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
185	0.05367	0.7607	lmo1631	trpD	-14.92	0.100424	142 -- 163	148 -- 170	anthranilate phosphoribosyltransferase	_____________141__________________164\n_____________\|____________________\|\n5'-UUC...UACGA____CG______________GAAAA...AAA-3'\n______________AUGA__GAAAACAAAUGAUG\n______________\|\|\|\|__\|\|\|\|\|\|\|\|\|\|:\|\|\|\n______________UACU__CUUUUGUUUAUUAC\n3'-GUU...UACUC____UA______________UAAAA...GGA-5'\n_____________\|____________________\|\n_____________171__________________147\n	153 -- 159	152 -- 158	-19.3831 kcal/mol	2.89443 kcal/mol	5.80116 kcal/mol	141 164@LB@ \| \|@LB@5'-UUC...UACGA CG GAAAA...AAA-3'@LB@ AUGA GAAAACAAAUGAUG@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|\|:\|\|\|@LB@ UACU CUUUUGUUUAUUAC@LB@3'-GUU...UACUC UA UAAAA...GGA-5'@LB@ \| \|@LB@ 171 147@LB@@LB@@LB@Energy -14.92 kcal/mol@LB@Hybridization Energy -19.3831 kcal/mol@LB@Unfolding Energy - mRNA 2.89443 kcal/mol@LB@Unfolding Energy - sRNA 5.80116 kcal/mol@LB@@LB@Position - mRNA 142 -- 163@LB@Position - sRNA 148 -- 170@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 152 -- 158@LB@
165	0.04532	0.7392	lmo2091	argH	-16.36	0.054421	189 -- 262	141 -- 199	argininosuccinate lyase	_____________188_________________263\n_____________\|___________________\|\n5'-UCA...GGUCA_______G__GAG______AAAUC...AAG-3'\n______________UGCCAUU_UA___GGAAGA\n______________\|\|\|\|\|\|\|_\|\|___\|\|\|\|\|\|\n______________ACGGUAA_AU___CCUUCU\n3'-GUU...GAUCA_______G__AA_______ACCUA...GGA-5'\n_____________\|___________________\|\n_____________200_________________140\n	20 -- 26	110 -- 116	-20.7676 kcal/mol	3.64063 kcal/mol	5.20705 kcal/mol	188 263@LB@ \| \|@LB@5'-UCA...GGUCA G GAG AAAUC...AAG-3'@LB@ UGCCAUU UA GGAAGA@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\|\|\|@LB@ ACGGUAA AU CCUUCU@LB@3'-GUU...GAUCA G AA ACCUA...GGA-5'@LB@ \| \|@LB@ 200 140@LB@@LB@@LB@Energy -16.36 kcal/mol@LB@Hybridization Energy -20.7676 kcal/mol@LB@Unfolding Energy - mRNA 3.64063 kcal/mol@LB@Unfolding Energy - sRNA 5.20705 kcal/mol@LB@@LB@Position - mRNA 189 -- 262@LB@Position - sRNA 141 -- 199@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 110 -- 116@LB@
96	0.02498	0.6733	lmo1278	clpQ	-17.33	0.035430	185 -- 216	173 -- 203	ATP-dependent protease peptidase subunit	_____________184_____217\n_____________\|_______\|\n5'-AAA...UCAAC_______AAAAG...UGA-3'\n______________AUGACGG\n______________\|\|:\|\|\|\|\n______________UAUUGCC\n3'-GUU...AUACG_______CUACU...GGA-5'\n_____________\|_______\|\n_____________204_____172\n	238 -- 244	203 -- 209	-8.20287 kcal/mol	1.40847 kcal/mol	0.374301 kcal/mol	184 217@LB@ \| \|@LB@5'-AAA...UCAAC AAAAG...UGA-3'@LB@ AUGACGG@LB@ \|\|:\|\|\|\|@LB@ UAUUGCC@LB@3'-GUU...AUACG CUACU...GGA-5'@LB@ \| \|@LB@ 204 172@LB@@LB@@LB@Energy -17.33 kcal/mol@LB@Hybridization Energy -8.20287 kcal/mol@LB@Unfolding Energy - mRNA 1.40847 kcal/mol@LB@Unfolding Energy - sRNA 0.374301 kcal/mol@LB@@LB@Position - mRNA 185 -- 216@LB@Position - sRNA 173 -- 203@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 203 -- 209@LB@
