Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
154	0.006224	0.1406	b0882	clpA	-11.36	0.017252	127 -- 158	2 -- 32	ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease chaperone activity	_____________126______________________________159\n_____________\|________________________________\|\n5'-UUU...CGCGA______AU_______CAUUG__G_____G___GAAAA...CGC-3'\n______________GGGAGA__GAGCAUC_____CU_UGUAC_CUA\n______________\|::\|\|\|__\|\|:\|\|\|\|_____\|\|_\|\|\|\|\|_\|\|\|\n______________CUUUCU__CUUGUAG_____GA_ACAUG_GAU\n3'-AUU...CCAGA______AU_______AAUG___G_____G___G-5'\n_____________\|________________________________\|\n_____________33_______________________________1\n	135 -- 141	18 -- 24	-27.9684 kcal/mol	7.80814 kcal/mol	8.82442 kcal/mol	126 159@LB@ \| \|@LB@5'-UUU...CGCGA AU CAUUG G G GAAAA...CGC-3'@LB@ GGGAGA GAGCAUC CU UGUAC CUA@LB@ \|::\|\|\| \|\|:\|\|\|\| \|\| \|\|\|\|\| \|\|\|@LB@ CUUUCU CUUGUAG GA ACAUG GAU@LB@3'-AUU...CCAGA AU AAUG G G G-5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -11.36 kcal/mol@LB@Hybridization Energy -27.9684 kcal/mol@LB@Unfolding Energy - mRNA 7.80814 kcal/mol@LB@Unfolding Energy - sRNA 8.82442 kcal/mol@LB@@LB@Position - mRNA 127 -- 158@LB@Position - sRNA 2 -- 32@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 18 -- 24@LB@
70	0.001199	0.05856	b0954	fabA	-10.37	0.035200	228 -- 254	4 -- 31	beta-hydroxydecanoyl thioester dehydrase	_____________227__________________________255\n_____________\|____________________________\|\n5'-GUG...AUACA_________C_U___________GU_G_GGUGA...ACA-3'\n______________AAAGA_AGA_C_UCUUGCCUCUG__C_C\n______________\|\|\|\|\|_\|\|\|_\|_\|\|\|\|:\|\|\|\|\|\|__\|_\|\n______________UUUCU_UCU_G_AGAAUGGAGAC__G_G\n3'-AUU...CAGAC_____A___U_U___________AU_G_AUG-5'\n_____________\|____________________________\|\n_____________32___________________________3\n	243 -- 249	9 -- 15	-26.2676 kcal/mol	7.86183 kcal/mol	8.05676 kcal/mol	227 255@LB@ \| \|@LB@5'-GUG...AUACA C U GU G GGUGA...ACA-3'@LB@ AAAGA AGA C UCUUGCCUCUG C C@LB@ \|\|\|\|\| \|\|\| \| \|\|\|\|:\|\|\|\|\|\| \| \|@LB@ UUUCU UCU G AGAAUGGAGAC G G@LB@3'-AUU...CAGAC A U U AU G AUG-5'@LB@ \| \|@LB@ 32 3@LB@@LB@@LB@Energy -10.37 kcal/mol@LB@Hybridization Energy -26.2676 kcal/mol@LB@Unfolding Energy - mRNA 7.86183 kcal/mol@LB@Unfolding Energy - sRNA 8.05676 kcal/mol@LB@@LB@Position - mRNA 228 -- 254@LB@Position - sRNA 4 -- 31@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 9 -- 15@LB@
157	0.006279	0.1407	b0312	betB	-8.02	0.153308	1 -- 12	52 -- 63	betaine aldehyde dehydrogenase NAD-dependent	______________1___________13\n______________\|___________\|\n___________5'-____________GAGCG...ACG-3'\n______________GUCGAAUCUGGU\n______________\|:\|:\|\|\|\|:\|:\|\n______________CGGUUUAGGCUA\n3'-AUU...UAAGU____________AUGCA...AUG-5'\n_____________\|____________\|\n_____________64___________51\n	6 -- 12	52 -- 58	-15.0997 kcal/mol	0.969406 kcal/mol	6.13017 kcal/mol	1 13@LB@ \| \|@LB@ 5'- GAGCG...ACG-3'@LB@ GUCGAAUCUGGU@LB@ \|:\|:\|\|\|\|:\|:\|@LB@ CGGUUUAGGCUA@LB@3'-AUU...UAAGU AUGCA...AUG-5'@LB@ \| \|@LB@ 64 51@LB@@LB@@LB@Energy -8.02 kcal/mol@LB@Hybridization Energy -15.0997 kcal/mol@LB@Unfolding Energy - mRNA 0.969406 kcal/mol@LB@Unfolding Energy - sRNA 6.13017 kcal/mol@LB@@LB@Position - mRNA 1 -- 12@LB@Position - sRNA 52 -- 63@LB@Position Seed - mRNA 6 -- 12@LB@Position Seed - sRNA 52 -- 58@LB@
