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
103	0.0104	0.3393	b2711	norW	-11.75	0.098250	192 -- 208	42 -- 58	NADH:flavorubredoxin oxidoreductase	_____________191_______________209\n_____________\|_________________\|\n5'-GAA...GCAUC________AA_______CGGCA...UUG-3'\n______________GGAGGCAA__UGAGUAA\n______________\|\|\|:\|\|\|\|__\|\|\|\|:\|\|\n______________CCUUCGUU__ACUCGUU\n3'-UUU...UAUGA________AC_______ACAGC...GCG-5'\n_____________\|_________________\|\n_____________59________________41\n	202 -- 208	42 -- 48	-20.2467 kcal/mol	5.28663 kcal/mol	3.2101 kcal/mol	191 209@LB@ \| \|@LB@5'-GAA...GCAUC AA CGGCA...UUG-3'@LB@ GGAGGCAA UGAGUAA@LB@ \|\|\|:\|\|\|\| \|\|\|\|:\|\|@LB@ CCUUCGUU ACUCGUU@LB@3'-UUU...UAUGA AC ACAGC...GCG-5'@LB@ \| \|@LB@ 59 41@LB@@LB@@LB@Energy -11.75 kcal/mol@LB@Hybridization Energy -20.2467 kcal/mol@LB@Unfolding Energy - mRNA 5.28663 kcal/mol@LB@Unfolding Energy - sRNA 3.2101 kcal/mol@LB@@LB@Position - mRNA 192 -- 208@LB@Position - sRNA 42 -- 58@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 42 -- 48@LB@
96	0.01001	0.3393	b2714	ascG	-11.75	0.098239	209 -- 220	53 -- 64	asc operon transcriptional repressor; prpBC operon repressor	_____________208__________221\n_____________\|____________\|\n5'-AAA...ACGAC____________GGCGA...AAG-3'\n______________GAUGCUGGAAGU\n______________:\|\|:\|\|\|\|\|\|\|:\n______________UUAUGACCUUCG\n3'-UUU...AUUCA____________UUACA...GCG-5'\n_____________\|____________\|\n_____________65___________52\n	214 -- 220	53 -- 59	-16.9486 kcal/mol	2.31342 kcal/mol	2.88502 kcal/mol	208 221@LB@ \| \|@LB@5'-AAA...ACGAC GGCGA...AAG-3'@LB@ GAUGCUGGAAGU@LB@ :\|\|:\|\|\|\|\|\|\|:@LB@ UUAUGACCUUCG@LB@3'-UUU...AUUCA UUACA...GCG-5'@LB@ \| \|@LB@ 65 52@LB@@LB@@LB@Energy -11.75 kcal/mol@LB@Hybridization Energy -16.9486 kcal/mol@LB@Unfolding Energy - mRNA 2.31342 kcal/mol@LB@Unfolding Energy - sRNA 2.88502 kcal/mol@LB@@LB@Position - mRNA 209 -- 220@LB@Position - sRNA 53 -- 64@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 53 -- 59@LB@
157	0.0194	0.4072	b2720	hycF	-4.41	0.858528	100 -- 115	42 -- 59	formate hydrogenlyase complex iron-sulfur protein	_____________99_________________116\n_____________\|__________________\|\n5'-CGA...GACCG___U_________C____GAAGA...CAG-3'\n______________UGG___CGAUGUG_GUAA\n______________\|\|\|___\|:\|\|\|\|\|_\|:\|\|\n______________ACC___GUUACAC_CGUU\n3'-UUU...UUAUG___UUC_______U____ACAGC...GCG-5'\n_____________\|__________________\|\n_____________60_________________41\n	104 -- 110	47 -- 53	-13.6757 kcal/mol	5.98921 kcal/mol	3.27185 kcal/mol	99 116@LB@ \| \|@LB@5'-CGA...GACCG U C GAAGA...CAG-3'@LB@ UGG CGAUGUG GUAA@LB@ \|\|\| \|:\|\|\|\|\| \|:\|\|@LB@ ACC GUUACAC CGUU@LB@3'-UUU...UUAUG UUC U ACAGC...GCG-5'@LB@ \| \|@LB@ 60 41@LB@@LB@@LB@Energy -4.41 kcal/mol@LB@Hybridization Energy -13.6757 kcal/mol@LB@Unfolding Energy - mRNA 5.98921 kcal/mol@LB@Unfolding Energy - sRNA 3.27185 kcal/mol@LB@@LB@Position - mRNA 100 -- 115@LB@Position - sRNA 42 -- 59@LB@Position Seed - mRNA 104 -- 110@LB@Position Seed - sRNA 47 -- 53@LB@
