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
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@
101	0.026	0.6733	lmo2768	N/A	-17.52	0.032492	230 -- 251	161 -- 179	hypothetical membrane protein	_____________229__________252\n_____________\|____________\|\n5'-UUA...GUAAU____________CUUUU...UAA-3'\n______________AUGAGAUGGAUG\n______________\|\|\|\|\|\|\|\|:\|\|\|\n______________UACUCUACUUAC\n3'-GUU...CCGGU____________UUUUG...GGA-5'\n_____________\|____________\|\n_____________180__________160\n	245 -- 251	161 -- 167	-15.292 kcal/mol	2.52317 kcal/mol	0.818518 kcal/mol	229 252@LB@ \| \|@LB@5'-UUA...GUAAU CUUUU...UAA-3'@LB@ AUGAGAUGGAUG@LB@ \|\|\|\|\|\|\|\|:\|\|\|@LB@ UACUCUACUUAC@LB@3'-GUU...CCGGU UUUUG...GGA-5'@LB@ \| \|@LB@ 180 160@LB@@LB@@LB@Energy -17.52 kcal/mol@LB@Hybridization Energy -15.292 kcal/mol@LB@Unfolding Energy - mRNA 2.52317 kcal/mol@LB@Unfolding Energy - sRNA 0.818518 kcal/mol@LB@@LB@Position - mRNA 230 -- 251@LB@Position - sRNA 161 -- 179@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 161 -- 167@LB@
180	0.05132	0.7607	lmo1643	N/A	-15.34	0.084306	231 -- 286	157 -- 207	lmo1643	_____________230_______________287\n_____________\|_________________\|\n5'-CGA...UAGUA_______GAU_______AGAAG...CUG-3'\n______________AGUGAGG___AUGAAAA\n______________\|:\|\|\|\|:___\|\|\|\|\|\|\|\n______________UUACUCU___UACUUUU\n3'-GUU...GCCGG_______ACU_______GUUUA...GGA-5'\n_____________\|_________________\|\n_____________208_______________156\n	280 -- 286	157 -- 163	-13.3165 kcal/mol	1.24234 kcal/mol	0.930085 kcal/mol	230 287@LB@ \| \|@LB@5'-CGA...UAGUA GAU AGAAG...CUG-3'@LB@ AGUGAGG AUGAAAA@LB@ \|:\|\|\|\|: \|\|\|\|\|\|\|@LB@ UUACUCU UACUUUU@LB@3'-GUU...GCCGG ACU GUUUA...GGA-5'@LB@ \| \|@LB@ 208 156@LB@@LB@@LB@Energy -15.34 kcal/mol@LB@Hybridization Energy -13.3165 kcal/mol@LB@Unfolding Energy - mRNA 1.24234 kcal/mol@LB@Unfolding Energy - sRNA 0.930085 kcal/mol@LB@@LB@Position - mRNA 231 -- 286@LB@Position - sRNA 157 -- 207@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 157 -- 163@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@
13	0.002947	0.4469	lmo0233	N/A	-20.88	0.006381	238 -- 276	156 -- 198	DNA repair protein RadA	_____________237_____________________________________________277\n_____________\|_______________________________________________\|\n5'-AAA...GUGUC______GU__________________AA___________________UCCGA...CNN-3'\n______________AGGCAU__GGAUAUGAAU____CGGC__AAUG_GAUGG__GAAAAUG\n______________\|\|\|\|\|\|__:\|\|:\|\|\|\|\|:____\|\|\|\|__\|\|\|\|_\|\|\|\|:__\|\|\|\|\|::\n______________UCCGUA__UCUGUACUUG____GCCG__UUAC_CUACU__CUUUUGU\n3'-GUU...CCUAC__________________AUGU____G_____U_____UA_______UUAUU...GGA-5'\n_____________\|_______________________________________________\|\n_____________199_____________________________________________155\n	271 -- 277	155 -- 161	-35.3246 kcal/mol	8.28493 kcal/mol	13.976 kcal/mol	237 277@LB@ \| \|@LB@5'-AAA...GUGUC GU AA UCCGA...CNN-3'@LB@ AGGCAU GGAUAUGAAU CGGC AAUG GAUGG GAAAAUG@LB@ \|\|\|\|\|\| :\|\|:\|\|\|\|\|: \|\|\|\| \|\|\|\| \|\|\|\|: \|\|\|\|\|::@LB@ UCCGUA UCUGUACUUG GCCG UUAC CUACU CUUUUGU@LB@3'-GUU...CCUAC AUGU G U UA UUAUU...GGA-5'@LB@ \| \|@LB@ 199 155@LB@@LB@@LB@Energy -20.88 kcal/mol@LB@Hybridization Energy -35.3246 kcal/mol@LB@Unfolding Energy - mRNA 8.28493 kcal/mol@LB@Unfolding Energy - sRNA 13.976 kcal/mol@LB@@LB@Position - mRNA 238 -- 276@LB@Position - sRNA 156 -- 198@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 155 -- 161@LB@
173	0.04847	0.7539	lmo1143	N/A	-15.38	0.082828	238 -- 287	171 -- 211	PduT protein	_____________237_______________________________288\n_____________\|_________________________________\|\n5'-GUG...GCAUC______GUC____C__U____AAA_________UCGGA...UUU-3'\n______________GAGGCG___GAUA_GA_GCUA___GCGGCCAAU\n______________\|\|\|\|\|:___\|\|:\|_\|\|_:\|\|\|___:\|\|\|\|\|\|\|\|\n______________CUCCGU___CUGU_CU_UGAU___UGCCGGUUA\n3'-GUU...CCCUA______AU_____A_______G___________CUCUA...GGA-5'\n_____________\|_________________________________\|\n_____________212_______________________________170\n	281 -- 287	171 -- 177	-30.6178 kcal/mol	10.0561 kcal/mol	13.341 kcal/mol	237 288@LB@ \| \|@LB@5'-GUG...GCAUC GUC C U AAA UCGGA...UUU-3'@LB@ GAGGCG GAUA GA GCUA GCGGCCAAU@LB@ \|\|\|\|\|: \|\|:\| \|\| :\|\|\| :\|\|\|\|\|\|\|\|@LB@ CUCCGU CUGU CU UGAU UGCCGGUUA@LB@3'-GUU...CCCUA AU A G CUCUA...GGA-5'@LB@ \| \|@LB@ 212 170@LB@@LB@@LB@Energy -15.38 kcal/mol@LB@Hybridization Energy -30.6178 kcal/mol@LB@Unfolding Energy - mRNA 10.0561 kcal/mol@LB@Unfolding Energy - sRNA 13.341 kcal/mol@LB@@LB@Position - mRNA 238 -- 287@LB@Position - sRNA 171 -- 211@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 171 -- 177@LB@
91	0.02389	0.6733	lmo2425	N/A	-16.15	0.059838	240 -- 263	146 -- 170	glycine cleavage system protein H	_____________239______________264\n_____________\|________________\|\n5'-CGA...AACAC________________GACGA...AUC-3'\n______________GA_AUGGGUGAAAGCA\n______________\|\|_\|\|\|::\|\|\|\|\|:\|\|\n______________CU_UACUUACUUUUGU\n3'-GUU...GGUUA__C_____________UUAUU...GGA-5'\n_____________\|________________\|\n_____________171______________145\n	248 -- 254	155 -- 161	-15.1065 kcal/mol	3.08859 kcal/mol	0.929544 kcal/mol	239 264@LB@ \| \|@LB@5'-CGA...AACAC GACGA...AUC-3'@LB@ GA AUGGGUGAAAGCA@LB@ \|\| \|\|\|::\|\|\|\|\|:\|\|@LB@ CU UACUUACUUUUGU@LB@3'-GUU...GGUUA C UUAUU...GGA-5'@LB@ \| \|@LB@ 171 145@LB@@LB@@LB@Energy -16.15 kcal/mol@LB@Hybridization Energy -15.1065 kcal/mol@LB@Unfolding Energy - mRNA 3.08859 kcal/mol@LB@Unfolding Energy - sRNA 0.929544 kcal/mol@LB@@LB@Position - mRNA 240 -- 263@LB@Position - sRNA 146 -- 170@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 155 -- 161@LB@
