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
118	0.005291	0.1553	b0481	ybaK	-9.02	0.349126	203 -- 225	45 -- 75	Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase	_____________202_____________________________226\n_____________\|_______________________________\|\n5'-AAU...ACCAU______C______UAAA______________AAAAA...UCG-3'\n______________GAC_AC_CGCAGU___________UUACUCG\n______________\|\|\|_\|\|_\|:\|\|\|:___________\|:\|\|\|\|:\n______________CUG_UG_GUGUCG___________AGUGAGU\n3'-UUU...CGUUU___A__U______UUAAGCAACAA_______CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	219 -- 225	45 -- 51	-15.8984 kcal/mol	3.13427 kcal/mol	3.74078 kcal/mol	202 226@LB@ \| \|@LB@5'-AAU...ACCAU C UAAA AAAAA...UCG-3'@LB@ GAC AC CGCAGU UUACUCG@LB@ \|\|\| \|\| \|:\|\|\|: \|:\|\|\|\|:@LB@ CUG UG GUGUCG AGUGAGU@LB@3'-UUU...CGUUU A U UUAAGCAACAA CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -9.02 kcal/mol@LB@Hybridization Energy -15.8984 kcal/mol@LB@Unfolding Energy - mRNA 3.13427 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 203 -- 225@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 45 -- 51@LB@
133	0.006126	0.1605	b0387	yaiI	-9.01	0.350598	46 -- 81	33 -- 74	UPF0178 family protein	_____________45_________________________________________82\n_____________\|__________________________________________\|\n5'-CAC...CCCAU____________CAAUAAAACCG______UCU__________UGCCU...CAA-3'\n______________AUUGC_CGCAGC_____________AUUU______UUUCCAU\n______________\|:\|:\|_\|:\|\|\|\|_____________\|:\|:______\|\|\|\|\|\|\|\n______________UGAUG_GUGUCG_____________UGAG______AAAGGUA\n3'-UUU...GUUUC_____U______UUAAGCAACAAAG____UCCCCU_______CGAAU...GCA-5'\n_____________\|__________________________________________\|\n_____________75_________________________________________32\n	75 -- 81	33 -- 39	-16.9561 kcal/mol	3.12923 kcal/mol	4.81602 kcal/mol	45 82@LB@ \| \|@LB@5'-CAC...CCCAU CAAUAAAACCG UCU UGCCU...CAA-3'@LB@ AUUGC CGCAGC AUUU UUUCCAU@LB@ \|:\|:\| \|:\|\|\|\| \|:\|: \|\|\|\|\|\|\|@LB@ UGAUG GUGUCG UGAG AAAGGUA@LB@3'-UUU...GUUUC U UUAAGCAACAAAG UCCCCU CGAAU...GCA-5'@LB@ \| \|@LB@ 75 32@LB@@LB@@LB@Energy -9.01 kcal/mol@LB@Hybridization Energy -16.9561 kcal/mol@LB@Unfolding Energy - mRNA 3.12923 kcal/mol@LB@Unfolding Energy - sRNA 4.81602 kcal/mol@LB@@LB@Position - mRNA 46 -- 81@LB@Position - sRNA 33 -- 74@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 33 -- 39@LB@
76	0.003141	0.1452	b0187	yaeR	-8.98	0.354982	261 -- 292	48 -- 78	putative lyase	_____________260_______________________________293\n_____________\|_________________________________\|\n5'-AAA...UGAGC_______UUC___U_____AU__UUG_______GCUGCAAA-3'\n______________AAAG_CU___UAC_GCGAU__UC___GUUUCAC\n______________\|\|\|\|_\|\|___:\|\|_\|\|:\|\|__\|\|___\|\|\|\|\|\|\|\n______________UUUC_GA___GUG_CGUUA__AG___CAAAGUG\n3'-UUU...ACCCG____U__UGU___U_________CAA_______AGUCC...GCA-5'\n_____________\|_________________________________\|\n_____________79________________________________47\n	286 -- 292	48 -- 54	-17.4111 kcal/mol	4.74942 kcal/mol	3.68736 kcal/mol	260 293@LB@ \| \|@LB@5'-AAA...UGAGC UUC U AU UUG GCUGCAAA-3'@LB@ AAAG CU UAC GCGAU UC GUUUCAC@LB@ \|\|\|\| \|\| :\|\| \|\|:\|\| \|\| \|\|\|\|\|\|\|@LB@ UUUC GA GUG CGUUA AG CAAAGUG@LB@3'-UUU...ACCCG U UGU U CAA AGUCC...GCA-5'@LB@ \| \|@LB@ 79 47@LB@@LB@@LB@Energy -8.98 kcal/mol@LB@Hybridization Energy -17.4111 kcal/mol@LB@Unfolding Energy - mRNA 4.74942 kcal/mol@LB@Unfolding Energy - sRNA 3.68736 kcal/mol@LB@@LB@Position - mRNA 261 -- 292@LB@Position - sRNA 48 -- 78@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 48 -- 54@LB@
