Input and runtime details for job 8257533 (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 8257533 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:34:31 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:34:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:30:38 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:30:45 CET 2018
	Job Completed		@ Fri Feb 16 22:31:01 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=8257533&toolName=CopraRNA ( 30 days expiry )

Description of the job

LhrA2

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_003210 Listeria monocytogenes EGD-e

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
151	0.03914	0.6976	lmo1466	N/A	-16.64	0.048271	185 -- 226	158 -- 202		_____________184_______________________________________________227\n_____________\|_________________________________________________\|\n5'-UGA...UUAGA____AGA__A_______A_____________________________G_UUGGU...UUC-3'\n______________GAGG___CA_AGAUGUG_AACUA____GCCAA_GA____AAUGGAGA_A\n______________\|\|\|\|___\|\|_\|\|\|::\|\|_\|\|\|\|\|____\|\|\|\|\|_\|\|____\|\|\|\|:\|:\|_\|\n______________CUCC___GU_UCUGUAC_UUGAU____CGGUU_CU____UUACUUUU_U\n3'-GUU...CCCUA_________A_____________GUGC_____A__CUAC________G_UUAUU...GGA-5'\n_____________\|_________________________________________________\|\n_____________203_______________________________________________157\n	218 -- 224	157 -- 163	-27.6675 kcal/mol	5.9878 kcal/mol	13.9822 kcal/mol	184 227@LB@ \| \|@LB@5'-UGA...UUAGA AGA A A G UUGGU...UUC-3'@LB@ GAGG CA AGAUGUG AACUA GCCAA GA AAUGGAGA A@LB@ \|\|\|\| \|\| \|\|\|::\|\| \|\|\|\|\| \|\|\|\|\| \|\| \|\|\|\|:\|:\| \|@LB@ CUCC GU UCUGUAC UUGAU CGGUU CU UUACUUUU U@LB@3'-GUU...CCCUA A GUGC A CUAC G UUAUU...GGA-5'@LB@ \| \|@LB@ 203 157@LB@@LB@@LB@Energy -16.64 kcal/mol@LB@Hybridization Energy -27.6675 kcal/mol@LB@Unfolding Energy - mRNA 5.9878 kcal/mol@LB@Unfolding Energy - sRNA 13.9822 kcal/mol@LB@@LB@Position - mRNA 185 -- 226@LB@Position - sRNA 158 -- 202@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 157 -- 163@LB@
152	0.04001	0.7027	lmo1203	cbiL	-16.49	0.051377	174 -- 199	155 -- 181	cobalt-precorrin-2 C(20)-methyltransferase	_____________173___________________200\n_____________\|_____________________\|\n5'-ACA...CACUG____A________________CGUGG...CAC-3'\n______________CAAU_GAGA_GGGUGAAAACA\n______________\|\|\|\|_\|\|\|\|_\|::\|\|\|\|\|\|\|\|\n______________GUUA_CUCU_CUUACUUUUGU\n3'-GUU...UGCCG_________A___________UUAUU...GGA-5'\n_____________\|_____________________\|\n_____________182___________________154\n	193 -- 199	155 -- 161	-18.5314 kcal/mol	4.87195 kcal/mol	0.95817 kcal/mol	173 200@LB@ \| \|@LB@5'-ACA...CACUG A CGUGG...CAC-3'@LB@ CAAU GAGA GGGUGAAAACA@LB@ \|\|\|\| \|\|\|\| \|::\|\|\|\|\|\|\|\|@LB@ GUUA CUCU CUUACUUUUGU@LB@3'-GUU...UGCCG A UUAUU...GGA-5'@LB@ \| \|@LB@ 182 154@LB@@LB@@LB@Energy -16.49 kcal/mol@LB@Hybridization Energy -18.5314 kcal/mol@LB@Unfolding Energy - mRNA 4.87195 kcal/mol@LB@Unfolding Energy - sRNA 0.95817 kcal/mol@LB@@LB@Position - mRNA 174 -- 199@LB@Position - sRNA 155 -- 181@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 155 -- 161@LB@
