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
158	0.04144	0.7058	lmo1958	fhuB	-14.94	0.099691	191 -- 222	150 -- 181	ferrichrome ABC transporter permease	_____________190_______________________________223\n_____________\|_________________________________\|\n5'-GUU...AAGGA_____U__A________A___C___________AAAUG...UCG-3'\n______________ACAUG_GC_GAUG_GAU_AGU_AAAACAGAUAA\n______________\|\|\|:\|_\|\|_:\|\|\|_\|\|\|_\|:\|_\|\|\|\|\|\|:\|\|\|\|\n______________UGUGC_CG_UUAC_CUA_UUA_UUUUGUUUAUU\n3'-GUU...CUUGA________G____U___C___C___________ACUAA...GGA-5'\n_____________\|_________________________________\|\n_____________182_______________________________149\n	214 -- 220	152 -- 158	-22.8664 kcal/mol	3.81003 kcal/mol	11.9534 kcal/mol	190 223@LB@ \| \|@LB@5'-GUU...AAGGA U A A C AAAUG...UCG-3'@LB@ ACAUG GC GAUG GAU AGU AAAACAGAUAA@LB@ \|\|\|:\| \|\| :\|\|\| \|\|\| \|:\| \|\|\|\|\|\|:\|\|\|\|@LB@ UGUGC CG UUAC CUA UUA UUUUGUUUAUU@LB@3'-GUU...CUUGA G U C C ACUAA...GGA-5'@LB@ \| \|@LB@ 182 149@LB@@LB@@LB@Energy -14.94 kcal/mol@LB@Hybridization Energy -22.8664 kcal/mol@LB@Unfolding Energy - mRNA 3.81003 kcal/mol@LB@Unfolding Energy - sRNA 11.9534 kcal/mol@LB@@LB@Position - mRNA 191 -- 222@LB@Position - sRNA 150 -- 181@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 152 -- 158@LB@
116	0.03152	0.6968	lmo1963	N/A	-17.16	0.038227	218 -- 258	130 -- 166		_____________217___________________________________________259\n_____________\|_____________________________________________\|\n5'-ACA...CACAU_________AAC________A__GUC___U___________U___GGUGA...UCC-3'\n______________UGAAUGGAA___GCGAAUAA_GA___UGG_UGUUUGGGCAG_UGU\n______________\|\|\|\|\|\|:\|\|___:\|:\|\|\|\|\|_\|\|___\|\|\|_\|\|\|:\|:::\|\|\|_\|\|\|\n______________ACUUACUUU___UGUUUAUU_CU___ACC_ACAGAUUUGUC_ACA\n3'-GUU...ACUCU____________________A__AAA_______________U___GACUG...GGA-5'\n_____________\|_____________________________________________\|\n_____________167___________________________________________129\n	220 -- 226	158 -- 164	-34.7415 kcal/mol	9.15867 kcal/mol	13.701 kcal/mol	217 259@LB@ \| \|@LB@5'-ACA...CACAU AAC A GUC U U GGUGA...UCC-3'@LB@ UGAAUGGAA GCGAAUAA GA UGG UGUUUGGGCAG UGU@LB@ \|\|\|\|\|\|:\|\| :\|:\|\|\|\|\| \|\| \|\|\| \|\|\|:\|:::\|\|\| \|\|\|@LB@ ACUUACUUU UGUUUAUU CU ACC ACAGAUUUGUC ACA@LB@3'-GUU...ACUCU A AAA U GACUG...GGA-5'@LB@ \| \|@LB@ 167 129@LB@@LB@@LB@Energy -17.16 kcal/mol@LB@Hybridization Energy -34.7415 kcal/mol@LB@Unfolding Energy - mRNA 9.15867 kcal/mol@LB@Unfolding Energy - sRNA 13.701 kcal/mol@LB@@LB@Position - mRNA 218 -- 258@LB@Position - sRNA 130 -- 166@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 158 -- 164@LB@
