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@
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@
68	0.01752	0.6733	lmo0547	N/A	-17.81	0.028341	205 -- 246	175 -- 207	DeoR family transcriptional regulator	_____________204_________________247\n_____________\|___________________\|\n5'-AGA...AAUGA_______A___AA____G_UAUGG...CUA-3'\n______________AAUGGGA_GAA__AAGA_A\n______________\|\|\|\|:\|\|_\|\|\|__\|\|:\|_\|\n______________UUACUCU_CUU__UUUU_U\n3'-GUU...GCCGG_______A___AC____G_UUAUU...GGA-5'\n_____________\|___________________\|\n_____________208_________________174\n	205 -- 211	167 -- 173	-10.1256 kcal/mol	0.951731 kcal/mol	0.954976 kcal/mol	204 247@LB@ \| \|@LB@5'-AGA...AAUGA A AA G UAUGG...CUA-3'@LB@ AAUGGGA GAA AAGA A@LB@ \|\|\|\|:\|\| \|\|\| \|\|:\| \|@LB@ UUACUCU CUU UUUU U@LB@3'-GUU...GCCGG A AC G UUAUU...GGA-5'@LB@ \| \|@LB@ 208 174@LB@@LB@@LB@Energy -17.81 kcal/mol@LB@Hybridization Energy -10.1256 kcal/mol@LB@Unfolding Energy - mRNA 0.951731 kcal/mol@LB@Unfolding Energy - sRNA 0.954976 kcal/mol@LB@@LB@Position - mRNA 205 -- 246@LB@Position - sRNA 175 -- 207@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 167 -- 173@LB@
82	0.02188	0.6733	lmo0200	prfA	-17.77	0.028863	191 -- 222	162 -- 204	listeriolysin positive regulatory protein	_____________190______223\n_____________\|________\|\n5'-UCA...AUUGG________ACAUG...AUC-3'\n______________GGGAUGAG\n______________\|\|\|\|\|\|\|\|\n______________CCCUACUC\n3'-GUU...UAUUG________CGUAU...GGA-5'\n_____________\|________\|\n_____________205______161\n	192 -- 198	197 -- 203	-14.1607 kcal/mol	1.90446 kcal/mol	0.386531 kcal/mol	190 223@LB@ \| \|@LB@5'-UCA...AUUGG ACAUG...AUC-3'@LB@ GGGAUGAG@LB@ \|\|\|\|\|\|\|\|@LB@ CCCUACUC@LB@3'-GUU...UAUUG CGUAU...GGA-5'@LB@ \| \|@LB@ 205 161@LB@@LB@@LB@Energy -17.77 kcal/mol@LB@Hybridization Energy -14.1607 kcal/mol@LB@Unfolding Energy - mRNA 1.90446 kcal/mol@LB@Unfolding Energy - sRNA 0.386531 kcal/mol@LB@@LB@Position - mRNA 191 -- 222@LB@Position - sRNA 162 -- 204@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 197 -- 203@LB@
90	0.02372	0.6733	lmo2712	N/A	-17.76	0.029098	218 -- 285	160 -- 210	gluconate kinase	_____________217________286\n_____________\|__________\|\n5'-AGA...AAAAU__________CUGUU...CGA-3'\n______________GCGGGGUGAG\n______________:\|\|\|\|:\|\|\|\|\n______________UGCCCUACUC\n3'-GUU...CGUAU__________CGUAU...GGA-5'\n_____________\|__________\|\n_____________211________159\n	190 -- 196	197 -- 203	-16.6296 kcal/mol	4.31289 kcal/mol	0.38676 kcal/mol	217 286@LB@ \| \|@LB@5'-AGA...AAAAU CUGUU...CGA-3'@LB@ GCGGGGUGAG@LB@ :\|\|\|\|:\|\|\|\|@LB@ UGCCCUACUC@LB@3'-GUU...CGUAU CGUAU...GGA-5'@LB@ \| \|@LB@ 211 159@LB@@LB@@LB@Energy -17.76 kcal/mol@LB@Hybridization Energy -16.6296 kcal/mol@LB@Unfolding Energy - mRNA 4.31289 kcal/mol@LB@Unfolding Energy - sRNA 0.38676 kcal/mol@LB@@LB@Position - mRNA 218 -- 285@LB@Position - sRNA 160 -- 210@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 197 -- 203@LB@
