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
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@
123	0.0134	0.3627	b3774	ilvC	-11.90	0.092739	9 -- 41	1 -- 25	ketol-acid reductoisomerase NAD(P)-binding	_____________8__________________________________42\n_____________\|__________________________________\|\n___5'-AUGGCGGC_______CAGAUGCAG__A_______A_______GUAAA...GCU-3'\n______________UUUCCGC_________GA_GGUUUUC__GAUCGC\n______________\|:\|\|\|\|\|_________\|\|_\|\|\|:\|\|\|__\|\|\|\|\|\|\n______________AGAGGCG_________CU_CCAGAAG__CUAGCG\n3'-UUU...GUCCA__________________C_______GA______-5'\n_____________\|_________________________________\|\n_____________26________________________________1\n	28 -- 34	9 -- 15	-28.1375 kcal/mol	8.51703 kcal/mol	7.71912 kcal/mol	8 42@LB@ \| \|@LB@ 5'-AUGGCGGC CAGAUGCAG A A GUAAA...GCU-3'@LB@ UUUCCGC GA GGUUUUC GAUCGC@LB@ \|:\|\|\|\|\| \|\| \|\|\|:\|\|\| \|\|\|\|\|\|@LB@ AGAGGCG CU CCAGAAG CUAGCG@LB@3'-UUU...GUCCA C GA -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -11.90 kcal/mol@LB@Hybridization Energy -28.1375 kcal/mol@LB@Unfolding Energy - mRNA 8.51703 kcal/mol@LB@Unfolding Energy - sRNA 7.71912 kcal/mol@LB@@LB@Position - mRNA 9 -- 41@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 9 -- 15@LB@
181	0.0223	0.4113	b3770	ilvE	-12.64	0.069830	250 -- 281	37 -- 61	branched-chain amino acid aminotransferase	_____________249______________________________282\n_____________\|________________________________\|\n5'-UUU...GGUUC_______AGAC____AG___CAU_________CACGC...GCA-3'\n______________GCUGGGA____GCGA__GUG___GUGAUGUCG\n______________:\|\|\|\|:\|____\|\|:\|__\|\|\|___\|::\|\|\|\|\|\|\n______________UGACCUU____CGUU__CAC___CGUUACAGC\n3'-UUU...CAUUA_______________A____U___________ACGAA...GCG-5'\n_____________\|________________________________\|\n_____________62_______________________________36\n	275 -- 281	37 -- 43	-25.0056 kcal/mol	9.06403 kcal/mol	3.30158 kcal/mol	249 282@LB@ \| \|@LB@5'-UUU...GGUUC AGAC AG CAU CACGC...GCA-3'@LB@ GCUGGGA GCGA GUG GUGAUGUCG@LB@ :\|\|\|\|:\| \|\|:\| \|\|\| \|::\|\|\|\|\|\|@LB@ UGACCUU CGUU CAC CGUUACAGC@LB@3'-UUU...CAUUA A U ACGAA...GCG-5'@LB@ \| \|@LB@ 62 36@LB@@LB@@LB@Energy -12.64 kcal/mol@LB@Hybridization Energy -25.0056 kcal/mol@LB@Unfolding Energy - mRNA 9.06403 kcal/mol@LB@Unfolding Energy - sRNA 3.30158 kcal/mol@LB@@LB@Position - mRNA 250 -- 281@LB@Position - sRNA 37 -- 61@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 37 -- 43@LB@
122	0.01331	0.3627	b0078	ilvH	-10.99	0.130728	66 -- 84	41 -- 61	acetolactate synthase 3 small subunit valine-sensitive	_____________65____________________85\n_____________\|_____________________\|\n5'-GCC...GAGGC_______________C_____AAUCG...UGA-3'\n______________GCUGGAA_CAG_GUG_GCAAU\n______________:\|\|\|\|\|\|_\|\|:_\|\|\|_\|\|\|\|\|\n______________UGACCUU_GUU_CAC_CGUUA\n3'-UUU...CAUUA_______C___A___U_____CAGCA...GCG-5'\n_____________\|_____________________\|\n_____________62____________________40\n	66 -- 72	55 -- 61	-20.2432 kcal/mol	5.95009 kcal/mol	3.30062 kcal/mol	65 85@LB@ \| \|@LB@5'-GCC...GAGGC C AAUCG...UGA-3'@LB@ GCUGGAA CAG GUG GCAAU@LB@ :\|\|\|\|\|\| \|\|: \|\|\| \|\|\|\|\|@LB@ UGACCUU GUU CAC CGUUA@LB@3'-UUU...CAUUA C A U CAGCA...GCG-5'@LB@ \| \|@LB@ 62 40@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -20.2432 kcal/mol@LB@Unfolding Energy - mRNA 5.95009 kcal/mol@LB@Unfolding Energy - sRNA 3.30062 kcal/mol@LB@@LB@Position - mRNA 66 -- 84@LB@Position - sRNA 41 -- 61@LB@Position Seed - mRNA 66 -- 72@LB@Position Seed - sRNA 55 -- 61@LB@
