Input and runtime details for job 3202356 (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 3202356 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:02 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:35 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:03:47 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:03:55 CET 2018
	Job Completed		@ Sat Feb 17 02:04:28 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

Description of the job

GcvB

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_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

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
105	0.005236	0.1728	stm4566	yjjI	-12.28	0.305832	96 -- 137	40 -- 77	YjjI family glycine radical enzyme	_____________95________________138\n_____________\|_________________\|\n5'-ACA...UUUUC____________U____CCGGC...UGG-3'\n______________UACAAUAGCGCA_CGUC\n______________:\|\|\|\|:\|:\|:\|\|_\|:\|\|\n______________GUGUUGUUGUGU_GUAG\n3'-UUU...CGUUU____________U____UGUUG...UCA-5'\n_____________\|_________________\|\n_____________78________________39\n	167 -- 173	74 -- 80	-18.3997 kcal/mol	3.44142 kcal/mol	3.92987 kcal/mol	95 138@LB@ \| \|@LB@5'-ACA...UUUUC U CCGGC...UGG-3'@LB@ UACAAUAGCGCA CGUC@LB@ :\|\|\|\|:\|:\|:\|\| \|:\|\|@LB@ GUGUUGUUGUGU GUAG@LB@3'-UUU...CGUUU U UGUUG...UCA-5'@LB@ \| \|@LB@ 78 39@LB@@LB@@LB@Energy -12.28 kcal/mol@LB@Hybridization Energy -18.3997 kcal/mol@LB@Unfolding Energy - mRNA 3.44142 kcal/mol@LB@Unfolding Energy - sRNA 3.92987 kcal/mol@LB@@LB@Position - mRNA 96 -- 137@LB@Position - sRNA 40 -- 77@LB@Position Seed - mRNA 167 -- 173@LB@Position Seed - sRNA 74 -- 80@LB@
70	0.003306	0.1596	stm2688	smpB	-12.25	0.308628	191 -- 230	36 -- 77	SsrA-binding protein	_____________190_________________231\n_____________\|___________________\|\n5'-AAU...GCAUA____UUCC__U________AUCGU...GUC-3'\n______________GCAA____CA_CAACAUAA\n______________\|\|\|\|____\|\|_\|\|\|\|\|:\|\|\n______________CGUU____GU_GUUGUGUU\n3'-UUU...GUUAA____UGU___U________GUAGU...UCA-5'\n_____________\|___________________\|\n_____________78__________________35\n	26 -- 32	73 -- 79	-12.551 kcal/mol	1.44298 kcal/mol	3.77104 kcal/mol	190 231@LB@ \| \|@LB@5'-AAU...GCAUA UUCC U AUCGU...GUC-3'@LB@ GCAA CA CAACAUAA@LB@ \|\|\|\| \|\| \|\|\|\|\|:\|\|@LB@ CGUU GU GUUGUGUU@LB@3'-UUU...GUUAA UGU U GUAGU...UCA-5'@LB@ \| \|@LB@ 78 35@LB@@LB@@LB@Energy -12.25 kcal/mol@LB@Hybridization Energy -12.551 kcal/mol@LB@Unfolding Energy - mRNA 1.44298 kcal/mol@LB@Unfolding Energy - sRNA 3.77104 kcal/mol@LB@@LB@Position - mRNA 191 -- 230@LB@Position - sRNA 36 -- 77@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 73 -- 79@LB@
