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
71	0.01891	0.6733	lmo2349	N/A	-17.22	0.037183	66 -- 119	160 -- 206	amino acid ABC transporter substrate-binding protein	_____________65______________________________________________________________________________________________________________________120\n_____________\|_______________________________________________________________________________________________________________________\|\n5'-ACC...GCACU___A_______CUUCUGCCAGA___________UG_______GA_____A__U__________________UU_______C__UUUU_A_______GA_G___________U_______UUAUG...AAG-3'\n______________GAC_CUUGGAA___________AAACA__UCCA__GUUGCUG__UAUGU_UC__GCGCC________GCGG__AUGAGGU_UA____G_ACAUGAG__A_ACGGC____GA_GUGGGUG\n______________\|\|\|_\|\|:\|:\|\|___________\|\|\|\|\|__\|\|\|\|__\|\|\|\|\|::__:\|\|\|\|_\|\|__\|\|\|\|\|________:\|\|\|__\|\|\|\|\|\|:_\|\|____\|_\|\|\|\|\|\|:__\|_\|\|\|\|\|____\|\|_:\|\|::\|\|\n______________CUG_GAGCUUU___________UUUGU__AGGU__CAACGGU__GUACA_AG__CGCGG________UGCC__UACUCCG_AU____C_UGUACUU__U_UGCCG____CU_UACUUAC\n___3'-GUUUUUUU___C_______A_______________AA____CG_______A_________CC_____AUACGUAU____C________U_______________GA_G_____GUUA__C_______UUUUG...GGA-5'\n_____________\|_______________________________________________________________________________________________________________________\|\n_____________207_____________________________________________________________________________________________________________________159\n	107 -- 113	161 -- 167	-71.8793 kcal/mol	29.0166 kcal/mol	34.5254 kcal/mol	65 120@LB@ \| \|@LB@5'-ACC...GCACU A CUUCUGCCAGA UG GA A U UU C UUUU A GA G U UUAUG...AAG-3'@LB@ GAC CUUGGAA AAACA UCCA GUUGCUG UAUGU UC GCGCC GCGG AUGAGGU UA G ACAUGAG A ACGGC GA GUGGGUG@LB@ \|\|\| \|\|:\|:\|\| \|\|\|\|\| \|\|\|\| \|\|\|\|\|:: :\|\|\|\| \|\| \|\|\|\|\| :\|\|\| \|\|\|\|\|\|: \|\| \| \|\|\|\|\|\|: \| \|\|\|\|\| \|\| :\|\|::\|\|@LB@ CUG GAGCUUU UUUGU AGGU CAACGGU GUACA AG CGCGG UGCC UACUCCG AU C UGUACUU U UGCCG CU UACUUAC@LB@ 3'-GUUUUUUU C A AA CG A CC AUACGUAU C U GA G GUUA C UUUUG...GGA-5'@LB@ \| \|@LB@ 207 159@LB@@LB@@LB@Energy -17.22 kcal/mol@LB@Hybridization Energy -71.8793 kcal/mol@LB@Unfolding Energy - mRNA 29.0166 kcal/mol@LB@Unfolding Energy - sRNA 34.5254 kcal/mol@LB@@LB@Position - mRNA 66 -- 119@LB@Position - sRNA 160 -- 206@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 161 -- 167@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@