153	0.04013	0.7027	lmo0979	N/A	-16.44	0.052648	251 -- 296	172 -- 207	daunorubicin resistance ATP-binding protein	_____________250_____________________________297\n_____________\|_______________________________\|\n5'-AAU...UUGAA__________UU____G_AAA_______G__AUUU-3'\n______________GGGUGUAGAU__UGAA_U___ACAUGGC_AA\n______________:\|\|::\|\|\|\|:__\|\|\|\|_\|___\|\|\|:\|\|\|_\|\|\n______________UCCGUAUCUG__ACUU_A___UGUGCCG_UU\n3'-GUU...CCUAC__________U_____G___________G__ACUCU...GGA-5'\n_____________\|_______________________________\|\n_____________208_____________________________171\n	287 -- 293	175 -- 181	-27.1075 kcal/mol	4.53663 kcal/mol	13.3233 kcal/mol	250 297@LB@ \| \|@LB@5'-AAU...UUGAA UU G AAA G AUUU-3'@LB@ GGGUGUAGAU UGAA U ACAUGGC AA@LB@ :\|\|::\|\|\|\|: \|\|\|\| \| \|\|\|:\|\|\| \|\|@LB@ UCCGUAUCUG ACUU A UGUGCCG UU@LB@3'-GUU...CCUAC U G G ACUCU...GGA-5'@LB@ \| \|@LB@ 208 171@LB@@LB@@LB@Energy -16.44 kcal/mol@LB@Hybridization Energy -27.1075 kcal/mol@LB@Unfolding Energy - mRNA 4.53663 kcal/mol@LB@Unfolding Energy - sRNA 13.3233 kcal/mol@LB@@LB@Position - mRNA 251 -- 296@LB@Position - sRNA 172 -- 207@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 175 -- 181@LB@
154	0.04021	0.7027	lmo2008	N/A	-17.88	0.027453	195 -- 258	157 -- 220	ABC transporter permease	_____________194___________________259\n_____________\|_____________________\|\n5'-CAG...UGAAG____________AU_______GUCCG...UUG-3'\n______________CAGUGAG_UGAA__AGAACAA\n______________\|\|:\|\|\|\|_\|\|\|\|__\|:\|\|\|\|\|\n______________GUUACUC_ACUU__UUUUGUU\n3'-GUU...UGCCG_______U____AC_______UAUUA...GGA-5'\n_____________\|_____________________\|\n_____________221___________________156\n	233 -- 239	154 -- 160	-15.5955 kcal/mol	3.58965 kcal/mol	0.962339 kcal/mol	194 259@LB@ \| \|@LB@5'-CAG...UGAAG AU GUCCG...UUG-3'@LB@ CAGUGAG UGAA AGAACAA@LB@ \|\|:\|\|\|\| \|\|\|\| \|:\|\|\|\|\|@LB@ GUUACUC ACUU UUUUGUU@LB@3'-GUU...UGCCG U AC UAUUA...GGA-5'@LB@ \| \|@LB@ 221 156@LB@@LB@@LB@Energy -17.88 kcal/mol@LB@Hybridization Energy -15.5955 kcal/mol@LB@Unfolding Energy - mRNA 3.58965 kcal/mol@LB@Unfolding Energy - sRNA 0.962339 kcal/mol@LB@@LB@Position - mRNA 195 -- 258@LB@Position - sRNA 157 -- 220@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 154 -- 160@LB@
155	0.04112	0.7058	lmo1165	N/A	-16.89	0.043077	88 -- 150	155 -- 206	ethanolamine utilization protein EutE	_____________87_______________________________151\n_____________\|________________________________\|\n5'-AAG...AAUGG____________G___C_______G_______UCCAC...CAA-3'\n______________GGAUUA_GCGGC_GAU_AG_UGGA_GAAGAUA\n______________\|:\|:\|\|_:\|\|\|\|_:\|\|_\|\|_\|\|:\|_\|\|\|:\|:\|\n______________CUUGAU_UGCCG_UUA_UC_ACUU_CUUUUGU\n3'-GUU...CUGUA______G_____G___C__U____A_______UUAUU...GGA-5'\n_____________\|________________________________\|\n_____________207______________________________154\n	144 -- 150	155 -- 161	-24.1777 kcal/mol	5.41964 kcal/mol	9.66922 kcal/mol	87 151@LB@ \| \|@LB@5'-AAG...AAUGG G C G UCCAC...CAA-3'@LB@ GGAUUA GCGGC GAU AG UGGA GAAGAUA@LB@ \|:\|:\|\| :\|\|\|\| :\|\| \|\| \|\|:\| \|\|\|:\|:\|@LB@ CUUGAU UGCCG UUA UC ACUU CUUUUGU@LB@3'-GUU...CUGUA G G C U A UUAUU...GGA-5'@LB@ \| \|@LB@ 207 154@LB@@LB@@LB@Energy -16.89 kcal/mol@LB@Hybridization Energy -24.1777 kcal/mol@LB@Unfolding Energy - mRNA 5.41964 kcal/mol@LB@Unfolding Energy - sRNA 9.66922 kcal/mol@LB@@LB@Position - mRNA 88 -- 150@LB@Position - sRNA 155 -- 206@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 155 -- 161@LB@