188	0.05492	0.7607	lmo1246	N/A	-15.64	0.074442	171 -- 206	183 -- 211	ATP-dependent RNA helicase	_____________170_______________207\n_____________\|_________________\|\n5'-GCC...AUGAU______A__________UGACA...CCU-3'\n______________AUGAGG__AAUGAGGAC\n______________\|\|\|\|\|:__\|\|\|\|\|::\|\|\n______________UACUCU__UUACUUUUG\n3'-GUU...CCGGU______AC_________UUUAU...GGA-5'\n_____________\|_________________\|\n_____________212_______________182\n	190 -- 196	156 -- 162	-13.5081 kcal/mol	2.39769 kcal/mol	0.922045 kcal/mol	170 207@LB@ \| \|@LB@5'-GCC...AUGAU A UGACA...CCU-3'@LB@ AUGAGG AAUGAGGAC@LB@ \|\|\|\|\|: \|\|\|\|\|::\|\|@LB@ UACUCU UUACUUUUG@LB@3'-GUU...CCGGU AC UUUAU...GGA-5'@LB@ \| \|@LB@ 212 182@LB@@LB@@LB@Energy -15.64 kcal/mol@LB@Hybridization Energy -13.5081 kcal/mol@LB@Unfolding Energy - mRNA 2.39769 kcal/mol@LB@Unfolding Energy - sRNA 0.922045 kcal/mol@LB@@LB@Position - mRNA 171 -- 206@LB@Position - sRNA 183 -- 211@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 156 -- 162@LB@
121	0.03234	0.6968	lmo0198	glmU	-15.85	0.067914	228 -- 259	153 -- 184	bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase	_____________227______________________________260\n_____________\|________________________________\|\n5'-UAC...UGCUU_____________GGCACAC________U___AACUU...UGG-3'\n______________GCUGC_UGGCCAA_______GGAUGAAA_CAA\n______________:\|\|:\|_:\|\|\|\|\|\|_______\|:\|\|\|\|\|\|_\|\|\|\n______________UGAUG_GCCGGUU_______CUUACUUU_GUU\n3'-GUU...GUACU_____U_______ACUCUA_________U___UAUUA...GGA-5'\n_____________\|________________________________\|\n_____________185______________________________152\n	248 -- 254	158 -- 164	-25.2592 kcal/mol	7.21839 kcal/mol	9.59579 kcal/mol	227 260@LB@ \| \|@LB@5'-UAC...UGCUU GGCACAC U AACUU...UGG-3'@LB@ GCUGC UGGCCAA GGAUGAAA CAA@LB@ :\|\|:\| :\|\|\|\|\|\| \|:\|\|\|\|\|\| \|\|\|@LB@ UGAUG GCCGGUU CUUACUUU GUU@LB@3'-GUU...GUACU U ACUCUA U UAUUA...GGA-5'@LB@ \| \|@LB@ 185 152@LB@@LB@@LB@Energy -15.85 kcal/mol@LB@Hybridization Energy -25.2592 kcal/mol@LB@Unfolding Energy - mRNA 7.21839 kcal/mol@LB@Unfolding Energy - sRNA 9.59579 kcal/mol@LB@@LB@Position - mRNA 228 -- 259@LB@Position - sRNA 153 -- 184@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 158 -- 164@LB@