55	0.005153	0.2905	b2727	hypB	-14.04	0.040392	194 -- 204	39 -- 49	GTP hydrolase involved in nickel liganding into hydrogenases	_____________193_________205\n_____________\|___________\|\n5'-GCC...CAGGA___________GUACA...CGG-3'\n______________GUGAGCGAUGU\n______________\|\|\|\|\|\|:\|\|\|\|\n______________CACUCGUUACA\n3'-UUU...CGUUA___________GCACG...GCG-5'\n_____________\|___________\|\n_____________50__________38\n	198 -- 204	39 -- 45	-18.0568 kcal/mol	2.85856 kcal/mol	1.15413 kcal/mol	193 205@LB@ \| \|@LB@5'-GCC...CAGGA GUACA...CGG-3'@LB@ GUGAGCGAUGU@LB@ \|\|\|\|\|\|:\|\|\|\|@LB@ CACUCGUUACA@LB@3'-UUU...CGUUA GCACG...GCG-5'@LB@ \| \|@LB@ 50 38@LB@@LB@@LB@Energy -14.04 kcal/mol@LB@Hybridization Energy -18.0568 kcal/mol@LB@Unfolding Energy - mRNA 2.85856 kcal/mol@LB@Unfolding Energy - sRNA 1.15413 kcal/mol@LB@@LB@Position - mRNA 194 -- 204@LB@Position - sRNA 39 -- 49@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 39 -- 45@LB@
161	0.02011	0.4072	b2820	recB	-12.55	0.072418	202 -- 213	37 -- 48	exonuclease V (RecBCD complex) beta subunit	_____________201__________214\n_____________\|____________\|\n5'-GGC...AAGAA____________CCGAG...UUG-3'\n______________UGAGUGAUGUCG\n______________\|\|\|\|::\|\|\|\|\|\|\n______________ACUCGUUACAGC\n3'-UUU...GUUAC____________ACGAA...GCG-5'\n_____________\|____________\|\n_____________49___________36\n	207 -- 213	37 -- 43	-16.4196 kcal/mol	2.71715 kcal/mol	1.1567 kcal/mol	201 214@LB@ \| \|@LB@5'-GGC...AAGAA CCGAG...UUG-3'@LB@ UGAGUGAUGUCG@LB@ \|\|\|\|::\|\|\|\|\|\|@LB@ ACUCGUUACAGC@LB@3'-UUU...GUUAC ACGAA...GCG-5'@LB@ \| \|@LB@ 49 36@LB@@LB@@LB@Energy -12.55 kcal/mol@LB@Hybridization Energy -16.4196 kcal/mol@LB@Unfolding Energy - mRNA 2.71715 kcal/mol@LB@Unfolding Energy - sRNA 1.1567 kcal/mol@LB@@LB@Position - mRNA 202 -- 213@LB@Position - sRNA 37 -- 48@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 37 -- 43@LB@
15	0.001024	0.2294	b2822	recC	-16.38	0.016046	234 -- 264	37 -- 63	exonuclease V (RecBCD complex) gamma chain	_____________233______________________________265\n_____________\|________________________________\|\n5'-AGU...UGGAC___________GUU_________UUAU_____AACGC...AGA-3'\n______________GUGCUGGAAGC___GAUG_GAGU____UGUCG\n______________:\|:\|\|\|\|\|\|\|\|___:\|\|\|_\|\|\|:____\|\|\|\|\|\n______________UAUGACCUUCG___UUAC_CUCG____ACAGC\n3'-UUU...UUCAU__________________A____UU_______ACGAA...GCG-5'\n_____________\|________________________________\|\n_____________64_______________________________36\n	238 -- 244	53 -- 59	-30.8262 