Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
86	0.003687	0.1509	b0774	bioA	-10.95	0.166636	92 -- 152	44 -- 98	7 8-diaminopelargonic acid synthase PLP-dependent	_____________91_____________________________________________________________153\n_____________\|______________________________________________________________\|\n5'-ACG...ACAAU_____G______C____A__CAU______UCUCCAAA___U__UU_________A_______UGUAG...AAG-3'\n______________GUCCA_CGUGGG_GGUG_GC___GGGGCU________ACG_GU__UUUGUUGUU__AUUCGG\n______________\|:\|\|\|_\|\|\|\|\|\|_\|:\|\|_\|\|___::\|:\|\|________\|\|:_\|:__\|\|:\|\|\|\|\|\|__\|:\|\|:\|\n______________CGGGU_GCACCC_CUAC_CG___UUCUGA________UGU_CG__AAGCAACAA__UGAGUC\n____3'-UUUUUUU_____A______U____C__U________UGUG__________UU_________AG______CCCUA...GCA-5'\n_____________\|______________________________________________________________\|\n_____________99_____________________________________________________________43\n	139 -- 145	52 -- 58	-48.0349 kcal/mol	20.1482 kcal/mol	16.9429 kcal/mol	91 153@LB@ \| \|@LB@5'-ACG...ACAAU G C A CAU UCUCCAAA U UU A UGUAG...AAG-3'@LB@ GUCCA CGUGGG GGUG GC GGGGCU ACG GU UUUGUUGUU AUUCGG@LB@ \|:\|\|\| \|\|\|\|\|\| \|:\|\| \|\| ::\|:\|\| \|\|: \|: \|\|:\|\|\|\|\|\| \|:\|\|:\|@LB@ CGGGU GCACCC CUAC CG UUCUGA UGU CG AAGCAACAA UGAGUC@LB@ 3'-UUUUUUU A U C U UGUG UU AG CCCUA...GCA-5'@LB@ \| \|@LB@ 99 43@LB@@LB@@LB@Energy -10.95 kcal/mol@LB@Hybridization Energy -48.0349 kcal/mol@LB@Unfolding Energy - mRNA 20.1482 kcal/mol@LB@Unfolding Energy - sRNA 16.9429 kcal/mol@LB@@LB@Position - mRNA 92 -- 152@LB@Position - sRNA 44 -- 98@LB@Position Seed - mRNA 139 -- 145@LB@Position Seed - sRNA 52 -- 58@LB@
28	0.0004009	0.04965	b3511	hdeD	-17.16	0.005105	126 -- 176	35 -- 75	acid-resistance membrane protein	_____________125__________________________________________________177\n_____________\|____________________________________________________\|\n5'-GAG...AAAUC________U_UUA__CG________G__AUAGAUUGAUAG____________UUCUU...UCG-3'\n______________GACUGCAU_C___GA__CGUU_UUU_GC____________CAGGGGAUUUUC\n______________\|\|\|\|:\|\|:_\|___:\|__\|\|\|\|_\|\|\|_:\|____________\|\|\|\|\|\|\|\|\|\|:\|\n______________CUGAUGUG_G___UU__GCAA_AAA_UG____________GUCCCCUAAAGG\n3'-UUU...CGUUU________U_UCG__AA____C___G__A_______________________UACGA...GCA-5'\n_____________\|____________________________________________________\|\n_____________76___________________________________________________34\n	170 -- 176	35 -- 41	-34.0299 kcal/mol	12.0619 kcal/mol	4.80541 kcal/mol	125 177@LB@ \| \|@LB@5'-GAG...AAAUC U UUA CG G AUAGAUUGAUAG UUCUU...UCG-3'@LB@ GACUGCAU C GA CGUU UUU GC CAGGGGAUUUUC@LB@ \|\|\|\|:\|\|: \| :\| \|\|\|\| \|\|\| :\| \|\|\|\|\|\|\|\|\|\|:\|@LB@ CUGAUGUG G UU GCAA AAA UG GUCCCCUAAAGG@LB@3'-UUU...CGUUU U UCG AA C G A UACGA...GCA-5'@LB@ \| \|@LB@ 76 34@LB@@LB@@LB@Energy -17.16 kcal/mol@LB@Hybridization Energy -34.0299 kcal/mol@LB@Unfolding Energy - mRNA 12.0619 kcal/mol@LB@Unfolding Energy - sRNA 4.80541 kcal/mol@LB@@LB@Position - mRNA 126 -- 176@LB@Position - sRNA 35 -- 75@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 35 -- 41@LB@
