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
131	0.03528	0.6968	lmo0788	N/A	-16.25	0.057193	177 -- 197	197 -- 213	lmo0788	_____________176______198\n_____________\|________\|\n5'-AAA...CGAAA________AAAAU...AUU-3'\n______________GGGAUGAG\n______________\|\|\|\|\|\|\|\|\n______________CCCUACUC\n3'-GUU...UAUUG________CGUAU...GGA-5'\n_____________\|________\|\n_____________214______196\n	191 -- 197	197 -- 203	-13.9782 kcal/mol	1.18818 kcal/mol	0.386531 kcal/mol	176 198@LB@ \| \|@LB@5'-AAA...CGAAA AAAAU...AUU-3'@LB@ GGGAUGAG@LB@ \|\|\|\|\|\|\|\|@LB@ CCCUACUC@LB@3'-GUU...UAUUG CGUAU...GGA-5'@LB@ \| \|@LB@ 214 196@LB@@LB@@LB@Energy -16.25 kcal/mol@LB@Hybridization Energy -13.9782 kcal/mol@LB@Unfolding Energy - mRNA 1.18818 kcal/mol@LB@Unfolding Energy - sRNA 0.386531 kcal/mol@LB@@LB@Position - mRNA 177 -- 197@LB@Position - sRNA 197 -- 213@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 197 -- 203@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@
109	0.02745	0.6733	lmo0843	N/A	-19.30	0.014041	79 -- 127	106 -- 151		_____________78____________________________________________________128\n_____________\|_____________________________________________________\|\n5'-CCG...GUCCA____C_________________________AUAAUUU__U_____________CCCUG...CUG-3'\n______________AGUG_UUUUGGUG_CU_GAC_GAUGUUUGA_______CU__UUGCCAUUUUAU\n______________\|:\|\|_\|\|\|\|\|\|\|\|_\|\|_:\|\|_\|\|\|\|\|:\|\|\|_______\|\|__\|\|\|\|\|\|\|\|:\|\|\|\n______________UUAC_AAAACCAC_GA_UUG_CUACAGACU_______GA__AACGGUAAGAUA\n3'-GUU...GUUUA____U________A__U___U__________________UC____________ACCUU...GGA-5'\n_____________\|_____________________________________________________\|\n_____________152___________________________________________________105\n	118 -- 124	109 -- 115	-38.6588 kcal/mol	9.72702 kcal/mol	18.7291 kcal/mol	78 128@LB@ \| \|@LB@5'-CCG...GUCCA C AUAAUUU U CCCUG...CUG-3'@LB@ AGUG UUUUGGUG CU GAC GAUGUUUGA CU UUGCCAUUUUAU@LB@ \|:\|\| \|\|\|\|\|\|\|\| \|\| :\|\| \|\|\|\|\|:\|\|\| \|\| \|\|\|\|\|\|\|\|:\|\|\|@LB@ UUAC AAAACCAC GA UUG CUACAGACU GA AACGGUAAGAUA@LB@3'-GUU...GUUUA U A U U UC ACCUU...GGA-5'@LB@ \| \|@LB@ 152 105@LB@@LB@@LB@Energy -19.30 kcal/mol@LB@Hybridization Energy -38.6588 kcal/mol@LB@Unfolding Energy - mRNA 9.72702 kcal/mol@LB@Unfolding Energy - sRNA 18.7291 kcal/mol@LB@@LB@Position - mRNA 79 -- 127@LB@Position - sRNA 106 -- 151@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 109 -- 115@LB@
50	0.01167	0.599	lmo0850	N/A	-18.65	0.019190	166 -- 190	141 -- 165		_____________165________________________191\n_____________\|__________________________\|\n5'-UGG...AAAGA____AAAAUAAAAA____________AUUUU...AAU-3'\n______________GAGA__________GAAUGAAAACAA\n______________\|\|\|\|__________\|\|\|\|\|\|\|\|\|\|\|\|\n______________CUCU__________CUUACUUUUGUU\n3'-GUU...GGUUA____A_____________________UAUUA...GGA-5'\n_____________\|__________________________\|\n_____________166________________________140\n	171 -- 177	154 -- 160	-14.3235 kcal/mol	1.0644 kcal/mol	0.933796 kcal/mol	165 191@LB@ \| \|@LB@5'-UGG...AAAGA AAAAUAAAAA AUUUU...AAU-3'@LB@ GAGA GAAUGAAAACAA@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|@LB@ CUCU CUUACUUUUGUU@LB@3'-GUU...GGUUA A UAUUA...GGA-5'@LB@ \| \|@LB@ 166 140@LB@@LB@@LB@Energy -18.65 kcal/mol@LB@Hybridization Energy -14.3235 kcal/mol@LB@Unfolding Energy - mRNA 1.0644 kcal/mol@LB@Unfolding Energy - sRNA 0.933796 kcal/mol@LB@@LB@Position - mRNA 166 -- 190@LB@Position - sRNA 141 -- 165@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 154 -- 160@LB@
