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
67	0.01689	0.6733	lmo0335	N/A	-16.81	0.044620	154 -- 214	153 -- 220	lmo0335	_____________153_____________________________________________________________215\n_____________\|_______________________________________________________________\|\n5'-AAA...CUACC______AUA______G____A____AUAUA______G_G____________A___________AUAAA...AUA-3'\n______________GGUGCU_____AUGA_GGGG__AGG_____CAUAGA_A_GAA__GCAU_GC_GAUGAGA_GAA\n______________\|\|:\|\|:_____\|\|:\|_\|\|\|:__\|\|\|_____\|\|\|\|\|\|_\|_\|\|\|__:\|\|:_\|\|_:\|\|\|\|\|\|_\|\|\|\n______________CCGCGG_____UAUU_CCCU__UCC_____GUAUCU_U_CUU__UGUG_CG_UUACUCU_CUU\n3'-GUU...CAAGC______AUACG____G____AC______________G_A___GA____C__G_______A___ACUUU...GGA-5'\n_____________\|_______________________________________________________________\|\n_____________221_____________________________________________________________152\n	200 -- 206	167 -- 173	-43.0643 kcal/mol	10.4394 kcal/mol	21.4092 kcal/mol	153 215@LB@ \| \|@LB@5'-AAA...CUACC AUA G A AUAUA G G A AUAAA...AUA-3'@LB@ GGUGCU AUGA GGGG AGG CAUAGA A GAA GCAU GC GAUGAGA GAA@LB@ \|\|:\|\|: \|\|:\| \|\|\|: \|\|\| \|\|\|\|\|\| \| \|\|\| :\|\|: \|\| :\|\|\|\|\|\| \|\|\|@LB@ CCGCGG UAUU CCCU UCC GUAUCU U CUU UGUG CG UUACUCU CUU@LB@3'-GUU...CAAGC AUACG G AC G A GA C G A ACUUU...GGA-5'@LB@ \| \|@LB@ 221 152@LB@@LB@@LB@Energy -16.81 kcal/mol@LB@Hybridization Energy -43.0643 kcal/mol@LB@Unfolding Energy - mRNA 10.4394 kcal/mol@LB@Unfolding Energy - sRNA 21.4092 kcal/mol@LB@@LB@Position - mRNA 154 -- 214@LB@Position - sRNA 153 -- 220@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 167 -- 173@LB@
127	0.03392	0.6968	lmo2096	N/A	-16.75	0.045974	122 -- 137	183 -- 198	PTS galacticol transporter subunit IIC	_____________121___________________138\n_____________\|_____________________\|\n5'-UAG...UUUCU____A__C_____________GAAGA...UGA-3'\n______________UAAC_GG_AUG_GGCAUGGAC\n______________\|\|\|\|_\|\|_\|\|\|_\|\|\|\|\|:\|\|\|\n______________AUUG_CC_UAC_CCGUAUCUG\n3'-GUU...UACGU____C______U_________UACUU...GGA-5'\n_____________\|_____________________\|\n_____________199___________________182\n	129 -- 135	191 -- 197	-23.3255 kcal/mol	4.68556 kcal/mol	9.82628 kcal/mol	121 138@LB@ \| \|@LB@5'-UAG...UUUCU A C GAAGA...UGA-3'@LB@ UAAC GG AUG GGCAUGGAC@LB@ \|\|\|\| \|\| \|\|\| \|\|\|\|\|:\|\|\|@LB@ AUUG CC UAC CCGUAUCUG@LB@3'-GUU...UACGU C U UACUU...GGA-5'@LB@ \| \|@LB@ 199 182@LB@@LB@@LB@Energy -16.75 kcal/mol@LB@Hybridization Energy -23.3255 kcal/mol@LB@Unfolding Energy - mRNA 4.68556 kcal/mol@LB@Unfolding Energy - sRNA 9.82628 kcal/mol@LB@@LB@Position - mRNA 122 -- 137@LB@Position - sRNA 183 -- 198@LB@Position Seed - mRNA 129 -- 135@LB@Position Seed - sRNA 191 -- 197@LB@