112	0.004986	0.1545	b0118	acnB	-15.18	0.018766	221 -- 251	38 -- 71	aconitate hydratase 2; aconitase B; 2-methyl-cis-aconitate hydratase	_____________220________________________________252\n_____________\|__________________________________\|\n5'-GAG...CGUAA_________UGAG___GC_______G________GCGCC...UGC-3'\n______________GCACGUAGC____CGU_____CGCU_AGGGGAUU\n______________:\|\|\|::\|\|\|____\|\|\|_____\|:\|\|_\|\|\|\|\|\|\|\|\n______________UGUGUGUCG____GCA_____GUGA_UCCCCUAA\n3'-UUU...UCUGA_________UUAA___ACAAA____G________AGGUA...GCA-5'\n_____________\|__________________________________\|\n_____________72_________________________________37\n	245 -- 251	38 -- 44	-33.2374 kcal/mol	13.3072 kcal/mol	4.74986 kcal/mol	220 252@LB@ \| \|@LB@5'-GAG...CGUAA UGAG GC G GCGCC...UGC-3'@LB@ GCACGUAGC CGU CGCU AGGGGAUU@LB@ :\|\|\|::\|\|\| \|\|\| \|:\|\| \|\|\|\|\|\|\|\|@LB@ UGUGUGUCG GCA GUGA UCCCCUAA@LB@3'-UUU...UCUGA UUAA ACAAA G AGGUA...GCA-5'@LB@ \| \|@LB@ 72 37@LB@@LB@@LB@Energy -15.18 kcal/mol@LB@Hybridization Energy -33.2374 kcal/mol@LB@Unfolding Energy - mRNA 13.3072 kcal/mol@LB@Unfolding Energy - sRNA 4.74986 kcal/mol@LB@@LB@Position - mRNA 221 -- 251@LB@Position - sRNA 38 -- 71@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 38 -- 44@LB@
73	0.00298	0.1437	b0474	adk	-13.48	0.049381	180 -- 198	34 -- 50	adenylate kinase	_____________179_________________199\n_____________\|___________________\|\n5'-ACC...CGACA_____UA____________CAAUG...AUA-3'\n______________CAUUU__AGGGGAUUUUCG\n______________\|\|:\|:__\|\|\|\|\|\|\|\|\|:\|:\n______________GUGAG__UCCCCUAAAGGU\n3'-UUU...ACAAA___________________ACGAA...GCA-5'\n_____________\|___________________\|\n_____________51__________________33\n	191 -- 197	35 -- 41	-19.9961 kcal/mol	4.64453 kcal/mol	1.87382 kcal/mol	179 199@LB@ \| \|@LB@5'-ACC...CGACA UA CAAUG...AUA-3'@LB@ CAUUU AGGGGAUUUUCG@LB@ \|\|:\|: \|\|\|\|\|\|\|\|\|:\|:@LB@ GUGAG UCCCCUAAAGGU@LB@3'-UUU...ACAAA ACGAA...GCA-5'@LB@ \| \|@LB@ 51 33@LB@@LB@@LB@Energy -13.48 kcal/mol@LB@Hybridization Energy -19.9961 kcal/mol@LB@Unfolding Energy - mRNA 4.64453 kcal/mol@LB@Unfolding Energy - sRNA 1.87382 kcal/mol@LB@@LB@Position - mRNA 180 -- 198@LB@Position - sRNA 34 -- 50@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 35 -- 41@LB@
149	0.006962	0.1638	b0935	ssuD	-8.45	0.421381	102 -- 123	48 -- 71	alkanesulfonate monooxygenase FMNH(2)-dependent	_____________101______________________124\n_____________\|________________________\|\n5'-AAA...CAGCA___A_______A____________GAAAA...AAC-3'\n______________GCA_ACGGCAG_UC__UGUUUUAU\n______________:\|\|_\|\|:\|\|\|:_\|\|__\|\|\|\|\|:\|:\n______________UGU_UGUCGUU_AG__ACAAAGUG\n3'-UUU...UCUGA___G_______A__CA________AGUCC...GCA-5'\n_____________\|________________________\|\n_____________72_______________________47\n	117 -- 123	48 -- 54	-17.2917 kcal/mol	5.19453 kcal/mol	3.65243 kcal/mol	101 124@LB@ \| \|@LB@5'-AAA...CAGCA A A GAAAA...AAC-3'@LB@ GCA ACGGCAG UC UGUUUUAU@LB@ :\|\| \|\|:\|\|\|: \|\| \|\|\|\|\|:\|:@LB@ UGU UGUCGUU AG ACAAAGUG@LB@3'-UUU...UCUGA G A CA AGUCC...GCA-5'@LB@ \| \|@LB@ 72 47@LB@@LB@@LB@Energy -8.45 kcal/mol@LB@Hybridization Energy -17.2917 kcal/mol@LB@Unfolding Energy - mRNA 5.19453 kcal/mol@LB@Unfolding Energy - sRNA 3.65243 kcal/mol@LB@@LB@Position - mRNA 102 -- 123@LB@Position - sRNA 48 -- 71@LB@Position Seed - mRNA 117 -- 123@LB@Position Seed - sRNA 48 -- 54@LB@
