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
136	0.03623	0.6968	lmo1567	citZ	-17.33	0.035419	8 -- 31	169 -- 198	citrate synthase	_____________7______________________________32\n_____________\|______________________________\|\n____5'-CGAAAAA__________________________U___UCCAC...ACG-3'\n______________AGGUGUAG______GCUAUAUGGCCG_UGA\n______________\|\|\|::\|\|\|______:\|\|\|:\|:\|\|\|\|:_\|\|\|\n______________UCCGUAUC______UGAUGUGCCGGU_ACU\n3'-GUU...CCUAC________UGUACU____________U___CUACU...GGA-5'\n_____________\|______________________________\|\n_____________199____________________________168\n	21 -- 27	173 -- 179	-29.4881 kcal/mol	5.57901 kcal/mol	13.3393 kcal/mol	7 32@LB@ \| \|@LB@ 5'-CGAAAAA U UCCAC...ACG-3'@LB@ AGGUGUAG GCUAUAUGGCCG UGA@LB@ \|\|\|::\|\|\| :\|\|\|:\|:\|\|\|\|: \|\|\|@LB@ UCCGUAUC UGAUGUGCCGGU ACU@LB@3'-GUU...CCUAC UGUACU U CUACU...GGA-5'@LB@ \| \|@LB@ 199 168@LB@@LB@@LB@Energy -17.33 kcal/mol@LB@Hybridization Energy -29.4881 kcal/mol@LB@Unfolding Energy - mRNA 5.57901 kcal/mol@LB@Unfolding Energy - sRNA 13.3393 kcal/mol@LB@@LB@Position - mRNA 8 -- 31@LB@Position - sRNA 169 -- 198@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 173 -- 179@LB@
32	0.006611	0.5515	lmo1649	N/A	-18.63	0.019340	118 -- 153	171 -- 207	lmo1649	_____________117_____________________________________________________________154\n_____________\|_______________________________________________________________\|\n5'-GUA...UGUUA_______AGUAAU__UA______CG__________A_____UC__A_____G___________UACAA...AAA-3'\n______________CAUCGUG______GU__CU_UGC__GAUGGG_UGA_GCAUA__CG_G_ACU_ACGCGGCCAGU\n______________\|\|\|\|:\|\|______\|:__\|\|_\|\|\|__:\|:\|\|\|_\|\|\|_\|\|\|\|\|__\|:_\|_\|\|\|_\|\|:\|\|\|\|\|\|:\|\n______________GUAGUAC______CG__GA_ACG__UUGCCC_ACU_CGUAU__GU_C_UGA_UGUGCCGGUUA\n3'-GUU...CAACG_______AAGCC___CG__U___UA______U___C_____CU__A_U_______________CUCUA...GGA-5'\n_____________\|_______________________________________________________________\|\n_____________208_____________________________________________________________170\n	147 -- 153	171 -- 177	-50.2657 kcal/mol	18.2787 kcal/mol	22.0434 kcal/mol	117 154@LB@ \| \|@LB@5'-GUA...UGUUA AGUAAU UA CG A UC A G UACAA...AAA-3'@LB@ CAUCGUG GU CU UGC GAUGGG UGA GCAUA CG G ACU ACGCGGCCAGU@LB@ \|\|\|\|:\|\| \|: \|\| \|\|\| :\|:\|\|\| \|\|\| \|\|\|\|\| \|: \| \|\|\| \|\|:\|\|\|\|\|\|:\|@LB@ GUAGUAC CG GA ACG UUGCCC ACU CGUAU GU C UGA UGUGCCGGUUA@LB@3'-GUU...CAACG AAGCC CG U UA U C CU A U CUCUA...GGA-5'@LB@ \| \|@LB@ 208 170@LB@@LB@@LB@Energy -18.63 kcal/mol@LB@Hybridization Energy -50.2657 kcal/mol@LB@Unfolding Energy - mRNA 18.2787 kcal/mol@LB@Unfolding Energy - sRNA 22.0434 kcal/mol@LB@@LB@Position - mRNA 118 -- 153@LB@Position - sRNA 171 -- 207@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 171 -- 177@LB@