196	0.01003	0.1776	b0344	lacZ	-8.86	0.369200	215 -- 237	48 -- 76	beta-D-galactosidase	_____________214___________________________238\n_____________\|_____________________________\|\n5'-ACC...AUUAC_____________________C_______AACGU...CUU-3'\n______________GGAUU_CAC_UGGC____CGU_GUUUUAC\n______________:\|\|:\|_\|\|\|_::\|\|____\|\|\|_\|\|\|\|:\|\|\n______________UCUGA_GUG_GUCG____GCA_CAAAGUG\n3'-UUU...CCGUU_____U___U____UUAA___A_______AGUCC...GCA-5'\n_____________\|_____________________________\|\n_____________77____________________________47\n	231 -- 237	48 -- 54	-17.9156 kcal/mol	5.37156 kcal/mol	3.68714 kcal/mol	214 238@LB@ \| \|@LB@5'-ACC...AUUAC C AACGU...CUU-3'@LB@ GGAUU CAC UGGC CGU GUUUUAC@LB@ :\|\|:\| \|\|\| ::\|\| \|\|\| \|\|\|\|:\|\|@LB@ UCUGA GUG GUCG GCA CAAAGUG@LB@3'-UUU...CCGUU U U UUAA A AGUCC...GCA-5'@LB@ \| \|@LB@ 77 47@LB@@LB@@LB@Energy -8.86 kcal/mol@LB@Hybridization Energy -17.9156 kcal/mol@LB@Unfolding Energy - mRNA 5.37156 kcal/mol@LB@Unfolding Energy - sRNA 3.68714 kcal/mol@LB@@LB@Position - mRNA 215 -- 237@LB@Position - sRNA 48 -- 76@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 48 -- 54@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@
124	0.005471	0.1553	b1249	clsA	-8.47	0.418250	164 -- 196	34 -- 71	cardiolipin synthase 1	_____________163____________________________________197\n_____________\|______________________________________\|\n5'-GUC...CGUAA__U____A____G__C_______AAA____________AUCUA...CAG-3'\n______________AC_CAUA_CAAU_CG___UUUCA______GGAUUUCUA\n______________\|\|_\|\|:\|_\|\|\|\|_\|\|___\|\|\|\|\|______\|\|\|\|\|\|\|:\|\n______________UG_GUGU_GUUA_GC___AAAGU______CCUAAAGGU\n3'-UUU...UCUGA__U____C____A__AAC_____GAGUCC_________ACGAA...GCA-5'\n_____________\|______________________________________\|\n_____________72_____________________________________33\n	190 -- 196	34 -- 40	-20.3655 kcal/mol	7.10457 kcal/mol	4.79237 kcal/mol	163 197@LB@ \| \|@LB@5'-GUC...CGUAA U A G C AAA AUCUA...CAG-3'@LB@ AC CAUA CAAU CG UUUCA GGAUUUCUA@LB@ \|\| \|\|:\| \|\|\|\| \|\| \|\|\|\|\| \|\|\|\|\|\|\|:\|@LB@ UG GUGU GUUA GC AAAGU CCUAAAGGU@LB@3'-UUU...UCUGA U C A AAC GAGUCC ACGAA...GCA-5'@LB@ \| \|@LB@ 72 33@LB@@LB@@LB@Energy -8.47 kcal/mol@LB@Hybridization Energy -20.3655 kcal/mol@LB@Unfolding Energy - mRNA 7.10457 kcal/mol@LB@Unfolding Energy - sRNA 4.79237 kcal/mol@LB@@LB@Position - mRNA 164 -- 196@LB@Position - sRNA 34 -- 71@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 34 -- 40@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@
