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
71	0.00621	0.2939	b0178	skp	-11.69	0.100677	99 -- 118	40 -- 66	periplasmic chaperone	_____________98__________________________119\n_____________\|___________________________\|\n5'-CUC...GGAAU___________________________ACUUU...UCC-3'\n______________GUAGU______GGUAGUGU_AGCGAUG\n______________\|\|\|:\|______:\|:\|:\|\|\|_\|\|\|:\|\|\|\n______________CAUUA______UCGUUACA_UCGUUAC\n3'-UUU...CGAUU_____UGACCU________C_______AGCAC...GCG-5'\n_____________\|___________________________\|\n_____________67__________________________39\n	112 -- 118	40 -- 46	-18.9809 kcal/mol	3.99027 kcal/mol	3.30497 kcal/mol	98 119@LB@ \| \|@LB@5'-CUC...GGAAU ACUUU...UCC-3'@LB@ GUAGU GGUAGUGU AGCGAUG@LB@ \|\|\|:\| :\|:\|:\|\|\| \|\|\|:\|\|\|@LB@ CAUUA UCGUUACA UCGUUAC@LB@3'-UUU...CGAUU UGACCU C AGCAC...GCG-5'@LB@ \| \|@LB@ 67 39@LB@@LB@@LB@Energy -11.69 kcal/mol@LB@Hybridization Energy -18.9809 kcal/mol@LB@Unfolding Energy - mRNA 3.99027 kcal/mol@LB@Unfolding Energy - sRNA 3.30497 kcal/mol@LB@@LB@Position - mRNA 99 -- 118@LB@Position - sRNA 40 -- 66@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 40 -- 46@LB@
72	0.00645	0.301	b2125	yehT	-9.24	0.246554	1 -- 8	14 -- 21	putative response regulator in two-component system withYehU	______________1_______9\n______________\|_______\|\n___________5'-________GCAAC...GUU-3'\n______________CGUGAGGG\n______________\|\|:\|\|\|\|\|\n______________GCGCUCCC\n3'-UUU...AAGAG________AGAAG...GCG-5'\n_____________\|________\|\n_____________22_______13\n	2 -- 8	14 -- 20	-15.432 kcal/mol	1.85513 kcal/mol	4.33947 kcal/mol	1 9@LB@ \| \|@LB@ 5'- GCAAC...GUU-3'@LB@ CGUGAGGG@LB@ \|\|:\|\|\|\|\|@LB@ GCGCUCCC@LB@3'-UUU...AAGAG AGAAG...GCG-5'@LB@ \| \|@LB@ 22 13@LB@@LB@@LB@Energy -9.24 kcal/mol@LB@Hybridization Energy -15.432 kcal/mol@LB@Unfolding Energy - mRNA 1.85513 kcal/mol@LB@Unfolding Energy - sRNA 4.33947 kcal/mol@LB@@LB@Position - mRNA 1 -- 8@LB@Position - sRNA 14 -- 21@LB@Position Seed - mRNA 2 -- 8@LB@Position Seed - sRNA 14 -- 20@LB@
73	0.006758	0.3082	b0073	leuB	-14.41	0.035044	252 -- 295	42 -- 89	3-isopropylmalate dehydrogenase NAD(+)-dependent	_____________251_______________________________________________296\n_____________\|_________________________________________________\|\n5'-AAA...GUCCG_____G_UG____A__________A__________U__C_____C____CCGCU-3'\n______________GAAGU_A__ACCC_GGC__GCUGA__AGUGCUGGA_GC___GUG_GCAA\n______________:\|\|\|:_\|__\|\|\|\|_\|\|\|__\|\|\|:\|__\|:\|:\|\|\|\|\|_\|\|___\|\|\|_\|\|\|\|\n______________UUUCG_U__UGGG_CCG__CGAUU__UUAUGACCU_CG___CAC_CGUU\n__________3'-U_____G_CG________AC_____CA_________U__UUA___U____ACAGC...GCG-5'\n_____________\|_________________________________________________\|\n_____________90________________________________________________41\n	277 -- 283	56 -- 62	-44.364 kcal/mol	15.0484 kcal/mol	14.9103 kcal/mol	251 296@LB@ \| \|@LB@5'-AAA...GUCCG G UG A A U C C CCGCU-3'@LB@ GAAGU A ACCC GGC GCUGA AGUGCUGGA GC GUG GCAA@LB@ :\|\|\|: \| \|\|\|\| \|\|\| \|\|\|:\| \|:\|:\|\|\|\|\| \|\| \|\|\| \|\|\|\|@LB@ UUUCG U UGGG CCG CGAUU UUAUGACCU CG CAC CGUU@LB@ 3'-U G CG AC CA U UUA U ACAGC...GCG-5'@LB@ \| \|@LB@ 90 41@LB@@LB@@LB@Energy -14.41 kcal/mol@LB@Hybridization Energy -44.364 kcal/mol@LB@Unfolding Energy - mRNA 15.0484 kcal/mol@LB@Unfolding Energy - sRNA 14.9103 kcal/mol@LB@@LB@Position - mRNA 252 -- 295@LB@Position - sRNA 42 -- 89@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 56 -- 62@LB@
