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
64	0.01603	0.6733	lmo0131	N/A	-19.25	0.014339	193 -- 248	149 -- 204	_____________192____________________________________________________249\n_____________\|______________________________________________________\|\n5'-UGU...AAAAG____G_____G______AUCUCGA______AAAU________C___UAG_____AUAGU...UCG-3'\n______________GAGG_AUA_A_AUGGAU_______GCACGG____AUGGGAUG_GAU___GAGAA\n______________\|\|\|\|_\|\|\|_\|_\|\|\|:\|:_______:\|\|\|\|\|____\|\|\|:\|\|\|\|_:\|\|___\|\|:\|\|\n______________CUCC_UAU_U_UACUUG_______UGUGCC____UACUCUAC_UUA___CUUUU\n3'-GUU...CCCUA____G___C_G______A____________GGU_____________________GUUUA...GGA-5'\n_____________\|______________________________________________________\|\n_____________205____________________________________________________148\n	225 -- 231	165 -- 171	-32.0138 kcal/mol	8.31689 kcal/mol	13.9574 kcal/mol	192 249@LB@ \| \|@LB@5'-UGU...AAAAG G G AUCUCGA AAAU C UAG AUAGU...UCG-3'@LB@ GAGG AUA A AUGGAU GCACGG AUGGGAUG GAU GAGAA@LB@ \|\|\|\| \|\|\| \| \|\|\|:\|: :\|\|\|\|\| \|\|\|:\|\|\|\| :\|\| \|\|:\|\|@LB@ CUCC UAU U UACUUG UGUGCC UACUCUAC UUA CUUUU@LB@3'-GUU...CCCUA G C G A GGU GUUUA...GGA-5'@LB@ \| \|@LB@ 205 148@LB@@LB@@LB@Energy -19.25 kcal/mol@LB@Hybridization Energy -32.0138 kcal/mol@LB@Unfolding Energy - mRNA 8.31689 kcal/mol@LB@Unfolding Energy - sRNA 13.9574 kcal/mol@LB@@LB@Position - mRNA 193 -- 248@LB@Position - sRNA 149 -- 204@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 165 -- 171@LB@
72	0.01905	0.6733	lmo2074	N/A	-18.09	0.024896	131 -- 158	147 -- 174	_____________130___________________159\n_____________\|_____________________\|\n5'-AUG...GAAAU________A____________AUAAG...CGC-3'\n______________UAAUG_GA_GAAUGGGAACAA\n______________:\|\|\|\|_\|\|_\|\|\|\|\|::\|\|\|\|\|\n______________GUUAC_CU_CUUACUUUUGUU\n3'-GUU...UGCCG_____U__A____________UAUUA...GGA-5'\n_____________\|_____________________\|\n_____________175___________________146\n	144 -- 150	154 -- 160	-16.7779 kcal/mol	1.50572 kcal/mol	0.962339 kcal/mol	130 159@LB@ \| \|@LB@5'-AUG...GAAAU A AUAAG...CGC-3'@LB@ UAAUG GA GAAUGGGAACAA@LB@ :\|\|\|\| \|\| \|\|\|\|\|::\|\|\|\|\|@LB@ GUUAC CU CUUACUUUUGUU@LB@3'-GUU...UGCCG U A UAUUA...GGA-5'@LB@ \| \|@LB@ 175 146@LB@@LB@@LB@Energy -18.09 kcal/mol@LB@Hybridization Energy -16.7779 kcal/mol@LB@Unfolding Energy - mRNA 1.50572 kcal/mol@LB@Unfolding Energy - sRNA 0.962339 kcal/mol@LB@@LB@Position - mRNA 131 -- 158@LB@Position - sRNA 147 -- 174@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 154 -- 160@LB@