55	0.01256	0.6043	lmo1725	N/A	-17.74	0.029271	269 -- 300	152 -- 185	GntR family tramscriptional regulator	_____________268______________________________301\n_____________\|________________________________\|\n5'-CAG...CAAAU___________G_______A___A________GU-3'\n______________GAUUACA_GGC_AAUG_GA_GGG_GAGGAUAA\n______________:\|:\|\|\|\|_\|\|\|_\|\|\|\|_\|\|_\|::_\|\|::\|:\|\|\n______________UUGAUGU_CCG_UUAC_CU_CUU_CUUUUGUU\n3'-GUU...UGUAC_______G___G____U__A___A________UAUUA...GGA-5'\n_____________\|________________________________\|\n_____________186______________________________151\n	291 -- 297	155 -- 161	-25.158 kcal/mol	5.52494 kcal/mol	9.66022 kcal/mol	268 301@LB@ \| \|@LB@5'-CAG...CAAAU G A A GU-3'@LB@ GAUUACA GGC AAUG GA GGG GAGGAUAA@LB@ :\|:\|\|\|\| \|\|\| \|\|\|\| \|\| \|:: \|\|::\|:\|\|@LB@ UUGAUGU CCG UUAC CU CUU CUUUUGUU@LB@3'-GUU...UGUAC G G U A A UAUUA...GGA-5'@LB@ \| \|@LB@ 186 151@LB@@LB@@LB@Energy -17.74 kcal/mol@LB@Hybridization Energy -25.158 kcal/mol@LB@Unfolding Energy - mRNA 5.52494 kcal/mol@LB@Unfolding Energy - sRNA 9.66022 kcal/mol@LB@@LB@Position - mRNA 269 -- 300@LB@Position - sRNA 152 -- 185@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 155 -- 161@LB@
86	0.02293	0.6733	lmo0853	N/A	-17.72	0.029549	77 -- 124	163 -- 214	SugE protein	_____________76__________________________________________________________125\n_____________\|___________________________________________________________\|\n5'-GAC...CGUUU________CUUCU______AC__________________________AUUUAU______ACGGA...UUU-3'\n______________UUUAUGCA_____UGAUGG__UGA_GUGUGGA________ACACGGC______GAUGAA\n______________::\|\|\|\|\|\|_____\|:\|:\|\|__\|\|\|_\|::\|:\|\|________\|\|\|\|\|\|\|______\|\|\|\|\|\|\n______________GGAUACGU_____AUUGCC__ACU_CGUAUCU________UGUGCCG______CUACUU\n3'-GUU...CCCGC___________________CU___C_______GUACUUGA_______GUUACU______ACUUU...GGA-5'\n_____________\|___________________________________________________________\|\n_____________215_________________________________________________________162\n	106 -- 112	175 -- 181	-38.3816 kcal/mol	10.3843 kcal/mol	19.6349 kcal/mol	76 125@LB@ \| \|@LB@5'-GAC...CGUUU CUUCU AC AUUUAU ACGGA...UUU-3'@LB@ UUUAUGCA UGAUGG UGA GUGUGGA ACACGGC GAUGAA@LB@ ::\|\|\|\|\|\| \|:\|:\|\| \|\|\| \|::\|:\|\| \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GGAUACGU AUUGCC ACU CGUAUCU UGUGCCG CUACUU@LB@3'-GUU...CCCGC CU C GUACUUGA GUUACU ACUUU...GGA-5'@LB@ \| \|@LB@ 215 162@LB@@LB@@LB@Energy -17.72 kcal/mol@LB@Hybridization Energy -38.3816 kcal/mol@LB@Unfolding Energy - mRNA 10.3843 kcal/mol@LB@Unfolding Energy - sRNA 19.6349 kcal/mol@LB@@LB@Position - mRNA 77 -- 124@LB@Position - sRNA 163 -- 214@LB@Position Seed - mRNA 106 -- 112@LB@Position Seed - sRNA 175 -- 181@LB@
