Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
141	0.0236	0.526	b3339	tufA	-10.69	0.070202	69 -- 84	1 -- 19	translation elongation factor EF-Tu 1	b3980	_____________68__________________85\n_____________\|___________________\|\n5'-AAU...AUUCC___________________GCCGA...CCA-3'\n______________UGAAGU__AUGAUGA_AGC\n______________\|:\|\|\|\|__\|\|\|\|\|\|\|_\|\|\|\n______________AUUUCA__UACUACU_UCG\n3'-UUU...UAUUU______AU_______A___-5'\n_____________\|__________________\|\n_____________20_________________1\n	75 -- 81	5 -- 11	-13.5879 kcal/mol	2.83361 kcal/mol	0.0638423 kcal/mol	68 85@LB@ \| \|@LB@5'-AAU...AUUCC GCCGA...CCA-3'@LB@ UGAAGU AUGAUGA AGC@LB@ \|:\|\|\|\| \|\|\|\|\|\|\| \|\|\|@LB@ AUUUCA UACUACU UCG@LB@3'-UUU...UAUUU AU A -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -10.69 kcal/mol@LB@Hybridization Energy -13.5879 kcal/mol@LB@Unfolding Energy - mRNA 2.83361 kcal/mol@LB@Unfolding Energy - sRNA 0.0638423 kcal/mol@LB@@LB@Position - mRNA 69 -- 84@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 5 -- 11@LB@
142	0.02395	0.526	b0192	nlpE	-14.44	0.009771	167 -- 226	1 -- 55	lipoprotein involved with copper homeostasis and adhesion		_____________166_______________________________________________________________227\n_____________\|_________________________________________________________________\|\n5'-UCA...GCAAA___C_______G________AAAAAGAAG____G________AA_______C____A____C___GAUGG...CGC-3'\n______________GUG_GCAG_CG_UCGGGAAU_________GAAU_GAUGGUGA_____AAAG__GAU_GUGA_AGC\n______________\|\|:_:\|\|\|_\|:_\|\|:\|:\|\|\|_________\|\|\|\|_\|\|:\|\|\|:\|_____\|\|\|\|__:\|\|_:\|\|\|_\|\|\|\n______________CAU_UGUC_GU_AGUCUUUA_________CUUA_CUGCCAUU_____UUUC__UUA_UACU_UCG\n3'-UUU...AUCCC___U____U__A______________________________AUUUA____AA___C____A___-5'\n_____________\|________________________________________________________________\|\n_____________56_______________________________________________________________1\n	201 -- 207	24 -- 30	-31.0616 kcal/mol	10.2836 kcal/mol	6.33758 kcal/mol	166 227@LB@ \| \|@LB@5'-UCA...GCAAA C G AAAAAGAAG G AA C A C GAUGG...CGC-3'@LB@ GUG GCAG CG UCGGGAAU GAAU GAUGGUGA AAAG GAU GUGA AGC@LB@ \|\|: :\|\|\| \|: \|\|:\|:\|\|\| \|\|\|\| \|\|:\|\|\|:\| \|\|\|\| :\|\| :\|\|\| \|\|\|@LB@ CAU UGUC GU AGUCUUUA CUUA CUGCCAUU UUUC UUA UACU UCG@LB@3'-UUU...AUCCC U U A AUUUA AA C A -5'@LB@ \| \|@LB@ 56 1@LB@@LB@@LB@Energy -14.44 kcal/mol@LB@Hybridization Energy -31.0616 kcal/mol@LB@Unfolding Energy - mRNA 10.2836 kcal/mol@LB@Unfolding Energy - sRNA 6.33758 kcal/mol@LB@@LB@Position - mRNA 167 -- 226@LB@Position - sRNA 1 -- 55@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 24 -- 30@LB@