38	0.001379	0.1215	stm0150	aroP	-12.21	0.313123	213 -- 232	63 -- 83	APC family aromatic amino acid transporter	_____________212_________________________233\n_____________\|___________________________\|\n5'-CAU...UGAUG____GU_____________A_______CAAGC...UGU-3'\n______________GACA__CAGCAGCACGGCG__GCAGCU\n______________:\|\|\|__\|\|:\|\|:\|\|\|::\|:__:\|\|:\|:\n______________UUGU__GUUGUUGUGUUGU__UGUUGG\n3'-UUU...AACGU___________________AG______CAUUC...UCA-5'\n_____________\|___________________________\|\n_____________84__________________________62\n	219 -- 225	71 -- 77	-26.8853 kcal/mol	7.73214 kcal/mol	8.28637 kcal/mol	212 233@LB@ \| \|@LB@5'-CAU...UGAUG GU A CAAGC...UGU-3'@LB@ GACA CAGCAGCACGGCG GCAGCU@LB@ :\|\|\| \|\|:\|\|:\|\|\|::\|: :\|\|:\|:@LB@ UUGU GUUGUUGUGUUGU UGUUGG@LB@3'-UUU...AACGU AG CAUUC...UCA-5'@LB@ \| \|@LB@ 84 62@LB@@LB@@LB@Energy -12.21 kcal/mol@LB@Hybridization Energy -26.8853 kcal/mol@LB@Unfolding Energy - mRNA 7.73214 kcal/mol@LB@Unfolding Energy - sRNA 8.28637 kcal/mol@LB@@LB@Position - mRNA 213 -- 232@LB@Position - sRNA 63 -- 83@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 71 -- 77@LB@
181	0.01001	0.1966	stm2266	apbE	-12.19	0.314808	267 -- 297	62 -- 90	FAD:protein FMN transferase ApbE	_____________266_____________________________298\n_____________\|_______________________________\|\n5'-ACC...AUGAG__UCCCGA______A__________CU____CUC-3'\n______________GC______AACGAC_ACAGCGUCAC__GCCG\n______________\|\|______\|\|\|:\|\|_\|\|\|:\|:\|\|\|\|__:\|\|\|\n______________CG______UUGUUG_UGUUGUAGUG__UGGC\n3'-UUU...GUUAA__UUUGUG_________________U_____AUUCG...UCA-5'\n_____________\|_______________________________\|\n_____________91______________________________61\n	285 -- 291	67 -- 73	-27.9543 kcal/mol	7.52451 kcal/mol	8.62576 kcal/mol	266 298@LB@ \| \|@LB@5'-ACC...AUGAG UCCCGA A CU CUC-3'@LB@ GC AACGAC ACAGCGUCAC GCCG@LB@ \|\| \|\|\|:\|\| \|\|\|:\|:\|\|\|\| :\|\|\|@LB@ CG UUGUUG UGUUGUAGUG UGGC@LB@3'-UUU...GUUAA UUUGUG U AUUCG...UCA-5'@LB@ \| \|@LB@ 91 61@LB@@LB@@LB@Energy -12.19 kcal/mol@LB@Hybridization Energy -27.9543 kcal/mol@LB@Unfolding Energy - mRNA 7.52451 kcal/mol@LB@Unfolding Energy - sRNA 8.62576 kcal/mol@LB@@LB@Position - mRNA 267 -- 297@LB@Position - sRNA 62 -- 90@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 67 -- 73@LB@
142	0.007269	0.182	stm4341	frdC	-12.15	0.319206	131 -- 234	54 -- 160	fumarate reductase subunit C	_____________130__________________235\n_____________\|____________________\|\n5'-AGA...AGGAG_______________UA___GCAAA...CGG-3'\n______________UGC_AACAUGACGAC__AAC\n______________\|\|\|_\|\|\|\|::\|\|:\|\|__\|\|\|\n______________ACG_UUGUGUUGUUG__UUG\n3'-UUU...GGUUA___U___________UG___UAGUG...UCA-5'\n_____________\|____________________\|\n_____________161__________________53\n	202 -- 208	77 -- 83	-18.8897 kcal/mol	4.02107 kcal/mol	3.80548 kcal/mol	130 235@LB@ \| \|@LB@5'-AGA...AGGAG UA GCAAA...CGG-3'@LB@ UGC AACAUGACGAC AAC@LB@ \|\|\| \|\|\|\|::\|\|:\|\| \|\|\|@LB@ ACG UUGUGUUGUUG UUG@LB@3'-UUU...GGUUA U UG UAGUG...UCA-5'@LB@ \| \|@LB@ 161 53@LB@@LB@@LB@Energy -12.15 kcal/mol@LB@Hybridization Energy -18.8897 kcal/mol@LB@Unfolding Energy - mRNA 4.02107 kcal/mol@LB@Unfolding Energy - sRNA 3.80548 kcal/mol@LB@@LB@Position - mRNA 131 -- 234@LB@Position - sRNA 54 -- 160@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 77 -- 83@LB@
