Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
171	0.02062	0.4033	b3192	mlaC	-11.25	0.065504	113 -- 124	47 -- 58	ABC transporter maintaining OM lipid asymmetry periplasmic binding protein	_____________112__________125\n_____________\|____________\|\n5'-GGA...AAGAA____________GCCAG...AGG-3'\n______________UAGUGGCGAUGC\n______________:\|\|\|\|\|\|:\|\|\|\|\n______________GUCACCGUUACG\n3'-UUU...UUUUA____________UUACC...UUG-5'\n_____________\|____________\|\n_____________59___________46\n	118 -- 124	47 -- 53	-20.0531 kcal/mol	5.42731 kcal/mol	3.37136 kcal/mol	112 125@LB@ \| \|@LB@5'-GGA...AAGAA GCCAG...AGG-3'@LB@ UAGUGGCGAUGC@LB@ :\|\|\|\|\|\|:\|\|\|\|@LB@ GUCACCGUUACG@LB@3'-UUU...UUUUA UUACC...UUG-5'@LB@ \| \|@LB@ 59 46@LB@@LB@@LB@Energy -11.25 kcal/mol@LB@Hybridization Energy -20.0531 kcal/mol@LB@Unfolding Energy - mRNA 5.42731 kcal/mol@LB@Unfolding Energy - sRNA 3.37136 kcal/mol@LB@@LB@Position - mRNA 113 -- 124@LB@Position - sRNA 47 -- 58@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 47 -- 53@LB@
172	0.02065	0.4033	b1015	putP	-10.70	0.086688	188 -- 205	52 -- 67	proline:sodium symporter	_____________187________________206\n_____________\|__________________\|\n5'-AGA...AUUUU_______CU____A____UAUUA...ACG-3'\n______________UUGGAGA__UUAG_UGGC\n______________\|\|\|\|\|:\|__\|:\|\|_\|\|\|\|\n______________AACCUUU__AGUC_ACCG\n3'-UUU...UAUAC_______U__________UUACG...UUG-5'\n_____________\|__________________\|\n_____________68_________________51\n	188 -- 194	61 -- 67	-15.9795 kcal/mol	2.37428 kcal/mol	2.90583 kcal/mol	187 206@LB@ \| \|@LB@5'-AGA...AUUUU CU A UAUUA...ACG-3'@LB@ UUGGAGA UUAG UGGC@LB@ \|\|\|\|\|:\| \|:\|\| \|\|\|\|@LB@ AACCUUU AGUC ACCG@LB@3'-UUU...UAUAC U UUACG...UUG-5'@LB@ \| \|@LB@ 68 51@LB@@LB@@LB@Energy -10.70 kcal/mol@LB@Hybridization Energy -15.9795 kcal/mol@LB@Unfolding Energy - mRNA 2.37428 kcal/mol@LB@Unfolding Energy - sRNA 2.90583 kcal/mol@LB@@LB@Position - mRNA 188 -- 205@LB@Position - sRNA 52 -- 67@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 61 -- 67@LB@
173	0.02087	0.4033	b2239	glpQ	-12.95	0.026326	256 -- 274	41 -- 66	periplasmic glycerophosphodiester phosphodiesterase	_____________255________________________275\n_____________\|__________________________\|\n5'-CGG...AGUCA__________________________GGCGG...UCA-3'\n______________UGGGAA_______GCAGUGCAAUGGC\n______________\|\|\|:\|\|_______\|\|\|:\|\|\|\|\|\|\|\|\|\n______________ACCUUU_______CGUUACGUUACCG\n3'-UUU...AUACA______UAGUCAC_____________GGUUG...UUG-5'\n_____________\|__________________________\|\n_____________67_________________________40\n	268 -- 274	41 -- 47	-26.6029 kcal/mol	7.82977 kcal/mol	5.82355 kcal/mol	255 275@LB@ \| \|@LB@5'-CGG...AGUCA GGCGG...UCA-3'@LB@ UGGGAA GCAGUGCAAUGGC@LB@ \|\|\|:\|\| \|\|\|:\|\|\|\|\|\|\|\|\|@LB@ ACCUUU CGUUACGUUACCG@LB@3'-UUU...AUACA UAGUCAC GGUUG...UUG-5'@LB@ \| \|@LB@ 67 40@LB@@LB@@LB@Energy -12.95 kcal/mol@LB@Hybridization Energy -26.6029 kcal/mol@LB@Unfolding Energy - mRNA 7.82977 kcal/mol@LB@Unfolding Energy - sRNA 5.82355 kcal/mol@LB@@LB@Position - mRNA 256 -- 274@LB@Position - sRNA 41 -- 66@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 41 -- 47@LB@