4	0.0009641	0.4469	lmo0851	N/A	-23.35	0.001728	188 -- 220	172 -- 201	lmo0851	_____________187_______________________________221\n_____________\|_________________________________\|\n5'-GGU...AUAGA__________U_______AAAAGAA________CCAAC...UAA-3'\n______________GUGAGGCAUA_ACAUGAA_______GCGGUUAA\n______________:\|\|\|\|\|\|\|\|\|_\|\|\|\|\|\|\|_______:\|\|\|::\|\|\n______________UACUCCGUAU_UGUACUU_______UGCCGGUU\n3'-GUU...UGCCC__________C_______GAUG___________ACUCU...GGA-5'\n_____________\|_________________________________\|\n_____________202_______________________________171\n	214 -- 220	172 -- 178	-33.261 kcal/mol	3.18896 kcal/mol	13.3764 kcal/mol	187 221@LB@ \| \|@LB@5'-GGU...AUAGA U AAAAGAA CCAAC...UAA-3'@LB@ GUGAGGCAUA ACAUGAA GCGGUUAA@LB@ :\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\| :\|\|\|::\|\|@LB@ UACUCCGUAU UGUACUU UGCCGGUU@LB@3'-GUU...UGCCC C GAUG ACUCU...GGA-5'@LB@ \| \|@LB@ 202 171@LB@@LB@@LB@Energy -23.35 kcal/mol@LB@Hybridization Energy -33.261 kcal/mol@LB@Unfolding Energy - mRNA 3.18896 kcal/mol@LB@Unfolding Energy - sRNA 13.3764 kcal/mol@LB@@LB@Position - mRNA 188 -- 220@LB@Position - sRNA 172 -- 201@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 172 -- 178@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@
199	0.05673	0.7607	lmo0888	N/A	-13.34	0.187096	200 -- 237	174 -- 211		_____________199___________________238\n_____________\|_____________________\|\n5'-AAG...GGCGG_____A__UAU__________ACGCA...AUA-3'\n______________AGUGA_GU___AAUGGAAGCA\n______________\|:\|\|\|_:\|___\|\|\|\|:\|\|:\|\|\n______________UUACU_UA___UUACUUUUGU\n3'-GUU...GCCGG_____C__C____________UUAUU...GGA-5'\n_____________\|_____________________\|\n_____________212___________________173\n	32 -- 38	155 -- 161	-11.9538 kcal/mol	2.24583 kcal/mol	0.954976 kcal/mol	199 238@LB@ \| \|@LB@5'-AAG...GGCGG A UAU ACGCA...AUA-3'@LB@ AGUGA GU AAUGGAAGCA@LB@ \|:\|\|\| :\| \|\|\|\|:\|\|:\|\|@LB@ UUACU UA UUACUUUUGU@LB@3'-GUU...GCCGG C C UUAUU...GGA-5'@LB@ \| \|@LB@ 212 173@LB@@LB@@LB@Energy -13.34 kcal/mol@LB@Hybridization Energy -11.9538 kcal/mol@LB@Unfolding Energy - mRNA 2.24583 kcal/mol@LB@Unfolding Energy - sRNA 0.954976 kcal/mol@LB@@LB@Position - mRNA 200 -- 237@LB@Position - sRNA 174 -- 211@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 155 -- 161@LB@
