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
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@
186	0.05422	0.7607	lmo2356	N/A	-15.92	0.066009	162 -- 205	129 -- 170	lmo2356	_____________161___________________206\n_____________\|_____________________\|\n5'-CUC...AAAGA_______AUUGAU________UUUGA...UUG-3'\n______________GAGAUGA______GUGAGGAU\n______________\|\|\|\|\|\|\|______:\|\|\|::\|:\n______________CUCUACU______UACUUUUG\n3'-GUU...GGUUA_____________________UUUAU...GGA-5'\n_____________\|_____________________\|\n_____________171___________________128\n	176 -- 182	156 -- 162	-14.0636 kcal/mol	2.1522 kcal/mol	0.916023 kcal/mol	161 206@LB@ \| \|@LB@5'-CUC...AAAGA AUUGAU UUUGA...UUG-3'@LB@ GAGAUGA GUGAGGAU@LB@ \|\|\|\|\|\|\| :\|\|\|::\|:@LB@ CUCUACU UACUUUUG@LB@3'-GUU...GGUUA UUUAU...GGA-5'@LB@ \| \|@LB@ 171 128@LB@@LB@@LB@Energy -15.92 kcal/mol@LB@Hybridization Energy -14.0636 kcal/mol@LB@Unfolding Energy - mRNA 2.1522 kcal/mol@LB@Unfolding Energy - sRNA 0.916023 kcal/mol@LB@@LB@Position - mRNA 162 -- 205@LB@Position - sRNA 129 -- 170@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 156 -- 162@LB@
120	0.03214	0.6968	lmo0368	N/A	-17.05	0.040150	163 -- 213	95 -- 164		_____________162______________________________________________214\n_____________\|________________________________________________\|\n5'-UGC...AAUGA_____A_____AA_______AGGGA___G______G_______A____AUUUG...UUC-3'\n______________AAGCA___GUC__UGAUUAG_____GCC_AUUUUA_UGGAAGA_UGGG\n______________\|\|:\|\|___\|\|\|__\|\|\|:\|\|\|_____\|\|\|_\|\|\|:\|\|_\|\|\|\|\|\|\|_\|\|\|:\n______________UUUGU___CAG__ACUGAUC_____CGG_UAAGAU_ACCUUCU_ACCU\n3'-GUU...ACAGA_____CUA____________AA_____________A____________AUGUG...GGA-5'\n_____________\|________________________________________________\|\n_____________165______________________________________________94\n	202 -- 208	99 -- 105	-32.1999 kcal/mol	10.9316 kcal/mol	9.49359 kcal/mol	162 214@LB@ \| \|@LB@5'-UGC...AAUGA A AA AGGGA G G A AUUUG...UUC-3'@LB@ AAGCA GUC UGAUUAG GCC AUUUUA UGGAAGA UGGG@LB@ \|\|:\|\| \|\|\| \|\|\|:\|\|\| \|\|\| \|\|\|:\|\| \|\|\|\|\|\|\| \|\|\|:@LB@ UUUGU CAG ACUGAUC CGG UAAGAU ACCUUCU ACCU@LB@3'-GUU...ACAGA CUA AA A AUGUG...GGA-5'@LB@ \| \|@LB@ 165 94@LB@@LB@@LB@Energy -17.05 kcal/mol@LB@Hybridization Energy -32.1999 kcal/mol@LB@Unfolding Energy - mRNA 10.9316 kcal/mol@LB@Unfolding Energy - sRNA 9.49359 kcal/mol@LB@@LB@Position - mRNA 163 -- 213@LB@Position - sRNA 95 -- 164@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 99 -- 105@LB@
29	0.005638	0.5232	lmo0014	qoxB	-19.61	0.012062	164 -- 215	168 -- 211	AA3-600 quinol oxidase subunit I	_____________163____________216\n_____________\|______________\|\n5'-CGG...CGCGA_____A________AAAUG...CUU-3'\n______________AGAUG_AAUGAAGA\n______________\|\|\|\|\|_\|\|\|\|\|\|:\|\n______________UCUAC_UUACUUUU\n3'-GUU...GUUAC______________GUUUA...GGA-5'\n_____________\|______________\|\n_____________212____________167\n	111 -- 117	157 -- 163	-11.9482 kcal/mol	0.56531 kcal/mol	0.884237 kcal/mol	163 216@LB@ \| \|@LB@5'-CGG...CGCGA A AAAUG...CUU-3'@LB@ AGAUG AAUGAAGA@LB@ \|\|\|\|\| \|\|\|\|\|\|:\|@LB@ UCUAC UUACUUUU@LB@3'-GUU...GUUAC GUUUA...GGA-5'@LB@ \| \|@LB@ 212 167@LB@@LB@@LB@Energy -19.61 kcal/mol@LB@Hybridization Energy -11.9482 kcal/mol@LB@Unfolding Energy - mRNA 0.56531 kcal/mol@LB@Unfolding Energy - sRNA 0.884237 kcal/mol@LB@@LB@Position - mRNA 164 -- 215@LB@Position - sRNA 168 -- 211@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 157 -- 163@LB@