174	0.02096	0.4033	b3929	rraA	-13.95	0.014802	2 -- 21	45 -- 66	ribonuclease E (RNase E) inhibitor protein	_____________1______________________22\n_____________\|______________________\|\n__________5'-A____CC________________CCAAU...GCG-3'\n______________UGGA____CGGUGGCGAUGCGA\n______________\|\|\|\|____\|:\|\|\|\|\|:\|\|\|\|:\|\n______________ACCU____GUCACCGUUACGUU\n3'-UUU...AUACA____UUUA______________ACCGG...UUG-5'\n_____________\|______________________\|\n_____________67_____________________44\n	15 -- 21	45 -- 51	-26.5083 kcal/mol	8.28748 kcal/mol	4.27166 kcal/mol	1 22@LB@ \| \|@LB@ 5'-A CC CCAAU...GCG-3'@LB@ UGGA CGGUGGCGAUGCGA@LB@ \|\|\|\| \|:\|\|\|\|\|:\|\|\|\|:\|@LB@ ACCU GUCACCGUUACGUU@LB@3'-UUU...AUACA UUUA ACCGG...UUG-5'@LB@ \| \|@LB@ 67 44@LB@@LB@@LB@Energy -13.95 kcal/mol@LB@Hybridization Energy -26.5083 kcal/mol@LB@Unfolding Energy - mRNA 8.28748 kcal/mol@LB@Unfolding Energy - sRNA 4.27166 kcal/mol@LB@@LB@Position - mRNA 2 -- 21@LB@Position - sRNA 45 -- 66@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 45 -- 51@LB@
175	0.02099	0.4033	b2913	serA	-5.57	0.642321	190 -- 257	5 -- 65	D-3-phosphoglycerate dehydrogenase	_____________189_____________________________________________________________________258\n_____________\|_______________________________________________________________________\|\n5'-UGU...AGACA___UU____AAA______AG___UCGC___AGAAA________U____UU____C________________CACCA...CCA-3'\n______________GGA__GGGU___UGGCAA__GUA____UGG_____GACA_AGA_UAAG__UCUG_UGGUA__GAAGGCGUG\n______________\|\|\|__:::\|___\|\|\|\|\|\|__\|:\|____\|\|\|_____:\|\|\|_\|:\|_\|\|\|:__\|\|\|\|_\|\|::\|__:\|\|\|\|\|:\|:\n______________CCU__UUUA___ACCGUU__CGU____ACC_____UUGU_UUU_AUUU__AGAC_ACUGU__UUUCCGUAU\n3'-UUU...UACAA_________GUC______A____U______GGG______C___U____U___________UA_________AUUG-5'\n_____________\|_______________________________________________________________________\|\n_____________66______________________________________________________________________4\n	251 -- 257	5 -- 11	-32.5395 kcal/mol	14.8085 kcal/mol	12.157 kcal/mol	189 258@LB@ \| \|@LB@5'-UGU...AGACA UU AAA AG UCGC AGAAA U UU C CACCA...CCA-3'@LB@ GGA GGGU UGGCAA GUA UGG GACA AGA UAAG UCUG UGGUA GAAGGCGUG@LB@ \|\|\| :::\| \|\|\|\|\|\| \|:\| \|\|\| :\|\|\| \|:\| \|\|\|: \|\|\|\| \|\|::\| :\|\|\|\|\|:\|:@LB@ CCU UUUA ACCGUU CGU ACC UUGU UUU AUUU AGAC ACUGU UUUCCGUAU@LB@3'-UUU...UACAA GUC A U GGG C U U UA AUUG-5'@LB@ \| \|@LB@ 66 4@LB@@LB@@LB@Energy -5.57 kcal/mol@LB@Hybridization Energy -32.5395 kcal/mol@LB@Unfolding Energy - mRNA 14.8085 kcal/mol@LB@Unfolding Energy - sRNA 12.157 kcal/mol@LB@@LB@Position - mRNA 190 -- 257@LB@Position - sRNA 5 -- 65@LB@Position Seed - mRNA 251 -- 257@LB@Position Seed - sRNA 5 -- 11@LB@