57	0.005292	0.2905	b0077	ilvI	-12.73	0.067491	188 -- 240	1 -- 67	acetolactate synthase 3 large subunit	_____________187__________________________________________________________________241\n_____________\|____________________________________________________________________\|\n5'-AAA...CAAAC___________C____C_________________________AG_____A__U____G__________UUAUC...UUU-3'\n______________AGUGA____GG_AGGC_AUG_GAG__AUGUUGU_CU____GG____CCG_GA_GGUC_UCC_GAUCGC\n______________\|\|\|:\|____\|\|_\|:\|\|_\|\|\|_\|\|\|__\|\|\|\|:\|\|_\|\|____\|\|____\|\|\|_\|\|_\|\|\|\|_\|\|\|_\|\|\|\|\|\|\n______________UCAUU____CC_UUCG_UAC_CUC__UACAGCA_GA____CC____GGC_CU_CCAG_AGG_CUAGCG\n3'-UUU...CCGAU_____AUGA_______U___A___GU_______C__AAGU__AAGA___G__C____A___A______-5'\n_____________\|___________________________________________________________________\|\n_____________68__________________________________________________________________1\n	207 -- 213	36 -- 42	-47.8903 kcal/mol	21.0378 kcal/mol	14.1245 kcal/mol	187 241@LB@ \| \|@LB@5'-AAA...CAAAC C C AG A U G UUAUC...UUU-3'@LB@ AGUGA GG AGGC AUG GAG AUGUUGU CU GG CCG GA GGUC UCC GAUCGC@LB@ \|\|\|:\| \|\| \|:\|\| \|\|\| \|\|\| \|\|\|\|:\|\| \|\| \|\| \|\|\| \|\| \|\|\|\| \|\|\| \|\|\|\|\|\|@LB@ UCAUU CC UUCG UAC CUC UACAGCA GA CC GGC CU CCAG AGG CUAGCG@LB@3'-UUU...CCGAU AUGA U A GU C AAGU AAGA G C A A -5'@LB@ \| \|@LB@ 68 1@LB@@LB@@LB@Energy -12.73 kcal/mol@LB@Hybridization Energy -47.8903 kcal/mol@LB@Unfolding Energy - mRNA 21.0378 kcal/mol@LB@Unfolding Energy - sRNA 14.1245 kcal/mol@LB@@LB@Position - mRNA 188 -- 240@LB@Position - sRNA 1 -- 67@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 36 -- 42@LB@
87	0.008915	0.3393	b2530	iscS	-12.30	0.079567	175 -- 203	40 -- 68	cysteine desulfurase (tRNA sulfurtransferase) PLP-dependent	_____________174___________________________204\n_____________\|_____________________________\|\n5'-AAG...GCAUU________UAC_____UUAUA________AAAUU...UUG-3'\n______________GAGUGAUG___GGAGU_____GAGCAAUG\n______________:\|\|\|:\|\|:___\|:\|\|:_____\|\|\|\|\|\|\|\|\n______________UUCAUUAU___CUUCG_____CUCGUUAC\n3'-UUU...ACCGA________GAC_____UUACA________AGCAC...GCG-5'\n_____________\|_____________________________\|\n_____________69____________________________39\n	197 -- 203	40 -- 46	-22.6486 kcal/mol	7.04226 kcal/mol	3.30507 kcal/mol	174 204@LB@ \| \|@LB@5'-AAG...GCAUU UAC UUAUA AAAUU...UUG-3'@LB@ GAGUGAUG GGAGU GAGCAAUG@LB@ :\|\|\|:\|\|: \|:\|\|: \|\|\|\|\|\|\|\|@LB@ UUCAUUAU CUUCG CUCGUUAC@LB@3'-UUU...ACCGA GAC UUACA AGCAC...GCG-5'@LB@ \| \|@LB@ 69 39@LB@@LB@@LB@Energy -12.30 kcal/mol@LB@Hybridization Energy -22.6486 kcal/mol@LB@Unfolding Energy - mRNA 7.04226 kcal/mol@LB@Unfolding Energy - sRNA 3.30507 kcal/mol@LB@@LB@Position - mRNA 175 -- 203@LB@Position - sRNA 40 -- 68@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 40 -- 46@LB@
33	0.003005	0.2776	b0698	kdpA	-12.81	0.065301	205 -- 229	1 -- 24	potassium translocating ATPase subunit A	_____________204_______________________230\n_____________\|_________________________\|\n5'-GCU...GAUGG__G___A____U___UA________CACGU...ACA-3'\n______________CU_CGC_AGGG_UCU__CUGAUCGC\n______________\|\|_\|\|\|_\|\|\|\|_\|\|\|__\|\|\|\|\|\|\|\|\n______________GA_GCG_UCCC_AGA__GACUAGCG\n3'-UUU...UCCAA__G___C________AG________-5'\n_____________\|________________________\|\n_____________25_______________________1\n	223 -- 229	1 -- 7	-32.8008 kcal/mol	12.2882 kcal/mol	7.69932 kcal/mol	204 230@LB@ \| \|@LB@5'-GCU...GAUGG G A U UA CACGU...ACA-3'@LB@ CU CGC AGGG UCU CUGAUCGC@LB@ \|\| \|\|\| \|\|\|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ GA GCG UCCC AGA GACUAGCG@LB@3'-UUU...UCCAA G C AG -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -12.81 kcal/mol@LB@Hybridization Energy -32.8008 kcal/mol@LB@Unfolding Energy - mRNA 12.2882 kcal/mol@LB@Unfolding Energy - sRNA 7.69932 kcal/mol@LB@@LB@Position - mRNA 205 -- 229@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 1 -- 7@LB@