98	0.02549	0.6733	lmo2155	N/A	-16.07	0.061955	240 -- 298	157 -- 207	ribonucleotide-diphosphate reductase subunit alpha	_____________239________299\n_____________\|__________\|\n5'-UAU...UAAAA__________AACAG...AAA-3'\n______________GACGGGG_GA\n______________:\|\|\|\|\|:_\|\|\n______________UUGCCCU_CU\n3'-GUU...ACGUA_______A__CCGUA...GGA-5'\n_____________\|__________\|\n_____________208________156\n	240 -- 246	201 -- 207	-11.5149 kcal/mol	1.00175 kcal/mol	0.374399 kcal/mol	239 299@LB@ \| \|@LB@5'-UAU...UAAAA AACAG...AAA-3'@LB@ GACGGGG GA@LB@ :\|\|\|\|\|: \|\|@LB@ UUGCCCU CU@LB@3'-GUU...ACGUA A CCGUA...GGA-5'@LB@ \| \|@LB@ 208 156@LB@@LB@@LB@Energy -16.07 kcal/mol@LB@Hybridization Energy -11.5149 kcal/mol@LB@Unfolding Energy - mRNA 1.00175 kcal/mol@LB@Unfolding Energy - sRNA 0.374399 kcal/mol@LB@@LB@Position - mRNA 240 -- 298@LB@Position - sRNA 157 -- 207@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 201 -- 207@LB@
117	0.03157	0.6968	lmo0079	N/A	-15.68	0.073126	244 -- 277	156 -- 185	lmo0079	_____________243________________________________278\n_____________\|__________________________________\|\n5'-UCG...AUACC_________CAA_______ACCAG___G______UAUCC...CCG-3'\n______________AGCUACGUG___CCAAUGA_____GAA_GAAAAC\n______________\|:\|\|\|\|::\|___\|\|\|\|\|\|\|_____\|\|\|_\|\|\|\|\|\|\n______________UUGAUGUGC___GGUUACU_____CUU_CUUUUG\n3'-GUU...UGUAC_________C_________CUA_____A______UUUAU...GGA-5'\n_____________\|__________________________________\|\n_____________186________________________________155\n	256 -- 262	169 -- 175	-22.638 kcal/mol	3.99376 kcal/mol	9.64492 kcal/mol	243 278@LB@ \| \|@LB@5'-UCG...AUACC CAA ACCAG G UAUCC...CCG-3'@LB@ AGCUACGUG CCAAUGA GAA GAAAAC@LB@ \|:\|\|\|\|::\| \|\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|@LB@ UUGAUGUGC GGUUACU CUU CUUUUG@LB@3'-GUU...UGUAC C CUA A UUUAU...GGA-5'@LB@ \| \|@LB@ 186 155@LB@@LB@@LB@Energy -15.68 kcal/mol@LB@Hybridization Energy -22.638 kcal/mol@LB@Unfolding Energy - mRNA 3.99376 kcal/mol@LB@Unfolding Energy - sRNA 9.64492 kcal/mol@LB@@LB@Position - mRNA 244 -- 277@LB@Position - sRNA 156 -- 185@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 169 -- 175@LB@
179	0.05074	0.7607	lmo1598	tyrS	-15.93	0.065557	245 -- 292	152 -- 211	tyrosyl-tRNA synthetase	_____________244_______________293\n_____________\|_________________\|\n5'-UAG...AAAAG____AU___________AUAUU...UGU-3'\n______________GAGA__GAUGAAAAUGA\n______________\|\|\|\|__:\|\|\|\|\|\|\|::\|\n______________CUCU__UUACUUUUGUU\n3'-GUU...GGUUA____AC___________UAUUA...GGA-5'\n_____________\|_________________\|\n_____________212_______________151\n	197 -- 203	155 -- 161	-12.3519 kcal/mol	1.69495 kcal/mol	0.933796 kcal/mol	244 293@LB@ \| \|@LB@5'-UAG...AAAAG AU AUAUU...UGU-3'@LB@ GAGA GAUGAAAAUGA@LB@ \|\|\|\| :\|\|\|\|\|\|\|::\|@LB@ CUCU UUACUUUUGUU@LB@3'-GUU...GGUUA AC UAUUA...GGA-5'@LB@ \| \|@LB@ 212 151@LB@@LB@@LB@Energy -15.93 kcal/mol@LB@Hybridization Energy -12.3519 kcal/mol@LB@Unfolding Energy - mRNA 1.69495 kcal/mol@LB@Unfolding Energy - sRNA 0.933796 kcal/mol@LB@@LB@Position - mRNA 245 -- 292@LB@Position - sRNA 152 -- 211@LB@Position Seed - mRNA 197 -- 203@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)

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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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