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	Additional homologs
122	0.005462	0.1553	b3143	yraI	-10.36	0.212908	69 -- 81	40 -- 51	putative periplasmic pilin chaperone	b0939 b4316 b0531	_____________68____________82\n_____________\|_____________\|\n5'-GGA...AGAAA____CC_______AGCAG...UGA-3'\n______________UCAC__CAGGGGA\n______________\|\|\|\|__\|\|\|\|\|\|\|\n______________AGUG__GUCCCCU\n3'-UUU...AACAA____A________AAAGG...GCA-5'\n_____________\|_____________\|\n_____________52____________39\n	75 -- 81	40 -- 46	-16.6795 kcal/mol	4.56539 kcal/mol	1.76028 kcal/mol	68 82@LB@ \| \|@LB@5'-GGA...AGAAA CC AGCAG...UGA-3'@LB@ UCAC CAGGGGA@LB@ \|\|\|\| \|\|\|\|\|\|\|@LB@ AGUG GUCCCCU@LB@3'-UUU...AACAA A AAAGG...GCA-5'@LB@ \| \|@LB@ 52 39@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -16.6795 kcal/mol@LB@Unfolding Energy - mRNA 4.56539 kcal/mol@LB@Unfolding Energy - sRNA 1.76028 kcal/mol@LB@@LB@Position - mRNA 69 -- 81@LB@Position - sRNA 40 -- 51@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 40 -- 46@LB@
35	0.0005607	0.05638	b1434	ydcN	-11.45	0.133710	242 -- 253	62 -- 74	putative DNA-binding transcriptional regulator	b1508 b1299	_____________241___________254\n_____________\|_____________\|\n5'-CGG...AAACA_____________GCGCG...CUA-3'\n______________ACUACGC_CAGCA\n______________\|\|\|\|\|:\|_\|\|\|\|\|\n______________UGAUGUG_GUCGU\n3'-UUU...GUUUC_______U_____UAAGC...GCA-5'\n_____________\|_____________\|\n_____________75____________61\n	242 -- 248	68 -- 74	-17.054 kcal/mol	2.36402 kcal/mol	3.24359 kcal/mol	241 254@LB@ \| \|@LB@5'-CGG...AAACA GCGCG...CUA-3'@LB@ ACUACGC CAGCA@LB@ \|\|\|\|\|:\| \|\|\|\|\|@LB@ UGAUGUG GUCGU@LB@3'-UUU...GUUUC U UAAGC...GCA-5'@LB@ \| \|@LB@ 75 61@LB@@LB@@LB@Energy -11.45 kcal/mol@LB@Hybridization Energy -17.054 kcal/mol@LB@Unfolding Energy - mRNA 2.36402 kcal/mol@LB@Unfolding Energy - sRNA 3.24359 kcal/mol@LB@@LB@Position - mRNA 242 -- 253@LB@Position - sRNA 62 -- 74@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 68 -- 74@LB@
36	0.0006028	0.05893	b2398	yfeC	-12.67	0.075056	159 -- 178	42 -- 76	DUF1323 family putative DNA-binding protein	b2399	_____________158_________________________________179\n_____________\|___________________________________\|\n5'-AUA...CUAAU____C______________________________AAUUG...GCG-3'\n______________AGAC__CACAUA______________CAUUCAGGG\n______________\|\|\|\|__\|\|\|\|:\|______________\|\|:\|\|\|\|\|\|\n______________UCUG__GUGUGU______________GUGAGUCCC\n3'-UUU...CCGUU____AU______CGUUAAGCAACAAA_________CUAAA...GCA-5'\n_____________\|___________________________________\|\n_____________77__________________________________41\n	172 -- 178	42 -- 48	-21.7854 kcal/mol	4.35612 kcal/mol	4.76453 kcal/mol	158 179@LB@ \| \|@LB@5'-AUA...CUAAU C AAUUG...GCG-3'@LB@ AGAC CACAUA CAUUCAGGG@LB@ \|\|\|\| \|\|\|\|:\| \|\|:\|\|\|\|\|\|@LB@ UCUG GUGUGU GUGAGUCCC@LB@3'-UUU...CCGUU AU CGUUAAGCAACAAA CUAAA...GCA-5'@LB@ \| \|@LB@ 77 41@LB@@LB@@LB@Energy -12.67 kcal/mol@LB@Hybridization Energy -21.7854 kcal/mol@LB@Unfolding Energy - mRNA 4.35612 kcal/mol@LB@Unfolding Energy - sRNA 4.76453 kcal/mol@LB@@LB@Position - mRNA 159 -- 178@LB@Position - sRNA 42 -- 76@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 42 -- 48@LB@
