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
193	0.008653	0.1558	b1677	lpp	-9.16	0.078007	273 -- 298	53 -- 76	murein lipoprotein	_____________272________________________299\n_____________\|__________________________\|\n5'-UCA...GCAAC________CGA______GUCU_____CG-3'\n______________GCUAAAAU___UCAGCU____UCUGA\n______________\|\|\|\|\|\|\|\|___\|\|\|\|\|:____\|\|:\|\|\n______________CGAUUUUA___AGUCGG____AGGCU\n3'-AUU...CCCGC________UA_______UUU______AAUGC...AUG-5'\n_____________\|__________________________\|\n_____________77_________________________52\n	273 -- 279	70 -- 76	-19.09 kcal/mol	3.58418 kcal/mol	6.36489 kcal/mol	272 299@LB@ \| \|@LB@5'-UCA...GCAAC CGA GUCU CG-3'@LB@ GCUAAAAU UCAGCU UCUGA@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|: \|\|:\|\|@LB@ CGAUUUUA AGUCGG AGGCU@LB@3'-AUU...CCCGC UA UUU AAUGC...AUG-5'@LB@ \| \|@LB@ 77 52@LB@@LB@@LB@Energy -9.16 kcal/mol@LB@Hybridization Energy -19.09 kcal/mol@LB@Unfolding Energy - mRNA 3.58418 kcal/mol@LB@Unfolding Energy - sRNA 6.36489 kcal/mol@LB@@LB@Position - mRNA 273 -- 298@LB@Position - sRNA 53 -- 76@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 70 -- 76@LB@
121	0.004045	0.1176	b1738	chbB	-6.64	0.311906	2 -- 15	34 -- 50	N N'-diacetylchitobiose-specific enzyme IIB component of PTS	_____________1_________________16\n_____________\|_________________\|\n__________5'-A_________________AUAAC...CGG-3'\n______________AUGUGAAG___AGGGUC\n______________\|:\|\|\|\|\|\|___\|:\|\|\|\|\n______________UGCACUUC___UUCCAG\n3'-AUU...GCUAA________AUU______ACUUU...AUG-5'\n_____________\|_________________\|\n_____________51________________33\n	3 -- 9	43 -- 49	-17.276 kcal/mol	2.8636 kcal/mol	7.69543 kcal/mol	1 16@LB@ \| \|@LB@ 5'-A AUAAC...CGG-3'@LB@ AUGUGAAG AGGGUC@LB@ \|:\|\|\|\|\|\| \|:\|\|\|\|@LB@ UGCACUUC UUCCAG@LB@3'-AUU...GCUAA AUU ACUUU...AUG-5'@LB@ \| \|@LB@ 51 33@LB@@LB@@LB@Energy -6.64 kcal/mol@LB@Hybridization Energy -17.276 kcal/mol@LB@Unfolding Energy - mRNA 2.8636 kcal/mol@LB@Unfolding Energy - sRNA 7.69543 kcal/mol@LB@@LB@Position - mRNA 2 -- 15@LB@Position - sRNA 34 -- 50@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 43 -- 49@LB@
74	0.001232	0.05856	b3139	agaC	-9.25	0.073815	213 -- 219	1 -- 7	N-acetylgalactosamine-specific enzyme IIC component of PTS	_____________212_____220\n_____________\|_______\|\n5'-AAC...AAAUA_______UUCAG...CGA-3'\n______________ACCCUAC\n______________\|\|\|\|\|\|\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	213 -- 219	1 -- 7	-11.8132 kcal/mol	0.545455 kcal/mol	2.03949 kcal/mol	212 220@LB@ \| \|@LB@5'-AAC...AAAUA UUCAG...CGA-3'@LB@ ACCCUAC@LB@ \|\|\|\|\|\|\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -11.8132 kcal/mol@LB@Unfolding Energy - mRNA 0.545455 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 213 -- 219@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 1 -- 7@LB@
33	0.0003369	0.03519	b0523	purE	-12.01	0.010423	150 -- 160	3 -- 13	N5-carboxyaminoimidazole ribonucleotide mutase	_____________149__________161\n_____________\|____________\|\n5'-UGG...GCUAU____________CUAAA...UGA-3'\n______________UCUCUGUGCCCU\n______________:\|\|\|\|\|\|:\|\|\|\|\n______________GGAGACAUGGGA\n3'-AUU...AGAAU____________UG-5'\n_____________\|____________\|\n_____________14___________2\n	154 -- 160	3 -- 9	-20.2448 kcal/mol	2.89849 kcal/mol	5.35591 kcal/mol	149 161@LB@ \| \|@LB@5'-UGG...GCUAU CUAAA...UGA-3'@LB@ UCUCUGUGCCCU@LB@ :\|\|\|\|\|\|:\|\|\|\|@LB@ GGAGACAUGGGA@LB@3'-AUU...AGAAU UG-5'@LB@ \| \|@LB@ 14 2@LB@@LB@@LB@Energy -12.01 kcal/mol@LB@Hybridization Energy -20.2448 kcal/mol@LB@Unfolding Energy - mRNA 2.89849 kcal/mol@LB@Unfolding Energy - sRNA 5.35591 kcal/mol@LB@@LB@Position - mRNA 150 -- 160@LB@Position - sRNA 3 -- 13@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 3 -- 9@LB@