74	0.006788	0.3082	b3525	yhjH	-16.42	0.015793	272 -- 288	44 -- 60	cyclic-di-GMP phosphodiesterase FlhDC-regulated	_____________271_______________289\n_____________\|_________________\|\n5'-UUA...CGUUU____UU___________GUGCU...CCU-3'\n______________UUGG__GCAGUGUGAGC\n______________:\|\|\|__\|\|\|:\|\|\|\|\|\|\|\n______________GACC__CGUUACACUCG\n3'-UUU...AUUAU____UU___________UUACA...GCG-5'\n_____________\|_________________\|\n_____________61________________43\n	279 -- 285	47 -- 53	-25.6078 kcal/mol	5.89114 kcal/mol	3.2985 kcal/mol	271 289@LB@ \| \|@LB@5'-UUA...CGUUU UU GUGCU...CCU-3'@LB@ UUGG GCAGUGUGAGC@LB@ :\|\|\| \|\|\|:\|\|\|\|\|\|\|@LB@ GACC CGUUACACUCG@LB@3'-UUU...AUUAU UU UUACA...GCG-5'@LB@ \| \|@LB@ 61 43@LB@@LB@@LB@Energy -16.42 kcal/mol@LB@Hybridization Energy -25.6078 kcal/mol@LB@Unfolding Energy - mRNA 5.89114 kcal/mol@LB@Unfolding Energy - sRNA 3.2985 kcal/mol@LB@@LB@Position - mRNA 272 -- 288@LB@Position - sRNA 44 -- 60@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 47 -- 53@LB@
75	0.007199	0.3134	b2167	fruA	-15.16	0.026023	90 -- 122	43 -- 84	fused fructose-specific PTS enzymes: IIBcomponent/IIC components	_____________89_________________________________________123\n_____________\|__________________________________________\|\n5'-CGC...UGUUG____________________CA____________________UUACC...AAA-3'\n______________CAGC_CCUGGC_GG_UAAGU________AAGCAAUGUGGGUA\n______________\|\|\|\|_\|\|:\|\|\|_\|\|_\|\|\|\|\|________\|\|\|\|\|\|\|\|\|\|:\|:\|\n______________GUCG_GGGCCG_CC_AUUCA________UUCGUUACACUCGU\n_____3'-UUUUCG____U______A__G_____UUAUGACC______________UACAG...GCG-5'\n_____________\|__________________________________________\|\n_____________85_________________________________________42\n	116 -- 122	43 -- 49	-41.7817 kcal/mol	11.7261 kcal/mol	14.8963 kcal/mol	89 123@LB@ \| \|@LB@5'-CGC...UGUUG CA UUACC...AAA-3'@LB@ CAGC CCUGGC GG UAAGU AAGCAAUGUGGGUA@LB@ \|\|\|\| \|\|:\|\|\| \|\| \|\|\|\|\| \|\|\|\|\|\|\|\|\|\|:\|:\|@LB@ GUCG GGGCCG CC AUUCA UUCGUUACACUCGU@LB@ 3'-UUUUCG U A G UUAUGACC UACAG...GCG-5'@LB@ \| \|@LB@ 85 42@LB@@LB@@LB@Energy -15.16 kcal/mol@LB@Hybridization Energy -41.7817 kcal/mol@LB@Unfolding Energy - mRNA 11.7261 kcal/mol@LB@Unfolding Energy - sRNA 14.8963 kcal/mol@LB@@LB@Position - mRNA 90 -- 122@LB@Position - sRNA 43 -- 84@LB@Position Seed - mRNA 116 -- 122@LB@Position Seed - sRNA 43 -- 49@LB@
