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
131	0.03528	0.6968	lmo0788	N/A	-16.25	0.057193	177 -- 197	197 -- 213	lmo0788	_____________176______198\n_____________\|________\|\n5'-AAA...CGAAA________AAAAU...AUU-3'\n______________GGGAUGAG\n______________\|\|\|\|\|\|\|\|\n______________CCCUACUC\n3'-GUU...UAUUG________CGUAU...GGA-5'\n_____________\|________\|\n_____________214______196\n	191 -- 197	197 -- 203	-13.9782 kcal/mol	1.18818 kcal/mol	0.386531 kcal/mol	176 198@LB@ \| \|@LB@5'-AAA...CGAAA AAAAU...AUU-3'@LB@ GGGAUGAG@LB@ \|\|\|\|\|\|\|\|@LB@ CCCUACUC@LB@3'-GUU...UAUUG CGUAU...GGA-5'@LB@ \| \|@LB@ 214 196@LB@@LB@@LB@Energy -16.25 kcal/mol@LB@Hybridization Energy -13.9782 kcal/mol@LB@Unfolding Energy - mRNA 1.18818 kcal/mol@LB@Unfolding Energy - sRNA 0.386531 kcal/mol@LB@@LB@Position - mRNA 177 -- 197@LB@Position - sRNA 197 -- 213@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 197 -- 203@LB@
132	0.03532	0.6968	lmo1773	purB	-14.78	0.106383	9 -- 45	147 -- 186	adenylosuccinate lyase	_____________8___________________________46\n_____________\|___________________________\|\n5'-AUA...AUGUU____CU_____________________AUUAU...CUU-3'\n______________GAUG__GUGAAU__AAACAAAUGGUGA\n______________:\|\|\|__:\|\|\|\|\|__\|\|\|\|\|\|\|\|::\|\|\|\n______________UUAC__UACUUA__UUUGUUUAUUACU\n3'-GUU...GCCGG____UC______CU_____________AAAAC...GGA-5'\n_____________\|___________________________\|\n_____________187_________________________146\n	33 -- 39	153 -- 159	-18.9825 kcal/mol	5.01078 kcal/mol	5.96192 kcal/mol	8 46@LB@ \| \|@LB@5'-AUA...AUGUU CU AUUAU...CUU-3'@LB@ GAUG GUGAAU AAACAAAUGGUGA@LB@ :\|\|\| :\|\|\|\|\| \|\|\|\|\|\|\|\|::\|\|\|@LB@ UUAC UACUUA UUUGUUUAUUACU@LB@3'-GUU...GCCGG UC CU AAAAC...GGA-5'@LB@ \| \|@LB@ 187 146@LB@@LB@@LB@Energy -14.78 kcal/mol@LB@Hybridization Energy -18.9825 kcal/mol@LB@Unfolding Energy - mRNA 5.01078 kcal/mol@LB@Unfolding Energy - sRNA 5.96192 kcal/mol@LB@@LB@Position - mRNA 9 -- 45@LB@Position - sRNA 147 -- 186@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 153 -- 159@LB@
133	0.03548	0.6968	lmo2772	N/A	-15.87	0.067267	191 -- 210	179 -- 199	PTS beta-glucoside transporter subunit IIABC	_____________190__________________211\n_____________\|____________________\|\n5'-GCG...UUUAG____AU______________AAUCA...AAU-3'\n______________GAGG__UAG_CAUGGACUAC\n______________\|\|\|\|__\|\|\|_\|\|\|\|:\|\|\|\|\|\n______________CUCC__AUC_GUACUUGAUG\n3'-GUU...CCCUA____GU___U__________UGCCG...GGA-5'\n_____________\|____________________\|\n_____________200__________________178\n	203 -- 209	180 -- 186	-24.3176 kcal/mol	4.09739 kcal/mol	10.4768 kcal/mol	190 211@LB@ \| \|@LB@5'-GCG...UUUAG AU AAUCA...AAU-3'@LB@ GAGG UAG CAUGGACUAC@LB@ \|\|\|\| \|\|\| \|\|\|\|:\|\|\|\|\|@LB@ CUCC AUC GUACUUGAUG@LB@3'-GUU...CCCUA GU U UGCCG...GGA-5'@LB@ \| \|@LB@ 200 178@LB@@LB@@LB@Energy -15.87 kcal/mol@LB@Hybridization Energy -24.3176 kcal/mol@LB@Unfolding Energy - mRNA 4.09739 kcal/mol@LB@Unfolding Energy - sRNA 10.4768 kcal/mol@LB@@LB@Position - mRNA 191 -- 210@LB@Position - sRNA 179 -- 199@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 180 -- 186@LB@