65	0.01641	0.6733	lmo0040	N/A	-17.01	0.040772	52 -- 100	171 -- 220	agmatine deiminase	_____________51______________101\n_____________\|_______________\|\n5'-GUC...AAUAG____A__________GGGAC...CUG-3'\n______________GAGG_GAAUGAGGAU\n______________\|\|\|:_\|\|\|\|\|\|::\|:\n______________CUCU_CUUACUUUUG\n3'-GUU...GGUUA____A__________UUUAU...GGA-5'\n_____________\|_______________\|\n_____________221_____________170\n	196 -- 202	156 -- 162	-15.5399 kcal/mol	0.994344 kcal/mol	0.916023 kcal/mol	51 101@LB@ \| \|@LB@5'-GUC...AAUAG A GGGAC...CUG-3'@LB@ GAGG GAAUGAGGAU@LB@ \|\|\|: \|\|\|\|\|\|::\|:@LB@ CUCU CUUACUUUUG@LB@3'-GUU...GGUUA A UUUAU...GGA-5'@LB@ \| \|@LB@ 221 170@LB@@LB@@LB@Energy -17.01 kcal/mol@LB@Hybridization Energy -15.5399 kcal/mol@LB@Unfolding Energy - mRNA 0.994344 kcal/mol@LB@Unfolding Energy - sRNA 0.916023 kcal/mol@LB@@LB@Position - mRNA 52 -- 100@LB@Position - sRNA 171 -- 220@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 156 -- 162@LB@
102	0.02619	0.6733	lmo1799	N/A	-17.02	0.040600	38 -- 69	171 -- 207	peptidoglycan binding protein	_____________37______________70\n_____________\|_______________\|\n5'-CUA...AAAAC__G____________UUGGC...UGG-3'\n______________GA_GGGA_GGGGCAU\n______________:\|_\|\|\|\|_\|:\|\|\|\|\|\n______________UU_CCCU_CUCCGUA\n3'-GUU...ACGUA__G____A_______UCUGU...GGA-5'\n_____________\|_______________\|\n_____________208_____________170\n	45 -- 51	193 -- 199	-19.1902 kcal/mol	1.80232 kcal/mol	8.95053 kcal/mol	37 70@LB@ \| \|@LB@5'-CUA...AAAAC G UUGGC...UGG-3'@LB@ GA GGGA GGGGCAU@LB@ :\| \|\|\|\| \|:\|\|\|\|\|@LB@ UU CCCU CUCCGUA@LB@3'-GUU...ACGUA G A UCUGU...GGA-5'@LB@ \| \|@LB@ 208 170@LB@@LB@@LB@Energy -17.02 kcal/mol@LB@Hybridization Energy -19.1902 kcal/mol@LB@Unfolding Energy - mRNA 1.80232 kcal/mol@LB@Unfolding Energy - sRNA 8.95053 kcal/mol@LB@@LB@Position - mRNA 38 -- 69@LB@Position - sRNA 171 -- 207@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 193 -- 199@LB@
173	0.04847	0.7539	lmo1143	N/A	-15.38	0.082828	238 -- 287	171 -- 211	PduT protein	_____________237_______________________________288\n_____________\|_________________________________\|\n5'-GUG...GCAUC______GUC____C__U____AAA_________UCGGA...UUU-3'\n______________GAGGCG___GAUA_GA_GCUA___GCGGCCAAU\n______________\|\|\|\|\|:___\|\|:\|_\|\|_:\|\|\|___:\|\|\|\|\|\|\|\|\n______________CUCCGU___CUGU_CU_UGAU___UGCCGGUUA\n3'-GUU...CCCUA______AU_____A_______G___________CUCUA...GGA-5'\n_____________\|_________________________________\|\n_____________212_______________________________170\n	281 -- 287	171 -- 177	-30.6178 kcal/mol	10.0561 kcal/mol	13.341 kcal/mol	237 288@LB@ \| \|@LB@5'-GUG...GCAUC GUC C U AAA UCGGA...UUU-3'@LB@ GAGGCG GAUA GA GCUA GCGGCCAAU@LB@ \|\|\|\|\|: \|\|:\| \|\| :\|\|\| :\|\|\|\|\|\|\|\|@LB@ CUCCGU CUGU CU UGAU UGCCGGUUA@LB@3'-GUU...CCCUA AU A G CUCUA...GGA-5'@LB@ \| \|@LB@ 212 170@LB@@LB@@LB@Energy -15.38 kcal/mol@LB@Hybridization Energy -30.6178 kcal/mol@LB@Unfolding Energy - mRNA 10.0561 kcal/mol@LB@Unfolding Energy - sRNA 13.341 kcal/mol@LB@@LB@Position - mRNA 238 -- 287@LB@Position - sRNA 171 -- 211@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 171 -- 177@LB@
4	0.0009641	0.4469	lmo0851	N/A	-23.35	0.001728	188 -- 220	172 -- 201	lmo0851	_____________187_______________________________221\n_____________\|_________________________________\|\n5'-GGU...AUAGA__________U_______AAAAGAA________CCAAC...UAA-3'\n______________GUGAGGCAUA_ACAUGAA_______GCGGUUAA\n______________:\|\|\|\|\|\|\|\|\|_\|\|\|\|\|\|\|_______:\|\|\|::\|\|\n______________UACUCCGUAU_UGUACUU_______UGCCGGUU\n3'-GUU...UGCCC__________C_______GAUG___________ACUCU...GGA-5'\n_____________\|_________________________________\|\n_____________202_______________________________171\n	214 -- 220	172 -- 178	-33.261 kcal/mol	3.18896 kcal/mol	13.3764 kcal/mol	187 221@LB@ \| \|@LB@5'-GGU...AUAGA U AAAAGAA CCAAC...UAA-3'@LB@ GUGAGGCAUA ACAUGAA GCGGUUAA@LB@ :\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\| :\|\|\|::\|\|@LB@ UACUCCGUAU UGUACUU UGCCGGUU@LB@3'-GUU...UGCCC C GAUG ACUCU...GGA-5'@LB@ \| \|@LB@ 202 171@LB@@LB@@LB@Energy -23.35 kcal/mol@LB@Hybridization Energy -33.261 kcal/mol@LB@Unfolding Energy - mRNA 3.18896 kcal/mol@LB@Unfolding Energy - sRNA 13.3764 kcal/mol@LB@@LB@Position - mRNA 188 -- 220@LB@Position - sRNA 172 -- 201@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 172 -- 178@LB@
144	0.03753	0.6968	lmo2422	N/A	-16.62	0.048504	29 -- 68	172 -- 209	two-component response regulator	_____________28___________________________________69\n_____________\|____________________________________\|\n5'-AUG...AUUCG____________AAAU_______G___U________UUUAU...AUG-3'\n______________CUAUGU__GACG____UGAGGCA_AGA_UAUGAAUU\n______________\|\|\|\|\|:__:\|\|\|____\|\|\|\|\|\|\|_\|\|\|_:\|\|\|\|\|:\|\n______________GAUACG__UUGC____ACUCCGU_UCU_GUACUUGA\n3'-GUU...CCGCG______UA____CCU________A____________UGUGC...GGA-5'\n_____________\|____________________________________\|\n_____________210__________________________________171\n	39 -- 45	194 -- 200	-29.3631 kcal/mol	6.47642 kcal/mol	13.3074 kcal/mol	28 69@LB@ \| \|@LB@5'-AUG...AUUCG AAAU G U UUUAU...AUG-3'@LB@ CUAUGU GACG UGAGGCA AGA UAUGAAUU@LB@ \|\|\|\|\|: :\|\|\| \|\|\|\|\|\|\| \|\|\| :\|\|\|\|\|:\|@LB@ GAUACG UUGC ACUCCGU UCU GUACUUGA@LB@3'-GUU...CCGCG UA CCU A UGUGC...GGA-5'@LB@ \| \|@LB@ 210 171@LB@@LB@@LB@Energy -16.62 kcal/mol@LB@Hybridization Energy -29.3631 kcal/mol@LB@Unfolding Energy - mRNA 6.47642 kcal/mol@LB@Unfolding Energy - sRNA 13.3074 kcal/mol@LB@@LB@Position - mRNA 29 -- 68@LB@Position - sRNA 172 -- 209@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 194 -- 200@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@
192	0.05535	0.7607	lmo2025	nadA	-15.59	0.075878	179 -- 223	172 -- 209	quinolinate synthetase	_____________178________________________________224\n_____________\|__________________________________\|\n5'-GAU...AAUAA_________U____UAGAA________ACA____ACAAU...CCC-3'\n______________AGGCAUGAA_UUAC_____ACGGUCGA___AGAU\n______________\|\|:\|\|\|\|\|\|_:\|\|\|_____\|\|\|\|:\|:\|___\|\|\|\|\n______________UCUGUACUU_GAUG_____UGCCGGUU___UCUA\n3'-GUU...CCGUA___________________________AC_____CUUAC...GGA-5'\n_____________\|__________________________________\|\n_____________210________________________________171\n	217 -- 223	172 -- 178	-24.6997 kcal/mol	5.14719 kcal/mol	11.5853 kcal/mol	178 224@LB@ \| \|@LB@5'-GAU...AAUAA U UAGAA ACA ACAAU...CCC-3'@LB@ AGGCAUGAA UUAC ACGGUCGA AGAU@LB@ \|\|:\|\|\|\|\|\| :\|\|\| \|\|\|\|:\|:\| \|\|\|\|@LB@ UCUGUACUU GAUG UGCCGGUU UCUA@LB@3'-GUU...CCGUA AC CUUAC...GGA-5'@LB@ \| \|@LB@ 210 171@LB@@LB@@LB@Energy -15.59 kcal/mol@LB@Hybridization Energy -24.6997 kcal/mol@LB@Unfolding Energy - mRNA 5.14719 kcal/mol@LB@Unfolding Energy - sRNA 11.5853 kcal/mol@LB@@LB@Position - mRNA 179 -- 223@LB@Position - sRNA 172 -- 209@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 172 -- 178@LB@
96	0.02498	0.6733	lmo1278	clpQ	-17.33	0.035430	185 -- 216	173 -- 203	ATP-dependent protease peptidase subunit	_____________184_____217\n_____________\|_______\|\n5'-AAA...UCAAC_______AAAAG...UGA-3'\n______________AUGACGG\n______________\|\|:\|\|\|\|\n______________UAUUGCC\n3'-GUU...AUACG_______CUACU...GGA-5'\n_____________\|_______\|\n_____________204_____172\n	238 -- 244	203 -- 209	-8.20287 kcal/mol	1.40847 kcal/mol	0.374301 kcal/mol	184 217@LB@ \| \|@LB@5'-AAA...UCAAC AAAAG...UGA-3'@LB@ AUGACGG@LB@ \|\|:\|\|\|\|@LB@ UAUUGCC@LB@3'-GUU...AUACG CUACU...GGA-5'@LB@ \| \|@LB@ 204 172@LB@@LB@@LB@Energy -17.33 kcal/mol@LB@Hybridization Energy -8.20287 kcal/mol@LB@Unfolding Energy - mRNA 1.40847 kcal/mol@LB@Unfolding Energy - sRNA 0.374301 kcal/mol@LB@@LB@Position - mRNA 185 -- 216@LB@Position - sRNA 173 -- 203@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 203 -- 209@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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