122	0.03252	0.6968	lmo0926	N/A	-16.71	0.046694	198 -- 274	155 -- 207	TetR family transcriptional regulator	_____________197______________275\n_____________\|________________\|\n5'-GCU...AACCA_____________G__GCGCC...UCG-3'\n______________AGAUGAGUGAAAA_CA\n______________\|\|\|\|\|\|:\|\|\|\|\|\|_\|\|\n______________UCUACUUACUUUU_GU\n3'-GUU...GUUAC________________UUAUU...GGA-5'\n_____________\|________________\|\n_____________208______________154\n	265 -- 271	157 -- 163	-16.1904 kcal/mol	1.95479 kcal/mol	0.920152 kcal/mol	197 275@LB@ \| \|@LB@5'-GCU...AACCA G GCGCC...UCG-3'@LB@ AGAUGAGUGAAAA CA@LB@ \|\|\|\|\|\|:\|\|\|\|\|\| \|\|@LB@ UCUACUUACUUUU GU@LB@3'-GUU...GUUAC UUAUU...GGA-5'@LB@ \| \|@LB@ 208 154@LB@@LB@@LB@Energy -16.71 kcal/mol@LB@Hybridization Energy -16.1904 kcal/mol@LB@Unfolding Energy - mRNA 1.95479 kcal/mol@LB@Unfolding Energy - sRNA 0.920152 kcal/mol@LB@@LB@Position - mRNA 198 -- 274@LB@Position - sRNA 155 -- 207@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 157 -- 163@LB@
94	0.02439	0.6733	lmo0952	N/A	-17.21	0.037353	188 -- 223	166 -- 199	lmo0952	_____________187__________________________________224\n_____________\|____________________________________\|\n5'-AAC...AAACG________UU__GAU_____A___AA__________AGUAC...UAA-3'\n______________GAGGCAUA__CA___GAUUA_ACG__CUGGUGAGAU\n______________\|\|\|\|\|\|\|\|__\|\|___:\|:\|\|_\|\|\|__\|:::\|\|\|\|\|\|\n______________CUCCGUAU__GU___UUGAU_UGC__GGUUACUCUA\n3'-GUU...CCCUA________CU__AC______G___C___________CUUAC...GGA-5'\n_____________\|____________________________________\|\n_____________200__________________________________165\n	217 -- 223	166 -- 172	-30.0979 kcal/mol	6.14462 kcal/mol	13.4403 kcal/mol	187 224@LB@ \| \|@LB@5'-AAC...AAACG UU GAU A AA AGUAC...UAA-3'@LB@ GAGGCAUA CA GAUUA ACG CUGGUGAGAU@LB@ \|\|\|\|\|\|\|\| \|\| :\|:\|\| \|\|\| \|:::\|\|\|\|\|\|@LB@ CUCCGUAU GU UUGAU UGC GGUUACUCUA@LB@3'-GUU...CCCUA CU AC G C CUUAC...GGA-5'@LB@ \| \|@LB@ 200 165@LB@@LB@@LB@Energy -17.21 kcal/mol@LB@Hybridization Energy -30.0979 kcal/mol@LB@Unfolding Energy - mRNA 6.14462 kcal/mol@LB@Unfolding Energy - sRNA 13.4403 kcal/mol@LB@@LB@Position - mRNA 188 -- 223@LB@Position - sRNA 166 -- 199@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 166 -- 172@LB@
66	0.01668	0.6733	lmo0959	N/A	-18.16	0.024105	185 -- 212	177 -- 206	undacaprenyl-phosphate N-acetylglucosaminyltransferase	_____________184________________213\n_____________\|__________________\|\n5'-GAA...AAGUA_____________A____AUUUG...CAG-3'\n______________UAAUGAGAUGAGU_AAAA\n______________:\|\|\|\|\|\|\|\|\|\|:\|_\|\|\|\|\n______________GUUACUCUACUUA_UUUU\n3'-GUU...UGCCG_____________C____GUUUA...GGA-5'\n_____________\|__________________\|\n_____________207________________176\n	169 -- 175	162 -- 168	-15.497 kcal/mol	1.5517 kcal/mol	0.933292 kcal/mol	184 213@LB@ \| \|@LB@5'-GAA...AAGUA A AUUUG...CAG-3'@LB@ UAAUGAGAUGAGU AAAA@LB@ :\|\|\|\|\|\|\|\|\|\|:\| \|\|\|\|@LB@ GUUACUCUACUUA UUUU@LB@3'-GUU...UGCCG C GUUUA...GGA-5'@LB@ \| \|@LB@ 207 176@LB@@LB@@LB@Energy -18.16 kcal/mol@LB@Hybridization Energy -15.497 kcal/mol@LB@Unfolding Energy - mRNA 1.5517 kcal/mol@LB@Unfolding Energy - sRNA 0.933292 kcal/mol@LB@@LB@Position - mRNA 185 -- 212@LB@Position - sRNA 177 -- 206@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 162 -- 168@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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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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