197	0.01006	0.1776	b0069	sgrR	-8.41	0.425671	7 -- 22	58 -- 74	transcriptional DNA-binding transcriptional activator of sgrS sRNA	_____________6_________________23\n_____________\|_________________\|\n_____5'-CAUCCC____________CC___AAGCA...UGA-3'\n______________ACUGCAU_CAGU__UUC\n______________\|\|\|:\|\|:_\|\|\|:__\|\|\|\n______________UGAUGUG_GUCG__AAG\n3'-UUU...GUUUC_______U____UU___CAACA...GCA-5'\n_____________\|_________________\|\n_____________75________________57\n	7 -- 13	68 -- 74	-13.3461 kcal/mol	1.63335 kcal/mol	3.3008 kcal/mol	6 23@LB@ \| \|@LB@ 5'-CAUCCC CC AAGCA...UGA-3'@LB@ ACUGCAU CAGU UUC@LB@ \|\|\|:\|\|: \|\|\|: \|\|\|@LB@ UGAUGUG GUCG AAG@LB@3'-UUU...GUUUC U UU CAACA...GCA-5'@LB@ \| \|@LB@ 75 57@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -13.3461 kcal/mol@LB@Unfolding Energy - mRNA 1.63335 kcal/mol@LB@Unfolding Energy - sRNA 3.3008 kcal/mol@LB@@LB@Position - mRNA 7 -- 22@LB@Position - sRNA 58 -- 74@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 68 -- 74@LB@
94	0.004209	0.1538	b1798	leuE	-8.23	0.450453	21 -- 61	47 -- 73	leucine efflux protein	_____________20_________________________________________62\n_____________\|__________________________________________\|\n5'-UGC...AAUUU____________U____CC_AGCACUACCCGAAUU_______GGAGC...AAA-3'\n______________UUACGC_CAGUA_UUUG__G_______________UUUCACU\n______________:\|\|\|:\|_\|\|\|:\|_\|\|:\|__\|_______________\|\|\|\|\|\|\|\n______________GAUGUG_GUCGU_AAGC__C_______________AAAGUGA\n3'-UUU...UUUCU______U_____U____AA_______________________GUCCC...GCA-5'\n_____________\|__________________________________________\|\n_____________74_________________________________________46\n	55 -- 61	47 -- 53	-16.3548 kcal/mol	4.43937 kcal/mol	3.69006 kcal/mol	20 62@LB@ \| \|@LB@5'-UGC...AAUUU U CC AGCACUACCCGAAUU GGAGC...AAA-3'@LB@ UUACGC CAGUA UUUG G UUUCACU@LB@ :\|\|\|:\| \|\|\|:\| \|\|:\| \| \|\|\|\|\|\|\|@LB@ GAUGUG GUCGU AAGC C AAAGUGA@LB@3'-UUU...UUUCU U U AA GUCCC...GCA-5'@LB@ \| \|@LB@ 74 46@LB@@LB@@LB@Energy -8.23 kcal/mol@LB@Hybridization Energy -16.3548 kcal/mol@LB@Unfolding Energy - mRNA 4.43937 kcal/mol@LB@Unfolding Energy - sRNA 3.69006 kcal/mol@LB@@LB@Position - mRNA 21 -- 61@LB@Position - sRNA 47 -- 73@LB@Position Seed - mRNA 55 -- 61@LB@Position Seed - sRNA 47 -- 53@LB@
58	0.002015	0.1223	b0189	rof	-8.06	0.473679	29 -- 61	40 -- 71	modulator of Rho-dependent transcription termination	_____________28_________________________________62\n_____________\|__________________________________\|\n5'-AGG...AGUUA_______A_____A__CG_AAA________C___GACUU...GCG-3'\n______________AUACGCA_GCGGU_CG__G___UCGC_CAG_GGA\n______________\|:\|\|:\|\|_\|\|::\|_\|\|__\|___\|\|:\|_\|\|\|_\|\|\|\n______________UGUGUGU_CGUUA_GC__C___AGUG_GUC_CCU\n3'-UUU...UCUGA_____________A__AA_AA_____A___C___AAAGG...GCA-5'\n_____________\|__________________________________\|\n_____________72_________________________________39\n	29 -- 35	65 -- 71	-25.5885 kcal/mol	12.7864 kcal/mol	4.74818 kcal/mol	28 62@LB@ \| \|@LB@5'-AGG...AGUUA A A CG AAA C GACUU...GCG-3'@LB@ AUACGCA GCGGU CG G UCGC CAG GGA@LB@ \|:\|\|:\|\| \|\|::\| \|\| \| \|\|:\| \|\|\| \|\|\|@LB@ UGUGUGU CGUUA GC C AGUG GUC CCU@LB@3'-UUU...UCUGA A AA AA A C AAAGG...GCA-5'@LB@ \| \|@LB@ 72 39@LB@@LB@@LB@Energy -8.06 kcal/mol@LB@Hybridization Energy -25.5885 kcal/mol@LB@Unfolding Energy - mRNA 12.7864 kcal/mol@LB@Unfolding Energy - sRNA 4.74818 kcal/mol@LB@@LB@Position - mRNA 29 -- 61@LB@Position - sRNA 40 -- 71@LB@Position Seed - mRNA 29 -- 35@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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