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
124	0.03258	0.6968	lmo1611	N/A	-17.32	0.035574	130 -- 182	121 -- 173	aminopeptidase	_____________129_______________________183\n_____________\|_________________________\|\n5'-CAU...AGAGA_______C___C_____________AUUUG...UUG-3'\n______________AGUGAGG_GAG_GGAAACGGAUAAU\n______________\|:\|\|\|\|:_\|\|:_\|:\|\|\|\|::\|\|\|\|\|\n______________UUACUCU_CUU_CUUUUGUUUAUUA\n3'-GUU...GCCGG_______A___A_____________CUAAA...GGA-5'\n_____________\|_________________________\|\n_____________174_______________________120\n	143 -- 149	154 -- 160	-22.8649 kcal/mol	4.94187 kcal/mol	5.58154 kcal/mol	129 183@LB@ \| \|@LB@5'-CAU...AGAGA C C AUUUG...UUG-3'@LB@ AGUGAGG GAG GGAAACGGAUAAU@LB@ \|:\|\|\|\|: \|\|: \|:\|\|\|\|::\|\|\|\|\|@LB@ UUACUCU CUU CUUUUGUUUAUUA@LB@3'-GUU...GCCGG A A CUAAA...GGA-5'@LB@ \| \|@LB@ 174 120@LB@@LB@@LB@Energy -17.32 kcal/mol@LB@Hybridization Energy -22.8649 kcal/mol@LB@Unfolding Energy - mRNA 4.94187 kcal/mol@LB@Unfolding Energy - sRNA 5.58154 kcal/mol@LB@@LB@Position - mRNA 130 -- 182@LB@Position - sRNA 121 -- 173@LB@Position Seed - mRNA 143 -- 149@LB@Position Seed - sRNA 154 -- 160@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@
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@
170	0.04745	0.7511	lmo2203	N/A	-15.31	0.085499	133 -- 190	99 -- 165	N-acetylmuramoyl-L-alanine amidase	_____________132___________________________________191\n_____________\|_____________________________________\|\n5'-AUA...AGGUU_________________A________AA_________ACUAA...CAG-3'\n______________AACAGA_____GAC_AG__GCCAUUU__AUUGGGGGA\n______________\|\|\|\|\|\|_____\|\|\|_\|\|__\|\|\|\|\|\|:__\|\|\|\|\|::\|\|\n______________UUGUCU_____CUG_UC__CGGUAAG__UAACCUUCU\n3'-GUU...CAGAU______ACAGA___A__AA_______A__________ACCUA...GGA-5'\n_____________\|_____________________________________\|\n_____________166___________________________________98\n	184 -- 190	99 -- 105	-25.8209 kcal/mol	4.57897 kcal/mol	9.42764 kcal/mol	132 191@LB@ \| \|@LB@5'-AUA...AGGUU A AA ACUAA...CAG-3'@LB@ AACAGA GAC AG GCCAUUU AUUGGGGGA@LB@ \|\|\|\|\|\| \|\|\| \|\| \|\|\|\|\|\|: \|\|\|\|\|::\|\|@LB@ UUGUCU CUG UC CGGUAAG UAACCUUCU@LB@3'-GUU...CAGAU ACAGA A AA A ACCUA...GGA-5'@LB@ \| \|@LB@ 166 98@LB@@LB@@LB@Energy -15.31 kcal/mol@LB@Hybridization Energy -25.8209 kcal/mol@LB@Unfolding Energy - mRNA 4.57897 kcal/mol@LB@Unfolding Energy - sRNA 9.42764 kcal/mol@LB@@LB@Position - mRNA 133 -- 190@LB@Position - sRNA 99 -- 165@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 99 -- 105@LB@
77	0.02006	0.6733	lmo1400	N/A	-17.16	0.038248	136 -- 215	157 -- 223	N-acetyltransferase	_____________135_____________216\n_____________\|_______________\|\n5'-AAA...GUUUU_______________AUUUU...AAG-3'\n______________UGAG_UGAGUGGAAA\n______________\|\|\|\|_\|\|\|:\|\|:\|\|\|\n______________ACUC_ACUUACUUUU\n3'-GUU...CGGUU____U__________GUUUA...GGA-5'\n_____________\|_______________\|\n_____________224_____________156\n	209 -- 215	157 -- 163	-14.2437 kcal/mol	2.95971 kcal/mol	0.905109 kcal/mol	