52	0.001789	0.121	b1799	dmlR	-11.56	0.127346	72 -- 108	34 -- 68	transcriptional activator of dmlA	b3060	_____________71_______________________________________109\n_____________\|________________________________________\|\n5'-CGC...GGGAU_________ACGCA_______________UU_____C___CUUCC...CGG-3'\n______________CGCAGCAAU_____UCGU__UUUCA_UCA__GGGUU_UCA\n______________\|:\|\|\|\|\|\|\|_____\|\|\|\|__\|\|\|\|\|_\|\|\|__\|\|:\|\|_:\|\|\n______________GUGUCGUUA_____AGCA__AAAGU_AGU__CCUAA_GGU\n3'-UUU...GAUGU__________________AC_____G___CC_____A___ACGAA...GCA-5'\n_____________\|________________________________________\|\n_____________69_______________________________________33\n	74 -- 80	60 -- 66	-24.8584 kcal/mol	8.52016 kcal/mol	4.78423 kcal/mol	71 109@LB@ \| \|@LB@5'-CGC...GGGAU ACGCA UU C CUUCC...CGG-3'@LB@ CGCAGCAAU UCGU UUUCA UCA GGGUU UCA@LB@ \|:\|\|\|\|\|\|\| \|\|\|\| \|\|\|\|\| \|\|\| \|\|:\|\| :\|\|@LB@ GUGUCGUUA AGCA AAAGU AGU CCUAA GGU@LB@3'-UUU...GAUGU AC G CC A ACGAA...GCA-5'@LB@ \| \|@LB@ 69 33@LB@@LB@@LB@Energy -11.56 kcal/mol@LB@Hybridization Energy -24.8584 kcal/mol@LB@Unfolding Energy - mRNA 8.52016 kcal/mol@LB@Unfolding Energy - sRNA 4.78423 kcal/mol@LB@@LB@Position - mRNA 72 -- 108@LB@Position - sRNA 34 -- 68@LB@Position Seed - mRNA 74 -- 80@LB@Position Seed - sRNA 60 -- 66@LB@
19	0.0001526	0.02826	b1040	csgD	-18.47	0.001904	103 -- 117	60 -- 74	csgBAC operon transcriptional regulator	b3520	_____________102_____________118\n_____________\|_______________\|\n5'-UUA...UUAUU_______________GCAAC...CGC-3'\n______________ACUACACACAGCAGU\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|:\|\n______________UGAUGUGUGUCGUUA\n3'-UUU...GUUUC_______________AGCAA...GCA-5'\n_____________\|_______________\|\n_____________75______________59\n	111 -- 117	60 -- 66	-23.4761 kcal/mol	1.72592 kcal/mol	3.27997 kcal/mol	102 118@LB@ \| \|@LB@5'-UUA...UUAUU GCAAC...CGC-3'@LB@ ACUACACACAGCAGU@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\|:\|@LB@ UGAUGUGUGUCGUUA@LB@3'-UUU...GUUUC AGCAA...GCA-5'@LB@ \| \|@LB@ 75 59@LB@@LB@@LB@Energy -18.47 kcal/mol@LB@Hybridization Energy -23.4761 kcal/mol@LB@Unfolding Energy - mRNA 1.72592 kcal/mol@LB@Unfolding Energy - sRNA 3.27997 kcal/mol@LB@@LB@Position - mRNA 103 -- 117@LB@Position - sRNA 60 -- 74@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 60 -- 66@LB@
160	0.007693	0.1668	b1671	ydhX	-11.21	0.148807	210 -- 235	39 -- 74	putative 4Fe-4S ferridoxin-type protein; FNR Nar NarP-regulated protein; putative subunit of YdhYVWXUT oxidoreductase complex	b4072	_____________209__________________________________236\n_____________\|____________________________________\|\n5'-CAC...CCUUC___CG________________________U______GGGAA...AGG-3'\n______________ACU__ACGCA__AAUUUGU________UC_GGGGAU\n______________\|\|\|__\|\|:\|\|__\|\|\|\|:\|\|________\|\|_\|\|\|\|\|\|\n______________UGA__UGUGU__UUAAGCA________AG_CCCCUA\n3'-UUU...GUUUC___UG_____CG_______ACAAAGUG__U______AAGGU...GCA-5'\n_____________\|____________________________________\|\n_____________75___________________________________38\n	