116	0.003844	0.1165	b1004	wrbA	-12.42	0.007537	123 -- 145	10 -- 35	NAD(P)H:quinone oxidoreductase	_____________122________________________146\n_____________\|__________________________\|\n5'-UUA...UGCAC__________________________AAAUA...AAG-3'\n______________UCUGAAA___AGGACGUCUUAUCUUU\n______________\|\|\|\|\|\|\|___\|\|:\|\|:\|\|\|\|\|:\|\|:\|\n______________AGACUUU___UCUUGUAGAAUGGAGA\n3'-AUU...UUUCC_______CUA________________CAUGG...AUG-5'\n_____________\|__________________________\|\n_____________36_________________________9\n	133 -- 139	16 -- 22	-25.4666 kcal/mol	4.32254 kcal/mol	8.70229 kcal/mol	122 146@LB@ \| \|@LB@5'-UUA...UGCAC AAAUA...AAG-3'@LB@ UCUGAAA AGGACGUCUUAUCUUU@LB@ \|\|\|\|\|\|\| \|\|:\|\|:\|\|\|\|\|:\|\|:\|@LB@ AGACUUU UCUUGUAGAAUGGAGA@LB@3'-AUU...UUUCC CUA CAUGG...AUG-5'@LB@ \| \|@LB@ 36 9@LB@@LB@@LB@Energy -12.42 kcal/mol@LB@Hybridization Energy -25.4666 kcal/mol@LB@Unfolding Energy - mRNA 4.32254 kcal/mol@LB@Unfolding Energy - sRNA 8.70229 kcal/mol@LB@@LB@Position - mRNA 123 -- 145@LB@Position - sRNA 10 -- 35@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 16 -- 22@LB@
109	0.003426	0.1101	b2280	nuoJ	-6.41	0.346318	31 -- 43	48 -- 59	NADH:ubiquinone oxidoreductase membrane subunit J	_____________30____________44\n_____________\|_____________\|\n5'-GAU...GCCAG_________U___AGAAA...UUA-3'\n______________GAUCUGGUU_ACG\n______________:\|\|\|:\|:\|\|_\|\|\|\n______________UUAGGCUAA_UGC\n3'-AUU...UCGGU_____________ACUUC...AUG-5'\n_____________\|_____________\|\n_____________60____________47\n	33 -- 39	51 -- 57	-11.2654 kcal/mol	3.27917 kcal/mol	1.55995 kcal/mol	30 44@LB@ \| \|@LB@5'-GAU...GCCAG U AGAAA...UUA-3'@LB@ GAUCUGGUU ACG@LB@ :\|\|\|:\|:\|\| \|\|\|@LB@ UUAGGCUAA UGC@LB@3'-AUU...UCGGU ACUUC...AUG-5'@LB@ \| \|@LB@ 60 47@LB@@LB@@LB@Energy -6.41 kcal/mol@LB@Hybridization Energy -11.2654 kcal/mol@LB@Unfolding Energy - mRNA 3.27917 kcal/mol@LB@Unfolding Energy - sRNA 1.55995 kcal/mol@LB@@LB@Position - mRNA 31 -- 43@LB@Position - sRNA 48 -- 59@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 51 -- 57@LB@
164	0.006623	0.1421	b2278	nuoL	-8.77	0.099276	203 -- 221	5 -- 24	NADH:ubiquinone oxidoreductase membrane subunit L	_____________202___________________222\n_____________\|_____________________\|\n5'-GGU...CGGAU______G________A_____AUUAU...UCG-3'\n______________GAACAU_CUUGCCUU___ACC\n______________\|\|\|\|\|\|_\|\|\|:\|\|\|:___\|\|\|\n______________CUUGUA_GAAUGGAG___UGG\n3'-AUU...UCUAU_______________ACA___GAUG-5'\n_____________\|_____________________\|\n_____________25____________________4\n	211 -- 217	11 -- 17	-20.7037 kcal/mol	3.94864 kcal/mol	8.01095 kcal/mol	202 222@LB@ \| \|@LB@5'-GGU...CGGAU G A AUUAU...UCG-3'@LB@ GAACAU CUUGCCUU ACC@LB@ \|\|\|\|\|\| \|\|\|:\|\|\|: \|\|\|@LB@ CUUGUA GAAUGGAG UGG@LB@3'-AUU...UCUAU ACA GAUG-5'@LB@ \| \|@LB@ 25 4@LB@@LB@@LB@Energy -8.77 kcal/mol@LB@Hybridization Energy -20.7037 kcal/mol@LB@Unfolding Energy - mRNA 3.94864 kcal/mol@LB@Unfolding Energy - sRNA 8.01095 kcal/mol@LB@@LB@Position - mRNA 203 -- 221@LB@Position - sRNA 5 -- 24@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 11 -- 17@LB@
