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
182	0.05242	0.7607	lmo2028	N/A	-14.74	0.108099	169 -- 210	158 -- 185		_____________168_________211\n_____________\|___________\|\n5'-CUU...AUUAU___________UUUAU...AAC-3'\n______________GAUGGAUGGAA\n______________\|\|\|\|:\|\|\|:\|\|\n______________CUACUUACUUU\n3'-GUU...UUACU___________UGUUU...GGA-5'\n_____________\|___________\|\n_____________186_________157\n	204 -- 210	158 -- 164	-12.4441 kcal/mol	2.18802 kcal/mol	0.806249 kcal/mol	168 211@LB@ \| \|@LB@5'-CUU...AUUAU UUUAU...AAC-3'@LB@ GAUGGAUGGAA@LB@ \|\|\|\|:\|\|\|:\|\|@LB@ CUACUUACUUU@LB@3'-GUU...UUACU UGUUU...GGA-5'@LB@ \| \|@LB@ 186 157@LB@@LB@@LB@Energy -14.74 kcal/mol@LB@Hybridization Energy -12.4441 kcal/mol@LB@Unfolding Energy - mRNA 2.18802 kcal/mol@LB@Unfolding Energy - sRNA 0.806249 kcal/mol@LB@@LB@Position - mRNA 169 -- 210@LB@Position - sRNA 158 -- 185@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 158 -- 164@LB@
191	0.0551	0.7607	lmo2853	N/A	-14.70	0.110014	201 -- 241	156 -- 201		_____________200_______________________________________________242\n_____________\|_________________________________________________\|\n5'-GGU...AGAAA________________________AA___U___ACGU____________UAUCC...UUC-3'\n______________GUGAG____AGAUAU_AACUGCGC__GGC_CAA_____UGAA__GAAGC\n______________:\|\|\|\|____\|\|\|:\|\|_\|\|\|\|:\|:\|__\|\|\|_\|\|\|_____\|\|\|\|__:\|\|:\|\n______________UACUC____UCUGUA_UUGAUGUG__CCG_GUU_____ACUU__UUUUG\n3'-GUU...UGCCC_____CGUA______C_________________ACUCU____AC_____UUUAU...GGA-5'\n_____________\|_________________________________________________\|\n_____________202_______________________________________________155\n	213 -- 219	178 -- 184	-28.7711 kcal/mol	7.06239 kcal/mol	14.0114 kcal/mol	200 242@LB@ \| \|@LB@5'-GGU...AGAAA AA U ACGU UAUCC...UUC-3'@LB@ GUGAG AGAUAU AACUGCGC GGC CAA UGAA GAAGC@LB@ :\|\|\|\| \|\|\|:\|\| \|\|\|\|:\|:\| \|\|\| \|\|\| \|\|\|\| :\|\|:\|@LB@ UACUC UCUGUA UUGAUGUG CCG GUU ACUU UUUUG@LB@3'-GUU...UGCCC CGUA C ACUCU AC UUUAU...GGA-5'@LB@ \| \|@LB@ 202 155@LB@@LB@@LB@Energy -14.70 kcal/mol@LB@Hybridization Energy -28.7711 kcal/mol@LB@Unfolding Energy - mRNA 7.06239 kcal/mol@LB@Unfolding Energy - sRNA 14.0114 kcal/mol@LB@@LB@Position - mRNA 201 -- 241@LB@Position - sRNA 156 -- 201@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 178 -- 184@LB@
190	0.0551	0.7607	lmo0641	N/A	-14.65	0.112053	196 -- 245	175 -- 211	heavy metal-transporting ATPase	_____________195_____________________246\n_____________\|_______________________\|\n5'-AUU...GAGCA______AA__U____________GAAUU...ACU-3'\n______________UAAUGA__GA_UGGAUGAAG_CA\n______________:\|\|\|\|\|__\|\|_\|\|:\|\|\|\|\|:_\|\|\n______________GUUACU__CU_ACUUACUUU_GU\n3'-GUU...UGCCG____________________U__UUAUU...GGA-5'\n_____________\|_______________________\|\n_____________212_____________________174\n	212 -- 218	158 -- 164	-12.4633 kcal/mol	2.08827 kcal/mol	0.95817 kcal/mol	195 246@LB@ \| \|@LB@5'-AUU...GAGCA AA U GAAUU...ACU-3'@LB@ UAAUGA GA UGGAUGAAG CA@LB@ :\|\|\|\|\| \|\| \|\|:\|\|\|\|\|: \|\|@LB@ GUUACU CU ACUUACUUU GU@LB@3'-GUU...UGCCG U UUAUU...GGA-5'@LB@ \| \|@LB@ 212 174@LB@@LB@@LB@Energy -14.65 kcal/mol@LB@Hybridization Energy -12.4633 kcal/mol@LB@Unfolding Energy - mRNA 2.08827 kcal/mol@LB@Unfolding Energy - sRNA 0.95817 kcal/mol@LB@@LB@Position - mRNA 196 -- 245@LB@Position - sRNA 175 -- 211@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 158 -- 164@LB@