186	0.01044	0.1967	stm1725	trpC	-12.00	0.335236	146 -- 174	55 -- 86	bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase	_____________145_______________175\n_____________\|_________________\|\n5'-AAA...GUUCU____________C____AUGAC...AGC-3'\n______________GCGCAACGGCAC_GCAU\n______________:\|:\|\|\|\|::\|\|\|_:\|\|\|\n______________UGUGUUGUUGUG_UGUA\n3'-UUU...ACGUU____________U____GUGUU...UCA-5'\n_____________\|_________________\|\n_____________87________________54\n	151 -- 157	75 -- 81	-20.8979 kcal/mol	6.12922 kcal/mol	3.85824 kcal/mol	145 175@LB@ \| \|@LB@5'-AAA...GUUCU C AUGAC...AGC-3'@LB@ GCGCAACGGCAC GCAU@LB@ :\|:\|\|\|\|::\|\|\| :\|\|\|@LB@ UGUGUUGUUGUG UGUA@LB@3'-UUU...ACGUU U GUGUU...UCA-5'@LB@ \| \|@LB@ 87 54@LB@@LB@@LB@Energy -12.00 kcal/mol@LB@Hybridization Energy -20.8979 kcal/mol@LB@Unfolding Energy - mRNA 6.12922 kcal/mol@LB@Unfolding Energy - sRNA 3.85824 kcal/mol@LB@@LB@Position - mRNA 146 -- 174@LB@Position - sRNA 55 -- 86@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 75 -- 81@LB@
60	0.002585	0.1534	stm0758	ybgR	-11.90	0.345594	235 -- 293	32 -- 91	cation transporter	_____________234_________________________294\n_____________\|___________________________\|\n5'-GGU...ACACC___CG___G__________U_______CUGCU...UCC-3'\n______________UGC__AAA_AUAAUAAUGC__CGUCGC\n______________\|\|\|__\|\|\|_\|:\|\|:\|\|::\|__\|:\|\|:\|\n______________ACG__UUU_UGUUGUUGUG__GUAGUG\n3'-UUU...GGUUA________G__________UU______UUGGC...UCA-5'\n_____________\|___________________________\|\n_____________92__________________________31\n	247 -- 253	75 -- 81	-19.147 kcal/mol	4.2306 kcal/mol	5.6854 kcal/mol	234 294@LB@ \| \|@LB@5'-GGU...ACACC CG G U CUGCU...UCC-3'@LB@ UGC AAA AUAAUAAUGC CGUCGC@LB@ \|\|\| \|\|\| \|:\|\|:\|\|::\| \|:\|\|:\|@LB@ ACG UUU UGUUGUUGUG GUAGUG@LB@3'-UUU...GGUUA G UU UUGGC...UCA-5'@LB@ \| \|@LB@ 92 31@LB@@LB@@LB@Energy -11.90 kcal/mol@LB@Hybridization Energy -19.147 kcal/mol@LB@Unfolding Energy - mRNA 4.2306 kcal/mol@LB@Unfolding Energy - sRNA 5.6854 kcal/mol@LB@@LB@Position - mRNA 235 -- 293@LB@Position - sRNA 32 -- 91@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 75 -- 81@LB@
67	0.003193	0.1596	stm0122	ftsI	-11.87	0.349270	199 -- 241	52 -- 90	peptidoglycan glycosyltransferase FtsI	_____________198_______________________242\n_____________\|_________________________\|\n5'-GUU...CGCGA____UUG_____UG___________CUGAU...UGG-3'\n______________UGCA___GACAU__AAUGGCGCAAC\n______________\|\|\|\|___:\|\|\|:__\|\|:::\|:\|\|\|\|\n______________ACGU___UUGUG__UUGUUGUGUUG\n3'-UUU...GGUUA_________________________UAGUG...UCA-5'\n_____________\|_________________________\|\n_____________91________________________51\n	62 -- 68	72 -- 78	-17.673 kcal/mol	4.85802 kcal/mol	3.80548 kcal/mol	198 