5	0.001245	0.4469	lmo1835	carB	-22.95	0.002153	176 -- 228	154 -- 207	carbamoyl-phosphate synthetase	_____________175____________________________________________________________229\n_____________\|______________________________________________________________\|\n5'-AAA...UGGAA___AUG_______AA_______________________C____AC_C__C__UAUA______AUUCU...CUU-3'\n______________AUG___AAUGGGA__GAGG___AGG_GUGAACUACAUG_CUAA__G_GA_GA____AAAACA\n______________\|\|\|___\|\|:\|\|\|\|__\|\|\|\|___\|\|:_:\|\|\|\|\|\|\|\|\|:\|_\|:\|\|__\|_\|\|_\|\|____\|\|\|\|\|\|\n______________UAC___UUGCCCU__CUCC___UCU_UACUUGAUGUGC_GGUU__C_CU_CU____UUUUGU\n3'-GUU...GCGGA___GUA_______A_____GUA___G____________C____A__U__A__UAC_______UUAUU...GGA-5'\n_____________\|______________________________________________________________\|\n_____________208____________________________________________________________153\n	194 -- 200	180 -- 186	-39.6119 kcal/mol	8.25276 kcal/mol	19.5968 kcal/mol	175 229@LB@ \| \|@LB@5'-AAA...UGGAA AUG AA C AC C C UAUA AUUCU...CUU-3'@LB@ AUG AAUGGGA GAGG AGG GUGAACUACAUG CUAA G GA GA AAAACA@LB@ \|\|\| \|\|:\|\|\|\| \|\|\|\| \|\|: :\|\|\|\|\|\|\|\|\|:\| \|:\|\| \| \|\| \|\| \|\|\|\|\|\|@LB@ UAC UUGCCCU CUCC UCU UACUUGAUGUGC GGUU C CU CU UUUUGU@LB@3'-GUU...GCGGA GUA A GUA G C A U A UAC UUAUU...GGA-5'@LB@ \| \|@LB@ 208 153@LB@@LB@@LB@Energy -22.95 kcal/mol@LB@Hybridization Energy -39.6119 kcal/mol@LB@Unfolding Energy - mRNA 8.25276 kcal/mol@LB@Unfolding Energy - sRNA 19.5968 kcal/mol@LB@@LB@Position - mRNA 176 -- 228@LB@Position - sRNA 154 -- 207@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 180 -- 186@LB@
62	0.01477	0.6412	lmo1163	N/A	-15.96	0.064740	175 -- 219	154 -- 212	carbon dioxide concentrating mechanism protein	_____________174_________________________________________________________220\n_____________\|___________________________________________________________\|\n5'-UAG...AAUAU____GU______A______GU_____UAUGUU______A____________________CAGGA...AUG-3'\n______________UGCA__GCGGGA__AGGCA__GACGU______UAUGGC______________AAAAUAA\n______________\|\|\|\|__:\|\|\|\|\|__\|\|\|\|\|__\|\|\|:\|______:\|:\|\|\|______________\|\|\|\|:\|\|\n______________ACGU__UGCCCU__UCCGU__CUGUA______GUGCCG______________UUUUGUU\n3'-GUU...CGGAU____AU______AC_____AU_____CUUGAU______GUUACUCUACUUAC_______UAUUA...GGA-5'\n_____________\|___________________________________________________________\|\n_____________213_________________________________________________________153\n	213 -- 219	154 -- 160	-36.6169 kcal/mol	12.1656 kcal/mol	19.5998 kcal/mol	174 220@LB@ \| \|@LB@5'-UAG...AAUAU GU A GU UAUGUU A CAGGA...AUG-3'@LB@ UGCA GCGGGA AGGCA GACGU UAUGGC AAAAUAA@LB@ \|\|\|\| :\|\|\|\|\| \|\|\|\|\| \|\|\|:\| :\|:\|\|\| \|\|\|\|:\|\|@LB@ ACGU UGCCCU UCCGU CUGUA GUGCCG UUUUGUU@LB@3'-GUU...CGGAU AU AC AU CUUGAU GUUACUCUACUUAC UAUUA...GGA-5'@LB@ \| \|@LB@ 213 153@LB@@LB@@LB@Energy -15.96 kcal/mol@LB@Hybridization Energy -36.6169 kcal/mol@LB@Unfolding Energy - mRNA 12.1656 kcal/mol@LB@Unfolding Energy - sRNA 19.5998 kcal/mol@LB@@LB@Position - mRNA 175 -- 219@LB@Position - sRNA 154 -- 212@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 154 -- 160@LB@