73	0.0193	0.6733	lmo0405	N/A	-18.50	0.020574	154 -- 209	155 -- 199	phosphate transporter	_____________153____________210\n_____________\|______________\|\n5'-GUG...UUAUG________U_____UACGA...CGA-3'\n______________AUGACGGG_AUGAG\n______________\|\|:\|\|\|\|\|_\|\|\|\|\|\n______________UAUUGCCC_UACUC\n3'-GUU...AUACG______________CGUAU...GGA-5'\n_____________\|______________\|\n_____________200____________154\n	50 -- 56	202 -- 208	-16.311 kcal/mol	2.72131 kcal/mol	0.386761 kcal/mol	153 210@LB@ \| \|@LB@5'-GUG...UUAUG U UACGA...CGA-3'@LB@ AUGACGGG AUGAG@LB@ \|\|:\|\|\|\|\| \|\|\|\|\|@LB@ UAUUGCCC UACUC@LB@3'-GUU...AUACG CGUAU...GGA-5'@LB@ \| \|@LB@ 200 154@LB@@LB@@LB@Energy -18.50 kcal/mol@LB@Hybridization Energy -16.311 kcal/mol@LB@Unfolding Energy - mRNA 2.72131 kcal/mol@LB@Unfolding Energy - sRNA 0.386761 kcal/mol@LB@@LB@Position - mRNA 154 -- 209@LB@Position - sRNA 155 -- 199@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 202 -- 208@LB@
74	0.01955	0.6733	lmo0190	ipk	-17.49	0.032930	174 -- 210	154 -- 192	4-diphosphocytidyl-2-C-methyl-D-erythritol kinase	_____________173_______________________________________211\n_____________\|_________________________________________\|\n5'-AUA...AAAAG____UU_________GA___________AA___________GCAUU...CAA-3'\n______________AGAU__UGAAC_GCG__GGCCA___AGA__AAUGAAAAUAA\n______________\|\|\|:__\|\|\|\|\|_:\|:__\|\|\|\|\|___\|\|\|__\|\|\|\|\|\|\|\|:\|\|\n______________UCUG__ACUUG_UGU__CCGGU___UCU__UUACUUUUGUU\n3'-GUU...CCGUA____U______A___G______UAC___AC___________UAUUA...GGA-5'\n_____________\|_________________________________________\|\n_____________193_______________________________________153\n	204 -- 210	154 -- 160	-28.6344 kcal/mol	5.15958 kcal/mol	12.1365 kcal/mol	173 211@LB@ \| \|@LB@5'-AUA...AAAAG UU GA AA GCAUU...CAA-3'@LB@ AGAU UGAAC GCG GGCCA AGA AAUGAAAAUAA@LB@ \|\|\|: \|\|\|\|\| :\|: \|\|\|\|\| \|\|\| \|\|\|\|\|\|\|\|:\|\|@LB@ UCUG ACUUG UGU CCGGU UCU UUACUUUUGUU@LB@3'-GUU...CCGUA U A G UAC AC UAUUA...GGA-5'@LB@ \| \|@LB@ 193 153@LB@@LB@@LB@Energy -17.49 kcal/mol@LB@Hybridization Energy -28.6344 kcal/mol@LB@Unfolding Energy - mRNA 5.15958 kcal/mol@LB@Unfolding Energy - sRNA 12.1365 kcal/mol@LB@@LB@Position - mRNA 174 -- 210@LB@Position - sRNA 154 -- 192@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 154 -- 160@LB@
75	0.01961	0.6733	lmo0383	N/A	-20.23	0.008871	224 -- 265	150 -- 186	methylmalonate-semialdehyde dehydrogenase	_____________223________________________________________266\n_____________\|__________________________________________\|\n5'-UUC...UUAAA_______AUUG_____G______UC___A_U___________AUAUG...AAG-3'\n______________GAAUUAU____ACGGC_AAUGGG__GAG_G_AAGACAGAUAA\n______________\|\|\|:\|\|:____\|\|\|\|\|_\|\|\|\|:\|__\|\|:_\|_\|\|:\|\|\|:\|\|\|\|\n______________CUUGAUG____UGCCG_UUACUC__CUU_C_UUUUGUUUAUU\n3'-GUU...CUGUA________________G______UA___A_____________ACUAA...GGA-5'\n_____________\|__________________________________________\|\n_____________187________________________________________149\n	257 -- 263	152 -- 158	-34.2826 kcal/mol	8.25616 kcal/mol	13.66 kcal/mol	223 266@LB@ \| \|@LB@5'-UUC...UUAAA AUUG G UC A U AUAUG...AAG-3'@LB@ GAAUUAU ACGGC AAUGGG GAG G AAGACAGAUAA@LB@ \|\|\|:\|\|: \|\|\|\|\| \|\|\|\|:\| \|\|: \| \|\|:\|\|\|:\|\|\|\|@LB@ CUUGAUG UGCCG UUACUC CUU C UUUUGUUUAUU@LB@3'-GUU...CUGUA G UA A ACUAA...GGA-5'@LB@ \| \|@LB@ 187 149@LB@@LB@@LB@Energy -20.23 kcal/mol@LB@Hybridization Energy -34.2826 kcal/mol@LB@Unfolding Energy - mRNA 8.25616 kcal/mol@LB@Unfolding Energy - sRNA 13.66 kcal/mol@LB@@LB@Position - mRNA 224 -- 265@LB@Position - sRNA 150 -- 186@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 152 -- 158@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@