88	0.02298	0.6733	lmo0666	N/A	-13.39	0.184164	127 -- 173	156 -- 211	_____________126__________________________________________________________________________________174\n_____________\|____________________________________________________________________________________\|\n5'-AAG...AUUCA____A__GAACC______AA__C___AGU____AC___A__AAA_____GUUA______G_____GC_________________UCGUU...AUG-3'\n______________GCCA_CA______GGCGC__AU_GCA___AUGG__GGU_AG___AUAGA____GA___A_ACGGC_________GAAUGGAGAC\n______________\|\|\|\|_\|\|______\|\|\|\|\|__\|\|_\|\|\|___\|:\|\|__\|:\|_\|\|___\|\|\|\|\|____\|\|___\|_\|\|\|\|\|_________\|\|\|\|\|:\|:\|\|\n______________CGGU_GU______CCGCG__UA_CGU___UGCC__CUA_UC___UAUCU____CU___U_UGCCG_________CUUACUUUUG\n3'-GUU...CGCAA____A__ACAAGC_____GA______AU__________C__CG______GUA___UGA_G_____GUUACUCUA__________UUUAU...GGA-5'\n_____________\|____________________________________________________________________________________\|\n_____________212__________________________________________________________________________________155\n	167 -- 173	156 -- 162	-45.3275 kcal/mol	14.8697 kcal/mol	22.6898 kcal/mol	126 174@LB@ \| \|@LB@5'-AAG...AUUCA A GAACC AA C AGU AC A AAA GUUA G GC UCGUU...AUG-3'@LB@ GCCA CA GGCGC AU GCA AUGG GGU AG AUAGA GA A ACGGC GAAUGGAGAC@LB@ \|\|\|\| \|\| \|\|\|\|\| \|\| \|\|\| \|:\|\| \|:\| \|\| \|\|\|\|\| \|\| \| \|\|\|\|\| \|\|\|\|\|:\|:\|\|@LB@ CGGU GU CCGCG UA CGU UGCC CUA UC UAUCU CU U UGCCG CUUACUUUUG@LB@3'-GUU...CGCAA A ACAAGC GA AU C CG GUA UGA G GUUACUCUA UUUAU...GGA-5'@LB@ \| \|@LB@ 212 155@LB@@LB@@LB@Energy -13.39 kcal/mol@LB@Hybridization Energy -45.3275 kcal/mol@LB@Unfolding Energy - mRNA 14.8697 kcal/mol@LB@Unfolding Energy - sRNA 22.6898 kcal/mol@LB@@LB@Position - mRNA 127 -- 173@LB@Position - sRNA 156 -- 211@LB@Position Seed - mRNA 167 -- 173@LB@Position Seed - sRNA 156 -- 162@LB@
97	0.02539	0.6733	lmo2585	N/A	-13.14	0.201793	84 -- 125	164 -- 211	_____________83______126\n_____________\|_______\|\n5'-ACA...GAUGC_______AAGGG...AAG-3'\n______________GGCGGGA\n______________::\|\|\|\|\|\n______________UUGCCCU\n3'-GUU...ACGUA_______ACUCC...GGA-5'\n_____________\|_______\|\n_____________212_____163\n	178 -- 184	201 -- 207	-10.7547 kcal/mol	3.27081 kcal/mol	0.326294 kcal/mol	83 126@LB@ \| \|@LB@5'-ACA...GAUGC AAGGG...AAG-3'@LB@ GGCGGGA@LB@ ::\|\|\|\|\|@LB@ UUGCCCU@LB@3'-GUU...ACGUA ACUCC...GGA-5'@LB@ \| \|@LB@ 212 163@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -10.7547 kcal/mol@LB@Unfolding Energy - mRNA 3.27081 kcal/mol@LB@Unfolding Energy - sRNA 0.326294 kcal/mol@LB@@LB@Position - mRNA 84 -- 125@LB@Position - sRNA 164 -- 211@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 201 -- 207@LB@
106	0.02722	0.6733	lmo1616	N/A	-15.61	0.075454	67 -- 108	167 -- 211	_____________66______________________109\n_____________\|_______________________\|\n5'-AAG...AUAAC_____U_____GACU________AGGGC...UUU-3'\n______________GAACA_AUGUU____UGACUAGU\n______________:\|\|\|\|_\|\|\|\|:____\|\|\|\|\|\|\|\|\n______________UUUGU_UACAG____ACUGAUCA\n3'-GUU...ACAGA_____C_________________ACGGU...GGA-5'\n_____________\|_______________________\|\n_____________212_____________________166\n	90 -- 96	117 -- 123	-17.5219 kcal/mol	5.32799 kcal/mol	5.058 kcal/mol	66 109@LB@ \| \|@LB@5'-AAG...AUAAC U GACU AGGGC...UUU-3'@LB@ GAACA AUGUU UGACUAGU@LB@ :\|\|\|\| \|\|\|\|: \|\|\|\|\|\|\|\|@LB@ UUUGU UACAG ACUGAUCA@LB@3'-GUU...ACAGA C ACGGU...GGA-5'@LB@ \| \|@LB@ 212 166@LB@@LB@@LB@Energy -15.61 kcal/mol@LB@Hybridization Energy -17.5219 kcal/mol@LB@Unfolding Energy - mRNA 5.32799 kcal/mol@LB@Unfolding Energy - sRNA 5.058 kcal/mol@LB@@LB@Position - mRNA 67 -- 108@LB@Position - sRNA 167 -- 211@LB@Position Seed - mRNA 90 -- 96@LB@Position Seed - sRNA 117 -- 123@LB@