kcal/mol	11.1454 kcal/mol	3.30267 kcal/mol	233 265@LB@ \| \|@LB@5'-AGU...UGGAC GUU UUAU AACGC...AGA-3'@LB@ GUGCUGGAAGC GAUG GAGU UGUCG@LB@ :\|:\|\|\|\|\|\|\|\| :\|\|\| \|\|\|: \|\|\|\|\|@LB@ UAUGACCUUCG UUAC CUCG ACAGC@LB@3'-UUU...UUCAU A UU ACGAA...GCG-5'@LB@ \| \|@LB@ 64 36@LB@@LB@@LB@Energy -16.38 kcal/mol@LB@Hybridization Energy -30.8262 kcal/mol@LB@Unfolding Energy - mRNA 11.1454 kcal/mol@LB@Unfolding Energy - sRNA 3.30267 kcal/mol@LB@@LB@Position - mRNA 234 -- 264@LB@Position - sRNA 37 -- 63@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 53 -- 59@LB@
154	0.01903	0.4072	b2823	ppdC	-17.47	0.010387	242 -- 260	40 -- 58	putative prepilin peptidase-dependent protein	_____________241_________________261\n_____________\|___________________\|\n5'-ACG...CUGCC___________U_______GUGUU...UCC-3'\n______________GGAGGUAAUGU_GGCGAUG\n______________\|\|\|:\|:\|\|\|\|\|_:\|\|:\|\|\|\n______________CCUUCGUUACA_UCGUUAC\n3'-UUU...UAUGA___________C_______AGCAC...GCG-5'\n_____________\|___________________\|\n_____________59__________________39\n	254 -- 260	40 -- 46	-26.2879 kcal/mol	5.60197 kcal/mol	3.21578 kcal/mol	241 261@LB@ \| \|@LB@5'-ACG...CUGCC U GUGUU...UCC-3'@LB@ GGAGGUAAUGU GGCGAUG@LB@ \|\|\|:\|:\|\|\|\|\| :\|\|:\|\|\|@LB@ CCUUCGUUACA UCGUUAC@LB@3'-UUU...UAUGA C AGCAC...GCG-5'@LB@ \| \|@LB@ 59 39@LB@@LB@@LB@Energy -17.47 kcal/mol@LB@Hybridization Energy -26.2879 kcal/mol@LB@Unfolding Energy - mRNA 5.60197 kcal/mol@LB@Unfolding Energy - sRNA 3.21578 kcal/mol@LB@@LB@Position - mRNA 242 -- 260@LB@Position - sRNA 40 -- 58@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 40 -- 46@LB@
173	0.02105	0.4072	b2840	ygeA	-11.88	0.093670	213 -- 233	44 -- 67	Asp/Glu_racemase family protein	_____________212______________________234\n_____________\|________________________\|\n5'-AAA...CAAUU___U__________G_________UGGGA...UUC-3'\n______________GGU__UGCUGGGAG_AA__UGAGC\n______________:\|\|__\|:\|\|\|\|:\|\|_\|\|__\|\|\|\|\|\n______________UCA__AUGACCUUC_UU__ACUCG\n3'-UUU...CCGAU___UU_________G__AC_____UUACA...GCG-5'\n_____________\|________________________\|\n_____________68_______________________43\n	219 -- 225	54 -- 60	-22.3324 kcal/mol	7.15309 kcal/mol	3.30407 kcal/mol	212 234@LB@ \| \|@LB@5'-AAA...CAAUU U G UGGGA...UUC-3'@LB@ GGU UGCUGGGAG AA UGAGC@LB@ :\|\| \|:\|\|\|\|:\|\| \|\| \|\|\|\|\|@LB@ UCA AUGACCUUC UU ACUCG@LB@3'-UUU...CCGAU UU G AC UUACA...GCG-5'@LB@ \| \|@LB@ 68 43@LB@@LB@@LB@Energy -11.88 kcal/mol@LB@Hybridization Energy -22.3324 kcal/mol@LB@Unfolding Energy - mRNA 7.15309 kcal/mol@LB@Unfolding Energy - sRNA 3.30407 kcal/mol@LB@@LB@Position - mRNA 213 -- 233@LB@Position - sRNA 44 -- 67@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 54 -- 60@LB@