173	0.007216	0.1466	b3650	spoT	-5.39	0.520602	11 -- 17	54 -- 60	bifunctional (p)ppGpp synthetase II/ guanosine-3' 5'-bis pyrophosphate 3'-pyrophosphohydrolase	_____________10______18\n_____________\|_______\|\n5'-UAG...GGAAA_______CUGGU...CUC-3'\n______________GGAUCCG\n______________::\|\|\|\|\|\n______________UUUAGGC\n3'-AUU...GUCGG_______UAAUG...AUG-5'\n_____________\|_______\|\n_____________61______53\n	11 -- 17	54 -- 60	-6.87427 kcal/mol	1.21245 kcal/mol	0.286889 kcal/mol	10 18@LB@ \| \|@LB@5'-UAG...GGAAA CUGGU...CUC-3'@LB@ GGAUCCG@LB@ ::\|\|\|\|\|@LB@ UUUAGGC@LB@3'-AUU...GUCGG UAAUG...AUG-5'@LB@ \| \|@LB@ 61 53@LB@@LB@@LB@Energy -5.39 kcal/mol@LB@Hybridization Energy -6.87427 kcal/mol@LB@Unfolding Energy - mRNA 1.21245 kcal/mol@LB@Unfolding Energy - sRNA 0.286889 kcal/mol@LB@@LB@Position - mRNA 11 -- 17@LB@Position - sRNA 54 -- 60@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 54 -- 60@LB@
122	0.004081	0.1177	b3940	metL	-10.48	0.032541	261 -- 280	41 -- 59	Bifunctional aspartokinase/homoserine dehydrogenase 2	_____________260__________________281\n_____________\|____________________\|\n5'-ACG...GCAGU_______CUG__________UUAUU...GCA-3'\n______________AGUCUGG___AUGUGAAGUG\n______________\|:\|\|:\|:___\|:\|\|\|\|\|\|\|:\n______________UUAGGCU___UGCACUUCAU\n3'-AUU...UCGGU_______AA___________UUUCC...AUG-5'\n_____________\|____________________\|\n_____________60___________________40\n	274 -- 280	41 -- 47	-17.3741 kcal/mol	3.59224 kcal/mol	3.31634 kcal/mol	260 281@LB@ \| \|@LB@5'-ACG...GCAGU CUG UUAUU...GCA-3'@LB@ AGUCUGG AUGUGAAGUG@LB@ \|:\|\|:\|: \|:\|\|\|\|\|\|\|:@LB@ UUAGGCU UGCACUUCAU@LB@3'-AUU...UCGGU AA UUUCC...AUG-5'@LB@ \| \|@LB@ 60 40@LB@@LB@@LB@Energy -10.48 kcal/mol@LB@Hybridization Energy -17.3741 kcal/mol@LB@Unfolding Energy - mRNA 3.59224 kcal/mol@LB@Unfolding Energy - sRNA 3.31634 kcal/mol@LB@@LB@Position - mRNA 261 -- 280@LB@Position - sRNA 41 -- 59@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 41 -- 47@LB@
111	0.003555	0.1127	b2938	speA	-9.18	0.077057	36 -- 48	46 -- 58	biosynthetic arginine decarboxylase PLP-binding	_____________35____________49\n_____________\|_____________\|\n5'-GUU...CUUAC_____________CUUAA...GCA-3'\n______________GUUCGGUUAUGUG\n______________:\|:\|\|:\|\|\|:\|\|\|\n______________UAGGCUAAUGCAC\n3'-AUU...CGGUU_____________UUCAU...AUG-5'\n_____________\|_____________\|\n_____________59____________45\n	42 -- 48	46 -- 52	-14.853 kcal/mol	3.8258 kcal/mol	1.8625 kcal/mol	35 49@LB@ \| \|@LB@5'-GUU...CUUAC CUUAA...GCA-3'@LB@ GUUCGGUUAUGUG@LB@ :\|:\|\|:\|\|\|:\|\|\|@LB@ UAGGCUAAUGCAC@LB@3'-AUU...CGGUU UUCAU...AUG-5'@LB@ \| \|@LB@ 59 45@LB@@LB@@LB@Energy -9.18 kcal/mol@LB@Hybridization Energy -14.853 kcal/mol@LB@Unfolding Energy - mRNA 3.8258 kcal/mol@LB@Unfolding Energy - sRNA 1.8625 kcal/mol@LB@@LB@Position - mRNA 36 -- 48@LB@Position - sRNA 46 -- 58@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 46 -- 52@LB@
45	0.0004826	0.03773	b4133	cadC	-9.27	0.072737	38 -- 110	5 -- 66	cadBA operon transcriptional activator	_____________37______________________________________________________________________________111\n_____________\|_______________________________________________________________________________\|\n5'-GAU...GGUUC_____A______U_______AAUACUAUGUAAUCAA_____UUAU_______UAAAAAU__________A_________AAUAA...UAA-3'\n______________UCAGU_AAAUCC__UU_CGU________________GAAGU____GG_CUGG_______AACGUCUUGC_UUC___ACC\n______________\|\|\|\|:_\|\|\|\|\|\|__\|\|_\|\|\|________________\|\|\|\|\|____\|\|_\|\|\|:_______\|\|\|:\|\|\|\|:\|_:\|\|___\|\|\|\n______________AGUCG_UUUAGG__AA_GCA________________CUUCA____CC_GACU_______UUGUAGAAUG_GAG___UGG\n3'-AUU...UUAUA_____G______CU__U________________________UUUU__A____UUCUAUC______________ACA___GAUG-5'\n_____________\|_______________________________________________________________________________\|\n_____________67______________________________________________________________________________4\n	