129	0.01401	0.3627	b0696	kdpC	-11.63	0.102829	282 -- 295	49 -- 63	potassium translocating ATPase subunit C	_____________281_____________296\n_____________\|_______________\|\n5'-GCG...CCACC_______________GUGGU-3'\n______________GUACUGG_GGCAAUG\n______________:\|\|\|\|\|\|_:\|\|\|\|\|\|\n______________UAUGACC_UCGUUAC\n3'-UUU...UUCAU_______U_______ACUCG...GCG-5'\n_____________\|_______________\|\n_____________64______________48\n	289 -- 295	49 -- 55	-18.0603 kcal/mol	3.42021 kcal/mol	3.01015 kcal/mol	281 296@LB@ \| \|@LB@5'-GCG...CCACC GUGGU-3'@LB@ GUACUGG GGCAAUG@LB@ :\|\|\|\|\|\| :\|\|\|\|\|\|@LB@ UAUGACC UCGUUAC@LB@3'-UUU...UUCAU U ACUCG...GCG-5'@LB@ \| \|@LB@ 64 48@LB@@LB@@LB@Energy -11.63 kcal/mol@LB@Hybridization Energy -18.0603 kcal/mol@LB@Unfolding Energy - mRNA 3.42021 kcal/mol@LB@Unfolding Energy - sRNA 3.01015 kcal/mol@LB@@LB@Position - mRNA 282 -- 295@LB@Position - sRNA 49 -- 63@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 49 -- 55@LB@
80	0.007461	0.3134	b0925	ldtD	-10.36	0.165445	187 -- 206	37 -- 61	murein L D-transpeptidase	_____________186_______________________207\n_____________\|_________________________\|\n5'-AAG...UAAAA__A______________G_______CUUAA...CUG-3'\n______________AC_GGGGGCA_____AG_GAUGUUG\n______________\|\|_\|\|::\|\|\|_____\|\|_:\|\|\|\|:\|\n______________UG_CCUUCGU_____UC_UUACAGC\n3'-UUU...CAUUA__A_______UACAC__G_______ACGAA...GCG-5'\n_____________\|_________________________\|\n_____________62________________________36\n	200 -- 206	37 -- 43	-19.2999 kcal/mol	5.64293 kcal/mol	3.30158 kcal/mol	186 207@LB@ \| \|@LB@5'-AAG...UAAAA A G CUUAA...CUG-3'@LB@ AC GGGGGCA AG GAUGUUG@LB@ \|\| \|\|::\|\|\| \|\| :\|\|\|\|:\|@LB@ UG CCUUCGU UC UUACAGC@LB@3'-UUU...CAUUA A UACAC G ACGAA...GCG-5'@LB@ \| \|@LB@ 62 36@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -19.2999 kcal/mol@LB@Unfolding Energy - mRNA 5.64293 kcal/mol@LB@Unfolding Energy - sRNA 3.30158 kcal/mol@LB@@LB@Position - mRNA 187 -- 206@LB@Position - sRNA 37 -- 61@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 37 -- 43@LB@
35	0.003076	0.2776	b1678	ldtE	-14.38	0.035403	2 -- 13	49 -- 60	murein L D-transpeptidase	_____________1____________14\n_____________\|____________\|\n__________5'-U____________AUUCG...GCC-3'\n______________CUGGAAGCGAUG\n______________\|\|\|\|\|\|\|\|:\|\|\|\n______________GACCUUCGUUAC\n3'-UUU...AUUAU____________ACUCG...GCG-5'\n_____________\|____________\|\n_____________61___________48\n	7 -- 13	49 -- 55	-19.7187 kcal/mol	2.33169 kcal/mol	3.00762 kcal/mol	1 14@LB@ \| \|@LB@ 5'-U AUUCG...GCC-3'@LB@ CUGGAAGCGAUG@LB@ \|\|\|\|\|\|\|\|:\|\|\|@LB@ GACCUUCGUUAC@LB@3'-UUU...AUUAU ACUCG...GCG-5'@LB@ \| \|@LB@ 61 48@LB@@LB@@LB@Energy -14.38 kcal/mol@LB@Hybridization Energy -19.7187 kcal/mol@LB@Unfolding Energy - mRNA 2.33169 kcal/mol@LB@Unfolding Energy - sRNA 3.00762 kcal/mol@LB@@LB@Position - mRNA 2 -- 13@LB@Position - sRNA 49 -- 60@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 49 -- 55@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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