77	0.02006	0.6733	lmo1400	N/A	-17.16	0.038248	136 -- 215	157 -- 223	N-acetyltransferase	_____________135_____________216\n_____________\|_______________\|\n5'-AAA...GUUUU_______________AUUUU...AAG-3'\n______________UGAG_UGAGUGGAAA\n______________\|\|\|\|_\|\|\|:\|\|:\|\|\|\n______________ACUC_ACUUACUUUU\n3'-GUU...CGGUU____U__________GUUUA...GGA-5'\n_____________\|_______________\|\n_____________224_____________156\n	209 -- 215	157 -- 163	-14.2437 kcal/mol	2.95971 kcal/mol	0.905109 kcal/mol	135 216@LB@ \| \|@LB@5'-AAA...GUUUU AUUUU...AAG-3'@LB@ UGAG UGAGUGGAAA@LB@ \|\|\|\| \|\|\|:\|\|:\|\|\|@LB@ ACUC ACUUACUUUU@LB@3'-GUU...CGGUU U GUUUA...GGA-5'@LB@ \| \|@LB@ 224 156@LB@@LB@@LB@Energy -17.16 kcal/mol@LB@Hybridization Energy -14.2437 kcal/mol@LB@Unfolding Energy - mRNA 2.95971 kcal/mol@LB@Unfolding Energy - sRNA 0.905109 kcal/mol@LB@@LB@Position - mRNA 136 -- 215@LB@Position - sRNA 157 -- 223@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 157 -- 163@LB@
78	0.02097	0.6733	lmo1196	N/A	-18.80	0.017871	157 -- 213	158 -- 203	cobalt-precorrin-6Y C(15)-methyltransferase	_____________156_________________________________________________________214\n_____________\|___________________________________________________________\|\n5'-CCU...AACCA____AA___GCAAAAAAAUAC_________GUAG____G_U__U_______AGA_____UAUUU...AAA-3'\n______________GAGG__GUA____________GAUAUGAAU____UGGU_A_UG_AGAUGAA___UGAAG\n______________\|\|\|\|__:\|\|____________\|\|:\|\|\|\|\|:____:\|\|:_\|_\|\|_\|\|\|\|\|\|\|___\|\|\|\|:\n______________CUCC__UAU____________CUGUACUUG____GCCG_U_AC_UCUACUU___ACUUU\n3'-GUU...CCCUA____G_________________________AUGU____G_U__________________UGUUU...GGA-5'\n_____________\|___________________________________________________________\|\n_____________204_________________________________________________________157\n	199 -- 205	163 -- 169	-30.6214 kcal/mol	5.96601 kcal/mol	13.8965 kcal/mol	156 214@LB@ \| \|@LB@5'-CCU...AACCA AA GCAAAAAAAUAC GUAG G U U AGA UAUUU...AAA-3'@LB@ GAGG GUA GAUAUGAAU UGGU A UG AGAUGAA UGAAG@LB@ \|\|\|\| :\|\| \|\|:\|\|\|\|\|: :\|\|: \| \|\| \|\|\|\|\|\|\| \|\|\|\|:@LB@ CUCC UAU CUGUACUUG GCCG U AC UCUACUU ACUUU@LB@3'-GUU...CCCUA G AUGU G U UGUUU...GGA-5'@LB@ \| \|@LB@ 204 157@LB@@LB@@LB@Energy -18.80 kcal/mol@LB@Hybridization Energy -30.6214 kcal/mol@LB@Unfolding Energy - mRNA 5.96601 kcal/mol@LB@Unfolding Energy - sRNA 13.8965 kcal/mol@LB@@LB@Position - mRNA 157 -- 213@LB@Position - sRNA 158 -- 203@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 163 -- 169@LB@