143	0.02405	0.526	b3292	zntR	-11.17	0.055543	275 -- 285	1 -- 12	zntA gene transcriptional activator		_____________274__________286\n_____________\|____________\|\n5'-UGA...CAGCA____________AUGAA...CUG-3'\n______________GAUGAUGG_AGC\n______________:\|\|\|\|\|\|:_\|\|\|\n______________UUACUACU_UCG\n3'-UUU...UUCAA________A___-5'\n_____________\|___________\|\n_____________13__________1\n	276 -- 282	5 -- 11	-12.3439 kcal/mol	1.13072 kcal/mol	0.0394463 kcal/mol	274 286@LB@ \| \|@LB@5'-UGA...CAGCA AUGAA...CUG-3'@LB@ GAUGAUGG AGC@LB@ :\|\|\|\|\|\|: \|\|\|@LB@ UUACUACU UCG@LB@3'-UUU...UUCAA A -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -11.17 kcal/mol@LB@Hybridization Energy -12.3439 kcal/mol@LB@Unfolding Energy - mRNA 1.13072 kcal/mol@LB@Unfolding Energy - sRNA 0.0394463 kcal/mol@LB@@LB@Position - mRNA 275 -- 285@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 5 -- 11@LB@
144	0.02445	0.526	b3441	yhhY	-11.04	0.059403	187 -- 218	22 -- 53	aminoacyl nucleotide detoxifying acetyltransferase		_____________186________________________________219\n_____________\|__________________________________\|\n5'-CCC...CCCCA__GA_____A______________GAUA______CGCCA...UGC-3'\n______________AA__GGACA___AGGAAUGAGUGA____GUAAUA\n______________\|\|__:\|\|\|\|___\|\|:\|\|\|\|\|:\|\|\|____\|\|\|\|\|\|\n______________UU__UCUGU___UCUUUACUUACU____CAUUAU\n3'-UUU...CCCCA__UG_____AAG____________GC________UUAUU...UCG-5'\n_____________\|__________________________________\|\n_____________54_________________________________21\n	202 -- 208	30 -- 36	-22.9472 kcal/mol	5.59747 kcal/mol	6.31329 kcal/mol	186 219@LB@ \| \|@LB@5'-CCC...CCCCA GA A GAUA CGCCA...UGC-3'@LB@ AA GGACA AGGAAUGAGUGA GUAAUA@LB@ \|\| :\|\|\|\| \|\|:\|\|\|\|\|:\|\|\| \|\|\|\|\|\|@LB@ UU UCUGU UCUUUACUUACU CAUUAU@LB@3'-UUU...CCCCA UG AAG GC UUAUU...UCG-5'@LB@ \| \|@LB@ 54 21@LB@@LB@@LB@Energy -11.04 kcal/mol@LB@Hybridization Energy -22.9472 kcal/mol@LB@Unfolding Energy - mRNA 5.59747 kcal/mol@LB@Unfolding Energy - sRNA 6.31329 kcal/mol@LB@@LB@Position - mRNA 187 -- 218@LB@Position - sRNA 22 -- 53@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 30 -- 36@LB@
145	0.02447	0.526	b4518	ymdF	-10.96	0.061577	258 -- 296	23 -- 64	KGG family protein		_____________257________________________________________________297\n_____________\|__________________________________________________\|\n5'-UUU...CAUCA____C___UAAAAAA_________C___GC_____________G______UUCA-3'\n______________GAAG_AGG_______GGUGGACAG_ACA_____________GG_GGUAAU\n______________\|\|\|:_\|\|\|_______\|\|\|::\|\|\|\|_\|\|\|_____________\|:_\|\|\|\|\|\|\n______________CUUU_UCC_______CCAUUUGUC_UGU_____________CU_CCAUUA\n3'-UUU...GCCAA____A_______________________AAGUCUUUACUUA__G______UUUAU...UCG-5'\n_____________\|__________________________________________________\|\n_____________65_________________________________________________22\n	275 -- 281	48 -- 54	-22.543 kcal/mol	5.2615 kcal/mol	6.31898 kcal/mol	257 297@LB@ \| \|@LB@5'-UUU...CAUCA C UAAAAAA C GC G UUCA-3'@LB@ GAAG AGG GGUGGACAG ACA GG GGUAAU@LB@ \|\|\|: \|\|\| \|\|\|::\|\|\|\| \|\|\| \|: \|\|\|\|\|\|@LB@ CUUU UCC CCAUUUGUC UGU CU CCAUUA@LB@3'-UUU...GCCAA A AAGUCUUUACUUA G UUUAU...UCG-5'@LB@ \| \|@LB@ 65 22@LB@@LB@@LB@Energy -10.96 kcal/mol@LB@Hybridization Energy -22.543 kcal/mol@LB@Unfolding Energy - mRNA 5.2615 kcal/mol@LB@Unfolding Energy - sRNA 6.31898 kcal/mol@LB@@LB@Position - mRNA 258 -- 296@LB@Position - sRNA 23 -- 64@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 48 -- 54@LB@