33	0.0005309	0.05552	b2905	gcvT	-15.66	0.013961	227 -- 265	34 -- 74	aminomethyltransferase tetrahydrofolate-dependent subunit (T protein) of glycine cleavage complex	_____________226___________________________________________266\n_____________\|_____________________________________________\|\n5'-CUG...UACGA__A_______________CG__________CAU__U_________CGGCU...AAA-3'\n______________AC_ACACAC_GC__UUUG__G___CGCUCG___GG_GGAUUUCCA\n______________\|\|_\|\|\|\|\|\|_\|\|__\|\|:\|__\|___\|:\|\|\|:___\|\|_\|\|\|\|\|\|\|\|\|\n______________UG_UGUGUG_CG__AAGC__C___GUGAGU___CC_CCUAAAGGU\n3'-UUU...GUUUC__A______U__UU____AA_AAA_____________________ACGAA...GCA-5'\n_____________\|_____________________________________________\|\n_____________75____________________________________________33\n	259 -- 265	34 -- 40	-32.8395 kcal/mol	12.3643 kcal/mol	4.81599 kcal/mol	226 266@LB@ \| \|@LB@5'-CUG...UACGA A CG CAU U CGGCU...AAA-3'@LB@ AC ACACAC GC UUUG G CGCUCG GG GGAUUUCCA@LB@ \|\| \|\|\|\|\|\| \|\| \|\|:\| \| \|:\|\|\|: \|\| \|\|\|\|\|\|\|\|\|@LB@ UG UGUGUG CG AAGC C GUGAGU CC CCUAAAGGU@LB@3'-UUU...GUUUC A U UU AA AAA ACGAA...GCA-5'@LB@ \| \|@LB@ 75 33@LB@@LB@@LB@Energy -15.66 kcal/mol@LB@Hybridization Energy -32.8395 kcal/mol@LB@Unfolding Energy - mRNA 12.3643 kcal/mol@LB@Unfolding Energy - sRNA 4.81599 kcal/mol@LB@@LB@Position - mRNA 227 -- 265@LB@Position - sRNA 34 -- 74@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 34 -- 40@LB@
177	0.008834	0.1747	b0932	pepN	-9.31	0.316043	123 -- 145	58 -- 78	aminopeptidase N	_____________122_____________________146\n_____________\|_______________________\|\n5'-GUA...AAGAU_____UU_______GC_______ACGCA...AGA-3'\n______________GAAGA__CUGCAUA__GCGAUUU\n______________:\|\|\|\|__\|\|:\|\|:\|__\|\|:\|\|\|:\n______________UUUCU__GAUGUGU__CGUUAAG\n3'-UUU...ACCCG______________GU_______CAACA...GCA-5'\n_____________\|_______________________\|\n_____________79______________________57\n	139 -- 145	58 -- 64	-18.0038 kcal/mol	5.38317 kcal/mol	3.31018 kcal/mol	122 146@LB@ \| \|@LB@5'-GUA...AAGAU UU GC ACGCA...AGA-3'@LB@ GAAGA CUGCAUA GCGAUUU@LB@ :\|\|\|\| \|\|:\|\|:\| \|\|:\|\|\|:@LB@ UUUCU GAUGUGU CGUUAAG@LB@3'-UUU...ACCCG GU CAACA...GCA-5'@LB@ \| \|@LB@ 79 57@LB@@LB@@LB@Energy -9.31 kcal/mol@LB@Hybridization Energy -18.0038 kcal/mol@LB@Unfolding Energy - mRNA 5.38317 kcal/mol@LB@Unfolding Energy - sRNA 3.31018 kcal/mol@LB@@LB@Position - mRNA 123 -- 145@LB@Position - sRNA 58 -- 78@LB@Position Seed - mRNA 139 -- 145@LB@Position Seed - sRNA 58 -- 64@LB@