167	0.02069	0.4072	b2897	sdhE	-17.17	0.011699	7 -- 68	8 -- 56	flavinator of succinate dehydrogenase; antitoxin of CptAB toxin-antitoxin pair	_____________6_______________________________________________________________69\n_____________\|_______________________________________________________________\|\n_____5'-GUAAAA____U___A________CAA_________CUACGCGAUCUGUGCC__________C_A_____AAAAA...ACA-3'\n______________GAGC_AUG__GGCAAUG___GUGCUUUCA________________UUCUGCGAGG_G_CUUCC\n______________:\|\|\|_\|\|\|__:\|\|\|\|\|\|___\|\|\|\|\|\|\|\|\|________________:\|\|:\|\|\|\|\|\|_\|_\|\|\|\|\|\n______________UUCG_UAC__UCGUUAC___CACGAAAGU________________GAGGCGCUCC_C_GAAGG\n3'-UUU...UGACC____U___AC_______AG__________CCAA________________________A_____ACUAGCG-5'\n_____________\|_______________________________________________________________\|\n_____________57______________________________________________________________7\n	54 -- 60	15 -- 21	-49.3967 kcal/mol	18.1865 kcal/mol	14.0385 kcal/mol	6 69@LB@ \| \|@LB@ 5'-GUAAAA U A CAA CUACGCGAUCUGUGCC C A AAAAA...ACA-3'@LB@ GAGC AUG GGCAAUG GUGCUUUCA UUCUGCGAGG G CUUCC@LB@ :\|\|\| \|\|\| :\|\|\|\|\|\| \|\|\|\|\|\|\|\|\| :\|\|:\|\|\|\|\|\| \| \|\|\|\|\|@LB@ UUCG UAC UCGUUAC CACGAAAGU GAGGCGCUCC C GAAGG@LB@3'-UUU...UGACC U AC AG CCAA A ACUAGCG-5'@LB@ \| \|@LB@ 57 7@LB@@LB@@LB@Energy -17.17 kcal/mol@LB@Hybridization Energy -49.3967 kcal/mol@LB@Unfolding Energy - mRNA 18.1865 kcal/mol@LB@Unfolding Energy - sRNA 14.0385 kcal/mol@LB@@LB@Position - mRNA 7 -- 68@LB@Position - sRNA 8 -- 56@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 15 -- 21@LB@
113	0.01187	0.3513	b2901	bglA	-10.39	0.163088	124 -- 152	36 -- 60	6-phospho-beta-glucosidase A	_____________123___________________________153\n_____________\|_____________________________\|\n5'-UUC...UCAUC______A__U__AAAAAA___________UUGGC...GGC-3'\n______________CUGGAA_CG_UG______AGUGAUGUCGU\n______________\|\|\|\|\|\|_\|:_\|\|______\|\|::\|\|\|\|\|\|\|\n______________GACCUU_GU_AC______UCGUUACAGCA\n3'-UUU...AUUAU______C__U__AC_______________CGAAA...GCG-5'\n_____________\|_____________________________\|\n_____________61____________________________35\n	146 -- 152	36 -- 42	-20.7652 kcal/mol	7.06987 kcal/mol	3.30077 kcal/mol	123 153@LB@ \| \|@LB@5'-UUC...UCAUC A U AAAAAA UUGGC...GGC-3'@LB@ CUGGAA CG UG AGUGAUGUCGU@LB@ \|\|\|\|\|\| \|: \|\| \|\|::\|\|\|\|\|\|\|@LB@ GACCUU GU AC UCGUUACAGCA@LB@3'-UUU...AUUAU C U AC CGAAA...GCG-5'@LB@ \| \|@LB@ 61 35@LB@@LB@@LB@Energy -10.39 kcal/mol@LB@Hybridization Energy -20.7652 kcal/mol@LB@Unfolding Energy - mRNA 7.06987 kcal/mol@LB@Unfolding Energy - sRNA 3.30077 kcal/mol@LB@@LB@Position - mRNA 124 -- 152@LB@Position - sRNA 36 -- 60@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 36 -- 42@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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