134	0.0358	0.6968	lmo2682	kdpA	-15.50	0.078936	69 -- 121	151 -- 202	potassium-transporting ATPase subunit A	_____________68_____________________________________________122\n_____________\|______________________________________________\|\n5'-ACA...UUGGU___AU___UG_____AAGAG______G___________CG______GGGUG...AAA-3'\n______________AGG__UAG__GUGGA_____UACGGU_AA_GGGGUGAA__GAAAAU\n______________\|\|\|__\|\|\|__:\|\|:\|_____:\|\|\|\|:_\|\|_\|:\|:\|\|\|\|__\|\|\|\|\|:\n______________UCC__AUC__UACUU_____GUGCCG_UU_CUCUACUU__CUUUUG\n3'-GUU...CCUAC___GU___UG_____GAU________G__A________A_______UUUAU...GGA-5'\n_____________\|______________________________________________\|\n_____________203____________________________________________150\n	102 -- 108	163 -- 169	-34.0107 kcal/mol	9.08348 kcal/mol	13.9626 kcal/mol	68 122@LB@ \| \|@LB@5'-ACA...UUGGU AU UG AAGAG G CG GGGUG...AAA-3'@LB@ AGG UAG GUGGA UACGGU AA GGGGUGAA GAAAAU@LB@ \|\|\| \|\|\| :\|\|:\| :\|\|\|\|: \|\| \|:\|:\|\|\|\| \|\|\|\|\|:@LB@ UCC AUC UACUU GUGCCG UU CUCUACUU CUUUUG@LB@3'-GUU...CCUAC GU UG GAU G A A UUUAU...GGA-5'@LB@ \| \|@LB@ 203 150@LB@@LB@@LB@Energy -15.50 kcal/mol@LB@Hybridization Energy -34.0107 kcal/mol@LB@Unfolding Energy - mRNA 9.08348 kcal/mol@LB@Unfolding Energy - sRNA 13.9626 kcal/mol@LB@@LB@Position - mRNA 69 -- 121@LB@Position - sRNA 151 -- 202@LB@Position Seed - mRNA 102 -- 108@LB@Position Seed - sRNA 163 -- 169@LB@
135	0.03605	0.6968	lmo1003	N/A	-16.96	0.041836	78 -- 154	154 -- 221	phosphotransferase system enzyme I	_____________77_______________________________________________________________________________________155\n_____________\|________________________________________________________________________________________\|\n5'-GUG...CUUAA____AUCA_____________CUCUUG___U___UAA______CU_____UACUAU______U_AA___A_C______AAA_______UUGAA...AAG-3'\n______________AUCA____UGGGCG_UUAUGU______GUA_UGG____AGGCG__GACAU______CUACAC_G__GGU_G_GAUGAA___GAAGCAA\n______________\|\|\|\|____:\|\|\|\|\|_:\|\|\|\|:______:\|\|_:\|\|____\|\|\|\|:__\|\|\|\|\|______\|\|\|\|\|\|_\|__::\|_\|_\|\|\|\|\|\|___:\|\|:\|\|\|\n______________UAGU____GCCCGC_GAUACG______UAU_GCC____UCCGU__CUGUA______GAUGUG_C__UUA_C_CUACUU___UUUUGUU\n3'-GUU...AACGG____ACAA______G_______________U___CUAC_____AU_____CUU_________C_GG_____U______AC________UAUUA...GGA-5'\n_____________\|________________________________________________________________________________________\|\n_____________222______________________________________________________________________________________153\n	148 -- 154	154 -- 160	-50.8348 kcal/mol	