41	0.008795	0.5772	lmo1984	ilvB	-19.06	0.015768	187 -- 229	157 -- 201	acetolactate synthase	_____________186____________________________________________230\n_____________\|______________________________________________\|\n5'-AUU...AAAAA_______G___A______UUG_____A_________CA________AGCGA...ACA-3'\n______________AUGAGGU_AUA_GCGUGA___AUACG__CGA__AGA__AAUGAAAA\n______________\|\|\|\|\|\|:_\|\|\|_:\|:\|\|\|___\|:\|\|\|__\|:\|__\|\|\|__\|\|\|\|\|\|\|\|\n______________UACUCCG_UAU_UGUACU___UGUGC__GUU__UCU__UUACUUUU\n3'-GUU...UGCCC___________C______UGA_____CG___AC___AC________GUUUA...GGA-5'\n_____________\|______________________________________________\|\n_____________202____________________________________________156\n	223 -- 229	157 -- 163	-31.6948 kcal/mol	5.6221 kcal/mol	13.9999 kcal/mol	186 230@LB@ \| \|@LB@5'-AUU...AAAAA G A UUG A CA AGCGA...ACA-3'@LB@ AUGAGGU AUA GCGUGA AUACG CGA AGA AAUGAAAA@LB@ \|\|\|\|\|\|: \|\|\| :\|:\|\|\| \|:\|\|\| \|:\| \|\|\| \|\|\|\|\|\|\|\|@LB@ UACUCCG UAU UGUACU UGUGC GUU UCU UUACUUUU@LB@3'-GUU...UGCCC C UGA CG AC AC GUUUA...GGA-5'@LB@ \| \|@LB@ 202 156@LB@@LB@@LB@Energy -19.06 kcal/mol@LB@Hybridization Energy -31.6948 kcal/mol@LB@Unfolding Energy - mRNA 5.6221 kcal/mol@LB@Unfolding Energy - sRNA 13.9999 kcal/mol@LB@@LB@Position - mRNA 187 -- 229@LB@Position - sRNA 157 -- 201@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 157 -- 163@LB@
128	0.03459	0.6968	lmo1993	pdp	-15.44	0.080912	179 -- 212	139 -- 174	pyrimidine-nucleoside phosphorylase	_____________178_________________213\n_____________\|___________________\|\n5'-AUU...GAAAG____A___GA_________GGUGG...UUC-3'\n______________GGUG_AGA__AAUGAGAAU\n______________::\|\|_\|\|\|__\|\|\|\|\|:\|\|:\n______________UUAC_UCU__UUACUUUUG\n3'-GUU...GCCGG________AC_________UUUAU...GGA-5'\n_____________\|___________________\|\n_____________175_________________138\n	202 -- 208	156 -- 162	-13.005 kcal/mol	2.24337 kcal/mol	0.941471 kcal/mol	178 213@LB@ \| \|@LB@5'-AUU...GAAAG A GA GGUGG...UUC-3'@LB@ GGUG AGA AAUGAGAAU@LB@ ::\|\| \|\|\| \|\|\|\|\|:\|\|:@LB@ UUAC UCU UUACUUUUG@LB@3'-GUU...GCCGG AC UUUAU...GGA-5'@LB@ \| \|@LB@ 175 138@LB@@LB@@LB@Energy -15.44 kcal/mol@LB@Hybridization Energy -13.005 kcal/mol@LB@Unfolding Energy - mRNA 2.24337 kcal/mol@LB@Unfolding Energy - sRNA 0.941471 kcal/mol@LB@@LB@Position - mRNA 179 -- 212@LB@Position - sRNA 139 -- 174@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 156 -- 162@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@
196	0.05638	0.7607	lmo2015	N/A	-14.78	0.106466	232 -- 254	163 -- 185	alpha-mannosidase	_____________231____________________________255\n_____________\|______________________________\|\n5'-GUA...ACUAA______________A___AGGCU_______GUUGC...UCC-3'\n______________AGAUA__AACUACG_GGC_____AGAUGAA\n______________\|\|\|:\|__\|\|\|\|\|\|:_\|\|\|_____\|\|\|\|\|\|\|\n______________UCUGU__UUGAUGU_CCG_____UCUACUU\n3'-GUU...CCGUA_____AC_______G___GUUAC_______ACUUU...GGA-5'\n_____________\|______________________________\|\n_____________186____________________________162\n	248 -- 254	163 -- 169	-25.0473 kcal/mol	4.43892 kcal/mol	11.8636 kcal/mol	231 255@LB@ \| \|@LB@5'-GUA...ACUAA A AGGCU GUUGC...UCC-3'@LB@ AGAUA AACUACG GGC