\|\|\|\|_\|\|:\|:\|\|\|_\|\|_\|\|\|\|\|__\|\|\|\|\|____\|\|____\|\|\|:\|:___\|:\|\|\|:\|\|\n______________UUCAU_A_GACC_UCGUUACA_UC_GUUAC__CACGA____CC____GGCGCU___AGAAGGAC\n3'-UUU...ACCGA_____U_U____U________C________AG_____AAGU__AAGA______CCC________UAGCG-5'\n_____________\|________________________________________________________________\|\n_____________69_______________________________________________________________5\n	147 -- 153	6 -- 12	-47.0166 kcal/mol	16.0597 kcal/mol	14.1245 kcal/mol	100 154@LB@ \| \|@LB@5'-UUA...ACCGG U U GG CU A CUGAU...AGC-3'@LB@ AAGUG U CUGG AGUAGUGU AG CAAUG GUGCU GG CCGUGG UUUUCUUG@LB@ \|\|\|\|: \| \|\|\|\| \|\|:\|:\|\|\| \|\| \|\|\|\|\| \|\|\|\|\| \|\| \|\|\|:\|: \|:\|\|\|:\|\|@LB@ UUCAU A GACC UCGUUACA UC GUUAC CACGA CC GGCGCU AGAAGGAC@LB@3'-UUU...ACCGA U U U C AG AAGU AAGA CCC UAGCG-5'@LB@ \| \|@LB@ 69 5@LB@@LB@@LB@Energy -16.83 kcal/mol@LB@Hybridization Energy -47.0166 kcal/mol@LB@Unfolding Energy - mRNA 16.0597 kcal/mol@LB@Unfolding Energy - sRNA 14.1245 kcal/mol@LB@@LB@Position - mRNA 101 -- 153@LB@Position - sRNA 6 -- 68@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 6 -- 12@LB@
150	0.01825	0.4072	b3255	accB	-12.43	0.075652	231 -- 278	1 -- 47	acetyl CoA carboxylase BCCP subunit	_____________230_______________________________________________279\n_____________\|_________________________________________________\|\n5'-UUU...UGAUC____UG_____AAGAA_____CA______AACU__AAA_______AG__GAAGA...GCC-3'\n______________GAGC___GUUG_____UCAGG__UCUCCG____GG___UUUCUGA__GC\n______________\|\|\|\|___\|\|:\|_____\|\|\|\|\|__\|\|\|\|\|\|____\|\|___\|\|:\|\|\|\|__\|\|\n______________CUCG___CAGC_____AGUCC__AGAGGC____CC___AAGGACU__CG\n3'-UUU...UUACA____UUA____ACGAA_____A_______GCU___CAG_______AG__-5'\n_____________\|________________________________________________\|\n_____________48_______________________________________________1\n	268 -- 274	5 -- 11	-38.2829 kcal/mol	12.4901 kcal/mol	13.3604 kcal/mol	230 279@LB@ \| \|@LB@5'-UUU...UGAUC UG AAGAA CA AACU AAA AG GAAGA...GCC-3'@LB@ GAGC GUUG UCAGG UCUCCG GG UUUCUGA GC@LB@ \|\|\|\| \|\|:\| \|\|\|\|\| \|\|\|\|\|\| \|\| \|\|:\|\|\|\| \|\|@LB@ CUCG CAGC AGUCC AGAGGC CC AAGGACU CG@LB@3'-UUU...UUACA UUA ACGAA A GCU CAG AG -5'@LB@ \| \|@LB@ 48 1@LB@@LB@@LB@Energy -12.43 kcal/mol@LB@Hybridization Energy -38.2829 kcal/mol@LB@Unfolding Energy - mRNA 12.4901 kcal/mol@LB@Unfolding Energy - sRNA 13.3604 kcal/mol@LB@@LB@Position - mRNA 231 -- 278@LB@Position - sRNA 1 -- 47@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 5 -- 11@LB@
63	0.005616	0.2905	b3261	fis	-12.93	0.062484	136 -- 161	37 -- 61	global DNA-binding transcriptional dual regulator	_____________135________________________162\n_____________\|__________________________\|\n5'-GGA...GAACA__________U__GA____UACU___AAAAU...AGG-3'\n______________GCUGGAGGCG_UG__GGCA____UCG\n______________:\|\|\|\|\|:\|\|:_\|\|__:\|\|\|____\|\|\|\n______________UGACCUUCGU_AC__UCGU____AGC\n3'-UUU...CAUUA__________U__AC____UAC____ACGAA...GCG-5'\n_____________\|__________________________\|\n_____________62_________________________36\n	139 -- 145	52 -- 58	-26.9705 kcal/mol	10.742 kcal/mol	3.30158 kcal/mol	135 162@LB@ \| \|@LB@5'-GGA...GAACA U GA UACU AAAAU...AGG-3'@LB@ GCUGGAGGCG UG GGCA UCG@LB@ :\|\|\|\|\|:\|\|: \|\| :\|\|\| \|\|\|@LB@ UGACCUUCGU AC UCGU AGC@LB@3'-UUU...CAUUA U AC UAC ACGAA...GCG-5'@LB@ \| \|@LB@ 62 36@LB@@LB@@LB@Energy -12.93 kcal/mol@LB@Hybridization Energy -26.9705 kcal/mol@LB@Unfolding Energy - mRNA 10.742 kcal/mol@LB@Unfolding Energy - sRNA 3.30158 kcal/mol@LB@@LB@Position - mRNA 136 -- 161@LB@Position - sRNA 37 -- 61@LB@Position Seed - mRNA 139 -- 145@LB@Position Seed - sRNA 52 -- 58@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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