162	0.04462	0.7375	lmo2840	N/A	-13.73	0.161226	169 -- 225	174 -- 208	sucrose phosphorylase	_____________168____________226\n_____________\|______________\|\n5'-UUU...AUAUU_______UG_____GAAUU...AUA-3'\n______________UAGCGGG__AUGAG\n______________\|\|:\|\|\|\|__\|\|\|\|\|\n______________AUUGCCC__UACUC\n3'-GUU...UACGU______________CGUAU...GGA-5'\n_____________\|______________\|\n_____________209____________173\n	169 -- 175	202 -- 208	-13.6832 kcal/mol	2.78278 kcal/mol	0.386761 kcal/mol	168 226@LB@ \| \|@LB@5'-UUU...AUAUU UG GAAUU...AUA-3'@LB@ UAGCGGG AUGAG@LB@ \|\|:\|\|\|\| \|\|\|\|\|@LB@ AUUGCCC UACUC@LB@3'-GUU...UACGU CGUAU...GGA-5'@LB@ \| \|@LB@ 209 173@LB@@LB@@LB@Energy -13.73 kcal/mol@LB@Hybridization Energy -13.6832 kcal/mol@LB@Unfolding Energy - mRNA 2.78278 kcal/mol@LB@Unfolding Energy - sRNA 0.386761 kcal/mol@LB@@LB@Position - mRNA 169 -- 225@LB@Position - sRNA 174 -- 208@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 202 -- 208@LB@
88	0.02298	0.6733	lmo0666	N/A	-13.39	0.184164	127 -- 173	156 -- 211		_____________126__________________________________________________________________________________174\n_____________\|____________________________________________________________________________________\|\n5'-AAG...AUUCA____A__GAACC______AA__C___AGU____AC___A__AAA_____GUUA______G_____GC_________________UCGUU...AUG-3'\n______________GCCA_CA______GGCGC__AU_GCA___AUGG__GGU_AG___AUAGA____GA___A_ACGGC_________GAAUGGAGAC\n______________\|\|\|\|_\|\|______\|\|\|\|\|__\|\|_\|\|\|___\|:\|\|__\|:\|_\|\|___\|\|\|\|\|____\|\|___\|_\|\|\|\|\|_________\|\|\|\|\|:\|:\|\|\n______________CGGU_GU______CCGCG__UA_CGU___UGCC__CUA_UC___UAUCU____CU___U_UGCCG_________CUUACUUUUG\n3'-GUU...CGCAA____A__ACAAGC_____GA______AU__________C__CG______GUA___UGA_G_____GUUACUCUA__________UUUAU...GGA-5'\n_____________\|____________________________________________________________________________________\|\n_____________212__________________________________________________________________________________155\n	167 -- 173	156 -- 162	-45.3275 kcal/mol	14.8697 kcal/mol	22.6898 kcal/mol	126 174@LB@ \| \|@LB@5'-AAG...AUUCA A GAACC AA C AGU AC A AAA GUUA G GC UCGUU...AUG-3'@LB@ GCCA CA GGCGC AU GCA AUGG GGU AG AUAGA GA A ACGGC GAAUGGAGAC@LB@ \|\|\|\| \|\| \|\|\|\|\| \|\| \|\|\| \|:\|\| \|:\| \|\| \|\|\|\|\| \|\| \| \|\|\|\|\| \|\|\|\|\|:\|:\|\|@LB@ CGGU GU CCGCG UA CGU UGCC CUA UC UAUCU CU U UGCCG CUUACUUUUG@LB@3'-GUU...CGCAA A ACAAGC GA AU C CG GUA UGA G GUUACUCUA UUUAU...GGA-5'@LB@ \| \|@LB@ 212 155@LB@@LB@@LB@Energy -13.39 kcal/mol@LB@Hybridization Energy -45.3275 kcal/mol@LB@Unfolding Energy - mRNA 14.8697 kcal/mol@LB@Unfolding Energy - sRNA 22.6898 kcal/mol@LB@@LB@Position - mRNA 127 -- 173@LB@Position - sRNA 156 -- 211@LB@Position Seed - mRNA 167 -- 173@LB@Position Seed - sRNA 156 -- 162@LB@