242@LB@ \| \|@LB@5'-GUU...CGCGA UUG UG CUGAU...UGG-3'@LB@ UGCA GACAU AAUGGCGCAAC@LB@ \|\|\|\| :\|\|\|: \|\|:::\|:\|\|\|\|@LB@ ACGU UUGUG UUGUUGUGUUG@LB@3'-UUU...GGUUA UAGUG...UCA-5'@LB@ \| \|@LB@ 91 51@LB@@LB@@LB@Energy -11.87 kcal/mol@LB@Hybridization Energy -17.673 kcal/mol@LB@Unfolding Energy - mRNA 4.85802 kcal/mol@LB@Unfolding Energy - sRNA 3.80548 kcal/mol@LB@@LB@Position - mRNA 199 -- 241@LB@Position - sRNA 52 -- 90@LB@Position Seed - mRNA 62 -- 68@LB@Position Seed - sRNA 72 -- 78@LB@
129	0.006472	0.1774	stm0158	acnB	-11.80	0.356459	140 -- 172	33 -- 60	bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase	_____________139________________173\n_____________\|__________________\|\n5'-AUU...CUUUU_________G_U______UUAAA...UGC-3'\n______________UUGUAAACA_A_UAACAC\n______________\|\|\|:\|\|\|\|\|_\|_:\|\|\|\|\|\n______________AACGUUUGU_U_GUUGUG\n3'-UUU...UGGUU_________G_U______UUGUA...UCA-5'\n_____________\|__________________\|\n_____________61_________________32\n	48 -- 54	84 -- 90	-17.8051 kcal/mol	3.41045 kcal/mol	3.73018 kcal/mol	139 173@LB@ \| \|@LB@5'-AUU...CUUUU G U UUAAA...UGC-3'@LB@ UUGUAAACA A UAACAC@LB@ \|\|\|:\|\|\|\|\| \| :\|\|\|\|\|@LB@ AACGUUUGU U GUUGUG@LB@3'-UUU...UGGUU G U UUGUA...UCA-5'@LB@ \| \|@LB@ 61 32@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -17.8051 kcal/mol@LB@Unfolding Energy - mRNA 3.41045 kcal/mol@LB@Unfolding Energy - sRNA 3.73018 kcal/mol@LB@@LB@Position - mRNA 140 -- 172@LB@Position - sRNA 33 -- 60@LB@Position Seed - mRNA 48 -- 54@LB@Position Seed - sRNA 84 -- 90@LB@
144	0.00736	0.182	stm4559	yjjG	-11.80	0.356804	189 -- 218	128 -- 159	putative haloacid dehalogenase-like hydrolase	_____________188_________________________________219\n_____________\|___________________________________\|\n5'-UUG...AUAAA_G_____A____U__________________CU__AUUUU...UCA-3'\n______________A_AGGCA_GGUG_AAUG_AU__GAAGUGGGA__GG\n______________\|_\|\|:\|\|_\|\|\|:_\|\|\|\|_\|:__\|\|\|\|\|\|::\|__\|\|\n______________U_UCUGU_CCAU_UUAC_UG__CUUCACUUU__CC\n3'-UUU...AUACC_G_____C_________A__UC_________UU__CAUCA...UCA-5'\n_____________\|___________________________________\|\n_____________160_________________________________127\n	208 -- 214	132 -- 138	-24.694 kcal/mol	5.33554 kcal/mol	7.83417 kcal/mol	188 219@LB@ \| \|@LB@5'-UUG...AUAAA G A U CU AUUUU...UCA-3'@LB@ A AGGCA GGUG AAUG AU GAAGUGGGA GG@LB@ \| \|\|:\|\| \|\|\|: \|\|\|\| \|: \|\|\|\|\|\|::\| \|\|@LB@ U UCUGU CCAU UUAC UG CUUCACUUU CC@LB@3'-UUU...AUACC G C A UC UU CAUCA...UCA-5'@LB@ \| \|@LB@ 160 127@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -24.694 kcal/mol@LB@Unfolding Energy - mRNA 5.33554 kcal/mol@LB@Unfolding Energy - sRNA 7.83417 kcal/mol@LB@@LB@Position - mRNA 189 -- 218@LB@Position - sRNA 128 -- 159@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 132 -- 138@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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