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
81	0.02179	0.6733	lmo0087	N/A	-17.84	0.027970	185 -- 226	166 -- 207	lmo0087	_____________184____________________227\n_____________\|______________________\|\n5'-ACU...AUUAU___AU____G____________AACCU...AUC-3'\n______________UGA__UGGA_GAGAGCAAAUGA\n______________\|\|\|__\|\|:\|_\|\|:\|:\|\|\|\|\|:\|\n______________ACU__ACUU_CUUUUGUUUAUU\n3'-GUU...CGGUU___CU____A____________ACUAA...GGA-5'\n_____________\|______________________\|\n_____________208____________________165\n	195 -- 201	153 -- 159	-17.3998 kcal/mol	2.37482 kcal/mol	5.01319 kcal/mol	184 227@LB@ \| \|@LB@5'-ACU...AUUAU AU G AACCU...AUC-3'@LB@ UGA UGGA GAGAGCAAAUGA@LB@ \|\|\| \|\|:\| \|\|:\|:\|\|\|\|\|:\|@LB@ ACU ACUU CUUUUGUUUAUU@LB@3'-GUU...CGGUU CU A ACUAA...GGA-5'@LB@ \| \|@LB@ 208 165@LB@@LB@@LB@Energy -17.84 kcal/mol@LB@Hybridization Energy -17.3998 kcal/mol@LB@Unfolding Energy - mRNA 2.37482 kcal/mol@LB@Unfolding Energy - sRNA 5.01319 kcal/mol@LB@@LB@Position - mRNA 185 -- 226@LB@Position - sRNA 166 -- 207@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 153 -- 159@LB@
51	0.01168	0.599	lmo0105	N/A	-17.88	0.027496	155 -- 205	153 -- 201	chitinase B	_____________154_________________206\n_____________\|___________________\|\n5'-ACC...GUGAA_________AA________AAAAG...AAA-3'\n______________GAGAUGAAU__GAAGAUGA\n______________\|\|\|\|\|\|\|\|\|__\|\|\|:\|::\|\n______________CUCUACUUA__CUUUUGUU\n3'-GUU...GGUUA___________________UAUUA...GGA-5'\n_____________\|___________________\|\n_____________202_________________152\n	197 -- 203	155 -- 161	-15.8376 kcal/mol	2.73398 kcal/mol	0.933796 kcal/mol	154 206@LB@ \| \|@LB@5'-ACC...GUGAA AA AAAAG...AAA-3'@LB@ GAGAUGAAU GAAGAUGA@LB@ \|\|\|\|\|\|\|\|\| \|\|\|:\|::\|@LB@ CUCUACUUA CUUUUGUU@LB@3'-GUU...GGUUA UAUUA...GGA-5'@LB@ \| \|@LB@ 202 152@LB@@LB@@LB@Energy -17.88 kcal/mol@LB@Hybridization Energy -15.8376 kcal/mol@LB@Unfolding Energy - mRNA 2.73398 kcal/mol@LB@Unfolding Energy - sRNA 0.933796 kcal/mol@LB@@LB@Position - mRNA 155 -- 205@LB@Position - sRNA 153 -- 201@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 155 -- 161@LB@
172	0.04804	0.7516	lmo0111	N/A	-17.34	0.035270	180 -- 204	147 -- 170	lmo0111	_____________179______________________205\n_____________\|________________________\|\n5'-AAU...AUAGA____A_A________G________GGACU...CAG-3'\n______________GAGG_G_AAUGAGAA_GGAUGAUG\n______________\|\|\|:_\|_\|\|\|\|\|:\|\|_::\|\|:\|\|\|\n______________CUCU_C_UUACUUUU_UUUAUUAC\n3'-GUU...GGUUA____A__________G________UAAAA...GGA-5'\n_____________\|________________________\|\n_____________171______________________146\n	188 -- 194	157 -- 163	-20.9699 kcal/mol	2.01501 kcal/mol	5.93381 kcal/mol	179 205@LB@ \| \|@LB@5'-AAU...AUAGA A A G GGACU...CAG-3'@LB@ GAGG G AAUGAGAA GGAUGAUG@LB@ \|\|\|: \| \|\|\|\|\|:\|\| ::\|\|:\|\|\|@LB@ CUCU C UUACUUUU UUUAUUAC@LB@3'-GUU...GGUUA A G UAAAA...GGA-5'@LB@ \| \|@LB@ 171 146@LB@@LB@@LB@Energy -17.34 kcal/mol@LB@Hybridization Energy -20.9699 kcal/mol@LB@Unfolding Energy - mRNA 2.01501 kcal/mol@LB@Unfolding Energy - sRNA 5.93381 kcal/mol@LB@@LB@Position - mRNA 180 -- 204@LB@Position - sRNA 147 -- 170@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 157 -- 163@LB@