146	0.02455	0.526	b0491	fetB	-8.60	0.179526	114 -- 156	14 -- 57	iron export ABC transporter permease; peroxide resistance protein		_____________113_______________________________________________157\n_____________\|_________________________________________________\|\n5'-GCC...GCUGU______C___C____AAGAC_____U___CAU_________________GAUUA...AGA-3'\n______________GGGUGA_ACA_GAUA_____GAAAU_AAU___GCGG______AUAAAGU\n______________\|\|\|\|:\|_\|\|\|_\|\|:\|_____\|\|\|\|\|_\|\|\|___:\|\|\|______\|\|\|\|\|\|\|\n______________CCCAUU_UGU_CUGU_____CUUUA_UUA___UGCC______UAUUUCA\n3'-UUU...UUAUC_______________AAGU______C___C______AUUAUU_______AUUAC...UCG-5'\n_____________\|_________________________________________________\|\n_____________58________________________________________________13\n	150 -- 156	14 -- 20	-22.3302 kcal/mol	7.40722 kcal/mol	6.32606 kcal/mol	113 157@LB@ \| \|@LB@5'-GCC...GCUGU C C AAGAC U CAU GAUUA...AGA-3'@LB@ GGGUGA ACA GAUA GAAAU AAU GCGG AUAAAGU@LB@ \|\|\|\|:\| \|\|\| \|\|:\| \|\|\|\|\| \|\|\| :\|\|\| \|\|\|\|\|\|\|@LB@ CCCAUU UGU CUGU CUUUA UUA UGCC UAUUUCA@LB@3'-UUU...UUAUC AAGU C C AUUAUU AUUAC...UCG-5'@LB@ \| \|@LB@ 58 13@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -22.3302 kcal/mol@LB@Unfolding Energy - mRNA 7.40722 kcal/mol@LB@Unfolding Energy - sRNA 6.32606 kcal/mol@LB@@LB@Position - mRNA 114 -- 156@LB@Position - sRNA 14 -- 57@LB@Position Seed - mRNA 150 -- 156@LB@Position Seed - sRNA 14 -- 20@LB@
147	0.02463	0.526	b2830	rppH	-8.72	0.170707	205 -- 218	1 -- 14	RNA pyrophosphohydrolase		_____________204____________219\n_____________\|______________\|\n5'-UUC...GGUGA_______C______UACCG...GGC-3'\n______________UUGAUGA_GAUGGC\n______________\|\|:\|\|\|\|_\|\|\|:\|\|\n______________AAUUACU_CUAUCG\n3'-UUU...AUUUC_______A______-5'\n_____________\|_____________\|\n_____________15____________1\n	205 -- 211	8 -- 14	-13.7427 kcal/mol	4.97796 kcal/mol	0.0473494 kcal/mol	204 219@LB@ \| \|@LB@5'-UUC...GGUGA C UACCG...GGC-3'@LB@ UUGAUGA GAUGGC@LB@ \|\|:\|\|\|\| \|\|\|:\|\|@LB@ AAUUACU CUAUCG@LB@3'-UUU...AUUUC A -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -13.7427 kcal/mol@LB@Unfolding Energy - mRNA 4.97796 kcal/mol@LB@Unfolding Energy - sRNA 0.0473494 kcal/mol@LB@@LB@Position - mRNA 205 -- 218@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 8 -- 14@LB@
148	0.02477	0.526	b2262	menB	-9.56	0.118602	261 -- 300	25 -- 56	dihydroxynaphthoic acid synthetase		_____________260______________________________________300\n_____________\|________________________________________\|\n5'-CGU...CCGAA___UUCGA__________UU_____AAAUCCACC_______-3'\n______________GGU_____GGACAUUC_G__AUGAA_________GACGGUA\n______________\|\|\|_____:\|\|\|\|\|\|\|_\|__\|\|\|\|\|_________\|\|\|\|\|\|\|\n______________CCA_____UCUGUAAG_C__UACUU_________CUGCCAU\n3'-UUU...UAUCC___UUUG_________U_UU_____A_______________UAUUU...UCG-5'\n_____________\|_________________________________________\|\n_____________57________________________________________24\n	294 -- 300	25 -- 31	-24.8577 kcal/mol	9.0019 kcal/mol	6.29869 kcal/mol	260 300@LB@ \| \|@LB@5'-CGU...CCGAA UUCGA UU AAAUCCACC -3'@LB@ GGU GGACAUUC G AUGAA GACGGUA@LB@ \|\|\| :\|\|\|\|\|\|\| \| \|\|\|\|\| \|\|\|\|\|\|\|@LB@ CCA UCUGUAAG C UACUU CUGCCAU@LB@3'-UUU...UAUCC UUUG U UU A UAUUU...UCG-5'@LB@ \| \|@LB@ 57 24@LB@@LB@@LB@Energy -9.56 kcal/mol@LB@Hybridization Energy -24.8577 kcal/mol@LB@Unfolding Energy - mRNA 9.0019 kcal/mol@LB@Unfolding Energy - sRNA 6.29869 kcal/mol@LB@@LB@Position - mRNA 261 -- 300@LB@Position - sRNA 25 -- 56@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 25 -- 31@LB@
149	0.02481	0.526	b2108	yehA	-13.80	0.014025	228 -- 241	1 -- 14	putative fimbrial-like adhesin protein		_____________227____________242\n_____________\|______________\|\n5'-GUU...UUAUA______________UAUGC...UUG-3'\n______________UUAAUGAUGAUGGU\n______________\|\|\|\|\|\|\|\|\|\|\|:\|:\n______________AAUUACUACUAUCG\n3'-UUU...AUUUC______________-5'\n_____________\|_____________\|\n_____________15____________1\n	235 -- 241	1 -- 7	-16.5389 kcal/mol	2.69058 kcal/mol	0.0473494 kcal/mol	227 242@LB@ \| \|@LB@5'-GUU...UUAUA UAUGC...UUG-3'@LB@ UUAAUGAUGAUGGU@LB@ \|\|\|\|\|\|\|\|\|\|\|:\|:@LB@ AAUUACUACUAUCG@LB@3'-UUU...AUUUC -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -13.80 kcal/mol@LB@Hybridization Energy -16.5389 kcal/mol@LB@Unfolding Energy - mRNA 2.69058 kcal/mol@LB@Unfolding Energy - sRNA 0.0473494 kcal/mol@LB@@LB@Position - mRNA 228 -- 241@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 1 -- 7@LB@
150	0.02489	0.526	b2088	insE1	-9.25	0.136086	235 -- 276	1 -- 55	IS3 transposase A	b0298 b0373 b0540 b1027	_____________234_____________________________________________________277\n_____________\|_______________________________________________________\|\n5'-ACC...ACCCC_______________CC_______UU__C____________CCC___________UUGCU...CUG-3'\n______________GUAAACAG_CAUUCG____UGAAU__CG______AGUGAAG____UGA____AGC\n______________\|\|\|\|\|\|\|\|_\|\|\|\|\|:____\|\|\|\|\|__\|\|______\|:\|:\|\|\|____\|\|\|____\|\|\|\n______________CAUUUGUC_GUAAGU____ACUUA__GC______UUAUUUC____ACU____UCG\n3'-UUU...AUCCC________U______CUUU_____CU__CAUUAU_______AAUU___ACUA___-5'\n_____________\|______________________________________________________\|\n_____________56_____________________________________________________1\n	261 -- 267	15 -- 21	-23.7484 kcal/mol	8.16492 kcal/mol	6.33758 kcal/mol	234 277@LB@ \| \|@LB@5'-ACC...ACCCC CC UU C CCC UUGCU...CUG-3'@LB@ GUAAACAG CAUUCG UGAAU CG AGUGAAG UGA AGC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|: \|\|\|\|\| \|\| \|:\|:\|\|\| \|\|\| \|\|\|@LB@ CAUUUGUC GUAAGU ACUUA GC UUAUUUC ACU UCG@LB@3'-UUU...AUCCC U CUUU CU CAUUAU AAUU ACUA -5'@LB@ \| \|@LB@ 56 1@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -23.7484 kcal/mol@LB@Unfolding Energy - mRNA 8.16492 kcal/mol@LB@Unfolding Energy - sRNA 6.33758 kcal/mol@LB@@LB@Position - mRNA 235 -- 276@LB@Position - sRNA 1 -- 55@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 15 -- 21@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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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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