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
57	0.01283	0.6057	lmo2379	N/A	-18.13	0.024463	194 -- 217	150 -- 173	monovalent cation/H+ antiporter subunit B	_____________193__________________218\n_____________\|____________________\|\n5'-GUA...AACGA_______AU___________AUGAC...AUA-3'\n______________GGUGAGA__GAUGAAAACGA\n______________::\|\|\|\|\|__:\|\|\|\|\|\|\|\|:\|\n______________UUACUCU__UUACUUUUGUU\n3'-GUU...GCCGG_______AC___________UAUUA...GGA-5'\n_____________\|____________________\|\n_____________174__________________149\n	207 -- 213	154 -- 160	-18.1864 kcal/mol	2.62553 kcal/mol	0.959215 kcal/mol	193 218@LB@ \| \|@LB@5'-GUA...AACGA AU AUGAC...AUA-3'@LB@ GGUGAGA GAUGAAAACGA@LB@ ::\|\|\|\|\| :\|\|\|\|\|\|\|\|:\|@LB@ UUACUCU UUACUUUUGUU@LB@3'-GUU...GCCGG AC UAUUA...GGA-5'@LB@ \| \|@LB@ 174 149@LB@@LB@@LB@Energy -18.13 kcal/mol@LB@Hybridization Energy -18.1864 kcal/mol@LB@Unfolding Energy - mRNA 2.62553 kcal/mol@LB@Unfolding Energy - sRNA 0.959215 kcal/mol@LB@@LB@Position - mRNA 194 -- 217@LB@Position - sRNA 150 -- 173@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 154 -- 160@LB@
84	0.02276	0.6733	lmo2467	N/A	-18.10	0.024762	166 -- 213	154 -- 198	chitin-binding protein	_____________165__________________________________________________214\n_____________\|____________________________________________________\|\n5'-UCA...CAAAA_____________________UGAAA__AA____CAUC______________CGAAG...AAC-3'\n______________AGGUAUA___AUGAACUAUAC_____GG__GGUG____AUGAA_GAAAAUGA\n______________\|\|\|:\|\|\|___\|\|\|\|\|\|\|\|:\|\|_____\|\|__::\|\|____\|\|\|\|\|_\|\|\|\|\|::\|\n______________UCCGUAU___UACUUGAUGUG_____CC__UUAC____UACUU_CUUUUGUU\n3'-GUU...CCUAC_______CUG__________________GG____UC_______A________UAUUA...GGA-5'\n_____________\|____________________________________________________\|\n_____________199__________________________________________________153\n	206 -- 212	155 -- 161	-31.7912 kcal/mol	6.75491 kcal/mol	13.9801 kcal/mol	165 214@LB@ \| \|@LB@5'-UCA...CAAAA UGAAA AA CAUC CGAAG...AAC-3'@LB@ AGGUAUA AUGAACUAUAC GG GGUG AUGAA GAAAAUGA@LB@ \|\|\|:\|\|\| \|\|\|\|\|\|\|\|:\|\| \|\| ::\|\| \|\|\|\|\| \|\|\|\|\|::\|@LB@ UCCGUAU UACUUGAUGUG CC UUAC UACUU CUUUUGUU@LB@3'-GUU...CCUAC CUG GG UC A UAUUA...GGA-5'@LB@ \| \|@LB@ 199 153@LB@@LB@@LB@Energy -18.10 kcal/mol@LB@Hybridization Energy -31.7912 kcal/mol@LB@Unfolding Energy - mRNA 6.75491 kcal/mol@LB@Unfolding Energy - sRNA 13.9801 kcal/mol@LB@@LB@Position - mRNA 166 -- 213@LB@Position - sRNA 154 -- 198@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 155 -- 161@LB@