135 216@LB@ \| \|@LB@5'-AAA...GUUUU AUUUU...AAG-3'@LB@ UGAG UGAGUGGAAA@LB@ \|\|\|\| \|\|\|:\|\|:\|\|\|@LB@ ACUC ACUUACUUUU@LB@3'-GUU...CGGUU U GUUUA...GGA-5'@LB@ \| \|@LB@ 224 156@LB@@LB@@LB@Energy -17.16 kcal/mol@LB@Hybridization Energy -14.2437 kcal/mol@LB@Unfolding Energy - mRNA 2.95971 kcal/mol@LB@Unfolding Energy - sRNA 0.905109 kcal/mol@LB@@LB@Position - mRNA 136 -- 215@LB@Position - sRNA 157 -- 223@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 157 -- 163@LB@
14	0.00304	0.4469	lmo1187	N/A	-19.26	0.014311	139 -- 172	153 -- 183	ethanolamine utilization protein EutQ	_____________138_______________________________173\n_____________\|_________________________________\|\n5'-UAA...GGUAU____________CC__AU______GA_______AGCAA...UUU-3'\n______________CUAUAUGGCUAA__GA__GAUGAA__AAAAUAA\n______________\|\|\|:\|:\|\|\|:\|\|__\|\|__\|\|\|\|\|\|__\|\|\|\|:\|\|\n______________GAUGUGCCGGUU__CU__CUACUU__UUUUGUU\n3'-GUU...UACUU____________A___________AC_______UAUUA...GGA-5'\n_____________\|_________________________________\|\n_____________184_______________________________152\n	165 -- 171	154 -- 160	-25.2263 kcal/mol	3.98561 kcal/mol	9.539 kcal/mol	138 173@LB@ \| \|@LB@5'-UAA...GGUAU CC AU GA AGCAA...UUU-3'@LB@ CUAUAUGGCUAA GA GAUGAA AAAAUAA@LB@ \|\|\|:\|:\|\|\|:\|\| \|\| \|\|\|\|\|\| \|\|\|\|:\|\|@LB@ GAUGUGCCGGUU CU CUACUU UUUUGUU@LB@3'-GUU...UACUU A AC UAUUA...GGA-5'@LB@ \| \|@LB@ 184 152@LB@@LB@@LB@Energy -19.26 kcal/mol@LB@Hybridization Energy -25.2263 kcal/mol@LB@Unfolding Energy - mRNA 3.98561 kcal/mol@LB@Unfolding Energy - sRNA 9.539 kcal/mol@LB@@LB@Position - mRNA 139 -- 172@LB@Position - sRNA 153 -- 183@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 154 -- 160@LB@
115	0.03087	0.6968	lmo0059	N/A	-17.38	0.034592	142 -- 189	155 -- 211		_____________141_______________________________________________190\n_____________\|_________________________________________________\|\n5'-AAG...UUAGC____G_____UU___U________________UUUU_____A_______GGGAG...CAU-3'\n______________AGGC__GGAU__AUG_GGCUGCGCG__CAAUG____UGAAU_GAAAGCG\n______________\|\|\|\|__:\|\|:__\|\|\|_::\|\|:\|:\|\|__\|\|\|\|\|____\|\|\|\|\|_\|\|\|\|:\|:\n______________UCCG__UCUG__UAC_UUGAUGUGC__GUUAC____ACUUA_CUUUUGU\n3'-GUU...CCUAC____UA___________________CG_____UCU______________UUAUU...GGA-5'\n_____________\|_________________________________________________\|\n_____________212_______________________________________________154\n	183 -- 189	155 -- 161	-35.3318 kcal/mol	12.9952 kcal/mol	13.976 kcal/mol	141 190@LB@ \| \|@LB@5'-AAG...UUAGC G UU U UUUU A GGGAG...CAU-3'@LB@ AGGC GGAU AUG GGCUGCGCG CAAUG UGAAU GAAAGCG@LB@ \|\|\|\| :\|\|: \|\|\| ::\|\|:\|:\|\| \|\|\|\|\| \|\|\|\|\| \|\|\|\|:\|:@LB@ UCCG UCUG UAC UUGAUGUGC GUUAC ACUUA CUUUUGU@LB@3'-GUU...CCUAC UA CG UCU UUAUU...GGA-5'@LB@ \| \|@LB@ 212 154@LB@@LB@@LB@Energy -17.38 kcal/mol@LB@Hybridization Energy -35.3318 kcal/mol@LB@Unfolding Energy - mRNA 12.9952 kcal/mol@LB@Unfolding Energy - sRNA 13.976 kcal/mol@LB@@LB@Position - mRNA 142 -- 189@LB@Position - sRNA 155 -- 211@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 155 -- 161@LB@