37	0.007696	0.5562	lmo0551	N/A	-17.72	0.029617	133 -- 210	151 -- 204	lmo0551	_____________132____________211\n_____________\|______________\|\n5'-AGA...UUAAG________G_____AAUUC...CUU-3'\n______________GAGGUGAG_GAAGA\n______________\|\|\|:\|\|\|:_\|\|\|:\|\n______________CUCUACUU_CUUUU\n3'-GUU...GGUUA________A_____GUUUA...GGA-5'\n_____________\|______________\|\n_____________205____________150\n	135 -- 141	163 -- 169	-13.8898 kcal/mol	2.56868 kcal/mol	0.904482 kcal/mol	132 211@LB@ \| \|@LB@5'-AGA...UUAAG G AAUUC...CUU-3'@LB@ GAGGUGAG GAAGA@LB@ \|\|\|:\|\|\|: \|\|\|:\|@LB@ CUCUACUU CUUUU@LB@3'-GUU...GGUUA A GUUUA...GGA-5'@LB@ \| \|@LB@ 205 150@LB@@LB@@LB@Energy -17.72 kcal/mol@LB@Hybridization Energy -13.8898 kcal/mol@LB@Unfolding Energy - mRNA 2.56868 kcal/mol@LB@Unfolding Energy - sRNA 0.904482 kcal/mol@LB@@LB@Position - mRNA 133 -- 210@LB@Position - sRNA 151 -- 204@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 163 -- 169@LB@
103	0.02634	0.6733	lmo2183	N/A	-17.72	0.029644	120 -- 189	95 -- 172	ferrichrome ABC transporter permease	_____________119_______________190\n_____________\|_________________\|\n5'-AGA...UGUGU____UU___________UUAUU...UCC-3'\n______________AUGA__UGGAUGAAAAU\n______________\|\|\|\|__\|\|:\|\|\|\|\|\|\|:\n______________UACU__ACUUACUUUUG\n3'-GUU...CCGGU____CU___________UUUAU...GGA-5'\n_____________\|_________________\|\n_____________173_______________94\n	130 -- 136	156 -- 162	-14.4355 kcal/mol	3.54286 kcal/mol	0.922045 kcal/mol	119 190@LB@ \| \|@LB@5'-AGA...UGUGU UU UUAUU...UCC-3'@LB@ AUGA UGGAUGAAAAU@LB@ \|\|\|\| \|\|:\|\|\|\|\|\|\|:@LB@ UACU ACUUACUUUUG@LB@3'-GUU...CCGGU CU UUUAU...GGA-5'@LB@ \| \|@LB@ 173 94@LB@@LB@@LB@Energy -17.72 kcal/mol@LB@Hybridization Energy -14.4355 kcal/mol@LB@Unfolding Energy - mRNA 3.54286 kcal/mol@LB@Unfolding Energy - sRNA 0.922045 kcal/mol@LB@@LB@Position - mRNA 120 -- 189@LB@Position - sRNA 95 -- 172@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 156 -- 162@LB@
60	0.01449	0.6412	lmo0835	N/A	-17.67	0.030280	187 -- 229	146 -- 187	peptidoglycan binding protein	_____________186______________________________________________230\n_____________\|________________________________________________\|\n5'-UUU...UAUGA_____UUGGAGGA____________UAAA____U____A_________UAACU...CAG-3'\n______________GAACU________AUGGUCAGUGAG____AAUG_AAAA_AAAUAGUGA\n______________\|\|\|\|\|________\|:\|\|:\|\|:\|\|\|\|____\|\|\|\|_\|\|\|\|_\|\|\|\|\|:\|\|\|\n______________CUUGA________UGCCGGUUACUC____UUAC_UUUU_UUUAUUACU\n3'-GUU...CUGUA_____UG__________________UAC__________G_________AAAAC...GGA-5'\n_____________\|________________________________________________\|\n_____________188______________________________________________145\n	199 -- 205	168 -- 174	-31.6389 kcal/mol	7.07372 kcal/mol	14.4129 kcal/mol	186 230@LB@ \| \|@LB@5'-UUU...UAUGA UUGGAGGA UAAA U A UAACU...CAG-3'@LB@ GAACU AUGGUCAGUGAG AAUG AAAA AAAUAGUGA@LB@ \|\|\|\|\| \|:\|\|:\|\|:\|\|\|\| \|\|\|\| \|\|\|\| \|\|\|\|\|:\|\|\|@LB@ CUUGA UGCCGGUUACUC UUAC UUUU UUUAUUACU@LB@3'-GUU...CUGUA UG UAC G AAAAC...GGA-5'@LB@ \| \|@LB@ 188 145@LB@@LB@@LB@Energy -17.67 kcal/mol@LB@Hybridization Energy -31.6389 kcal/mol@LB@Unfolding Energy - mRNA 7.07372 kcal/mol@LB@Unfolding Energy - sRNA 14.4129 kcal/mol@LB@@LB@Position - mRNA 187 -- 229@LB@Position - sRNA 146 -- 187@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 168 -- 174@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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