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
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@
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@
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@
150	0.03884	0.6968	lmo1709	N/A	-16.64	0.048121	221 -- 241	163 -- 181	methionine aminopeptidase	_____________220__________242\n_____________\|____________\|\n5'-UCA...GAAAU____________AGCAG...CUG-3'\n______________CGAUGAGAUGAA\n______________\|:\|\|\|\|\|\|\|\|\|\|\n______________GUUACUCUACUU\n3'-GUU...UGCCG____________ACUUU...GGA-5'\n_____________\|____________\|\n_____________182__________162\n	235 -- 241	163 -- 169	-15.3561 kcal/mol	3.44721 kcal/mol	0.694462 kcal/mol	220 242@LB@ \| \|@LB@5'-UCA...GAAAU AGCAG...CUG-3'@LB@ CGAUGAGAUGAA@LB@ \|:\|\|\|\|\|\|\|\|\|\|@LB@ GUUACUCUACUU@LB@3'-GUU...UGCCG ACUUU...GGA-5'@LB@ \| \|@LB@ 182 162@LB@@LB@@LB@Energy -16.64 kcal/mol@LB@Hybridization Energy -15.3561 kcal/mol@LB@Unfolding Energy - mRNA 3.44721 kcal/mol@LB@Unfolding Energy - sRNA 0.694462 kcal/mol@LB@@LB@Position - mRNA 221 -- 241@LB@Position - sRNA 163 -- 181@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 163 -- 169@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@
97	0.02539	0.6733	lmo2585	N/A	-13.14	0.201793	84 -- 125	164 -- 211		_____________83______126\n_____________\|_______\|\n5'-ACA...GAUGC_______AAGGG...AAG-3'\n______________GGCGGGA\n______________::\|\|\|\|\|\n______________UUGCCCU\n3'-GUU...ACGUA_______ACUCC...GGA-5'\n_____________\|_______\|\n_____________212_____163\n	178 -- 184	201 -- 207	-10.7547 kcal/mol	3.27081 kcal/mol	0.326294 kcal/mol	83 126@LB@ \| \|@LB@5'-ACA...GAUGC AAGGG...AAG-3'@LB@ GGCGGGA@LB@ ::\|\|\|\|\|@LB@ UUGCCCU@LB@3'-GUU...ACGUA ACUCC...GGA-5'@LB@ \| \|@LB@ 212 163@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -10.7547 kcal/mol@LB@Unfolding Energy - mRNA 3.27081 kcal/mol@LB@Unfolding Energy - sRNA 0.326294 kcal/mol@LB@@LB@Position - mRNA 84 -- 125@LB@Position - sRNA 164 -- 211@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 201 -- 207@LB@
85	0.0229	0.6733	lmo1788	N/A	-18.82	0.017630	177 -- 227	165 -- 211	transcriptional regulator	_____________176______________________________________________________228\n_____________\|________________________________________________________\|\n5'-UCU...AAAUG_______C______G____AA__G_____AAAA__A____CUGCUUAU________UUCAG...GGC-3'\n______________GAGGUGU_AGAUAU_GAAC__UG_ACGGU____GA_AUGG________GUGGGGAU\n______________\|\|\|\|::\|_\|\|\|:\|\|_\|\|\|\|__\|:_\|\|\|\|:____\|\|_\|\|\|:________:\|\|:::\|:\n______________CUCCGUA_UCUGUA_CUUG__AU_UGCCG____CU_UACU________UACUUUUG\n3'-GUU...CCCUA_______________________G_____GUUA__C____________________UUUAU...GGA-5'\n_____________\|________________________________________________________\|\n_____________212______________________________________________________164\n	238 -- 244	156 -- 162	-32.2408 kcal/mol	14.3369 kcal/mol	13.9689 kcal/mol	176 228@LB@ \| \|@LB@5'-UCU...AAAUG C G AA G AAAA A CUGCUUAU UUCAG...GGC-3'@LB@ GAGGUGU AGAUAU GAAC UG ACGGU GA AUGG GUGGGGAU@LB@ \|\|\|\|::\| \|\|\|:\|\| \|\|\|\| \|: \|\|\|\|: \|\| \|\|\|: :\|\|:::\|:@LB@ CUCCGUA UCUGUA CUUG AU UGCCG CU UACU UACUUUUG@LB@3'-GUU...CCCUA G GUUA C UUUAU...GGA-5'@LB@ \| \|@LB@ 212 164@LB@@LB@@LB@Energy -18.82 kcal/mol@LB@Hybridization Energy -32.2408 kcal/mol@LB@Unfolding Energy - mRNA 14.3369 kcal/mol@LB@Unfolding Energy - sRNA 13.9689 kcal/mol@LB@@LB@Position - mRNA 177 -- 227@LB@Position - sRNA 165 -- 211@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 156 -- 162@LB@
27	0.005046	0.5029	lmo2370	N/A	-21.11	0.005698	252 -- 287	166 -- 205	aminotransferase	_____________251_____________288\n_____________\|_______________\|\n5'-CCU...AUAAU_____C_________AGAAG...UGU-3'\n______________UGAGG_GAAUGAAAG\n______________\|\|\|\|:_\|\|\|\|\|\|\|\|:\n______________ACUCU_CUUACUUUU\n3'-GUU...CGGUU_____A_________GUUUA...GGA-5'\n_____________\|_______________\|\n_____________206_____________165\n	176 -- 182	157 -- 163	-15.2487 kcal/mol	2.36926 kcal/mol	0.905109 kcal/mol	251 288@LB@ \| \|@LB@5'-CCU...AUAAU C AGAAG...UGU-3'@LB@ UGAGG GAAUGAAAG@LB@ \|\|\|\|: \|\|\|\|\|\|\|\|:@LB@ ACUCU CUUACUUUU@LB@3'-GUU...CGGUU A GUUUA...GGA-5'@LB@ \| \|@LB@ 206 165@LB@@LB@@LB@Energy -21.11 kcal/mol@LB@Hybridization Energy -15.2487 kcal/mol@LB@Unfolding Energy - mRNA 2.36926 kcal/mol@LB@Unfolding Energy - sRNA 0.905109 kcal/mol@LB@@LB@Position - mRNA 252 -- 287@LB@Position - sRNA 166 -- 205@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 157 -- 163@LB@
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@
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@

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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