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	Additional homologs
107	0.02737	0.6733	lmo1575	N/A	-17.23	0.037041	80 -- 118	156 -- 205			_____________79______119\n_____________\|_______\|\n5'-GUA...UCACA_______C-3'\n______________AAUGGGG\n______________\|\|:\|\|\|:\n______________UUGCCCU\n3'-GUU...ACGUA_______ACUCC...GGA-5'\n_____________\|_______\|\n_____________206_____155\n	293 -- 299	201 -- 207	-8.20946 kcal/mol	0.611387 kcal/mol	0.326294 kcal/mol	79 119@LB@ \| \|@LB@5'-GUA...UCACA C-3'@LB@ AAUGGGG@LB@ \|\|:\|\|\|:@LB@ UUGCCCU@LB@3'-GUU...ACGUA ACUCC...GGA-5'@LB@ \| \|@LB@ 206 155@LB@@LB@@LB@Energy -17.23 kcal/mol@LB@Hybridization Energy -8.20946 kcal/mol@LB@Unfolding Energy - mRNA 0.611387 kcal/mol@LB@Unfolding Energy - sRNA 0.326294 kcal/mol@LB@@LB@Position - mRNA 80 -- 118@LB@Position - sRNA 156 -- 205@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 201 -- 207@LB@
117	0.03157	0.6968	lmo0079	N/A	-15.68	0.073126	244 -- 277	156 -- 185	lmo0079		_____________243________________________________278\n_____________\|__________________________________\|\n5'-UCG...AUACC_________CAA_______ACCAG___G______UAUCC...CCG-3'\n______________AGCUACGUG___CCAAUGA_____GAA_GAAAAC\n______________\|:\|\|\|\|::\|___\|\|\|\|\|\|\|_____\|\|\|_\|\|\|\|\|\|\n______________UUGAUGUGC___GGUUACU_____CUU_CUUUUG\n3'-GUU...UGUAC_________C_________CUA_____A______UUUAU...GGA-5'\n_____________\|__________________________________\|\n_____________186________________________________155\n	256 -- 262	169 -- 175	-22.638 kcal/mol	3.99376 kcal/mol	9.64492 kcal/mol	243 278@LB@ \| \|@LB@5'-UCG...AUACC CAA ACCAG G UAUCC...CCG-3'@LB@ AGCUACGUG CCAAUGA GAA GAAAAC@LB@ \|:\|\|\|\|::\| \|\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|@LB@ UUGAUGUGC GGUUACU CUU CUUUUG@LB@3'-GUU...UGUAC C CUA A UUUAU...GGA-5'@LB@ \| \|@LB@ 186 155@LB@@LB@@LB@Energy -15.68 kcal/mol@LB@Hybridization Energy -22.638 kcal/mol@LB@Unfolding Energy - mRNA 3.99376 kcal/mol@LB@Unfolding Energy - sRNA 9.64492 kcal/mol@LB@@LB@Position - mRNA 244 -- 277@LB@Position - sRNA 156 -- 185@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 169 -- 175@LB@
118	0.03209	0.6968	lmo0654	N/A	-17.15	0.038336	200 -- 225	156 -- 180	lmo0654		_____________199________________________226\n_____________\|__________________________\|\n5'-GAA...GCGCG_______C______AUUUAA______UAGAA...CAC-3'\n______________UAUGGCC_AUGAGA______GAGAAC\n______________:\|:\|\|\|\|_\|\|\|\|\|\|______\|\|:\|\|\|\n______________GUGCCGG_UACUCU______CUUUUG\n3'-GUU...UUGAU_______U______ACUUA_______UUUAU...GGA-5'\n_____________\|__________________________\|\n_____________181________________________155\n	200 -- 206	174 -- 180	-23.3306 kcal/mol	3.96502 kcal/mol	8.29586 kcal/mol	199 226@LB@ \| \|@LB@5'-GAA...GCGCG C AUUUAA UAGAA...CAC-3'@LB@ UAUGGCC AUGAGA GAGAAC@LB@ :\|:\|\|\|\| \|\|\|\|\|\| \|\|:\|\|\|@LB@ GUGCCGG UACUCU CUUUUG@LB@3'-GUU...UUGAU U ACUUA UUUAU...GGA-5'@LB@ \| \|@LB@ 181 155@LB@@LB@@LB@Energy -17.15 kcal/mol@LB@Hybridization Energy -23.3306 kcal/mol@LB@Unfolding Energy - mRNA 3.96502 kcal/mol@LB@Unfolding Energy - sRNA 8.29586 kcal/mol@LB@@LB@Position - mRNA 200 -- 225@LB@Position - sRNA 156 -- 180@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 174 -- 180@LB@
