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
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@
142	0.03693	0.6968	lmo2586	N/A	-16.96	0.041696	196 -- 266	151 -- 227	formate dehydrogenase subunit alpha	_____________195______267\n_____________\|________\|\n5'-UUU...GUGGC________UGGUG...AUC-3'\n______________GCGGGAUG\n______________:\|\|\|\|\|\|\|\n______________UGCCCUAC\n3'-GUU...CGUAU________UCCGU...GGA-5'\n_____________\|________\|\n_____________228______150\n	240 -- 246	199 -- 205	-13.0644 kcal/mol	3.68871 kcal/mol	0.331032 kcal/mol	195 267@LB@ \| \|@LB@5'-UUU...GUGGC UGGUG...AUC-3'@LB@ GCGGGAUG@LB@ :\|\|\|\|\|\|\|@LB@ UGCCCUAC@LB@3'-GUU...CGUAU UCCGU...GGA-5'@LB@ \| \|@LB@ 228 150@LB@@LB@@LB@Energy -16.96 kcal/mol@LB@Hybridization Energy -13.0644 kcal/mol@LB@Unfolding Energy - mRNA 3.68871 kcal/mol@LB@Unfolding Energy - sRNA 0.331032 kcal/mol@LB@@LB@Position - mRNA 196 -- 266@LB@Position - sRNA 151 -- 227@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 199 -- 205@LB@
143	0.03726	0.6968	lmo2701	N/A	-17.97	0.026314	78 -- 126	156 -- 198		_____________77_________________________________________________127\n_____________\|__________________________________________________\|\n5'-GAA...CCUUC_______AAAGUA___A____AGC________UUCCA_____________UUAGA...UCA-3'\n______________AGGCAUA______ACG_GAAU___GCAUGGCC______GUGGGUGGAGAC\n______________\|\|\|\|\|\|\|______\|\|:_\|\|\|:___:\|\|:\|\|\|\|______:\|\|::\|\|:\|:\|\|\n______________UCCGUAU______UGU_CUUG___UGUGCCGG______UACUUACUUUUG\n3'-GUU...CCUAC_______C________A____A__________UUACUC____________UUUAU...GGA-5'\n_____________\|__________________________________________________\|\n_____________199________________________________________________155\n	120 -- 126	156 -- 162	-37.6493 kcal/mol	12.7788 kcal/mol	13.9626 kcal/mol	77 127@LB@ \| \|@LB@5'-GAA...CCUUC AAAGUA A AGC UUCCA UUAGA...UCA-3'@LB@ AGGCAUA ACG GAAU GCAUGGCC GUGGGUGGAGAC@LB@ \|\|\|\|\|\|\| \|\|: \|\|\|: :\|\|:\|\|\|\| :\|\|::\|\|:\|:\|\|@LB@ UCCGUAU UGU CUUG UGUGCCGG UACUUACUUUUG@LB@3'-GUU...CCUAC C A A UUACUC UUUAU...GGA-5'@LB@ \| \|@LB@ 199 155@LB@@LB@@LB@Energy -17.97 kcal/mol@LB@Hybridization Energy -37.6493 kcal/mol@LB@Unfolding Energy - mRNA 12.7788 kcal/mol@LB@Unfolding Energy - sRNA 13.9626 kcal/mol@LB@@LB@Position - mRNA 78 -- 126@LB@Position - sRNA 156 -- 198@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 156 -- 162@LB@
144	0.03753	0.6968	lmo2422	N/A	-16.62	0.048504	29 -- 68	172 -- 209	two-component response regulator	_____________28___________________________________69\n_____________\|____________________________________\|\n5'-AUG...AUUCG____________AAAU_______G___U________UUUAU...AUG-3'\n______________CUAUGU__GACG____UGAGGCA_AGA_UAUGAAUU\n______________\|\|\|\|\|:__:\|\|\|____\|\|\|\|\|\|\|_\|\|\|_:\|\|\|\|\|:\|\n______________GAUACG__UUGC____ACUCCGU_UCU_GUACUUGA\n3'-GUU...CCGCG______UA____CCU________A____________UGUGC...GGA-5'\n_____________\|____________________________________\|\n_____________210__________________________________171\n	