199	0.05673	0.7607	lmo0888	N/A	-13.34	0.187096	200 -- 237	174 -- 211		_____________199___________________238\n_____________\|_____________________\|\n5'-AAG...GGCGG_____A__UAU__________ACGCA...AUA-3'\n______________AGUGA_GU___AAUGGAAGCA\n______________\|:\|\|\|_:\|___\|\|\|\|:\|\|:\|\|\n______________UUACU_UA___UUACUUUUGU\n3'-GUU...GCCGG_____C__C____________UUAUU...GGA-5'\n_____________\|_____________________\|\n_____________212___________________173\n	32 -- 38	155 -- 161	-11.9538 kcal/mol	2.24583 kcal/mol	0.954976 kcal/mol	199 238@LB@ \| \|@LB@5'-AAG...GGCGG A UAU ACGCA...AUA-3'@LB@ AGUGA GU AAUGGAAGCA@LB@ \|:\|\|\| :\| \|\|\|\|:\|\|:\|\|@LB@ UUACU UA UUACUUUUGU@LB@3'-GUU...GCCGG C C UUAUU...GGA-5'@LB@ \| \|@LB@ 212 173@LB@@LB@@LB@Energy -13.34 kcal/mol@LB@Hybridization Energy -11.9538 kcal/mol@LB@Unfolding Energy - mRNA 2.24583 kcal/mol@LB@Unfolding Energy - sRNA 0.954976 kcal/mol@LB@@LB@Position - mRNA 200 -- 237@LB@Position - sRNA 174 -- 211@LB@Position Seed - mRNA 32 -- 38@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@
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@
174	0.04903	0.7583	lmo1615	trmB	-12.39	0.264018	169 -- 243	157 -- 213	tRNA (guanine-N(7)-)-methyltransferase	_____________168________________244\n_____________\|__________________\|\n5'-AAU...AAGAU_________U__A_____AUGCG...AAG-3'\n______________GAUGAGGUG_AA_GAAAG\n______________:\|\|\|\|\|:\|\|_\|\|_\|\|\|\|:\n______________UUACUCUAC_UU_CUUUU\n3'-GUU...GCCGG____________A_____GUUUA...GGA-5'\n_____________\|__________________\|\n_____________214________________156\n	185 -- 191	165 -- 171	-13.3606 kcal/mol	4.29808 kcal/mol	0.930085 kcal/mol	168 244@LB@ \| \|@LB@5'-AAU...AAGAU U A AUGCG...AAG-3'@LB@ GAUGAGGUG AA GAAAG@LB@ :\|\|\|\|\|:\|\| \|\| \|\|\|\|:@LB@ UUACUCUAC UU CUUUU@LB@3'-GUU...GCCGG A GUUUA...GGA-5'@LB@ \| \|@LB@ 214 156@LB@@LB@@LB@Energy -12.39 kcal/mol@LB@Hybridization Energy -13.3606 kcal/mol@LB@Unfolding Energy - mRNA 4.29808 kcal/mol@LB@Unfolding Energy - sRNA 0.930085 kcal/mol@LB@@LB@Position - mRNA 169 -- 243@LB@Position - sRNA 157 -- 213@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 165 -- 171@LB@
145	0.03765	0.6968	lmo0134	N/A	-12.36	0.267504	193 -- 220	147 -- 170		_____________192__________________________221\n_____________\|____________________________\|\n5'-GGG...AGGAG_____UA_______UAUAA_________AAAUA...UUA-3'\n______________GAGAU__AAUGGAA_____AAAUGGUGA\n______________\|\|\|\|\|__\|\|\|\|:\|\|_____\|\|\|\|::\|\|\|\n______________CUCUA__UUACUUU_____UUUAUUACU\n3'-GUU...GGUUA_____C________UG____________AAAAC...GGA-5'\n_____________\|____________________________\|\n_____________171__________________________146\n	200 -- 206	158 -- 164	-15.5721 kcal/mol	1.73331 kcal/mol	5.93585 kcal/mol	192 221@LB@ \| \|@LB@5'-GGG...AGGAG UA UAUAA AAAUA...UUA-3'@LB@ GAGAU AAUGGAA AAAUGGUGA@LB@ \|\|\|\|\| \|\|\|\|:\|\| \|\|\|\|::\|\|\|@LB@ CUCUA UUACUUU UUUAUUACU@LB@3'-GUU...GGUUA C UG AAAAC...GGA-5'@LB@ \| \|@LB@ 171 146@LB@@LB@@LB@Energy -12.36 kcal/mol@LB@Hybridization Energy -15.5721 kcal/mol@LB@Unfolding Energy - mRNA 1.73331 kcal/mol@LB@Unfolding Energy - sRNA 5.93585 kcal/mol@LB@@LB@Position - mRNA 193 -- 220@LB@Position - sRNA 147 -- 170@LB@Position Seed - mRNA 200 -- 206@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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