79	0.02126	0.6733	lmo1172	N/A	-17.83	0.028138	200 -- 242	163 -- 210	two-component response regulator	_____________199_________243\n_____________\|___________\|\n5'-CAC...CAGGA___________AAUUG...UAG-3'\n______________AUGAAUGGAAG\n______________\|\|\|\|\|\|\|:\|\|:\n______________UACUUACUUUU\n3'-GUU...UACUC___________GUUUA...GGA-5'\n_____________\|___________\|\n_____________211_________162\n	214 -- 220	157 -- 163	-10.013 kcal/mol	1.15656 kcal/mol	0.82573 kcal/mol	199 243@LB@ \| \|@LB@5'-CAC...CAGGA AAUUG...UAG-3'@LB@ AUGAAUGGAAG@LB@ \|\|\|\|\|\|\|:\|\|:@LB@ UACUUACUUUU@LB@3'-GUU...UACUC GUUUA...GGA-5'@LB@ \| \|@LB@ 211 162@LB@@LB@@LB@Energy -17.83 kcal/mol@LB@Hybridization Energy -10.013 kcal/mol@LB@Unfolding Energy - mRNA 1.15656 kcal/mol@LB@Unfolding Energy - sRNA 0.82573 kcal/mol@LB@@LB@Position - mRNA 200 -- 242@LB@Position - sRNA 163 -- 210@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 157 -- 163@LB@
80	0.02141	0.6733	lmo1147	N/A	-19.90	0.010431	143 -- 214	146 -- 207	cobalamin biosynthesis protein CopB	_____________142____________________________________________________________________215\n_____________\|______________________________________________________________________\|\n5'-UAU...AUUUG_______AUUUUUA________A____AUC____UGU_______A_______GAAUGGAC__________UGAUG...CAA-3'\n______________AGCGGGA_______GGGGC_UA_ACGU___GGAU___UACGCGG__AAUGAG________AUGAGUGAAA\n______________\|:\|\|\|\|\|_______\|:\|\|\|_\|\|_\|\|:\|___\|:\|:___\|\|\|:\|\|\|__\|\|\|\|\|\|________\|\|\|\|:\|\|\|\|\|\n______________UUGCCCU_______CUCCG_AU_UGUA___CUUG___AUGUGCC__UUACUC________UACUUACUUU\n3'-GUU...ACGUA_______A___________U__C_____________________GG________________________UGUUU...GGA-5'\n_____________\|______________________________________________________________________\|\n_____________208____________________________________________________________________145\n	204 -- 210	158 -- 164	-42.8674 kcal/mol	12.3523 kcal/mol	18.5828 kcal/mol	142 215@LB@ \| \|@LB@5'-UAU...AUUUG AUUUUUA A AUC UGU A GAAUGGAC UGAUG...CAA-3'@LB@ AGCGGGA GGGGC UA ACGU GGAU UACGCGG AAUGAG AUGAGUGAAA@LB@ \|:\|\|\|\|\| \|:\|\|\| \|\| \|\|:\| \|:\|: \|\|\|:\|\|\| \|\|\|\|\|\| \|\|\|\|:\|\|\|\|\|@LB@ UUGCCCU CUCCG AU UGUA CUUG AUGUGCC UUACUC UACUUACUUU@LB@3'-GUU...ACGUA A U C GG UGUUU...GGA-5'@LB@ \| \|@LB@ 208 145@LB@@LB@@LB@Energy -19.90 kcal/mol@LB@Hybridization Energy -42.8674 kcal/mol@LB@Unfolding Energy - mRNA 12.3523 kcal/mol@LB@Unfolding Energy - sRNA 18.5828 kcal/mol@LB@@LB@Position - mRNA 143 -- 214@LB@Position - sRNA 146 -- 207@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 158 -- 164@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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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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