176	0.02144	0.4097	b0948	rlmL	-6.91	0.434425	184 -- 201	13 -- 33	23S rRNA m(2)G2445 and m(7)G2069 methyltransferases SAM-dependent	_____________183___________________202\n_____________\|_____________________\|\n5'-GAC...CUCUU_____________________UGAAU...GUG-3'\n______________AGAGUAAAA___GUGACGAUA\n______________\|:\|:\|\|\|\|\|___\|\|\|\|\|:\|\|\|\n______________UUUUAUUUU___CACUGUUAU\n3'-UUU...UUGUC_________AGA_________UUCCG...UUG-5'\n_____________\|_____________________\|\n_____________34____________________12\n	195 -- 201	13 -- 19	-14.282 kcal/mol	2.4415 kcal/mol	4.9341 kcal/mol	183 202@LB@ \| \|@LB@5'-GAC...CUCUU UGAAU...GUG-3'@LB@ AGAGUAAAA GUGACGAUA@LB@ \|:\|:\|\|\|\|\| \|\|\|\|\|:\|\|\|@LB@ UUUUAUUUU CACUGUUAU@LB@3'-UUU...UUGUC AGA UUCCG...UUG-5'@LB@ \| \|@LB@ 34 12@LB@@LB@@LB@Energy -6.91 kcal/mol@LB@Hybridization Energy -14.282 kcal/mol@LB@Unfolding Energy - mRNA 2.4415 kcal/mol@LB@Unfolding Energy - sRNA 4.9341 kcal/mol@LB@@LB@Position - mRNA 184 -- 201@LB@Position - sRNA 13 -- 33@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 13 -- 19@LB@
177	0.02174	0.4127	b1725	yniA	-12.81	0.028485	66 -- 113	12 -- 55	fructosamine kinase family protein	_____________65__________________________________________________114\n_____________\|___________________________________________________\|\n5'-GAG...CGACC___G____G_____AAUAG______________UGGUU_____________UCAGU...GGC-3'\n______________UGG_A__G_AAUGG_____CAACAGAAAAUAAA_____UUUG_GGCAAUAA\n______________\|\|\|_\|__\|_\|\|\|\|\|_____\|\|\|\|\|\|\|\|\|\|\|\|\|\|_____\|:\|\|_\|:\|\|\|\|\|\|\n______________ACC_U__C_UUACC_____GUUGUCUUUUAUUU_____AGAC_CUGUUAUU\n3'-UUU...UAGUC___G_UA_G_____GG_________________U________A________UCCGU...UUG-5'\n_____________\|___________________________________________________\|\n_____________56__________________________________________________11\n	107 -- 113	12 -- 18	-33.1768 kcal/mol	9.27067 kcal/mol	11.0975 kcal/mol	65 114@LB@ \| \|@LB@5'-GAG...CGACC G G AAUAG UGGUU UCAGU...GGC-3'@LB@ UGG A G AAUGG CAACAGAAAAUAAA UUUG GGCAAUAA@LB@ \|\|\| \| \| \|\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|\|\| \|:\|\| \|:\|\|\|\|\|\|@LB@ ACC U C UUACC GUUGUCUUUUAUUU AGAC CUGUUAUU@LB@3'-UUU...UAGUC G UA G GG U A UCCGU...UUG-5'@LB@ \| \|@LB@ 56 11@LB@@LB@@LB@Energy -12.81 kcal/mol@LB@Hybridization Energy -33.1768 kcal/mol@LB@Unfolding Energy - mRNA 9.27067 kcal/mol@LB@Unfolding Energy - sRNA 11.0975 kcal/mol@LB@@LB@Position - mRNA 66 -- 113@LB@Position - sRNA 12 -- 55@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 12 -- 18@LB@