35	0.0003501	0.03519	b2700	pncC	-8.73	0.102058	11 -- 28	20 -- 37	nicotinamide-nucleotide amidohydrolase; NMN amidohydrolase	_____________10_________________29\n_____________\|__________________\|\n5'-ACG...AUGGC_______C__U_______AGCCG...GUU-3'\n______________GGUCUGG_AG_UAGGACA\n______________\|\|\|\|\|\|:_\|\|_\|\|\|:\|\|\|\n______________CCAGACU_UC_AUCUUGU\n3'-AUU...AUUUU_______U__U_______AGAAU...AUG-5'\n_____________\|__________________\|\n_____________38_________________19\n	22 -- 28	20 -- 26	-19.0339 kcal/mol	5.51285 kcal/mol	4.72108 kcal/mol	10 29@LB@ \| \|@LB@5'-ACG...AUGGC C U AGCCG...GUU-3'@LB@ GGUCUGG AG UAGGACA@LB@ \|\|\|\|\|\|: \|\| \|\|\|:\|\|\|@LB@ CCAGACU UC AUCUUGU@LB@3'-AUU...AUUUU U U AGAAU...AUG-5'@LB@ \| \|@LB@ 38 19@LB@@LB@@LB@Energy -8.73 kcal/mol@LB@Hybridization Energy -19.0339 kcal/mol@LB@Unfolding Energy - mRNA 5.51285 kcal/mol@LB@Unfolding Energy - sRNA 4.72108 kcal/mol@LB@@LB@Position - mRNA 11 -- 28@LB@Position - sRNA 20 -- 37@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 20 -- 26@LB@
155	0.00623	0.1406	b4178	nsrR	-8.53	0.114937	220 -- 228	48 -- 56	nitric oxide-sensitive repressor for NO regulon	_____________219_______229\n_____________\|_________\|\n5'-GGU...UUUCA_________GAUUA...ACG-3'\n______________CUGAUUACG\n______________\|:\|\|\|\|\|\|\|\n______________GGCUAAUGC\n3'-AUU...GUUUA_________ACUUC...AUG-5'\n_____________\|_________\|\n_____________57________47\n	222 -- 228	48 -- 54	-11.8869 kcal/mol	1.78283 kcal/mol	1.55919 kcal/mol	219 229@LB@ \| \|@LB@5'-GGU...UUUCA GAUUA...ACG-3'@LB@ CUGAUUACG@LB@ \|:\|\|\|\|\|\|\|@LB@ GGCUAAUGC@LB@3'-AUU...GUUUA ACUUC...AUG-5'@LB@ \| \|@LB@ 57 47@LB@@LB@@LB@Energy -8.53 kcal/mol@LB@Hybridization Energy -11.8869 kcal/mol@LB@Unfolding Energy - mRNA 1.78283 kcal/mol@LB@Unfolding Energy - sRNA 1.55919 kcal/mol@LB@@LB@Position - mRNA 220 -- 228@LB@Position - sRNA 48 -- 56@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 48 -- 54@LB@
69	0.001182	0.05856	b2962	yggX	-12.92	0.004967	226 -- 272	1 -- 57	oxidative damage protective factor for iron-sulfur proteins	_____________225________________________________________________________273\n_____________\|__________________________________________________________\|\n5'-UCA...UACUU___UGCA________C____________________G_______AG________CG__GAGCU...AGA-3'\n______________UCC____ACGUGAAG_AGAAGGUC__________AG_AUUUU_C__CUGUACCC__GC\n______________\|\|\|____\|\|\|\|\|\|\|\|_\|:\|\|\|\|\|\|__________\|:_\|\|:\|\|_\|__\|\|\|\|\|\|\|\|__:\|\n______________AGG____UGCACUUC_UUUUCCAG__________UU_UAGAA_G__GACAUGGG__UG\n3'-AUU...GGUUU___CUAA________A________ACUUUCUAUC__G_____U_GA________A___-5'\n_____________\|_________________________________________________________\|\n_____________58________________________________________________________1\n	262 -- 268	4 -- 10	-42.3698 kcal/mol	16.7751 kcal/mol	12.7026 kcal/mol	225 273@LB@ \| \|@LB@5'-UCA...UACUU UGCA C G AG CG GAGCU...AGA-3'@LB@ UCC ACGUGAAG AGAAGGUC AG AUUUU C CUGUACCC GC@LB@ \|\|\| \|\|\|\|\|\|\|\| \|:\|\|\|\|\|\| \|: \|\|:\|\| \| \|\|\|\|\|\|\|\| :\|@LB@ AGG UGCACUUC UUUUCCAG UU UAGAA G GACAUGGG UG@LB@3'-AUU...GGUUU CUAA A ACUUUCUAUC G U GA A -5'@LB@ \| \|@LB@ 58 1@LB@@LB@@LB@Energy -12.92 kcal/mol@LB@Hybridization Energy -42.3698 kcal/mol@LB@Unfolding Energy - mRNA 16.7751 kcal/mol@LB@Unfolding Energy - sRNA 12.7026 kcal/mol@LB@@LB@Position - mRNA 226 -- 272@LB@Position - sRNA 1 -- 57@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 4 -- 10@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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