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
51	0.01168	0.599	lmo0105	N/A	-17.88	0.027496	155 -- 205	153 -- 201	chitinase B	_____________154_________________206\n_____________\|___________________\|\n5'-ACC...GUGAA_________AA________AAAAG...AAA-3'\n______________GAGAUGAAU__GAAGAUGA\n______________\|\|\|\|\|\|\|\|\|__\|\|\|:\|::\|\n______________CUCUACUUA__CUUUUGUU\n3'-GUU...GGUUA___________________UAUUA...GGA-5'\n_____________\|___________________\|\n_____________202_________________152\n	197 -- 203	155 -- 161	-15.8376 kcal/mol	2.73398 kcal/mol	0.933796 kcal/mol	154 206@LB@ \| \|@LB@5'-ACC...GUGAA AA AAAAG...AAA-3'@LB@ GAGAUGAAU GAAGAUGA@LB@ \|\|\|\|\|\|\|\|\| \|\|\|:\|::\|@LB@ CUCUACUUA CUUUUGUU@LB@3'-GUU...GGUUA UAUUA...GGA-5'@LB@ \| \|@LB@ 202 152@LB@@LB@@LB@Energy -17.88 kcal/mol@LB@Hybridization Energy -15.8376 kcal/mol@LB@Unfolding Energy - mRNA 2.73398 kcal/mol@LB@Unfolding Energy - sRNA 0.933796 kcal/mol@LB@@LB@Position - mRNA 155 -- 205@LB@Position - sRNA 153 -- 201@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 155 -- 161@LB@
61	0.01458	0.6412	lmo2589	N/A	-18.59	0.019740	180 -- 258	153 -- 210	TetR family transcriptional regulator	_____________179__________259\n_____________\|____________\|\n5'-ACU...AACAG____________UGUUU...CUG-3'\n______________AAC_GGGUGGGG\n______________\|\|\|_\|\|:\|\|:\|\|\n______________UUG_CCUACUCC\n3'-GUU...ACGUA___C________GUAUC...GGA-5'\n_____________\|____________\|\n_____________211__________152\n	186 -- 192	197 -- 203	-13.3669 kcal/mol	1.19489 kcal/mol	3.58567 kcal/mol	179 259@LB@ \| \|@LB@5'-ACU...AACAG UGUUU...CUG-3'@LB@ AAC GGGUGGGG@LB@ \|\|\| \|\|:\|\|:\|\|@LB@ UUG CCUACUCC@LB@3'-GUU...ACGUA C GUAUC...GGA-5'@LB@ \| \|@LB@ 211 152@LB@@LB@@LB@Energy -18.59 kcal/mol@LB@Hybridization Energy -13.3669 kcal/mol@LB@Unfolding Energy - mRNA 1.19489 kcal/mol@LB@Unfolding Energy - sRNA 3.58567 kcal/mol@LB@@LB@Position - mRNA 180 -- 258@LB@Position - sRNA 153 -- 210@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 197 -- 203@LB@
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@
114	0.02972	0.6968	lmo2166	N/A	-15.48	0.079589	75 -- 119	153 -- 198	lmo2166	_____________74_________________________________________________120\n_____________\|__________________________________________________\|\n5'-GGA...UAUUC___U_____UG___U______CAU________________AA________ACCCA...AAA-3'\n______________AGG_CAUGG__AUG_AACUAC___CGGUCA______UGAA__GAAGACAA\n______________\|\|\|_\|\|\|:\|__\|\|\|_\|\|\|\|\|\|___\|\|\|:\|\|______\|\|\|\|__\|\|\|:\|\|\|\|\n______________UCC_GUAUC__UAC_UUGAUG___GCCGGU______ACUU__CUUUUGUU\n3'-GUU...CCUAC_________UG__________U________UACUCU____A_________UAUUA...GGA-5'\n_____________\|__________________________________________________\|\n_____________199________________________________________________152\n	112 -- 118	154 -- 160	-33.2648 kcal/mol	10.6544 kcal/mol	13.9801 kcal/mol	74 120@LB@ \| \|@LB@5'-GGA...UAUUC U UG U CAU AA ACCCA...AAA-3'@LB@ AGG CAUGG AUG AACUAC CGGUCA UGAA GAAGACAA@LB@ \|\|\| \|\|\|:\| \|\|\| \|\|\|\|\|\| \|\|\|:\|\| \|\|\|\| \|\|\|:\|\|\|\|@LB@ UCC GUAUC UAC UUGAUG GCCGGU ACUU CUUUUGUU@LB@3'-GUU...CCUAC UG U UACUCU A UAUUA...GGA-5'@LB@ \| \|@LB@ 199 152@LB@@LB@@LB@Energy -15.48 kcal/mol@LB@Hybridization Energy -33.2648 kcal/mol@LB@Unfolding Energy - mRNA 10.6544 kcal/mol@LB@Unfolding Energy - sRNA 13.9801 kcal/mol@LB@@LB@Position - mRNA 75 -- 119@LB@Position - sRNA 153 -- 198@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 154 -- 160@LB@