178	0.02184	0.4127	b1466	narW	-11.23	0.066200	254 -- 267	42 -- 56	nitrate reductase 2 (NRZ) delta subunit (assembly subunit)	_____________253_____________268\n_____________\|_______________\|\n5'-AUU...CUGUU____G__________AGGAC...CGC-3'\n______________GUGG_AAUGCAA_GG\n______________\|\|\|\|_\|\|\|\|\|\|\|_\|\|\n______________CACC_UUACGUU_CC\n3'-UUU...UUAGU____G_______A__GGGUU...UUG-5'\n_____________\|_______________\|\n_____________57______________41\n	259 -- 265	45 -- 51	-17.8423 kcal/mol	3.07693 kcal/mol	3.53153 kcal/mol	253 268@LB@ \| \|@LB@5'-AUU...CUGUU G AGGAC...CGC-3'@LB@ GUGG AAUGCAA GG@LB@ \|\|\|\| \|\|\|\|\|\|\| \|\|@LB@ CACC UUACGUU CC@LB@3'-UUU...UUAGU G A GGGUU...UUG-5'@LB@ \| \|@LB@ 57 41@LB@@LB@@LB@Energy -11.23 kcal/mol@LB@Hybridization Energy -17.8423 kcal/mol@LB@Unfolding Energy - mRNA 3.07693 kcal/mol@LB@Unfolding Energy - sRNA 3.53153 kcal/mol@LB@@LB@Position - mRNA 254 -- 267@LB@Position - sRNA 42 -- 56@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 45 -- 51@LB@
179	0.02223	0.4143	b2167	fruA	-7.15	0.399094	192 -- 200	5 -- 13	fused fructose-specific PTS enzymes: IIBcomponent/IIC components	_____________191_______201\n_____________\|_________\|\n5'-CGC...GCAGG_________AUGAA...AAA-3'\n______________AGAGGCAUA\n______________\|:\|\|\|\|\|\|\|\n______________UUUCCGUAU\n3'-UUU...UGUUA_________AUUG-5'\n_____________\|_________\|\n_____________14________4\n	194 -- 200	5 -- 11	-11.8443 kcal/mol	1.8873 kcal/mol	2.80332 kcal/mol	191 201@LB@ \| \|@LB@5'-CGC...GCAGG AUGAA...AAA-3'@LB@ AGAGGCAUA@LB@ \|:\|\|\|\|\|\|\|@LB@ UUUCCGUAU@LB@3'-UUU...UGUUA AUUG-5'@LB@ \| \|@LB@ 14 4@LB@@LB@@LB@Energy -7.15 kcal/mol@LB@Hybridization Energy -11.8443 kcal/mol@LB@Unfolding Energy - mRNA 1.8873 kcal/mol@LB@Unfolding Energy - sRNA 2.80332 kcal/mol@LB@@LB@Position - mRNA 192 -- 200@LB@Position - sRNA 5 -- 13@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 5 -- 11@LB@
180	0.02233	0.4143	b0435	bolA	-10.38	0.101210	35 -- 46	39 -- 51	stationary-phase morphogene transcriptional repressor for mreB; also regulator for dacA dacC and ampC	_____________34____________47\n_____________\|_____________\|\n5'-UGA...ACACU_____________GUGUU...CCG-3'\n______________GAUGCGA_GGCCU\n______________:\|\|\|\|:\|_\|\|\|\|:\n______________UUACGUU_CCGGG\n3'-UUU...CACCG_______A_____UUGUC...UUG-5'\n_____________\|_____________\|\n_____________52____________38\n	35 -- 41	45 -- 51	-16.689 kcal/mol	1.55914 kcal/mol	4.74571 kcal/mol	34 47@LB@ \| \|@LB@5'-UGA...ACACU GUGUU...CCG-3'@LB@ GAUGCGA GGCCU@LB@ :\|\|\|\|:\| \|\|\|\|:@LB@ UUACGUU CCGGG@LB@3'-UUU...CACCG A UUGUC...UUG-5'@LB@ \| \|@LB@ 52 38@LB@@LB@@LB@Energy -10.38 kcal/mol@LB@Hybridization Energy -16.689 kcal/mol@LB@Unfolding Energy - mRNA 1.55914 kcal/mol@LB@Unfolding Energy - sRNA 4.74571 kcal/mol@LB@@LB@Position - mRNA 35 -- 46@LB@Position - sRNA 39 -- 51@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 45 -- 51@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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