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@
52	0.01176	0.599	lmo0302	N/A	-19.32	0.013869	143 -- 287	107 -- 220	lmo0302	_____________142________________288\n_____________\|__________________\|\n5'-CGA...CAUAG_________A__U_____AAAAA...AUA-3'\n______________GAGAUGAAU_GA_GAUGA\n______________\|\|\|\|\|\|\|\|\|_\|\|_:\|::\|\n______________CUCUACUUA_CU_UUGUU\n3'-GUU...GGUUA____________U_____UAUUA...GGA-5'\n_____________\|__________________\|\n_____________221________________106\n	189 -- 195	162 -- 168	-14.2485 kcal/mol	1.08239 kcal/mol	0.933796 kcal/mol	142 288@LB@ \| \|@LB@5'-CGA...CAUAG A U AAAAA...AUA-3'@LB@ GAGAUGAAU GA GAUGA@LB@ \|\|\|\|\|\|\|\|\| \|\| :\|::\|@LB@ CUCUACUUA CU UUGUU@LB@3'-GUU...GGUUA U UAUUA...GGA-5'@LB@ \| \|@LB@ 221 106@LB@@LB@@LB@Energy -19.32 kcal/mol@LB@Hybridization Energy -14.2485 kcal/mol@LB@Unfolding Energy - mRNA 1.08239 kcal/mol@LB@Unfolding Energy - sRNA 0.933796 kcal/mol@LB@@LB@Position - mRNA 143 -- 287@LB@Position - sRNA 107 -- 220@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 162 -- 168@LB@
80	0.02141	0.6733	lmo1147	N/A	-19.90	0.010431	143 -- 214	146 -- 207	cobalamin biosynthesis protein CopB	_____________142____________________________________________________________________215\n_____________\|______________________________________________________________________\|\n5'-UAU...AUUUG_______AUUUUUA________A____AUC____UGU_______A_______GAAUGGAC__________UGAUG...CAA-3'\n______________AGCGGGA_______GGGGC_UA_ACGU___GGAU___UACGCGG__AAUGAG________AUGAGUGAAA\n______________\|:\|\|\|\|\|_______\|:\|\|\|_\|\|_\|\|:\|___\|:\|:___\|\|\|:\|\|\|__\|\|\|\|\|\|________\|\|\|\|:\|\|\|\|\|\n______________UUGCCCU_______CUCCG_AU_UGUA___CUUG___AUGUGCC__UUACUC________UACUUACUUU\n3'-GUU...ACGUA_______A___________U__C_____________________GG________________________UGUUU...GGA-5'\n_____________\|______________________________________________________________________\|\n_____________208____________________________________________________________________145\n	204 -- 210	158 -- 164	-42.8674 kcal/mol	12.3523 kcal/mol	18.5828 kcal/mol	142 215@LB@ \| \|@LB@5'-UAU...AUUUG AUUUUUA A AUC UGU A GAAUGGAC UGAUG...CAA-3'@LB@ AGCGGGA GGGGC UA ACGU GGAU UACGCGG AAUGAG AUGAGUGAAA@LB@ \|:\|\|\|\|\| \|:\|\|\| \|\| \|\|:\| \|:\|: \|\|\|:\|\|\| \|\|\|\|\|\| \|\|\|\|:\|\|\|\|\|@LB@ UUGCCCU CUCCG AU UGUA CUUG AUGUGCC UUACUC UACUUACUUU@LB@3'-GUU...ACGUA A U C GG UGUUU...GGA-5'@LB@ \| \|@LB@ 208 145@LB@@LB@@LB@Energy -19.90 kcal/mol@LB@Hybridization Energy -42.8674 kcal/mol@LB@Unfolding Energy - mRNA 12.3523 kcal/mol@LB@Unfolding Energy - sRNA 18.5828 kcal/mol@LB@@LB@Position - mRNA 143 -- 214@LB@Position - sRNA 146 -- 207@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 158 -- 164@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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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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