143	0.03726	0.6968	lmo2701	N/A	-17.97	0.026314	78 -- 126	156 -- 198			_____________77_________________________________________________127\n_____________\|__________________________________________________\|\n5'-GAA...CCUUC_______AAAGUA___A____AGC________UUCCA_____________UUAGA...UCA-3'\n______________AGGCAUA______ACG_GAAU___GCAUGGCC______GUGGGUGGAGAC\n______________\|\|\|\|\|\|\|______\|\|:_\|\|\|:___:\|\|:\|\|\|\|______:\|\|::\|\|:\|:\|\|\n______________UCCGUAU______UGU_CUUG___UGUGCCGG______UACUUACUUUUG\n3'-GUU...CCUAC_______C________A____A__________UUACUC____________UUUAU...GGA-5'\n_____________\|__________________________________________________\|\n_____________199________________________________________________155\n	120 -- 126	156 -- 162	-37.6493 kcal/mol	12.7788 kcal/mol	13.9626 kcal/mol	77 127@LB@ \| \|@LB@5'-GAA...CCUUC AAAGUA A AGC UUCCA UUAGA...UCA-3'@LB@ AGGCAUA ACG GAAU GCAUGGCC GUGGGUGGAGAC@LB@ \|\|\|\|\|\|\| \|\|: \|\|\|: :\|\|:\|\|\|\| :\|\|::\|\|:\|:\|\|@LB@ UCCGUAU UGU CUUG UGUGCCGG UACUUACUUUUG@LB@3'-GUU...CCUAC C A A UUACUC UUUAU...GGA-5'@LB@ \| \|@LB@ 199 155@LB@@LB@@LB@Energy -17.97 kcal/mol@LB@Hybridization Energy -37.6493 kcal/mol@LB@Unfolding Energy - mRNA 12.7788 kcal/mol@LB@Unfolding Energy - sRNA 13.9626 kcal/mol@LB@@LB@Position - mRNA 78 -- 126@LB@Position - sRNA 156 -- 198@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 156 -- 162@LB@
148	0.03863	0.6968	lmo1766	purN	-15.06	0.094934	1 -- 35	156 -- 188	phosphoribosylglycinamide formyltransferase		______________1__________________________________36\n______________\|__________________________________\|\n___________5'-_____GAA___________UAAAC_A_________GUAUG...AUA-3'\n______________GUGAA___AUACGGCCAAU_____G_AAUGGAAAU\n______________:\|\|\|\|___\|:\|\|\|\|\|\|\|\|\|_____\|_\|\|\|\|:\|\|\|:\n______________UACUU___UGUGCCGGUUA_____C_UUACUUUUG\n3'-GUU...AUCUG_____GA____________CUCUA___________UUUAU...GGA-5'\n_____________\|___________________________________\|\n_____________189_________________________________155\n	29 -- 35	156 -- 162	-25.7257 kcal/mol	7.32217 kcal/mol	9.72027 kcal/mol	1 36@LB@ \| \|@LB@ 5'- GAA UAAAC A GUAUG...AUA-3'@LB@ GUGAA AUACGGCCAAU G AAUGGAAAU@LB@ :\|\|\|\| \|:\|\|\|\|\|\|\|\|\| \| \|\|\|\|:\|\|\|:@LB@ UACUU UGUGCCGGUUA C UUACUUUUG@LB@3'-GUU...AUCUG GA CUCUA UUUAU...GGA-5'@LB@ \| \|@LB@ 189 155@LB@@LB@@LB@Energy -15.06 kcal/mol@LB@Hybridization Energy -25.7257 kcal/mol@LB@Unfolding Energy - mRNA 7.32217 kcal/mol@LB@Unfolding Energy - sRNA 9.72027 kcal/mol@LB@@LB@Position - mRNA 1 -- 35@LB@Position - sRNA 156 -- 188@LB@Position Seed - mRNA 29 -- 35@LB@Position Seed - sRNA 156 -- 162@LB@