97 -- 103	14 -- 20	-38.0459 kcal/mol	10.2122 kcal/mol	18.5819 kcal/mol	37 111@LB@ \| \|@LB@5'-GAU...GGUUC A U AAUACUAUGUAAUCAA UUAU UAAAAAU A AAUAA...UAA-3'@LB@ UCAGU AAAUCC UU CGU GAAGU GG CUGG AACGUCUUGC UUC ACC@LB@ \|\|\|\|: \|\|\|\|\|\| \|\| \|\|\| \|\|\|\|\| \|\| \|\|\|: \|\|\|:\|\|\|\|:\| :\|\| \|\|\|@LB@ AGUCG UUUAGG AA GCA CUUCA CC GACU UUGUAGAAUG GAG UGG@LB@3'-AUU...UUAUA G CU U UUUU A UUCUAUC ACA GAUG-5'@LB@ \| \|@LB@ 67 4@LB@@LB@@LB@Energy -9.27 kcal/mol@LB@Hybridization Energy -38.0459 kcal/mol@LB@Unfolding Energy - mRNA 10.2122 kcal/mol@LB@Unfolding Energy - sRNA 18.5819 kcal/mol@LB@@LB@Position - mRNA 38 -- 110@LB@Position - sRNA 5 -- 66@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 14 -- 20@LB@
94	0.002669	0.09947	b2659	csiD	-13.62	0.002680	28 -- 48	1 -- 21	carbon starvation protein	_____________27____________________49\n_____________\|_____________________\|\n5'-GUU...UGUCU__C________AA________GUUAA...UGG-3'\n______________CA_UUUGCCUU__UACCCUAC\n______________\|\|_:\|\|:\|\|\|:__\|\|\|\|\|\|\|\|\n______________GU_GAAUGGAG__AUGGGAUG\n3'-AUU...AUCUU__A________AC________-5'\n_____________\|____________________\|\n_____________22___________________1\n	42 -- 48	1 -- 7	-22.7197 kcal/mol	1.13457 kcal/mol	7.99195 kcal/mol	27 49@LB@ \| \|@LB@5'-GUU...UGUCU C AA GUUAA...UGG-3'@LB@ CA UUUGCCUU UACCCUAC@LB@ \|\| :\|\|:\|\|\|: \|\|\|\|\|\|\|\|@LB@ GU GAAUGGAG AUGGGAUG@LB@3'-AUU...AUCUU A AC -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -13.62 kcal/mol@LB@Hybridization Energy -22.7197 kcal/mol@LB@Unfolding Energy - mRNA 1.13457 kcal/mol@LB@Unfolding Energy - sRNA 7.99195 kcal/mol@LB@@LB@Position - mRNA 28 -- 48@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 1 -- 7@LB@
190	0.008456	0.1558	b0036	caiD	-8.40	0.123663	110 -- 117	1 -- 8	carnitinyl-CoA dehydratase	_____________109______118\n_____________\|________\|\n5'-UGG...GGAAC________CAGCU...AAA-3'\n______________UACCCUGC\n______________\|\|\|\|\|\|:\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	111 -- 117	1 -- 7	-12.4513 kcal/mol	1.95818 kcal/mol	2.11603 kcal/mol	109 118@LB@ \| \|@LB@5'-UGG...GGAAC CAGCU...AAA-3'@LB@ UACCCUGC@LB@ \|\|\|\|\|\|:\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -8.40 kcal/mol@LB@Hybridization Energy -12.4513 kcal/mol@LB@Unfolding Energy - mRNA 1.95818 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 110 -- 117@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 1 -- 7@LB@
49	0.0005477	0.03933	b2715	ascF	-9.59	0.059292	173 -- 180	1 -- 8	cellobiose/arbutin/salicin-specific PTS enzymes IIB and IC components	_____________172______181\n_____________\|________\|\n5'-UGC...ACAUC________UGAUA...GCU-3'\n______________UACCCUAC\n______________\|\|\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	174 -- 180	1 -- 7	-12.1729 kcal/mol	0.486168 kcal/mol	2.11603 kcal/mol	172 181@LB@ \| \|@LB@5'-UGC...ACAUC UGAUA...GCU-3'@LB@ UACCCUAC@LB@ \|\|\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -12.1729 kcal/mol@LB@Unfolding Energy - mRNA 0.486168 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 173 -- 180@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 1 -- 7@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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