107	0.02737	0.6733	lmo1575	N/A	-17.23	0.037041	80 -- 118	156 -- 205	_____________79______119\n_____________\|_______\|\n5'-GUA...UCACA_______C-3'\n______________AAUGGGG\n______________\|\|:\|\|\|:\n______________UUGCCCU\n3'-GUU...ACGUA_______ACUCC...GGA-5'\n_____________\|_______\|\n_____________206_____155\n	293 -- 299	201 -- 207	-8.20946 kcal/mol	0.611387 kcal/mol	0.326294 kcal/mol	79 119@LB@ \| \|@LB@5'-GUA...UCACA C-3'@LB@ AAUGGGG@LB@ \|\|:\|\|\|:@LB@ UUGCCCU@LB@3'-GUU...ACGUA ACUCC...GGA-5'@LB@ \| \|@LB@ 206 155@LB@@LB@@LB@Energy -17.23 kcal/mol@LB@Hybridization Energy -8.20946 kcal/mol@LB@Unfolding Energy - mRNA 0.611387 kcal/mol@LB@Unfolding Energy - sRNA 0.326294 kcal/mol@LB@@LB@Position - mRNA 80 -- 118@LB@Position - sRNA 156 -- 205@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 201 -- 207@LB@
108	0.02743	0.6733	lmo2330	N/A	-16.53	0.050546	195 -- 214	191 -- 207	_____________194_________215\n_____________\|___________\|\n5'-ACG...GAGAA___________CAAGU...UUU-3'\n______________AGCGGGAUGAG\n______________\|:\|\|\|\|\|\|\|\|\|\n______________UUGCCCUACUC\n3'-GUU...ACGUA___________CGUAU...GGA-5'\n_____________\|___________\|\n_____________208_________190\n	199 -- 205	197 -- 203	-18.6004 kcal/mol	2.16538 kcal/mol	0.386761 kcal/mol	194 215@LB@ \| \|@LB@5'-ACG...GAGAA CAAGU...UUU-3'@LB@ AGCGGGAUGAG@LB@ \|:\|\|\|\|\|\|\|\|\|@LB@ UUGCCCUACUC@LB@3'-GUU...ACGUA CGUAU...GGA-5'@LB@ \| \|@LB@ 208 190@LB@@LB@@LB@Energy -16.53 kcal/mol@LB@Hybridization Energy -18.6004 kcal/mol@LB@Unfolding Energy - mRNA 2.16538 kcal/mol@LB@Unfolding Energy - sRNA 0.386761 kcal/mol@LB@@LB@Position - mRNA 195 -- 214@LB@Position - sRNA 191 -- 207@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 197 -- 203@LB@
109	0.02745	0.6733	lmo0843	N/A	-19.30	0.014041	79 -- 127	106 -- 151	_____________78____________________________________________________128\n_____________\|_____________________________________________________\|\n5'-CCG...GUCCA____C_________________________AUAAUUU__U_____________CCCUG...CUG-3'\n______________AGUG_UUUUGGUG_CU_GAC_GAUGUUUGA_______CU__UUGCCAUUUUAU\n______________\|:\|\|_\|\|\|\|\|\|\|\|_\|\|_:\|\|_\|\|\|\|\|:\|\|\|_______\|\|__\|\|\|\|\|\|\|\|:\|\|\|\n______________UUAC_AAAACCAC_GA_UUG_CUACAGACU_______GA__AACGGUAAGAUA\n3'-GUU...GUUUA____U________A__U___U__________________UC____________ACCUU...GGA-5'\n_____________\|_____________________________________________________\|\n_____________152___________________________________________________105\n	118 -- 124	109 -- 115	-38.6588 kcal/mol	9.72702 kcal/mol	18.7291 kcal/mol	78 128@LB@ \| \|@LB@5'-CCG...GUCCA C AUAAUUU U CCCUG...CUG-3'@LB@ AGUG UUUUGGUG CU GAC GAUGUUUGA CU