149	0.0387	0.6968	lmo1809	plsX	-16.53	0.050633	188 -- 233	156 -- 203	glycerol-3-phosphate acyltransferase PlsX		_____________187________________234\n_____________\|__________________\|\n5'-ACA...CUGUA____C_____________CACGC...UUC-3'\n______________GAUG_GAUGGGUGGAGAU\n______________:\|\|\|_\|\|\|\|::\|\|:\|:\|:\n______________UUAC_CUACUUACUUUUG\n3'-GUU...GCCGG____U_____________UUUAU...GGA-5'\n_____________\|__________________\|\n_____________204________________155\n	227 -- 233	156 -- 162	-17.4325 kcal/mol	7.3364 kcal/mol	0.941471 kcal/mol	187 234@LB@ \| \|@LB@5'-ACA...CUGUA C CACGC...UUC-3'@LB@ GAUG GAUGGGUGGAGAU@LB@ :\|\|\| \|\|\|\|::\|\|:\|:\|:@LB@ UUAC CUACUUACUUUUG@LB@3'-GUU...GCCGG U UUUAU...GGA-5'@LB@ \| \|@LB@ 204 155@LB@@LB@@LB@Energy -16.53 kcal/mol@LB@Hybridization Energy -17.4325 kcal/mol@LB@Unfolding Energy - mRNA 7.3364 kcal/mol@LB@Unfolding Energy - sRNA 0.941471 kcal/mol@LB@@LB@Position - mRNA 188 -- 233@LB@Position - sRNA 156 -- 203@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 156 -- 162@LB@
161	0.04429	0.7375	lmo0588	N/A	-15.80	0.069486	3 -- 42	156 -- 202	DNA photolyase		_____________2____________43\n_____________\|____________\|\n5'-UUG...CUUAU____________UAUGA...AAG-3'\n______________GUGGAUGAAAGC\n______________:\|\|:\|\|\|\|\|\|:\|\n______________UACUUACUUUUG\n3'-GUU...UACUC____________UUUAU...GGA-5'\n_____________\|____________\|\n_____________203__________155\n	36 -- 42	156 -- 162	-13.6691 kcal/mol	1.75048 kcal/mol	0.849227 kcal/mol	2 43@LB@ \| \|@LB@5'-UUG...CUUAU UAUGA...AAG-3'@LB@ GUGGAUGAAAGC@LB@ :\|\|:\|\|\|\|\|\|:\|@LB@ UACUUACUUUUG@LB@3'-GUU...UACUC UUUAU...GGA-5'@LB@ \| \|@LB@ 203 155@LB@@LB@@LB@Energy -15.80 kcal/mol@LB@Hybridization Energy -13.6691 kcal/mol@LB@Unfolding Energy - mRNA 1.75048 kcal/mol@LB@Unfolding Energy - sRNA 0.849227 kcal/mol@LB@@LB@Position - mRNA 3 -- 42@LB@Position - sRNA 156 -- 202@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 156 -- 162@LB@
191	0.0551	0.7607	lmo2853	N/A	-14.70	0.110014	201 -- 241	156 -- 201			_____________200_______________________________________________242\n_____________\|_________________________________________________\|\n5'-GGU...AGAAA________________________AA___U___ACGU____________UAUCC...UUC-3'\n______________GUGAG____AGAUAU_AACUGCGC__GGC_CAA_____UGAA__GAAGC\n______________:\|\|\|\|____\|\|\|:\|\|_\|\|\|\|:\|:\|__\|\|\|_\|\|\|_____\|\|\|\|__:\|\|:\|\n______________UACUC____UCUGUA_UUGAUGUG__CCG_GUU_____ACUU__UUUUG\n3'-GUU...UGCCC_____CGUA______C_________________ACUCU____AC_____UUUAU...GGA-5'\n_____________\|_________________________________________________\|\n_____________202_______________________________________________155\n	