156	0.04133	0.7058	lmo1481	holA	-16.45	0.052293	189 -- 224	151 -- 199	DNA polymerase III subunit delta	_____________188_________225\n_____________\|___________\|\n5'-CAA...UGCCA___________GAUAC...UUU-3'\n______________GAAUGGAAACA\n______________\|\|\|\|\|:\|\|\|\|\|\n______________CUUACUUUUGU\n3'-GUU...CUCUA___________UUAUU...GGA-5'\n_____________\|___________\|\n_____________200_________150\n	213 -- 219	156 -- 162	-12.8572 kcal/mol	1.78423 kcal/mol	0.853601 kcal/mol	188 225@LB@ \| \|@LB@5'-CAA...UGCCA GAUAC...UUU-3'@LB@ GAAUGGAAACA@LB@ \|\|\|\|\|:\|\|\|\|\|@LB@ CUUACUUUUGU@LB@3'-GUU...CUCUA UUAUU...GGA-5'@LB@ \| \|@LB@ 200 150@LB@@LB@@LB@Energy -16.45 kcal/mol@LB@Hybridization Energy -12.8572 kcal/mol@LB@Unfolding Energy - mRNA 1.78423 kcal/mol@LB@Unfolding Energy - sRNA 0.853601 kcal/mol@LB@@LB@Position - mRNA 189 -- 224@LB@Position - sRNA 151 -- 199@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 156 -- 162@LB@
157	0.0414	0.7058	lmo0010	N/A	-15.41	0.081879	188 -- 219	167 -- 203	mevalonate kinase	_____________187_____220\n_____________\|_______\|\n5'-AUC...AUGCG_______UGCAG...UAG-3'\n______________GAGAACA\n______________\|\|:\|\|\|\|\n______________CUUUUGU\n3'-GUU...ACUUA_______UUAUU...GGA-5'\n_____________\|_______\|\n_____________204_____166\n	241 -- 247	155 -- 161	-5.76961 kcal/mol	0.621388 kcal/mol	0.528569 kcal/mol	187 220@LB@ \| \|@LB@5'-AUC...AUGCG UGCAG...UAG-3'@LB@ GAGAACA@LB@ \|\|:\|\|\|\|@LB@ CUUUUGU@LB@3'-GUU...ACUUA UUAUU...GGA-5'@LB@ \| \|@LB@ 204 166@LB@@LB@@LB@Energy -15.41 kcal/mol@LB@Hybridization Energy -5.76961 kcal/mol@LB@Unfolding Energy - mRNA 0.621388 kcal/mol@LB@Unfolding Energy - sRNA 0.528569 kcal/mol@LB@@LB@Position - mRNA 188 -- 219@LB@Position - sRNA 167 -- 203@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 155 -- 161@LB@
158	0.04144	0.7058	lmo1958	fhuB	-14.94	0.099691	191 -- 222	150 -- 181	ferrichrome ABC transporter permease	_____________190_______________________________223\n_____________\|_________________________________\|\n5'-GUU...AAGGA_____U__A________A___C___________AAAUG...UCG-3'\n______________ACAUG_GC_GAUG_GAU_AGU_AAAACAGAUAA\n______________\|\|\|:\|_\|\|_:\|\|\|_\|\|\|_\|:\|_\|\|\|\|\|\|:\|\|\|\|\n______________UGUGC_CG_UUAC_CUA_UUA_UUUUGUUUAUU\n3'-GUU...CUUGA________G____U___C___C___________ACUAA...GGA-5'\n_____________\|_________________________________\|\n_____________182_______________________________149\n	214 -- 220	152 -- 158	-22.8664 kcal/mol	3.81003 kcal/mol	11.9534 kcal/mol	190 223@LB@ \| \|@LB@5'-GUU...AAGGA U A A C AAAUG...UCG-3'@LB@ ACAUG GC GAUG GAU AGU AAAACAGAUAA@LB@ \|\|\|:\| \|\| :\|\|\| \|\|\| \|:\| \|\|\|\|\|\|:\|\|\|\|@LB@ UGUGC CG UUAC CUA UUA UUUUGUUUAUU@LB@3'-GUU...CUUGA G U C C ACUAA...GGA-5'@LB@ \| \|@LB@ 182 149@LB@@LB@@LB@Energy -14.94 kcal/mol@LB@Hybridization Energy -22.8664 kcal/mol@LB@Unfolding Energy - mRNA 3.81003 kcal/mol@LB@Unfolding Energy - sRNA 11.9534 kcal/mol@LB@@LB@Position - mRNA 191 -- 222@LB@Position - sRNA 150 -- 181@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 152 -- 158@LB@