AGAUGAA@LB@ \|\|\|:\| \|\|\|\|\|\|: \|\|\| \|\|\|\|\|\|\|@LB@ UCUGU UUGAUGU CCG UCUACUU@LB@3'-GUU...CCGUA AC G GUUAC ACUUU...GGA-5'@LB@ \| \|@LB@ 186 162@LB@@LB@@LB@Energy -14.78 kcal/mol@LB@Hybridization Energy -25.0473 kcal/mol@LB@Unfolding Energy - mRNA 4.43892 kcal/mol@LB@Unfolding Energy - sRNA 11.8636 kcal/mol@LB@@LB@Position - mRNA 232 -- 254@LB@Position - sRNA 163 -- 185@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 163 -- 169@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@
182	0.05242	0.7607	lmo2028	N/A	-14.74	0.108099	169 -- 210	158 -- 185		_____________168_________211\n_____________\|___________\|\n5'-CUU...AUUAU___________UUUAU...AAC-3'\n______________GAUGGAUGGAA\n______________\|\|\|\|:\|\|\|:\|\|\n______________CUACUUACUUU\n3'-GUU...UUACU___________UGUUU...GGA-5'\n_____________\|___________\|\n_____________186_________157\n	204 -- 210	158 -- 164	-12.4441 kcal/mol	2.18802 kcal/mol	0.806249 kcal/mol	168 211@LB@ \| \|@LB@5'-CUU...AUUAU UUUAU...AAC-3'@LB@ GAUGGAUGGAA@LB@ \|\|\|\|:\|\|\|:\|\|@LB@ CUACUUACUUU@LB@3'-GUU...UUACU UGUUU...GGA-5'@LB@ \| \|@LB@ 186 157@LB@@LB@@LB@Energy -14.74 kcal/mol@LB@Hybridization Energy -12.4441 kcal/mol@LB@Unfolding Energy - mRNA 2.18802 kcal/mol@LB@Unfolding Energy - sRNA 0.806249 kcal/mol@LB@@LB@Position - mRNA 169 -- 210@LB@Position - sRNA 158 -- 185@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 158 -- 164@LB@
93	0.02416	0.6733	lmo2042	N/A	-17.13	0.038629	149 -- 196	158 -- 206	cell division protein MraZ	_____________148_____________________________________________197\n_____________\|_______________________________________________\|\n5'-UUU...GCGAA_________________UAAAG_____AUGU____AA__________UCUAA...CCC-3'\n______________GUGGGG___AGAUGUGG______UGGU____AUGA__GUGGGUGAAG\n______________:\|\|:\|\|___\|\|\|::\|\|:______:\|\|:____\|\|\|\|__:\|\|::\|\|\|\|:\n______________UACUCC___UCUGUACU______GCCG____UACU__UACUUACUUU\n3'-GUU...UGCCC______GUA________UGAUGU____GU______C___________UGUUU...GGA-5'\n_____________\|_______________________________________________\|\n_____________207_____________________________________________157\n	190 -- 196	158 -- 164	-27.738 kcal/mol	5.20754 kcal/mol	13.9391 kcal/mol	148 197@LB@ \| \|@LB@5'-UUU...GCGAA UAAAG AUGU AA UCUAA...CCC-3'@LB@ GUGGGG AGAUGUGG UGGU AUGA GUGGGUGAAG@LB@ :\|\|:\|\| \|\|\|::\|\|: :\|\|: \|\|\|\| :\|\|::\|\|\|\|:@LB@ UACUCC UCUGUACU GCCG UACU UACUUACUUU@LB@3'-GUU...UGCCC GUA UGAUGU GU C UGUUU...GGA-5'@LB@ \| \|@LB@ 207 157@LB@@LB@@LB@Energy -17.13 kcal/mol@LB@Hybridization Energy -27.738 kcal/mol@LB@Unfolding Energy - mRNA 5.20754 kcal/mol@LB@Unfolding Energy - sRNA 13.9391 kcal/mol@LB@@LB@Position - mRNA 149 -- 196@LB@Position - sRNA 158 -- 206@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 158 -- 164@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@

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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