39 -- 45	194 -- 200	-29.3631 kcal/mol	6.47642 kcal/mol	13.3074 kcal/mol	28 69@LB@ \| \|@LB@5'-AUG...AUUCG AAAU G U UUUAU...AUG-3'@LB@ CUAUGU GACG UGAGGCA AGA UAUGAAUU@LB@ \|\|\|\|\|: :\|\|\| \|\|\|\|\|\|\| \|\|\| :\|\|\|\|\|:\|@LB@ GAUACG UUGC ACUCCGU UCU GUACUUGA@LB@3'-GUU...CCGCG UA CCU A UGUGC...GGA-5'@LB@ \| \|@LB@ 210 171@LB@@LB@@LB@Energy -16.62 kcal/mol@LB@Hybridization Energy -29.3631 kcal/mol@LB@Unfolding Energy - mRNA 6.47642 kcal/mol@LB@Unfolding Energy - sRNA 13.3074 kcal/mol@LB@@LB@Position - mRNA 29 -- 68@LB@Position - sRNA 172 -- 209@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 194 -- 200@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@
146	0.03799	0.6968	lmo1526	N/A	-15.66	0.073786	160 -- 215	153 -- 207		_____________159____________________216\n_____________\|______________________\|\n5'-AUG...AGGAG____AAACA____A________AGUAC...UAA-3'\n______________GAGA_____UGAA_GAAAAUAA\n______________\|\|\|\|_____\|\|\|\|_\|\|\|\|\|:\|\|\n______________CUCU_____ACUU_CUUUUGUU\n3'-GUU...GGUUA_____________A________UAUUA...GGA-5'\n_____________\|______________________\|\n_____________208____________________152\n	208 -- 214	154 -- 160	-11.4679 kcal/mol	1.00795 kcal/mol	0.933796 kcal/mol	159 216@LB@ \| \|@LB@5'-AUG...AGGAG AAACA A AGUAC...UAA-3'@LB@ GAGA UGAA GAAAAUAA@LB@ \|\|\|\| \|\|\|\| \|\|\|\|\|:\|\|@LB@ CUCU ACUU CUUUUGUU@LB@3'-GUU...GGUUA A UAUUA...GGA-5'@LB@ \| \|@LB@ 208 152@LB@@LB@@LB@Energy -15.66 kcal/mol@LB@Hybridization Energy -11.4679 kcal/mol@LB@Unfolding Energy - mRNA 1.00795 kcal/mol@LB@Unfolding Energy - sRNA 0.933796 kcal/mol@LB@@LB@Position - mRNA 160 -- 215@LB@Position - sRNA 153 -- 207@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 154 -- 160@LB@
147	0.03815	0.6968	lmo0655	N/A	-15.78	0.070044	227 -- 290	154 -- 212	phosphoprotein phosphatase	_____________226_____________291\n_____________\|_______________\|\n______5'-AACAA______UU_______CCACA...UUG-3'\n______________GAGA_G__UGAAGAC\n______________\|\|\|\|_\|__\|\|\|\|:\|\|\n______________CUCU_C__ACUUUUG\n3'-GUU...GGUUA____A_UU_______UUUAU...GGA-5'\n_____________\|_______________\|\n_____________213_____________153\n	13 -- 19	156 -- 162	-12.8457 kcal/mol	3.32795 kcal/mol	0.916023 kcal/mol	226 291@LB@ \| \|@LB@ 5'-AACAA UU CCACA...UUG-3'@LB@ GAGA G UGAAGAC@LB@ \|\|\|\| \| \|\|\|\|:\|\|@LB@ CUCU C ACUUUUG@LB@3'-GUU...GGUUA A UU UUUAU...GGA-5'@LB@ \| \|@LB@ 213 153@LB@@LB@@LB@Energy -15.78 kcal/mol@LB@Hybridization Energy -12.8457 kcal/mol@LB@Unfolding Energy - mRNA 3.32795 kcal/mol@LB@Unfolding Energy - sRNA 0.916023 kcal/mol@LB@@LB@Position - mRNA 227 -- 290@LB@Position - sRNA 154 -- 212@LB@Position Seed - mRNA 13 -- 19@LB@Position Seed - sRNA 156 -- 162@LB@