200	0.05675	0.7607	lmo0115	lmaD	-15.21	0.089253	167 -- 203	151 -- 184		_____________166_________________204\n_____________\|___________________\|\n5'-AUG...GUGGG____________A______UUUUA...UGG-3'\n______________AAUG_GAUGGAU_GAAAAC\n______________\|\|\|\|_\|\|\|\|:\|\|_\|\|\|\|\|\|\n______________UUAC_CUACUUA_CUUUUG\n3'-GUU...GCCGG____U______________UUUAU...GGA-5'\n_____________\|___________________\|\n_____________185_________________150\n	200 -- 206	162 -- 168	-16.3044 kcal/mol	1.75857 kcal/mol	0.941471 kcal/mol	166 204@LB@ \| \|@LB@5'-AUG...GUGGG A UUUUA...UGG-3'@LB@ AAUG GAUGGAU GAAAAC@LB@ \|\|\|\| \|\|\|\|:\|\| \|\|\|\|\|\|@LB@ UUAC CUACUUA CUUUUG@LB@3'-GUU...GCCGG U UUUAU...GGA-5'@LB@ \| \|@LB@ 185 150@LB@@LB@@LB@Energy -15.21 kcal/mol@LB@Hybridization Energy -16.3044 kcal/mol@LB@Unfolding Energy - mRNA 1.75857 kcal/mol@LB@Unfolding Energy - sRNA 0.941471 kcal/mol@LB@@LB@Position - mRNA 167 -- 203@LB@Position - sRNA 151 -- 184@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 162 -- 168@LB@
18	0.003504	0.4469	lmo0129	N/A	-18.06	0.025228	187 -- 226	176 -- 203	N-acetylmuramoyl-L-alanine amidase	_____________186____________227\n_____________\|______________\|\n5'-UUU...GUCAG______________AAAAC...AAC-3'\n______________GAGA_GGAUGAGGA\n______________\|\|\|\|_\|:\|\|\|\|::\|\n______________CUCU_CUUACUUUU\n3'-GUU...GGUUA____A_________GUUUA...GGA-5'\n_____________\|______________\|\n_____________204____________175\n	189 -- 195	157 -- 163	-12.9517 kcal/mol	0.542108 kcal/mol	0.904482 kcal/mol	186 227@LB@ \| \|@LB@5'-UUU...GUCAG AAAAC...AAC-3'@LB@ GAGA GGAUGAGGA@LB@ \|\|\|\| \|:\|\|\|\|::\|@LB@ CUCU CUUACUUUU@LB@3'-GUU...GGUUA A GUUUA...GGA-5'@LB@ \| \|@LB@ 204 175@LB@@LB@@LB@Energy -18.06 kcal/mol@LB@Hybridization Energy -12.9517 kcal/mol@LB@Unfolding Energy - mRNA 0.542108 kcal/mol@LB@Unfolding Energy - sRNA 0.904482 kcal/mol@LB@@LB@Position - mRNA 187 -- 226@LB@Position - sRNA 176 -- 203@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 157 -- 163@LB@
64	0.01603	0.6733	lmo0131	N/A	-19.25	0.014339	193 -- 248	149 -- 204		_____________192____________________________________________________249\n_____________\|______________________________________________________\|\n5'-UGU...AAAAG____G_____G______AUCUCGA______AAAU________C___UAG_____AUAGU...UCG-3'\n______________GAGG_AUA_A_AUGGAU_______GCACGG____AUGGGAUG_GAU___GAGAA\n______________\|\|\|\|_\|\|\|_\|_\|\|\|:\|:_______:\|\|\|\|\|____\|\|\|:\|\|\|\|_:\|\|___\|\|:\|\|\n______________CUCC_UAU_U_UACUUG_______UGUGCC____UACUCUAC_UUA___CUUUU\n3'-GUU...CCCUA____G___C_G______A____________GGU_____________________GUUUA...GGA-5'\n_____________\|______________________________________________________\|\n_____________205____________________________________________________148\n	