126	0.03359	0.6968	lmo1599	ccpA	-16.59	0.049230	178 -- 221	146 -- 188	catabolite control protein A	_____________177______________222\n_____________\|________________\|\n5'-UUU...GAAUA__________U_____AUUUA...CAA-3'\n______________GAGAUGAAUG__AACA\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\|\|\n______________CUCUACUUAC__UUGU\n3'-GUU...GGUUA__________UU____UUAUU...GGA-5'\n_____________\|________________\|\n_____________189______________145\n	201 -- 207	161 -- 167	-17.207 kcal/mol	2.33031 kcal/mol	0.929544 kcal/mol	177 222@LB@ \| \|@LB@5'-UUU...GAAUA U AUUUA...CAA-3'@LB@ GAGAUGAAUG AACA@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ CUCUACUUAC UUGU@LB@3'-GUU...GGUUA UU UUAUU...GGA-5'@LB@ \| \|@LB@ 189 145@LB@@LB@@LB@Energy -16.59 kcal/mol@LB@Hybridization Energy -17.207 kcal/mol@LB@Unfolding Energy - mRNA 2.33031 kcal/mol@LB@Unfolding Energy - sRNA 0.929544 kcal/mol@LB@@LB@Position - mRNA 178 -- 221@LB@Position - sRNA 146 -- 188@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 161 -- 167@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@
84	0.02276	0.6733	lmo2467	N/A	-18.10	0.024762	166 -- 213	154 -- 198	chitin-binding protein	_____________165__________________________________________________214\n_____________\|____________________________________________________\|\n5'-UCA...CAAAA_____________________UGAAA__AA____CAUC______________CGAAG...AAC-3'\n______________AGGUAUA___AUGAACUAUAC_____GG__GGUG____AUGAA_GAAAAUGA\n______________\|\|\|:\|\|\|___\|\|\|\|\|\|\|\|:\|\|_____\|\|__::\|\|____\|\|\|\|\|_\|\|\|\|\|::\|\n______________UCCGUAU___UACUUGAUGUG_____CC__UUAC____UACUU_CUUUUGUU\n3'-GUU...CCUAC_______CUG__________________GG____UC_______A________UAUUA...GGA-5'\n_____________\|____________________________________________________\|\n_____________199__________________________________________________153\n	206 -- 212	155 -- 161	-31.7912 kcal/mol	6.75491 kcal/mol	13.9801 kcal/mol	165 214@LB@ \| \|@LB@5'-UCA...CAAAA UGAAA AA CAUC CGAAG...AAC-3'@LB@ AGGUAUA AUGAACUAUAC GG GGUG AUGAA GAAAAUGA@LB@ \|\|\|:\|\|\| \|\|\|\|\|\|\|\|:\|\| \|\| ::\|\| \|\|\|\|\| \|\|\|\|\|::\|@LB@ UCCGUAU UACUUGAUGUG CC UUAC UACUU CUUUUGUU@LB@3'-GUU...CCUAC CUG GG UC A UAUUA...GGA-5'@LB@ \| \|@LB@ 199 153@LB@@LB@@LB@Energy -18.10 kcal/mol@LB@Hybridization Energy -31.7912 kcal/mol@LB@Unfolding Energy - mRNA 6.75491 kcal/mol@LB@Unfolding Energy - sRNA 13.9801 kcal/mol@LB@@LB@Position - mRNA 166 -- 213@LB@Position - sRNA 154 -- 198@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 155 -- 161@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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