76	0.007246	0.3134	b4174	hflK	-10.43	0.160892	249 -- 292	51 -- 90	modulator for HflB protease specific for phage lambda cII repressor	_____________248_____________________________________________293\n_____________\|_______________________________________________\|\n5'-AGA...CGUGG__________AA___________AACUC____GGAAA______A___AGGCGGUC-3'\n______________GGAAG_CAGC__ACCUGGC_GGC_____UGAG______UGGAA_CAA\n______________::\|\|\|_\|\|\|\|__\|\|\|:\|\|\|_\|\|\|_____\|:\|\|______\|\|\|\|\|_\|\|\|\n______________UUUUC_GUCG__UGGGCCG_CCG_____AUUC______ACCUU_GUU\n___________3'-_____G_____________A____________AUUAUG_____C___ACACU...GCG-5'\n______________\|______________________________________________\|\n______________90_____________________________________________50\n	260 -- 266	74 -- 80	-34.0568 kcal/mol	9.12339 kcal/mol	14.5017 kcal/mol	248 293@LB@ \| \|@LB@5'-AGA...CGUGG AA AACUC GGAAA A AGGCGGUC-3'@LB@ GGAAG CAGC ACCUGGC GGC UGAG UGGAA CAA@LB@ ::\|\|\| \|\|\|\| \|\|\|:\|\|\| \|\|\| \|:\|\| \|\|\|\|\| \|\|\|@LB@ UUUUC GUCG UGGGCCG CCG AUUC ACCUU GUU@LB@ 3'- G A AUUAUG C ACACU...GCG-5'@LB@ \| \|@LB@ 90 50@LB@@LB@@LB@Energy -10.43 kcal/mol@LB@Hybridization Energy -34.0568 kcal/mol@LB@Unfolding Energy - mRNA 9.12339 kcal/mol@LB@Unfolding Energy - sRNA 14.5017 kcal/mol@LB@@LB@Position - mRNA 249 -- 292@LB@Position - sRNA 51 -- 90@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 74 -- 80@LB@
77	0.00734	0.3134	b1793	yoaF	-12.59	0.071143	233 -- 250	68 -- 86	DUF333 family outer membrane lipoprotein	_____________232_________________251\n_____________\|___________________\|\n5'-GAU...UGCUU___________________UUCAA...UGG-3'\n______________GCUGGU_CCUGGCUGGUUG\n______________\|\|::\|:_\|\|:\|\|\|\|\|\|:\|:\n______________CGGUCG_GGGCCGACCGAU\n_______3'-UUUU______U____________UCAUU...GCG-5'\n_____________\|___________________\|\n_____________87__________________67\n	243 -- 249	69 -- 75	-29.581 kcal/mol	5.32768 kcal/mol	11.6617 kcal/mol	232 251@LB@ \| \|@LB@5'-GAU...UGCUU UUCAA...UGG-3'@LB@ GCUGGU CCUGGCUGGUUG@LB@ \|\|::\|: \|\|:\|\|\|\|\|\|:\|:@LB@ CGGUCG GGGCCGACCGAU@LB@ 3'-UUUU U UCAUU...GCG-5'@LB@ \| \|@LB@ 87 67@LB@@LB@@LB@Energy -12.59 kcal/mol@LB@Hybridization Energy -29.581 kcal/mol@LB@Unfolding Energy - mRNA 5.32768 kcal/mol@LB@Unfolding Energy - sRNA 11.6617 kcal/mol@LB@@LB@Position - mRNA 233 -- 250@LB@Position - sRNA 68 -- 86@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 69 -- 75@LB@
78	0.00737	0.3134	b2299	yfcD	-10.35	0.165972	38 -- 78	49 -- 90	putative NUDIX hydrolase	_____________37__________________________________________79\n_____________\|___________________________________________\|\n5'-AGA...AUUCC_____G____A_______GA____U_GC_______________ACGUA...AGU-3'\n______________GAAAG_CGGU_AUCCGGC__GUUA_G__AUGCUGGA__UAAUG\n______________:\|\|\|\|_\|:\|:_\|:\|\|\|\|\|__\|:\|\|_\|__\|\|:\|\|\|\|\|__:\|\|\|\|\n______________UUUUC_GUCG_UGGGCCG__CGAU_C__UAUGACCU__GUUAC\n___________3'-_____G____________AC____U_AU________UC_____ACUCG...GCG-5'\n______________\|__________________________________________\|\n______________90_________________________________________48\n	67 -- 73	56 -- 62	-41.1069 kcal/mol	16.14 kcal/mol	14.6203 kcal/mol	37 79@LB@ \| \|@LB@5'-AGA...AUUCC G A GA U GC ACGUA...AGU-3'@LB@ GAAAG CGGU AUCCGGC GUUA G AUGCUGGA UAAUG@LB@ :\|\|\|\| \|:\|: \|:\|\|\|\|\| \|:\|\| \| \|\|:\|\|\|\|\| :\|\|\|\|@LB@ UUUUC GUCG UGGGCCG CGAU C UAUGACCU GUUAC@LB@ 3'- G AC U AU UC ACUCG...GCG-5'@LB@ \| \|@LB@ 90 48@LB@@LB@@LB@Energy -10.35 kcal/mol@LB@Hybridization Energy -41.1069 kcal/mol@LB@Unfolding Energy - mRNA 16.14 kcal/mol@LB@Unfolding Energy - sRNA 14.6203 kcal/mol@LB@@LB@Position - mRNA 38 -- 78@LB@Position - sRNA 49 -- 90@LB@Position Seed - mRNA 67 -- 73@LB@Position Seed - sRNA 56 -- 62@LB@