119	0.03213	0.6968	lmo2454	N/A	-17.21	0.037384	166 -- 217	153 -- 209	lmo2454	_____________165_____________218\n_____________\|_______________\|\n5'-GUG...GACGC__U____C_______AAGCC...AAA-3'\n______________UG_GGUG_AUGAAAA\n______________\|\|_\|:\|\|_\|\|\|\|\|\|\|\n______________AC_CUAC_UACUUUU\n3'-GUU...CGGUU__U____U_______GUUUA...GGA-5'\n_____________\|_______________\|\n_____________210_____________152\n	274 -- 280	157 -- 163	-10.6243 kcal/mol	2.77636 kcal/mol	0.905109 kcal/mol	165 218@LB@ \| \|@LB@5'-GUG...GACGC U C AAGCC...AAA-3'@LB@ UG GGUG AUGAAAA@LB@ \|\| \|:\|\| \|\|\|\|\|\|\|@LB@ AC CUAC UACUUUU@LB@3'-GUU...CGGUU U U GUUUA...GGA-5'@LB@ \| \|@LB@ 210 152@LB@@LB@@LB@Energy -17.21 kcal/mol@LB@Hybridization Energy -10.6243 kcal/mol@LB@Unfolding Energy - mRNA 2.77636 kcal/mol@LB@Unfolding Energy - sRNA 0.905109 kcal/mol@LB@@LB@Position - mRNA 166 -- 217@LB@Position - sRNA 153 -- 209@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 157 -- 163@LB@
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@
123	0.03258	0.6968	lmo1821	N/A	-14.83	0.104144	189 -- 278	153 -- 220	phosphoprotein phosphatase	_____________188_________279\n_____________\|___________\|\n5'-AGA...AUCAU___________CGGCG...UUG-3'\n______________AAUGAAGACAA\n______________\|\|\|\|\|\|:\|\|\|\|\n______________UUACUUUUGUU\n3'-GUU...UCUAC___________UAUUA...GGA-5'\n_____________\|___________\|\n_____________221_________152\n	250 -- 256	154 -- 160	-9.76744 kcal/mol	1.01794 kcal/mol	0.610258 kcal/mol	188 279@LB@ \| \|@LB@5'-AGA...AUCAU CGGCG...UUG-3'@LB@ AAUGAAGACAA@LB@ \|\|\|\|\|\|:\|\|\|\|@LB@ UUACUUUUGUU@LB@3'-GUU...UCUAC UAUUA...GGA-5'@LB@ \| \|@LB@ 221 152@LB@@LB@@LB@Energy -14.83 kcal/mol@LB@Hybridization Energy -9.76744 kcal/mol@LB@Unfolding Energy - mRNA 1.01794 kcal/mol@LB@Unfolding Energy - sRNA 0.610258 kcal/mol@LB@@LB@Position - mRNA 189 -- 278@LB@Position - sRNA 153 -- 220@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 154 -- 160@LB@
137	0.03627	0.6968	lmo2666	N/A	-15.01	0.096662	42 -- 111	153 -- 211	PTS galacticol transporter subunit IIB	_____________41__________________112\n_____________\|___________________\|\n5'-CUC...ACUCA___CGAAA___________AGUAA...UGG-3'\n______________GAG_____GAUGAAGACGA\n______________\|\|\|_____:\|\|\|\|\|:\|\|:\|\n______________CUC_____UUACUUUUGUU\n3'-GUU...GGUUA___UAC_____________UAUUA...GGA-5'\n_____________\|___________________\|\n_____________212_________________152\n	104 -- 110	154 -- 160	-11.8615 kcal/mol	1.60013 kcal/mol	0.933796 kcal/mol	41 112@LB@ \| \|@LB@5'-CUC...ACUCA CGAAA AGUAA...UGG-3'@LB@ GAG GAUGAAGACGA@LB@ \|\|\| :\|\|\|\|\|:\|\|:\|@LB@ CUC UUACUUUUGUU@LB@3'-GUU...GGUUA UAC UAUUA...GGA-5'@LB@ \| \|@LB@ 212 152@LB@@LB@@LB@Energy -15.01 kcal/mol@LB@Hybridization Energy -11.8615 kcal/mol@LB@Unfolding Energy - mRNA 1.60013 kcal/mol@LB@Unfolding Energy - sRNA 0.933796 kcal/mol@LB@@LB@Position - mRNA 42 -- 111@LB@Position - sRNA 153 -- 211@LB@Position Seed - mRNA 104 -- 110@LB@Position Seed - sRNA 154 -- 160@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@
159	0.04218	0.7139	lmo1454	rpoD	-16.27	0.056776	172 -- 217	153 -- 211	RNA polymerase sigma factor RpoD	_____________171_______________218\n_____________\|_________________\|\n5'-AGA...GUUAA___G________U____UAAUA...UAA-3'\n______________ACA_CGGCCAAU_GGAU\n______________\|\|\|_\|\|\|\|\|\|\|\|_:\|\|\|\n______________UGU_GCCGGUUA_UCUA\n3'-GUU...CUUGA____________C____CUUAC...GGA-5'\n_____________\|_________________\|\n_____________212_______________152\n	92 -- 98	171 -- 177	-19.258 kcal/mol	2.66151 kcal/mol	6.2749 kcal/mol	171 218@LB@ \| \|@LB@5'-AGA...GUUAA G U UAAUA...UAA-3'@LB@ ACA CGGCCAAU GGAU@LB@ \|\|\| \|\|\|\|\|\|\|\| :\|\|\|@LB@ UGU GCCGGUUA UCUA@LB@3'-GUU...CUUGA C CUUAC...GGA-5'@LB@ \| \|@LB@ 212 152@LB@@LB@@LB@Energy -16.27 kcal/mol@LB@Hybridization Energy -19.258 kcal/mol@LB@Unfolding Energy - mRNA 2.66151 kcal/mol@LB@Unfolding Energy - sRNA 6.2749 kcal/mol@LB@@LB@Position - mRNA 172 -- 217@LB@Position - sRNA 153 -- 211@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 171 -- 177@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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