225 -- 231	165 -- 171	-32.0138 kcal/mol	8.31689 kcal/mol	13.9574 kcal/mol	192 249@LB@ \| \|@LB@5'-UGU...AAAAG G G AUCUCGA AAAU C UAG AUAGU...UCG-3'@LB@ GAGG AUA A AUGGAU GCACGG AUGGGAUG GAU GAGAA@LB@ \|\|\|\| \|\|\| \| \|\|\|:\|: :\|\|\|\|\| \|\|\|:\|\|\|\| :\|\| \|\|:\|\|@LB@ CUCC UAU U UACUUG UGUGCC UACUCUAC UUA CUUUU@LB@3'-GUU...CCCUA G C G A GGU GUUUA...GGA-5'@LB@ \| \|@LB@ 205 148@LB@@LB@@LB@Energy -19.25 kcal/mol@LB@Hybridization Energy -32.0138 kcal/mol@LB@Unfolding Energy - mRNA 8.31689 kcal/mol@LB@Unfolding Energy - sRNA 13.9574 kcal/mol@LB@@LB@Position - mRNA 193 -- 248@LB@Position - sRNA 149 -- 204@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 165 -- 171@LB@
145	0.03765	0.6968	lmo0134	N/A	-12.36	0.267504	193 -- 220	147 -- 170		_____________192__________________________221\n_____________\|____________________________\|\n5'-GGG...AGGAG_____UA_______UAUAA_________AAAUA...UUA-3'\n______________GAGAU__AAUGGAA_____AAAUGGUGA\n______________\|\|\|\|\|__\|\|\|\|:\|\|_____\|\|\|\|::\|\|\|\n______________CUCUA__UUACUUU_____UUUAUUACU\n3'-GUU...GGUUA_____C________UG____________AAAAC...GGA-5'\n_____________\|____________________________\|\n_____________171__________________________146\n	200 -- 206	158 -- 164	-15.5721 kcal/mol	1.73331 kcal/mol	5.93585 kcal/mol	192 221@LB@ \| \|@LB@5'-GGG...AGGAG UA UAUAA AAAUA...UUA-3'@LB@ GAGAU AAUGGAA AAAUGGUGA@LB@ \|\|\|\|\| \|\|\|\|:\|\| \|\|\|\|::\|\|\|@LB@ CUCUA UUACUUU UUUAUUACU@LB@3'-GUU...GGUUA C UG AAAAC...GGA-5'@LB@ \| \|@LB@ 171 146@LB@@LB@@LB@Energy -12.36 kcal/mol@LB@Hybridization Energy -15.5721 kcal/mol@LB@Unfolding Energy - mRNA 1.73331 kcal/mol@LB@Unfolding Energy - sRNA 5.93585 kcal/mol@LB@@LB@Position - mRNA 193 -- 220@LB@Position - sRNA 147 -- 170@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 158 -- 164@LB@
47	0.01063	0.599	lmo0138	N/A	-20.04	0.009767	146 -- 210	158 -- 213	lmo0138	_____________145_________________________________________________________________________211\n_____________\|___________________________________________________________________________\|\n5'-AAA...AAUGC____G_____U_____UAA_____A____UUCAUUAUU________________A___GCA___A__________UAAAA...GCA-3'\n______________GUGC__AUGC_AUAAU___GGGAU_AGGU_________AUAGACA_GAG__AUG_GGC____GA_AUGAGUGAAA\n______________\|:\|\|__\|\|\|\|_\|\|\|\|:___\|\|\|\|\|_\|\|\|:_________\|\|\|\|\|\|\|_\|\|:__\|::_\|\|\|____\|\|_\|\|\|\|:\|\|\|\|\|\n______________CGCG__UACG_UAUUG___CCCUA_UCCG_________UAUCUGU_CUU__UGU_CCG____CU_UACUUACUUU\n3'-GUU...AAGCC____GA__________________C____________________A___GA___G___GUUA__C__________UGUUU...GGA-5'\n_____________\|___________________________________________________________________________\|\n_____________214_________________________________________________________________________157\n	