18.1196 kcal/mol	22.592 kcal/mol	77 155@LB@ \| \|@LB@5'-GUG...CUUAA AUCA CUCUUG U UAA CU UACUAU U AA A C AAA UUGAA...AAG-3'@LB@ AUCA UGGGCG UUAUGU GUA UGG AGGCG GACAU CUACAC G GGU G GAUGAA GAAGCAA@LB@ \|\|\|\| :\|\|\|\|\| :\|\|\|\|: :\|\| :\|\| \|\|\|\|: \|\|\|\|\| \|\|\|\|\|\| \| ::\| \| \|\|\|\|\|\| :\|\|:\|\|\|@LB@ UAGU GCCCGC GAUACG UAU GCC UCCGU CUGUA GAUGUG C UUA C CUACUU UUUUGUU@LB@3'-GUU...AACGG ACAA G U CUAC AU CUU C GG U AC UAUUA...GGA-5'@LB@ \| \|@LB@ 222 153@LB@@LB@@LB@Energy -16.96 kcal/mol@LB@Hybridization Energy -50.8348 kcal/mol@LB@Unfolding Energy - mRNA 18.1196 kcal/mol@LB@Unfolding Energy - sRNA 22.592 kcal/mol@LB@@LB@Position - mRNA 78 -- 154@LB@Position - sRNA 154 -- 221@LB@Position Seed - mRNA 148 -- 154@LB@Position Seed - sRNA 154 -- 160@LB@
136	0.03623	0.6968	lmo1567	citZ	-17.33	0.035419	8 -- 31	169 -- 198	citrate synthase	_____________7______________________________32\n_____________\|______________________________\|\n____5'-CGAAAAA__________________________U___UCCAC...ACG-3'\n______________AGGUGUAG______GCUAUAUGGCCG_UGA\n______________\|\|\|::\|\|\|______:\|\|\|:\|:\|\|\|\|:_\|\|\|\n______________UCCGUAUC______UGAUGUGCCGGU_ACU\n3'-GUU...CCUAC________UGUACU____________U___CUACU...GGA-5'\n_____________\|______________________________\|\n_____________199____________________________168\n	21 -- 27	173 -- 179	-29.4881 kcal/mol	5.57901 kcal/mol	13.3393 kcal/mol	7 32@LB@ \| \|@LB@ 5'-CGAAAAA U UCCAC...ACG-3'@LB@ AGGUGUAG GCUAUAUGGCCG UGA@LB@ \|\|\|::\|\|\| :\|\|\|:\|:\|\|\|\|: \|\|\|@LB@ UCCGUAUC UGAUGUGCCGGU ACU@LB@3'-GUU...CCUAC UGUACU U CUACU...GGA-5'@LB@ \| \|@LB@ 199 168@LB@@LB@@LB@Energy -17.33 kcal/mol@LB@Hybridization Energy -29.4881 kcal/mol@LB@Unfolding Energy - mRNA 5.57901 kcal/mol@LB@Unfolding Energy - sRNA 13.3393 kcal/mol@LB@@LB@Position - mRNA 8 -- 31@LB@Position - sRNA 169 -- 198@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 173 -- 179@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@
138	0.03642	0.6968	lmo0509	prs	-15.18	0.090372	180 -- 241	157 -- 211	phosphoribosyl pyrophosphate synthetase	_____________179____________________________________242\n_____________\|______________________________________\|\n5'-AAC...GAAGA_____G______G__AG_____A_C_____C_______AUGAA...UCC-3'\n______________AAUUA_UAUGGC_GA__GAGAU_G_AAUGG_AGGCAAA\n______________\|\|:\|\|_:\|:\|\|\|_:\|__\|\|\|\|\|_\|_\|\|\|\|:_\|::\|\|\|\|\n______________UUGAU_GUGCCG_UU__CUCUA_C_UUACU_UUUGUUU\n3'-GUU...UGUAC____________G__A______________________AUUAC...GGA-5'\n_____________\|______________________________________\|\n_____________212____________________________________156\n	206 -- 212	153 -- 159	-24.2745 kcal/mol	6.00947 kcal/mol	10.6652 kcal/mol	179 242@LB@ \| \|@LB@5'-AAC...GAAGA G G AG A C C AUGAA...UCC-3'@LB@ AAUUA UAUGGC GA GAGAU G AAUGG AGGCAAA@LB@ \|\|:\|\| :\|:\|\|\| :\| \|\|\|\|\| \| \|\|\|\|: \|::\|\|\|\|@LB@ UUGAU GUGCCG UU CUCUA C UUACU UUUGUUU@LB@3'-GUU...UGUAC G A AUUAC...GGA-5'@LB@ \| \|@LB@ 212 156@LB@@LB@@LB@Energy -15.18 kcal/mol@LB@Hybridization Energy -24.2745 kcal/mol@LB@Unfolding Energy - mRNA 6.00947 kcal/mol@LB@Unfolding Energy - sRNA 10.6652 kcal/mol@LB@@LB@Position - mRNA 180 -- 241@LB@Position - sRNA 157 -- 211@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 153 -- 159@LB@
139	0.03644	0.6968	lmo2566	N/A	-16.54	0.050390	198 -- 240	121 -- 170	lmo2566	_____________197_________________241\n_____________\|___________________\|\n5'-GAA...ACAUA_________AUA_______CCUUA...CAG-3'\n______________GAGAUGAAU___GAAAACA\n______________\|\|\|\|\|\|\|\|\|___\|\|\|\|\|\|\|\n______________CUCUACUUA___CUUUUGU\n3'-GUU...GGUUA___________________UUAUU...GGA-5'\n_____________\|___________________\|\n_____________171_________________120\n	210 -- 216	155 -- 161	-17.6586 kcal/mol	1.26524 kcal/mol	0.929544 kcal/mol	197 241@LB@ \| \|@LB@5'-GAA...ACAUA AUA CCUUA...CAG-3'@LB@ GAGAUGAAU GAAAACA@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ CUCUACUUA CUUUUGU@LB@3'-GUU...GGUUA UUAUU...GGA-5'@LB@ \| \|@LB@ 171 120@LB@@LB@@LB@Energy -16.54 kcal/mol@LB@Hybridization Energy -17.6586 kcal/mol@LB@Unfolding Energy - mRNA 1.26524 kcal/mol@LB@Unfolding Energy - sRNA 0.929544 kcal/mol@LB@@LB@Position - mRNA 198 -- 240@LB@Position - sRNA 121 -- 170@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 155 -- 161@LB@
140	0.0365	0.6968	lmo1717	N/A	-17.46	0.033387	195 -- 217	147 -- 170		_____________194______________________218\n_____________\|________________________\|\n5'-UAG...AGUAG____C___________________AACAC...AAA-3'\n______________GAGA__GAUGAAAAUGGAUAGUGA\n______________\|\|\|\|__:\|\|\|\|\|\|\|:::\|\|\|:\|\|\|\n______________CUCU__UUACUUUUGUUUAUUACU\n3'-GUU...GGUUA____AC__________________AAAAC...GGA-5'\n_____________\|________________________\|\n_____________171______________________146\n	203 -- 209	155 -- 161	-21.6361 kcal/mol	2.67158 kcal/mol	5.93585 kcal/mol	194 218@LB@ \| \|@LB@5'-UAG...AGUAG C AACAC...AAA-3'@LB@ GAGA GAUGAAAAUGGAUAGUGA@LB@ \|\|\|\| :\|\|\|\|\|\|\|:::\|\|\|:\|\|\|@LB@ CUCU UUACUUUUGUUUAUUACU@LB@3'-GUU...GGUUA AC AAAAC...GGA-5'@LB@ \| \|@LB@ 171 146@LB@@LB@@LB@Energy -17.46 kcal/mol@LB@Hybridization Energy -21.6361 kcal/mol@LB@Unfolding Energy - mRNA 2.67158 kcal/mol@LB@Unfolding Energy - sRNA 5.93585 kcal/mol@LB@@LB@Position - mRNA 195 -- 217@LB@Position - sRNA 147 -- 170@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 155 -- 161@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

Use the following button if you want to resubmit the job with altered input or parameterization:

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service.

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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