72	0.01905	0.6733	lmo2074	N/A	-18.09	0.024896	131 -- 158	147 -- 174		_____________130___________________159\n_____________\|_____________________\|\n5'-AUG...GAAAU________A____________AUAAG...CGC-3'\n______________UAAUG_GA_GAAUGGGAACAA\n______________:\|\|\|\|_\|\|_\|\|\|\|\|::\|\|\|\|\|\n______________GUUAC_CU_CUUACUUUUGUU\n3'-GUU...UGCCG_____U__A____________UAUUA...GGA-5'\n_____________\|_____________________\|\n_____________175___________________146\n	144 -- 150	154 -- 160	-16.7779 kcal/mol	1.50572 kcal/mol	0.962339 kcal/mol	130 159@LB@ \| \|@LB@5'-AUG...GAAAU A AUAAG...CGC-3'@LB@ UAAUG GA GAAUGGGAACAA@LB@ :\|\|\|\| \|\| \|\|\|\|\|::\|\|\|\|\|@LB@ GUUAC CU CUUACUUUUGUU@LB@3'-GUU...UGCCG U A UAUUA...GGA-5'@LB@ \| \|@LB@ 175 146@LB@@LB@@LB@Energy -18.09 kcal/mol@LB@Hybridization Energy -16.7779 kcal/mol@LB@Unfolding Energy - mRNA 1.50572 kcal/mol@LB@Unfolding Energy - sRNA 0.962339 kcal/mol@LB@@LB@Position - mRNA 131 -- 158@LB@Position - sRNA 147 -- 174@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 154 -- 160@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@
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@
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@
58	0.0137	0.6248	lmo1724	N/A	-17.96	0.026530	144 -- 212	156 -- 211	ABC transporter ATP-binding protein	_____________143__________213\n_____________\|____________\|\n5'-UUA...CAACC____________CUGAU...UCA-3'\n______________AUGAAUGAAAAC\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________UACUUACUUUUG\n3'-GUU...UACUC____________UUUAU...GGA-5'\n_____________\|____________\|\n_____________212__________155\n	206 -- 212	156 -- 162	-13.4321 kcal/mol	1.37849 kcal/mol	0.849227 kcal/mol	143 213@LB@ \| \|@LB@5'-UUA...CAACC CUGAU...UCA-3'@LB@ AUGAAUGAAAAC@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ UACUUACUUUUG@LB@3'-GUU...UACUC UUUAU...GGA-5'@LB@ \| \|@LB@ 212 155@LB@@LB@@LB@Energy -17.96 kcal/mol@LB@Hybridization Energy -13.4321 kcal/mol@LB@Unfolding Energy - mRNA 1.37849 kcal/mol@LB@Unfolding Energy - sRNA 0.849227 kcal/mol@LB@@LB@Position - mRNA 144 -- 212@LB@Position - sRNA 156 -- 211@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 156 -- 162@LB@
76	0.01998	0.6733	lmo1751	N/A	-17.90	0.027246	260 -- 292	176 -- 211	Uncharacterized RNA methyltransferase lmo1751	_____________259______________293\n_____________\|________________\|\n5'-GAA...GGCAA____CUU_________UCCCU...CAU-3'\n______________GGGA____UGGAAGCA\n______________\|:\|\|____\|\|:\|\|:\|\|\n______________CUCU____ACUUUUGU\n3'-GUU...GGUUA____ACUU________UUAUU...GGA-5'\n_____________\|________________\|\n_____________212______________175\n	203 -- 209	155 -- 161	-10.7582 kcal/mol	2.48877 kcal/mol	0.929544 kcal/mol	259 293@LB@ \| \|@LB@5'-GAA...GGCAA CUU UCCCU...CAU-3'@LB@ GGGA UGGAAGCA@LB@ \|:\|\| \|\|:\|\|:\|\|@LB@ CUCU ACUUUUGU@LB@3'-GUU...GGUUA ACUU UUAUU...GGA-5'@LB@ \| \|@LB@ 212 175@LB@@LB@@LB@Energy -17.90 kcal/mol@LB@Hybridization Energy -10.7582 kcal/mol@LB@Unfolding Energy - mRNA 2.48877 kcal/mol@LB@Unfolding Energy - sRNA 0.929544 kcal/mol@LB@@LB@Position - mRNA 260 -- 292@LB@Position - sRNA 176 -- 211@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 155 -- 161@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@
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@

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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