56	0.01257	0.6043	lmo2205	N/A	-16.72	0.046467	190 -- 249	147 -- 203	phosphoglyceromutase	_____________189_____________________250\n_____________\|_______________________\|\n5'-AUG...GCGAA____GAA________________AAUUA...UGG-3'\n______________AAUG___GGAUGAG_GAAGAUGA\n______________\|\|\|\|___:\|\|\|\|\|:_\|\|\|:\|::\|\n______________UUAC___UCUACUU_CUUUUGUU\n3'-GUU...GCCGG______________A________UAUUA...GGA-5'\n_____________\|_______________________\|\n_____________204_____________________146\n	197 -- 203	155 -- 161	-13.1674 kcal/mol	1.25432 kcal/mol	0.959215 kcal/mol	189 250@LB@ \| \|@LB@5'-AUG...GCGAA GAA AAUUA...UGG-3'@LB@ AAUG GGAUGAG GAAGAUGA@LB@ \|\|\|\| :\|\|\|\|\|: \|\|\|:\|::\|@LB@ UUAC UCUACUU CUUUUGUU@LB@3'-GUU...GCCGG A UAUUA...GGA-5'@LB@ \| \|@LB@ 204 146@LB@@LB@@LB@Energy -16.72 kcal/mol@LB@Hybridization Energy -13.1674 kcal/mol@LB@Unfolding Energy - mRNA 1.25432 kcal/mol@LB@Unfolding Energy - sRNA 0.959215 kcal/mol@LB@@LB@Position - mRNA 190 -- 249@LB@Position - sRNA 147 -- 203@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 155 -- 161@LB@
122	0.03252	0.6968	lmo0926	N/A	-16.71	0.046694	198 -- 274	155 -- 207	TetR family transcriptional regulator	_____________197______________275\n_____________\|________________\|\n5'-GCU...AACCA_____________G__GCGCC...UCG-3'\n______________AGAUGAGUGAAAA_CA\n______________\|\|\|\|\|\|:\|\|\|\|\|\|_\|\|\n______________UCUACUUACUUUU_GU\n3'-GUU...GUUAC________________UUAUU...GGA-5'\n_____________\|________________\|\n_____________208______________154\n	265 -- 271	157 -- 163	-16.1904 kcal/mol	1.95479 kcal/mol	0.920152 kcal/mol	197 275@LB@ \| \|@LB@5'-GCU...AACCA G GCGCC...UCG-3'@LB@ AGAUGAGUGAAAA CA@LB@ \|\|\|\|\|\|:\|\|\|\|\|\| \|\|@LB@ UCUACUUACUUUU GU@LB@3'-GUU...GUUAC UUAUU...GGA-5'@LB@ \| \|@LB@ 208 154@LB@@LB@@LB@Energy -16.71 kcal/mol@LB@Hybridization Energy -16.1904 kcal/mol@LB@Unfolding Energy - mRNA 1.95479 kcal/mol@LB@Unfolding Energy - sRNA 0.920152 kcal/mol@LB@@LB@Position - mRNA 198 -- 274@LB@Position - sRNA 155 -- 207@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 157 -- 163@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@
151	0.03914	0.6976	lmo1466	N/A	-16.64	0.048271	185 -- 226	158 -- 202		_____________184_______________________________________________227\n_____________\|_________________________________________________\|\n5'-UGA...UUAGA____AGA__A_______A_____________________________G_UUGGU...UUC-3'\n______________GAGG___CA_AGAUGUG_AACUA____GCCAA_GA____AAUGGAGA_A\n______________\|\|\|\|___\|\|_\|\|\|::\|\|_\|\|\|\|\|____\|\|\|\|\|_\|\|____\|\|\|\|:\|:\|_\|\n______________CUCC___GU_UCUGUAC_UUGAU____CGGUU_CU____UUACUUUU_U\n3'-GUU...CCCUA_________A_____________GUGC_____A__CUAC________G_UUAUU...GGA-5'\n_____________\|_________________________________________________\|\n_____________203_______________________________________________157\n	218 -- 224	157 -- 163	-27.6675 kcal/mol	5.9878 kcal/mol	13.9822 kcal/mol	184 227@LB@ \| \|@LB@5'-UGA...UUAGA AGA A A G UUGGU...UUC-3'@LB@ GAGG CA AGAUGUG AACUA GCCAA GA AAUGGAGA A@LB@ \|\|\|\| \|\| \|\|\|::\|\| \|\|\|\|\| \|\|\|\|\| \|\| \|\|\|\|:\|:\| \|@LB@ CUCC GU UCUGUAC UUGAU CGGUU CU UUACUUUU U@LB@3'-GUU...CCCUA A GUGC A CUAC G UUAUU...GGA-5'@LB@ \| \|@LB@ 203 157@LB@@LB@@LB@Energy -16.64 kcal/mol@LB@Hybridization Energy -27.6675 kcal/mol@LB@Unfolding Energy - mRNA 5.9878 kcal/mol@LB@Unfolding Energy - sRNA 13.9822 kcal/mol@LB@@LB@Position - mRNA 185 -- 226@LB@Position - sRNA 158 -- 202@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 157 -- 163@LB@