148	0.03863	0.6968	lmo1766	purN	-15.06	0.094934	1 -- 35	156 -- 188	phosphoribosylglycinamide formyltransferase	______________1__________________________________36\n______________\|__________________________________\|\n___________5'-_____GAA___________UAAAC_A_________GUAUG...AUA-3'\n______________GUGAA___AUACGGCCAAU_____G_AAUGGAAAU\n______________:\|\|\|\|___\|:\|\|\|\|\|\|\|\|\|_____\|_\|\|\|\|:\|\|\|:\n______________UACUU___UGUGCCGGUUA_____C_UUACUUUUG\n3'-GUU...AUCUG_____GA____________CUCUA___________UUUAU...GGA-5'\n_____________\|___________________________________\|\n_____________189_________________________________155\n	29 -- 35	156 -- 162	-25.7257 kcal/mol	7.32217 kcal/mol	9.72027 kcal/mol	1 36@LB@ \| \|@LB@ 5'- GAA UAAAC A GUAUG...AUA-3'@LB@ GUGAA AUACGGCCAAU G AAUGGAAAU@LB@ :\|\|\|\| \|:\|\|\|\|\|\|\|\|\| \| \|\|\|\|:\|\|\|:@LB@ UACUU UGUGCCGGUUA C UUACUUUUG@LB@3'-GUU...AUCUG GA CUCUA UUUAU...GGA-5'@LB@ \| \|@LB@ 189 155@LB@@LB@@LB@Energy -15.06 kcal/mol@LB@Hybridization Energy -25.7257 kcal/mol@LB@Unfolding Energy - mRNA 7.32217 kcal/mol@LB@Unfolding Energy - sRNA 9.72027 kcal/mol@LB@@LB@Position - mRNA 1 -- 35@LB@Position - sRNA 156 -- 188@LB@Position Seed - mRNA 29 -- 35@LB@Position Seed - sRNA 156 -- 162@LB@
149	0.0387	0.6968	lmo1809	plsX	-16.53	0.050633	188 -- 233	156 -- 203	glycerol-3-phosphate acyltransferase PlsX	_____________187________________234\n_____________\|__________________\|\n5'-ACA...CUGUA____C_____________CACGC...UUC-3'\n______________GAUG_GAUGGGUGGAGAU\n______________:\|\|\|_\|\|\|\|::\|\|:\|:\|:\n______________UUAC_CUACUUACUUUUG\n3'-GUU...GCCGG____U_____________UUUAU...GGA-5'\n_____________\|__________________\|\n_____________204________________155\n	227 -- 233	156 -- 162	-17.4325 kcal/mol	7.3364 kcal/mol	0.941471 kcal/mol	187 234@LB@ \| \|@LB@5'-ACA...CUGUA C CACGC...UUC-3'@LB@ GAUG GAUGGGUGGAGAU@LB@ :\|\|\| \|\|\|\|::\|\|:\|:\|:@LB@ UUAC CUACUUACUUUUG@LB@3'-GUU...GCCGG U UUUAU...GGA-5'@LB@ \| \|@LB@ 204 155@LB@@LB@@LB@Energy -16.53 kcal/mol@LB@Hybridization Energy -17.4325 kcal/mol@LB@Unfolding Energy - mRNA 7.3364 kcal/mol@LB@Unfolding Energy - sRNA 0.941471 kcal/mol@LB@@LB@Position - mRNA 188 -- 233@LB@Position - sRNA 156 -- 203@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 156 -- 162@LB@
150	0.03884	0.6968	lmo1709	N/A	-16.64	0.048121	221 -- 241	163 -- 181	methionine aminopeptidase	_____________220__________242\n_____________\|____________\|\n5'-UCA...GAAAU____________AGCAG...CUG-3'\n______________CGAUGAGAUGAA\n______________\|:\|\|\|\|\|\|\|\|\|\|\n______________GUUACUCUACUU\n3'-GUU...UGCCG____________ACUUU...GGA-5'\n_____________\|____________\|\n_____________182__________162\n	235 -- 241	163 -- 169	-15.3561 kcal/mol	3.44721 kcal/mol	0.694462 kcal/mol	220 242@LB@ \| \|@LB@5'-UCA...GAAAU AGCAG...CUG-3'@LB@ CGAUGAGAUGAA@LB@ \|:\|\|\|\|\|\|\|\|\|\|@LB@ GUUACUCUACUU@LB@3'-GUU...UGCCG ACUUU...GGA-5'@LB@ \| \|@LB@ 182 162@LB@@LB@@LB@Energy -16.64 kcal/mol@LB@Hybridization Energy -15.3561 kcal/mol@LB@Unfolding Energy - mRNA 3.44721 kcal/mol@LB@Unfolding Energy - sRNA 0.694462 kcal/mol@LB@@LB@Position - mRNA 221 -- 241@LB@Position - sRNA 163 -- 181@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 163 -- 169@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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