213 -- 219	178 -- 184	-28.7711 kcal/mol	7.06239 kcal/mol	14.0114 kcal/mol	200 242@LB@ \| \|@LB@5'-GGU...AGAAA AA U ACGU UAUCC...UUC-3'@LB@ GUGAG AGAUAU AACUGCGC GGC CAA UGAA GAAGC@LB@ :\|\|\|\| \|\|\|:\|\| \|\|\|\|:\|:\| \|\|\| \|\|\| \|\|\|\| :\|\|:\|@LB@ UACUC UCUGUA UUGAUGUG CCG GUU ACUU UUUUG@LB@3'-GUU...UGCCC CGUA C ACUCU AC UUUAU...GGA-5'@LB@ \| \|@LB@ 202 155@LB@@LB@@LB@Energy -14.70 kcal/mol@LB@Hybridization Energy -28.7711 kcal/mol@LB@Unfolding Energy - mRNA 7.06239 kcal/mol@LB@Unfolding Energy - sRNA 14.0114 kcal/mol@LB@@LB@Position - mRNA 201 -- 241@LB@Position - sRNA 156 -- 201@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 178 -- 184@LB@
2	0.0002774	0.3688	lmo1666	N/A	-21.94	0.003684	151 -- 207	157 -- 207	peptidoglycan-linked protein	lmo0333	_____________150____________208\n_____________\|______________\|\n5'-GUG...AGAUG______________GUAAA...CUC-3'\n______________GGGAUGAAUGAAAA\n______________\|:\|\|\|\|\|\|\|\|\|\|\|\|\n______________CUCUACUUACUUUU\n3'-GUU...GGUUA______________GUUUA...GGA-5'\n_____________\|______________\|\n_____________208____________156\n	201 -- 207	157 -- 163	-18.267 kcal/mol	1.529 kcal/mol	0.904482 kcal/mol	150 208@LB@ \| \|@LB@5'-GUG...AGAUG GUAAA...CUC-3'@LB@ GGGAUGAAUGAAAA@LB@ \|:\|\|\|\|\|\|\|\|\|\|\|\|@LB@ CUCUACUUACUUUU@LB@3'-GUU...GGUUA GUUUA...GGA-5'@LB@ \| \|@LB@ 208 156@LB@@LB@@LB@Energy -21.94 kcal/mol@LB@Hybridization Energy -18.267 kcal/mol@LB@Unfolding Energy - mRNA 1.529 kcal/mol@LB@Unfolding Energy - sRNA 0.904482 kcal/mol@LB@@LB@Position - mRNA 151 -- 207@LB@Position - sRNA 157 -- 207@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 157 -- 163@LB@
7	0.001816	0.4469	lmo1666	N/A	-21.94	0.003684	151 -- 207	157 -- 207	peptidoglycan-linked protein	lmo0333	_____________150____________208\n_____________\|______________\|\n5'-GUG...AGAUG______________GUAAA...CUC-3'\n______________GGGAUGAAUGAAAA\n______________\|:\|\|\|\|\|\|\|\|\|\|\|\|\n______________CUCUACUUACUUUU\n3'-GUU...GGUUA______________GUUUA...GGA-5'\n_____________\|______________\|\n_____________208____________156\n	201 -- 207	157 -- 163	-18.267 kcal/mol	1.529 kcal/mol	0.904482 kcal/mol	150 208@LB@ \| \|@LB@5'-GUG...AGAUG GUAAA...CUC-3'@LB@ GGGAUGAAUGAAAA@LB@ \|:\|\|\|\|\|\|\|\|\|\|\|\|@LB@ CUCUACUUACUUUU@LB@3'-GUU...GGUUA GUUUA...GGA-5'@LB@ \| \|@LB@ 208 156@LB@@LB@@LB@Energy -21.94 kcal/mol@LB@Hybridization Energy -18.267 kcal/mol@LB@Unfolding Energy - mRNA 1.529 kcal/mol@LB@Unfolding Energy - sRNA 0.904482 kcal/mol@LB@@LB@Position - mRNA 151 -- 207@LB@Position - sRNA 157 -- 207@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 157 -- 163@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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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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