92	0.02404	0.6733	lmo1947	resE	-16.63	0.048416	181 -- 212	141 -- 170	two-component sensor histidine kinas	_____________180_________________213\n_____________\|___________________\|\n5'-AAG...ACCGA_______AUA_________UUGGA...UUU-3'\n______________GGUGAGA___GAUGAAGAU\n______________::\|\|\|\|\|___:\|\|\|\|\|:\|:\n______________UUACUCU___UUACUUUUG\n3'-GUU...GCCGG_______AC__________UUUAU...GGA-5'\n_____________\|___________________\|\n_____________171_________________140\n	202 -- 208	156 -- 162	-13.4823 kcal/mol	2.25638 kcal/mol	0.941471 kcal/mol	180 213@LB@ \| \|@LB@5'-AAG...ACCGA AUA UUGGA...UUU-3'@LB@ GGUGAGA GAUGAAGAU@LB@ ::\|\|\|\|\| :\|\|\|\|\|:\|:@LB@ UUACUCU UUACUUUUG@LB@3'-GUU...GCCGG AC UUUAU...GGA-5'@LB@ \| \|@LB@ 171 140@LB@@LB@@LB@Energy -16.63 kcal/mol@LB@Hybridization Energy -13.4823 kcal/mol@LB@Unfolding Energy - mRNA 2.25638 kcal/mol@LB@Unfolding Energy - sRNA 0.941471 kcal/mol@LB@@LB@Position - mRNA 181 -- 212@LB@Position - sRNA 141 -- 170@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 156 -- 162@LB@
176	0.04979	0.7607	lmo1340	N/A	-16.63	0.048446	193 -- 216	151 -- 177		_____________192_____________217\n_____________\|_______________\|\n5'-UGC...UUGGA_______________AAAAU...CUG-3'\n______________GGCCA__GAGAUGAA\n______________\|\|\|\|\|__\|\|\|\|\|\|\|\|\n______________CCGGU__CUCUACUU\n3'-GUU...AUGUG_____UA________ACUUU...GGA-5'\n_____________\|_______________\|\n_____________178_____________150\n	199 -- 205	163 -- 169	-19.0992 kcal/mol	1.80937 kcal/mol	7.44208 kcal/mol	192 217@LB@ \| \|@LB@5'-UGC...UUGGA AAAAU...CUG-3'@LB@ GGCCA GAGAUGAA@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ CCGGU CUCUACUU@LB@3'-GUU...AUGUG UA ACUUU...GGA-5'@LB@ \| \|@LB@ 178 150@LB@@LB@@LB@Energy -16.63 kcal/mol@LB@Hybridization Energy -19.0992 kcal/mol@LB@Unfolding Energy - mRNA 1.80937 kcal/mol@LB@Unfolding Energy - sRNA 7.44208 kcal/mol@LB@@LB@Position - mRNA 193 -- 216@LB@Position - sRNA 151 -- 177@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 163 -- 169@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@
125	0.03321	0.6968	lmo2357	N/A	-16.59	0.049158	2 -- 27	152 -- 176		_____________1_____________________28\n_____________\|_____________________\|\n_______5'-AGCU___AU________C_______AUCUU...CAC-3'\n______________GAU__GAUGGAUG_AAAACAA\n______________:\|\|__\|\|\|\|:\|\|\|_\|\|\|\|\|\|\|\n______________UUA__CUACUUAC_UUUUGUU\n3'-GUU...GCCGG___CU________________UAUUA...GGA-5'\n_____________\|_____________________\|\n_____________177___________________151\n	19 -- 25	154 -- 160	-15.1634 kcal/mol	3.68151 kcal/mol	0.959215 kcal/mol	1 28@LB@ \| \|@LB@ 5'-AGCU AU C AUCUU...CAC-3'@LB@ GAU GAUGGAUG AAAACAA@LB@ :\|\| \|\|\|\|:\|\|\| \|\|\|\|\|\|\|@LB@ UUA CUACUUAC UUUUGUU@LB@3'-GUU...GCCGG CU UAUUA...GGA-5'@LB@ \| \|@LB@ 177 151@LB@@LB@@LB@Energy -16.59 kcal/mol@LB@Hybridization Energy -15.1634 kcal/mol@LB@Unfolding Energy - mRNA 3.68151 kcal/mol@LB@Unfolding Energy - sRNA 0.959215 kcal/mol@LB@@LB@Position - mRNA 2 -- 27@LB@Position - sRNA 152 -- 176@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 154 -- 160@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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