204 -- 210	158 -- 164	-47.7003 kcal/mol	15.2802 kcal/mol	21.9717 kcal/mol	145 211@LB@ \| \|@LB@5'-AAA...AAUGC G U UAA A UUCAUUAUU A GCA A UAAAA...GCA-3'@LB@ GUGC AUGC AUAAU GGGAU AGGU AUAGACA GAG AUG GGC GA AUGAGUGAAA@LB@ \|:\|\| \|\|\|\| \|\|\|\|: \|\|\|\|\| \|\|\|: \|\|\|\|\|\|\| \|\|: \|:: \|\|\| \|\| \|\|\|\|:\|\|\|\|\|@LB@ CGCG UACG UAUUG CCCUA UCCG UAUCUGU CUU UGU CCG CU UACUUACUUU@LB@3'-GUU...AAGCC GA C A GA G GUUA C UGUUU...GGA-5'@LB@ \| \|@LB@ 214 157@LB@@LB@@LB@Energy -20.04 kcal/mol@LB@Hybridization Energy -47.7003 kcal/mol@LB@Unfolding Energy - mRNA 15.2802 kcal/mol@LB@Unfolding Energy - sRNA 21.9717 kcal/mol@LB@@LB@Position - mRNA 146 -- 210@LB@Position - sRNA 158 -- 213@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 158 -- 164@LB@
49	0.01139	0.599	lmo0181	N/A	-18.25	0.023109	147 -- 168	157 -- 179	sugar ABC transporter substrate-binding protein	_____________146________________169\n_____________\|__________________\|\n5'-AAG...AAUGG_______CG_________AAUAA...UUA-3'\n______________CAAUGAG__GAAUGAAAG\n______________\|\|\|\|\|\|\|__\|\|\|\|\|\|\|\|:\n______________GUUACUC__CUUACUUUU\n3'-GUU...UGCCG_______UA_________GUUUA...GGA-5'\n_____________\|__________________\|\n_____________180________________156\n	162 -- 168	157 -- 163	-17.3464 kcal/mol	2.46271 kcal/mol	0.933292 kcal/mol	146 169@LB@ \| \|@LB@5'-AAG...AAUGG CG AAUAA...UUA-3'@LB@ CAAUGAG GAAUGAAAG@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|\|\|:@LB@ GUUACUC CUUACUUUU@LB@3'-GUU...UGCCG UA GUUUA...GGA-5'@LB@ \| \|@LB@ 180 156@LB@@LB@@LB@Energy -18.25 kcal/mol@LB@Hybridization Energy -17.3464 kcal/mol@LB@Unfolding Energy - mRNA 2.46271 kcal/mol@LB@Unfolding Energy - sRNA 0.933292 kcal/mol@LB@@LB@Position - mRNA 147 -- 168@LB@Position - sRNA 157 -- 179@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 157 -- 163@LB@
48	0.01096	0.599	lmo0184	N/A	-18.00	0.026009	159 -- 211	157 -- 203	oligo-1 6-glucosidase	_____________158_____212\n_____________\|_______\|\n5'-ACG...ACAAG_______AUUUA...GAA-3'\n______________GGCGGGA\n______________::\|\|\|\|\|\n______________UUGCCCU\n3'-GUU...ACGUA_______ACUCC...GGA-5'\n_____________\|_______\|\n_____________204_____156\n	185 -- 191	201 -- 207	-10.9952 kcal/mol	1.94403 kcal/mol	0.326294 kcal/mol	158 212@LB@ \| \|@LB@5'-ACG...ACAAG AUUUA...GAA-3'@LB@ GGCGGGA@LB@ ::\|\|\|\|\|@LB@ UUGCCCU@LB@3'-GUU...ACGUA ACUCC...GGA-5'@LB@ \| \|@LB@ 204 156@LB@@LB@@LB@Energy -18.00 kcal/mol@LB@Hybridization Energy -10.9952 kcal/mol@LB@Unfolding Energy - mRNA 1.94403 kcal/mol@LB@Unfolding Energy - sRNA 0.326294 kcal/mol@LB@@LB@Position - mRNA 159 -- 211@LB@Position - sRNA 157 -- 203@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 201 -- 207@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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