79	0.007454	0.3134	b1912	pgsA	-16.66	0.014365	232 -- 294	1 -- 48	phosphatidylglycerophosphate synthetase	_____________231_____________________________________________________________295\n_____________\|_______________________________________________________________\|\n5'-GUC...UACAC__UU_C_____AUC___A__CCA________AUU______UUAUCUGCCUGUCA_________CGUUUG-3'\n______________UG__C_GUGUC___CUU_UC___UUCUUUGU___GGUCUU______________CCUGGUCGC\n______________\|\|__\|_:\|\|\|\|___\|\|\|_\|\|___\|\|\|\|::\|:___\|\|\|\|\|\|______________\|\|\|\|:\|\|\|\|\n______________AC__G_UACAG___GAA_AG___AAGAGGCG___CCAGAA______________GGACUAGCG\n3'-UUU...GUUAC__UC_U_____CAC______UCC________CUC_____________________________-5'\n_____________\|______________________________________________________________\|\n_____________49_____________________________________________________________1\n	288 -- 294	1 -- 7	-35.4585 kcal/mol	5.43289 kcal/mol	13.3693 kcal/mol	231 295@LB@ \| \|@LB@5'-GUC...UACAC UU C AUC A CCA AUU UUAUCUGCCUGUCA CGUUUG-3'@LB@ UG C GUGUC CUU UC UUCUUUGU GGUCUU CCUGGUCGC@LB@ \|\| \| :\|\|\|\| \|\|\| \|\| \|\|\|\|::\|: \|\|\|\|\|\| \|\|\|\|:\|\|\|\|@LB@ AC G UACAG GAA AG AAGAGGCG CCAGAA GGACUAGCG@LB@3'-UUU...GUUAC UC U CAC UCC CUC -5'@LB@ \| \|@LB@ 49 1@LB@@LB@@LB@Energy -16.66 kcal/mol@LB@Hybridization Energy -35.4585 kcal/mol@LB@Unfolding Energy - mRNA 5.43289 kcal/mol@LB@Unfolding Energy - sRNA 13.3693 kcal/mol@LB@@LB@Position - mRNA 232 -- 294@LB@Position - sRNA 1 -- 48@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 1 -- 7@LB@
80	0.007461	0.3134	b0925	ldtD	-10.36	0.165445	187 -- 206	37 -- 61	murein L D-transpeptidase	_____________186_______________________207\n_____________\|_________________________\|\n5'-AAG...UAAAA__A______________G_______CUUAA...CUG-3'\n______________AC_GGGGGCA_____AG_GAUGUUG\n______________\|\|_\|\|::\|\|\|_____\|\|_:\|\|\|\|:\|\n______________UG_CCUUCGU_____UC_UUACAGC\n3'-UUU...CAUUA__A_______UACAC__G_______ACGAA...GCG-5'\n_____________\|_________________________\|\n_____________62________________________36\n	200 -- 206	37 -- 43	-19.2999 kcal/mol	5.64293 kcal/mol	3.30158 kcal/mol	186 207@LB@ \| \|@LB@5'-AAG...UAAAA A G CUUAA...CUG-3'@LB@ AC GGGGGCA AG GAUGUUG@LB@ \|\| \|\|::\|\|\| \|\| :\|\|\|\|:\|@LB@ UG CCUUCGU UC UUACAGC@LB@3'-UUU...CAUUA A UACAC G ACGAA...GCG-5'@LB@ \| \|@LB@ 62 36@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -19.2999 kcal/mol@LB@Unfolding Energy - mRNA 5.64293 kcal/mol@LB@Unfolding Energy - sRNA 3.30158 kcal/mol@LB@@LB@Position - mRNA 187 -- 206@LB@Position - sRNA 37 -- 61@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 37 -- 43@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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