50	0.01167	0.599	lmo0850	N/A	-18.65	0.019190	166 -- 190	141 -- 165		_____________165________________________191\n_____________\|__________________________\|\n5'-UGG...AAAGA____AAAAUAAAAA____________AUUUU...AAU-3'\n______________GAGA__________GAAUGAAAACAA\n______________\|\|\|\|__________\|\|\|\|\|\|\|\|\|\|\|\|\n______________CUCU__________CUUACUUUUGUU\n3'-GUU...GGUUA____A_____________________UAUUA...GGA-5'\n_____________\|__________________________\|\n_____________166________________________140\n	171 -- 177	154 -- 160	-14.3235 kcal/mol	1.0644 kcal/mol	0.933796 kcal/mol	165 191@LB@ \| \|@LB@5'-UGG...AAAGA AAAAUAAAAA AUUUU...AAU-3'@LB@ GAGA GAAUGAAAACAA@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|@LB@ CUCU CUUACUUUUGUU@LB@3'-GUU...GGUUA A UAUUA...GGA-5'@LB@ \| \|@LB@ 166 140@LB@@LB@@LB@Energy -18.65 kcal/mol@LB@Hybridization Energy -14.3235 kcal/mol@LB@Unfolding Energy - mRNA 1.0644 kcal/mol@LB@Unfolding Energy - sRNA 0.933796 kcal/mol@LB@@LB@Position - mRNA 166 -- 190@LB@Position - sRNA 141 -- 165@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 154 -- 160@LB@
84	0.02276	0.6733	lmo2467	N/A	-18.10	0.024762	166 -- 213	154 -- 198	chitin-binding protein	_____________165__________________________________________________214\n_____________\|____________________________________________________\|\n5'-UCA...CAAAA_____________________UGAAA__AA____CAUC______________CGAAG...AAC-3'\n______________AGGUAUA___AUGAACUAUAC_____GG__GGUG____AUGAA_GAAAAUGA\n______________\|\|\|:\|\|\|___\|\|\|\|\|\|\|\|:\|\|_____\|\|__::\|\|____\|\|\|\|\|_\|\|\|\|\|::\|\n______________UCCGUAU___UACUUGAUGUG_____CC__UUAC____UACUU_CUUUUGUU\n3'-GUU...CCUAC_______CUG__________________GG____UC_______A________UAUUA...GGA-5'\n_____________\|____________________________________________________\|\n_____________199__________________________________________________153\n	206 -- 212	155 -- 161	-31.7912 kcal/mol	6.75491 kcal/mol	13.9801 kcal/mol	165 214@LB@ \| \|@LB@5'-UCA...CAAAA UGAAA AA CAUC CGAAG...AAC-3'@LB@ AGGUAUA AUGAACUAUAC GG GGUG AUGAA GAAAAUGA@LB@ \|\|\|:\|\|\| \|\|\|\|\|\|\|\|:\|\| \|\| ::\|\| \|\|\|\|\| \|\|\|\|\|::\|@LB@ UCCGUAU UACUUGAUGUG CC UUAC UACUU CUUUUGUU@LB@3'-GUU...CCUAC CUG GG UC A UAUUA...GGA-5'@LB@ \| \|@LB@ 199 153@LB@@LB@@LB@Energy -18.10 kcal/mol@LB@Hybridization Energy -31.7912 kcal/mol@LB@Unfolding Energy - mRNA 6.75491 kcal/mol@LB@Unfolding Energy - sRNA 13.9801 kcal/mol@LB@@LB@Position - mRNA 166 -- 213@LB@Position - sRNA 154 -- 198@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 155 -- 161@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@
200	0.05675	0.7607	lmo0115	lmaD	-15.21	0.089253	167 -- 203	151 -- 184		_____________166_________________204\n_____________\|___________________\|\n5'-AUG...GUGGG____________A______UUUUA...UGG-3'\n______________AAUG_GAUGGAU_GAAAAC\n______________\|\|\|\|_\|\|\|\|:\|\|_\|\|\|\|\|\|\n______________UUAC_CUACUUA_CUUUUG\n3'-GUU...GCCGG____U______________UUUAU...GGA-5'\n_____________\|___________________\|\n_____________185_________________150\n	200 -- 206	162 -- 168	-16.3044 kcal/mol	1.75857 kcal/mol	0.941471 kcal/mol	166 204@LB@ \| \|@LB@5'-AUG...GUGGG A UUUUA...UGG-3'@LB@ AAUG GAUGGAU GAAAAC@LB@ \|\|\|\| \|\|\|\|:\|\| \|\|\|\|\|\|@LB@ UUAC CUACUUA CUUUUG@LB@3'-GUU...GCCGG U UUUAU...GGA-5'@LB@ \| \|@LB@ 185 150@LB@@LB@@LB@Energy -15.21 kcal/mol@LB@Hybridization Energy -16.3044 kcal/mol@LB@Unfolding Energy - mRNA 1.75857 kcal/mol@LB@Unfolding Energy - sRNA 0.941471 kcal/mol@LB@@LB@Position - mRNA 167 -- 203@LB@Position - sRNA 151 -- 184@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 162 -- 168@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@
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@

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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