220 -- 226	56 -- 62	-21.5478 kcal/mol	5.56457 kcal/mol	4.77831 kcal/mol	209 236@LB@ \| \|@LB@5'-CAC...CCUUC CG U GGGAA...AGG-3'@LB@ ACU ACGCA AAUUUGU UC GGGGAU@LB@ \|\|\| \|\|:\|\| \|\|\|\|:\|\| \|\| \|\|\|\|\|\|@LB@ UGA UGUGU UUAAGCA AG CCCCUA@LB@3'-UUU...GUUUC UG CG ACAAAGUG U AAGGU...GCA-5'@LB@ \| \|@LB@ 75 38@LB@@LB@@LB@Energy -11.21 kcal/mol@LB@Hybridization Energy -21.5478 kcal/mol@LB@Unfolding Energy - mRNA 5.56457 kcal/mol@LB@Unfolding Energy - sRNA 4.77831 kcal/mol@LB@@LB@Position - mRNA 210 -- 235@LB@Position - sRNA 39 -- 74@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 56 -- 62@LB@
1	5.015e-10	1.765e-06	b0680	glnS	-23.71	0.000006	155 -- 198	34 -- 77	glutamyl-tRNA synthetase		_____________154___________________________________________199\n_____________\|_____________________________________________\|\n5'-UGC...CUUAU_____C______C__U__A________A_____U_A___A_____CGAUG...CGC-3'\n______________AAGAU_AUACGC_GU_AU_CGUUGUUU_CGCUU_G_GGA__UCCA\n______________\|\|\|\|:_\|:\|\|:\|_\|:_\|\|_\|\|\|\|\|\|\|\|_\|:\|\|:_\|_\|\|\|__\|\|\|\|\n______________UUCUG_UGUGUG_CG_UA_GCAACAAA_GUGAG_C_CCU__AGGU\n3'-UUU...CCCGU_____A______U__U__A______________U_C___AA____ACGAA...GCA-5'\n_____________\|_____________________________________________\|\n_____________78____________________________________________33\n	175 -- 181	51 -- 57	-34.8912 kcal/mol	6.37021 kcal/mol	4.81601 kcal/mol	154 199@LB@ \| \|@LB@5'-UGC...CUUAU C C U A A U A A CGAUG...CGC-3'@LB@ AAGAU AUACGC GU AU CGUUGUUU CGCUU G GGA UCCA@LB@ \|\|\|\|: \|:\|\|:\| \|: \|\| \|\|\|\|\|\|\|\| \|:\|\|: \| \|\|\| \|\|\|\|@LB@ UUCUG UGUGUG CG UA GCAACAAA GUGAG C CCU AGGU@LB@3'-UUU...CCCGU A U U A U C AA ACGAA...GCA-5'@LB@ \| \|@LB@ 78 33@LB@@LB@@LB@Energy -23.71 kcal/mol@LB@Hybridization Energy -34.8912 kcal/mol@LB@Unfolding Energy - mRNA 6.37021 kcal/mol@LB@Unfolding Energy - sRNA 4.81601 kcal/mol@LB@@LB@Position - mRNA 155 -- 198@LB@Position - sRNA 34 -- 77@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 51 -- 57@LB@
2	1.464e-07	0.0002576	b2741	rpoS	-16.90	0.006155	67 -- 107	33 -- 71	RNA polymerase sigma S (sigma 38) factor		_____________66______________________________________________108\n_____________\|_______________________________________________\|\n5'-CGG...GUUCA______UU___UUUUGAA______________A_______AA_____AAACC...AGG-3'\n______________ACACGC__GCA_______AUUCGUU_____AC__AGGGGA__UCCGU\n______________\|\|\|\|:\|__\|\|\|_______\|\|\|\|\|\|\|_____\|\|__\|\|\|\|\|\|__\|\|\|:\|\n______________UGUGUG__CGU_______UAAGCAA_____UG__UCCCCU__AGGUA\n3'-UUU...UCUGA______U__________________CAAAG__AG______AA_____CGAAU...GCA-5'\n_____________\|_______________________________________________\|\n_____________72______________________________________________32\n	85 -- 91	55 -- 61	-29.972 kcal/mol	8.28292 kcal/mol	4.7924 kcal/mol	66 108@LB@ \| \|@LB@5'-CGG...GUUCA UU UUUUGAA A AA AAACC...AGG-3'@LB@ ACACGC GCA AUUCGUU AC AGGGGA UCCGU@LB@ \|\|\|\|:\| \|\|\| \|\|\|\|\|\|\| \|\| \|\|\|\|\|\| \|\|\|:\|@LB@ UGUGUG CGU UAAGCAA UG UCCCCU AGGUA@LB@3'-UUU...UCUGA U CAAAG AG AA CGAAU...GCA-5'@LB@ \| \|@LB@ 72 32@LB@@LB@@LB@Energy -16.90 kcal/mol@LB@Hybridization Energy -29.972 kcal/mol@LB@Unfolding Energy - mRNA 8.28292 kcal/mol@LB@Unfolding Energy - sRNA 4.7924 kcal/mol@LB@@LB@Position - mRNA 67 -- 107@LB@Position - sRNA 33 -- 71@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 55 -- 61@LB@
3	3.356e-06	0.003937	b3724	phoU	-15.84	0.012477	157 -- 192	43 -- 78	negative regulator of PhoR/PhoB two-component regulator		_____________156____________________________________193\n_____________\|______________________________________\|\n5'-ACC...AAACA______________C_________ACGG__G_______AGUGC...AGC-3'\n______________GAAGACUACAU_CA_CGG_UCGUU____UU_AUUCAGG\n______________:\|\|\|\|\|\|\|\|\|:_\|\|_\|::_\|\|\|\|\|____\|\|_\|:\|\|\|\|\|\n______________UUUCUGAUGUG_GU_GUU_AGCAA____AA_UGAGUCC\n3'-UUU...ACCCG___________U__C___A_____CA____G_______CCUAA...GCA-5'\n_____________\|______________________________________\|\n_____________79_____________________________________42\n	186 -- 192	43 -- 49	-29.823 kcal/mol	9.63349 kcal/mol	4.35315 kcal/mol	156 193@LB@ \| \|@LB@5'-ACC...AAACA C ACGG G AGUGC...AGC-3'@LB@ GAAGACUACAU CA CGG UCGUU UU AUUCAGG@LB@ :\|\|\|\|\|\|\|\|\|: \|\| \|:: \|\|\|\|\| \|\| \|:\|\|\|\|\|@LB@ UUUCUGAUGUG GU GUU AGCAA AA UGAGUCC@LB@3'-UUU...ACCCG U C A CA G CCUAA...GCA-5'@LB@ \| \|@LB@ 79 42@LB@@LB@@LB@Energy -15.84 kcal/mol@LB@Hybridization Energy -29.823 kcal/mol@LB@Unfolding Energy - mRNA 9.63349 kcal/mol@LB@Unfolding Energy - sRNA 4.35315 kcal/mol@LB@@LB@Position - mRNA 157 -- 192@LB@Position - sRNA 43 -- 78@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 43 -- 49@LB@
4	8.9e-06	0.006694	b3281	aroE	-13.87	0.039990	230 -- 259	45 -- 75	dehydroshikimate reductase NAD(P)-binding		_____________229_____________________________260\n_____________\|_______________________________\|\n5'-UUU...AAUCC___A__C________A___CCA_________UCAGC...AUG-3'\n______________GAU_GC_CACAGCAA_UCG____UUCAUUCA\n______________\|\|:_:\|_\|\|\|\|\|\|\|\|_\|\|\|____\|\|\|\|:\|\|\|\n______________CUG_UG_GUGUCGUU_AGC____AAGUGAGU\n3'-UUU...CGUUU___A__U________A___AACA________CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	253 -- 259	45 -- 51	-26.2723 kcal/mol	8.66309 kcal/mol	3.74078 kcal/mol	229 260@LB@ \| \|@LB@5'-UUU...AAUCC A C A CCA UCAGC...AUG-3'@LB@ GAU GC CACAGCAA UCG UUCAUUCA@LB@ \|\|: :\| \|\|\|\|\|\|\|\| \|\|\| \|\|\|\|:\|\|\|@LB@ CUG UG GUGUCGUU AGC AAGUGAGU@LB@3'-UUU...CGUUU A U A AACA CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -13.87 kcal/mol@LB@Hybridization Energy -26.2723 kcal/mol@LB@Unfolding Energy - mRNA 8.66309 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 230 -- 259@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 253 -- 259@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)

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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