116	0.005119	0.155	b2513	yfgM	-8.84	0.371642	84 -- 101	60 -- 75	ancillary SecYEG translocon subunit; putative anti-RcsB factor	_____________83_________________102\n_____________\|__________________\|\n5'-GGC...GAAGU_____ACG__________AGUGA...UUG-3'\n______________GGCUA___GCACAGCAGU\n______________\|:\|\|\|___:\|\|\|\|\|\|\|:\|\n______________CUGAU___UGUGUCGUUA\n3'-UUU...CGUUU_____G____________AGCAA...GCA-5'\n_____________\|__________________\|\n_____________76_________________59\n	95 -- 101	60 -- 66	-19.484 kcal/mol	7.35825 kcal/mol	3.28851 kcal/mol	83 102@LB@ \| \|@LB@5'-GGC...GAAGU ACG AGUGA...UUG-3'@LB@ GGCUA GCACAGCAGU@LB@ \|:\|\|\| :\|\|\|\|\|\|\|:\|@LB@ CUGAU UGUGUCGUUA@LB@3'-UUU...CGUUU G AGCAA...GCA-5'@LB@ \| \|@LB@ 76 59@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -19.484 kcal/mol@LB@Unfolding Energy - mRNA 7.35825 kcal/mol@LB@Unfolding Energy - sRNA 3.28851 kcal/mol@LB@@LB@Position - mRNA 84 -- 101@LB@Position - sRNA 60 -- 75@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 60 -- 66@LB@
121	0.005439	0.1553	b1640	anmK	-7.89	0.496680	290 -- 297	63 -- 70	anhydro-N-acetylmuramic acid kinase	_____________289______298\n_____________\|________\|\n5'-CCA...CGGGU________UGG-3'\n______________CGCACAGC\n______________\|:\|\|\|\|\|\|\n______________GUGUGUCG\n3'-UUU...CUGAU________UUAAG...GCA-5'\n_____________\|________\|\n_____________71_______62\n	291 -- 297	63 -- 69	-13.0848 kcal/mol	2.06561 kcal/mol	3.13161 kcal/mol	289 298@LB@ \| \|@LB@5'-CCA...CGGGU UGG-3'@LB@ CGCACAGC@LB@ \|:\|\|\|\|\|\|@LB@ GUGUGUCG@LB@3'-UUU...CUGAU UUAAG...GCA-5'@LB@ \| \|@LB@ 71 62@LB@@LB@@LB@Energy -7.89 kcal/mol@LB@Hybridization Energy -13.0848 kcal/mol@LB@Unfolding Energy - mRNA 2.06561 kcal/mol@LB@Unfolding Energy - sRNA 3.13161 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 63 -- 70@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 63 -- 69@LB@
34	0.0005364	0.05552	b4244	pyrI	-10.55	0.196904	198 -- 215	60 -- 77	aspartate carbamoyltransferase regulatory subunit	_____________197________________216\n_____________\|__________________\|\n5'-UUC...AAAUA_____G_______A____AAAUU...UCA-3'\n______________GAGAU_ACACACG_UAAU\n______________:\|\|\|:_\|\|\|\|\|\|:_:\|\|\|\n______________UUCUG_UGUGUGU_GUUA\n3'-UUU...CCCGU_____A_______C____AGCAA...GCA-5'\n_____________\|__________________\|\n_____________78_________________59\n	204 -- 210	65 -- 71	-15.1619 kcal/mol	1.32522 kcal/mol	3.29036 kcal/mol	197 216@LB@ \| \|@LB@5'-UUC...AAAUA G A AAAUU...UCA-3'@LB@ GAGAU ACACACG UAAU@LB@ :\|\|\|: \|\|\|\|\|\|: :\|\|\|@LB@ UUCUG UGUGUGU GUUA@LB@3'-UUU...CCCGU A C AGCAA...GCA-5'@LB@ \| \|@LB@ 78 59@LB@@LB@@LB@Energy -10.55 kcal/mol@LB@Hybridization Energy -15.1619 kcal/mol@LB@Unfolding Energy - mRNA 1.32522 kcal/mol@LB@Unfolding Energy - sRNA 3.29036 kcal/mol@LB@@LB@Position - mRNA 198 -- 215@LB@Position - sRNA 60 -- 77@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 65 -- 71@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

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service.

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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