159	0.04218	0.7139	lmo1454	rpoD	-16.27	0.056776	172 -- 217	153 -- 211	RNA polymerase sigma factor RpoD	_____________171_______________218\n_____________\|_________________\|\n5'-AGA...GUUAA___G________U____UAAUA...UAA-3'\n______________ACA_CGGCCAAU_GGAU\n______________\|\|\|_\|\|\|\|\|\|\|\|_:\|\|\|\n______________UGU_GCCGGUUA_UCUA\n3'-GUU...CUUGA____________C____CUUAC...GGA-5'\n_____________\|_________________\|\n_____________212_______________152\n	92 -- 98	171 -- 177	-19.258 kcal/mol	2.66151 kcal/mol	6.2749 kcal/mol	171 218@LB@ \| \|@LB@5'-AGA...GUUAA G U UAAUA...UAA-3'@LB@ ACA CGGCCAAU GGAU@LB@ \|\|\| \|\|\|\|\|\|\|\| :\|\|\|@LB@ UGU GCCGGUUA UCUA@LB@3'-GUU...CUUGA C CUUAC...GGA-5'@LB@ \| \|@LB@ 212 152@LB@@LB@@LB@Energy -16.27 kcal/mol@LB@Hybridization Energy -19.258 kcal/mol@LB@Unfolding Energy - mRNA 2.66151 kcal/mol@LB@Unfolding Energy - sRNA 6.2749 kcal/mol@LB@@LB@Position - mRNA 172 -- 217@LB@Position - sRNA 153 -- 211@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 171 -- 177@LB@
160	0.04276	0.7192	lmo0415	N/A	-19.07	0.015641	183 -- 241	108 -- 171	endo-1 4-beta-xylanase	_____________182_________________________________________________________________242\n_____________\|___________________________________________________________________\|\n5'-UUU...UUUUC_________GU______UAAU____AAA__A____GA______________C_______________CAUUA...AGU-3'\n______________UGAGGUGAG_____GCA____GUGA___UU_GGUG__UUAGAC_____UUU_ACUAGUUGCCAUUCU\n______________\|\|\|\|:\|\|\|:_____:\|\|____:\|\|\|___\|\|_\|\|\|\|__:\|\|:\|\|_____\|:\|_\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________ACUCUACUU_____UGU____UACU___AA_CCAC__GAUUUG_____AGA_UGAUCAACGGUAAGA\n3'-GUU...CGGUU_________ACUUU___UUAU____A____A____A_______UCUAC___C_______________UAACC...GGA-5'\n_____________\|___________________________________________________________________\|\n_____________172_________________________________________________________________107\n	235 -- 241	108 -- 114	-46.29 kcal/mol	15.9956 kcal/mol	19.2069 kcal/mol	182 242@LB@ \| \|@LB@5'-UUU...UUUUC GU UAAU AAA A GA C CAUUA...AGU-3'@LB@ UGAGGUGAG GCA GUGA UU GGUG UUAGAC UUU ACUAGUUGCCAUUCU@LB@ \|\|\|\|:\|\|\|: :\|\| :\|\|\| \|\| \|\|\|\| :\|\|:\|\| \|:\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ ACUCUACUU UGU UACU AA CCAC GAUUUG AGA UGAUCAACGGUAAGA@LB@3'-GUU...CGGUU ACUUU UUAU A A A UCUAC C UAACC...GGA-5'@LB@ \| \|@LB@ 172 107@LB@@LB@@LB@Energy -19.07 kcal/mol@LB@Hybridization Energy -46.29 kcal/mol@LB@Unfolding Energy - mRNA 15.9956 kcal/mol@LB@Unfolding Energy - sRNA 19.2069 kcal/mol@LB@@LB@Position - mRNA 183 -- 241@LB@Position - sRNA 108 -- 171@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 108 -- 114@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)

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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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