UUGCCAUUUUAU@LB@ \|:\|\| \|\|\|\|\|\|\|\| \|\| :\|\| \|\|\|\|\|:\|\|\| \|\| \|\|\|\|\|\|\|\|:\|\|\|@LB@ UUAC AAAACCAC GA UUG CUACAGACU GA AACGGUAAGAUA@LB@3'-GUU...GUUUA U A U U UC ACCUU...GGA-5'@LB@ \| \|@LB@ 152 105@LB@@LB@@LB@Energy -19.30 kcal/mol@LB@Hybridization Energy -38.6588 kcal/mol@LB@Unfolding Energy - mRNA 9.72702 kcal/mol@LB@Unfolding Energy - sRNA 18.7291 kcal/mol@LB@@LB@Position - mRNA 79 -- 127@LB@Position - sRNA 106 -- 151@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 109 -- 115@LB@
110	0.02752	0.6733	lmo0057	N/A	-17.32	0.035592	178 -- 213	150 -- 185	_____________177_________________214\n_____________\|___________________\|\n5'-AAA...GCGGG_______CA__________AAGUA...AAG-3'\n______________AGUGGGA__UGAAUGAAGA\n______________\|:\|\|:\|\|__\|\|\|\|\|\|\|\|:\|\n______________UUACUCU__ACUUACUUUU\n3'-GUU...GCCGG___________________GUUUA...GGA-5'\n_____________\|___________________\|\n_____________186_________________149\n	201 -- 207	157 -- 163	-16.939 kcal/mol	2.5385 kcal/mol	0.930085 kcal/mol	177 214@LB@ \| \|@LB@5'-AAA...GCGGG CA AAGUA...AAG-3'@LB@ AGUGGGA UGAAUGAAGA@LB@ \|:\|\|:\|\| \|\|\|\|\|\|\|\|:\|@LB@ UUACUCU ACUUACUUUU@LB@3'-GUU...GCCGG GUUUA...GGA-5'@LB@ \| \|@LB@ 186 149@LB@@LB@@LB@Energy -17.32 kcal/mol@LB@Hybridization Energy -16.939 kcal/mol@LB@Unfolding Energy - mRNA 2.5385 kcal/mol@LB@Unfolding Energy - sRNA 0.930085 kcal/mol@LB@@LB@Position - mRNA 178 -- 213@LB@Position - sRNA 150 -- 185@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 157 -- 163@LB@
115	0.03087	0.6968	lmo0059	N/A	-17.38	0.034592	142 -- 189	155 -- 211	_____________141_______________________________________________190\n_____________\|_________________________________________________\|\n5'-AAG...UUAGC____G_____UU___U________________UUUU_____A_______GGGAG...CAU-3'\n______________AGGC__GGAU__AUG_GGCUGCGCG__CAAUG____UGAAU_GAAAGCG\n______________\|\|\|\|__:\|\|:__\|\|\|_::\|\|:\|:\|\|__\|\|\|\|\|____\|\|\|\|\|_\|\|\|\|:\|:\n______________UCCG__UCUG__UAC_UUGAUGUGC__GUUAC____ACUUA_CUUUUGU\n3'-GUU...CCUAC____UA___________________CG_____UCU______________UUAUU...GGA-5'\n_____________\|_________________________________________________\|\n_____________212_______________________________________________154\n	183 -- 189	155 -- 161	-35.3318 kcal/mol	12.9952 kcal/mol	13.976 kcal/mol	141 190@LB@ \| \|@LB@5'-AAG...UUAGC G UU U UUUU A GGGAG...CAU-3'@LB@ AGGC GGAU AUG GGCUGCGCG CAAUG UGAAU GAAAGCG@LB@ \|\|\|\| :\|\|: \|\|\| ::\|\|:\|:\|\| \|\|\|\|\| \|\|\|\|\| \|\|\|\|:\|:@LB@ UCCG UCUG UAC UUGAUGUGC GUUAC ACUUA CUUUUGU@LB@3'-GUU...CCUAC UA CG UCU UUAUU...GGA-5'@LB@ \| \|@LB@ 212 154@LB@@LB@@LB@Energy -17.38 kcal/mol@LB@Hybridization Energy -35.3318 kcal/mol@LB@Unfolding Energy - mRNA 12.9952 kcal/mol@LB@Unfolding Energy - sRNA 13.976 kcal/mol@LB@@LB@Position - mRNA 142 -- 189@LB@Position - sRNA 155 -- 211@LB@Position Seed - mRNA 183 -- 189@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:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching