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
153	0.04013	0.7027	lmo0979	N/A	-16.44	0.052648	251 -- 296	172 -- 207	daunorubicin resistance ATP-binding protein	_____________250_____________________________297\n_____________\|_______________________________\|\n5'-AAU...UUGAA__________UU____G_AAA_______G__AUUU-3'\n______________GGGUGUAGAU__UGAA_U___ACAUGGC_AA\n______________:\|\|::\|\|\|\|:__\|\|\|\|_\|___\|\|\|:\|\|\|_\|\|\n______________UCCGUAUCUG__ACUU_A___UGUGCCG_UU\n3'-GUU...CCUAC__________U_____G___________G__ACUCU...GGA-5'\n_____________\|_______________________________\|\n_____________208_____________________________171\n	287 -- 293	175 -- 181	-27.1075 kcal/mol	4.53663 kcal/mol	13.3233 kcal/mol	250 297@LB@ \| \|@LB@5'-AAU...UUGAA UU G AAA G AUUU-3'@LB@ GGGUGUAGAU UGAA U ACAUGGC AA@LB@ :\|\|::\|\|\|\|: \|\|\|\| \| \|\|\|:\|\|\| \|\|@LB@ UCCGUAUCUG ACUU A UGUGCCG UU@LB@3'-GUU...CCUAC U G G ACUCU...GGA-5'@LB@ \| \|@LB@ 208 171@LB@@LB@@LB@Energy -16.44 kcal/mol@LB@Hybridization Energy -27.1075 kcal/mol@LB@Unfolding Energy - mRNA 4.53663 kcal/mol@LB@Unfolding Energy - sRNA 13.3233 kcal/mol@LB@@LB@Position - mRNA 251 -- 296@LB@Position - sRNA 172 -- 207@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 175 -- 181@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@
193	0.05586	0.7607	lmo1772	purC	-15.19	0.089756	256 -- 291	97 -- 135	phosphoribosylaminoimidazole-succinocarboxamide synthase	_____________255_____________________________________292\n_____________\|_______________________________________\|\n5'-UUA...AGAAG____________U__GU______UAUAA______C____CGACA...CGC-3'\n______________AAGCAGGUGUCU_GC__GUUGCU________GGA_GAUG\n______________\|\|:\|\|\|:\|\|\|\|\|_:\|__\|\|\|\|\|:________\|\|\|_\|\|\|\|\n______________UUUGUCUACAGA_UG__CAACGG________CCU_CUAC\n3'-GUU...ACAGA____________C__AU______UAAGAUAA___U____CUAUG...GGA-5'\n_____________\|_______________________________________\|\n_____________136_____________________________________96\n	261 -- 267	124 -- 130	-33.6761 kcal/mol	9.14329 kcal/mol	9.45249 kcal/mol	255 292@LB@ \| \|@LB@5'-UUA...AGAAG U GU UAUAA C CGACA...CGC-3'@LB@ AAGCAGGUGUCU GC GUUGCU GGA GAUG@LB@ \|\|:\|\|\|:\|\|\|\|\| :\| \|\|\|\|\|: \|\|\| \|\|\|\|@LB@ UUUGUCUACAGA UG CAACGG CCU CUAC@LB@3'-GUU...ACAGA C AU UAAGAUAA U CUAUG...GGA-5'@LB@ \| \|@LB@ 136 96@LB@@LB@@LB@Energy -15.19 kcal/mol@LB@Hybridization Energy -33.6761 kcal/mol@LB@Unfolding Energy - mRNA 9.14329 kcal/mol@LB@Unfolding Energy - sRNA 9.45249 kcal/mol@LB@@LB@Position - mRNA 256 -- 291@LB@Position - sRNA 97 -- 135@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 124 -- 130@LB@
76	0.01998	0.6733	lmo1751	N/A	-17.90	0.027246	260 -- 292	176 -- 211	Uncharacterized RNA methyltransferase lmo1751	_____________259______________293\n_____________\|________________\|\n5'-GAA...GGCAA____CUU_________UCCCU...CAU-3'\n______________GGGA____UGGAAGCA\n______________\|:\|\|____\|\|:\|\|:\|\|\n______________CUCU____ACUUUUGU\n3'-GUU...GGUUA____ACUU________UUAUU...GGA-5'\n_____________\|________________\|\n_____________212______________175\n	203 -- 209	155 -- 161	-10.7582 kcal/mol	2.48877 kcal/mol	0.929544 kcal/mol	259 293@LB@ \| \|@LB@5'-GAA...GGCAA CUU UCCCU...CAU-3'@LB@ GGGA UGGAAGCA@LB@ \|:\|\| \|\|:\|\|:\|\|@LB@ CUCU ACUUUUGU@LB@3'-GUU...GGUUA ACUU UUAUU...GGA-5'@LB@ \| \|@LB@ 212 175@LB@@LB@@LB@Energy -17.90 kcal/mol@LB@Hybridization Energy -10.7582 kcal/mol@LB@Unfolding Energy - mRNA 2.48877 kcal/mol@LB@Unfolding Energy - sRNA 0.929544 kcal/mol@LB@@LB@Position - mRNA 260 -- 292@LB@Position - sRNA 176 -- 211@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 155 -- 161@LB@
43	0.009411	0.5889	lmo0325	N/A	-15.65	0.074138	261 -- 289	174 -- 199	transcriptional regulator	______________261_________________________290\n______________\|___________________________\|\n___________5'-_______AAUACUUAAAAAA________ACGAU...UCG-3'\n______________UGCUAUU_____________GGAAGAUG\n______________\|\|\|:\|\|\|_____________\|\|\|\|\|\|\|\|\n______________ACGGUAA_____________CCUUCUAC\n3'-GUU...GAUCA_______GAUAA________________CUAUG...GGA-5'\n_____________\|____________________________\|\n_____________200__________________________173\n	22 -- 28	97 -- 103	-16.3216 kcal/mol	2.64423 kcal/mol	5.20765 kcal/mol	261 290@LB@ \| \|@LB@ 5'- AAUACUUAAAAAA ACGAU...UCG-3'@LB@ UGCUAUU GGAAGAUG@LB@ \|\|\|:\|\|\| \|\|\|\|\|\|\|\|@LB@ ACGGUAA CCUUCUAC@LB@3'-GUU...GAUCA GAUAA CUAUG...GGA-5'@LB@ \| \|@LB@ 200 173@LB@@LB@@LB@Energy -15.65 kcal/mol@LB@Hybridization Energy -16.3216 kcal/mol@LB@Unfolding Energy - mRNA 2.64423 kcal/mol@LB@Unfolding Energy - sRNA 5.20765 kcal/mol@LB@@LB@Position - mRNA 261 -- 289@LB@Position - sRNA 174 -- 199@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 97 -- 103@LB@
197	0.05638	0.7607	lmo0344	N/A	-15.66	0.073858	267 -- 298	182 -- 211	short chain dehydrogenase	_____________266______299\n_____________\|________\|\n5'-CAG...CAGCA________UGGUA...UUU-3'\n______________AGCGGGAU\n______________\|:\|\|\|\|\|\|\n______________UUGCCCUA\n3'-GUU...ACGUA________CUCCG...GGA-5'\n_____________\|________\|\n_____________212______181\n	271 -- 277	200 -- 206	-11.8444 kcal/mol	1.0403 kcal/mol	0.330969 kcal/mol	266 299@LB@ \| \|@LB@5'-CAG...CAGCA UGGUA...UUU-3'@LB@ AGCGGGAU@LB@ \|:\|\|\|\|\|\|@LB@ UUGCCCUA@LB@3'-GUU...ACGUA CUCCG...GGA-5'@LB@ \| \|@LB@ 212 181@LB@@LB@@LB@Energy -15.66 kcal/mol@LB@Hybridization Energy -11.8444 kcal/mol@LB@Unfolding Energy - mRNA 1.0403 kcal/mol@LB@Unfolding Energy - sRNA 0.330969 kcal/mol@LB@@LB@Position - mRNA 267 -- 298@LB@Position - sRNA 182 -- 211@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 200 -- 206@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@
100	0.02596	0.6733	lmo2805	N/A	-13.33	0.188364	273 -- 298	147 -- 172	hypothetical secreted protein	_____________272_______________________________________299\n_____________\|_________________________________________\|\n5'-GAA...CAUAC______GG_____AG_____AAAAA________________AAUAG...AAA-3'\n______________AACAGA____UGA__AGUUG____________GAGAUGGAU\n______________\|\|\|\|\|\|____\|\|\|__\|\|\|\|\|____________:\|\|\|\|\|\|\|\|\n______________UUGUCU____ACU__UCAAC____________UUCUACCUA\n3'-GUU...CAGAU______ACAG___GA_____GGUAAGAUAACC_________UGUGG...GGA-5'\n_____________\|_________________________________________\|\n_____________173_______________________________________146\n	211 -- 217	94 -- 100	-22.9496 kcal/mol	2.56346 kcal/mol	9.49359 kcal/mol	272 299@LB@ \| \|@LB@5'-GAA...CAUAC GG AG AAAAA AAUAG...AAA-3'@LB@ AACAGA UGA AGUUG GAGAUGGAU@LB@ \|\|\|\|\|\| \|\|\| \|\|\|\|\| :\|\|\|\|\|\|\|\|@LB@ UUGUCU ACU UCAAC UUCUACCUA@LB@3'-GUU...CAGAU ACAG GA GGUAAGAUAACC UGUGG...GGA-5'@LB@ \| \|@LB@ 173 146@LB@@LB@@LB@Energy -13.33 kcal/mol@LB@Hybridization Energy -22.9496 kcal/mol@LB@Unfolding Energy - mRNA 2.56346 kcal/mol@LB@Unfolding Energy - sRNA 9.49359 kcal/mol@LB@@LB@Position - mRNA 273 -- 298@LB@Position - sRNA 147 -- 172@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 94 -- 100@LB@
169	0.04649	0.7403	lmo0268	N/A	-16.22	0.057928	275 -- 284	195 -- 204	phosphoglycerate mutase	_____________274________285\n_____________\|__________\|\n5'-ACC...AUGCA__________GAUUC...UUG-3'\n______________GGGAUGGGGC\n______________\|\|\|\|\|\|:\|\|\|\n______________CCCUACUCCG\n3'-GUU...UAUUG__________UAUCU...GGA-5'\n_____________\|__________\|\n_____________205________194\n	278 -- 284	195 -- 201	-19.94 kcal/mol	1.96731 kcal/mol	6.55531 kcal/mol	274 285@LB@ \| \|@LB@5'-ACC...AUGCA GAUUC...UUG-3'@LB@ GGGAUGGGGC@LB@ \|\|\|\|\|\|:\|\|\|@LB@ CCCUACUCCG@LB@3'-GUU...UAUUG UAUCU...GGA-5'@LB@ \| \|@LB@ 205 194@LB@@LB@@LB@Energy -16.22 kcal/mol@LB@Hybridization Energy -19.94 kcal/mol@LB@Unfolding Energy - mRNA 1.96731 kcal/mol@LB@Unfolding Energy - sRNA 6.55531 kcal/mol@LB@@LB@Position - mRNA 275 -- 284@LB@Position - sRNA 195 -- 204@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 195 -- 201@LB@
141	0.03665	0.6968	lmo1798	N/A	-14.74	0.108024	280 -- 295	194 -- 209		_____________279_______296\n_____________\|_________\|\n5'-GAU...CACUU_________AAUGG...GUU-3'\n______________AUAACGGGA\n______________\|\|\|\|\|\|\|\|\|\n______________UAUUGCCCU\n3'-GUU...AUACG_________ACUCC...GGA-5'\n_____________\|_________\|\n_____________210_______193\n	282 -- 288	201 -- 207	-12.5707 kcal/mol	0.27177 kcal/mol	0.374318 kcal/mol	279 296@LB@ \| \|@LB@5'-GAU...CACUU AAUGG...GUU-3'@LB@ AUAACGGGA@LB@ \|\|\|\|\|\|\|\|\|@LB@ UAUUGCCCU@LB@3'-GUU...AUACG ACUCC...GGA-5'@LB@ \| \|@LB@ 210 193@LB@@LB@@LB@Energy -14.74 kcal/mol@LB@Hybridization Energy -12.5707 kcal/mol@LB@Unfolding Energy - mRNA 0.27177 kcal/mol@LB@Unfolding Energy - sRNA 0.374318 kcal/mol@LB@@LB@Position - mRNA 280 -- 295@LB@Position - sRNA 194 -- 209@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 201 -- 207@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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