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
191	0.0551	0.7607	lmo2853	N/A	-14.70	0.110014	201 -- 241	156 -- 201		_____________200_______________________________________________242\n_____________\|_________________________________________________\|\n5'-GGU...AGAAA________________________AA___U___ACGU____________UAUCC...UUC-3'\n______________GUGAG____AGAUAU_AACUGCGC__GGC_CAA_____UGAA__GAAGC\n______________:\|\|\|\|____\|\|\|:\|\|_\|\|\|\|:\|:\|__\|\|\|_\|\|\|_____\|\|\|\|__:\|\|:\|\n______________UACUC____UCUGUA_UUGAUGUG__CCG_GUU_____ACUU__UUUUG\n3'-GUU...UGCCC_____CGUA______C_________________ACUCU____AC_____UUUAU...GGA-5'\n_____________\|_________________________________________________\|\n_____________202_______________________________________________155\n	213 -- 219	178 -- 184	-28.7711 kcal/mol	7.06239 kcal/mol	14.0114 kcal/mol	200 242@LB@ \| \|@LB@5'-GGU...AGAAA AA U ACGU UAUCC...UUC-3'@LB@ GUGAG AGAUAU AACUGCGC GGC CAA UGAA GAAGC@LB@ :\|\|\|\| \|\|\|:\|\| \|\|\|\|:\|:\| \|\|\| \|\|\| \|\|\|\| :\|\|:\|@LB@ UACUC UCUGUA UUGAUGUG CCG GUU ACUU UUUUG@LB@3'-GUU...UGCCC CGUA C ACUCU AC UUUAU...GGA-5'@LB@ \| \|@LB@ 202 155@LB@@LB@@LB@Energy -14.70 kcal/mol@LB@Hybridization Energy -28.7711 kcal/mol@LB@Unfolding Energy - mRNA 7.06239 kcal/mol@LB@Unfolding Energy - sRNA 14.0114 kcal/mol@LB@@LB@Position - mRNA 201 -- 241@LB@Position - sRNA 156 -- 201@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 178 -- 184@LB@
68	0.01752	0.6733	lmo0547	N/A	-17.81	0.028341	205 -- 246	175 -- 207	DeoR family transcriptional regulator	_____________204_________________247\n_____________\|___________________\|\n5'-AGA...AAUGA_______A___AA____G_UAUGG...CUA-3'\n______________AAUGGGA_GAA__AAGA_A\n______________\|\|\|\|:\|\|_\|\|\|__\|\|:\|_\|\n______________UUACUCU_CUU__UUUU_U\n3'-GUU...GCCGG_______A___AC____G_UUAUU...GGA-5'\n_____________\|___________________\|\n_____________208_________________174\n	205 -- 211	167 -- 173	-10.1256 kcal/mol	0.951731 kcal/mol	0.954976 kcal/mol	204 247@LB@ \| \|@LB@5'-AGA...AAUGA A AA G UAUGG...CUA-3'@LB@ AAUGGGA GAA AAGA A@LB@ \|\|\|\|:\|\| \|\|\| \|\|:\| \|@LB@ UUACUCU CUU UUUU U@LB@3'-GUU...GCCGG A AC G UUAUU...GGA-5'@LB@ \| \|@LB@ 208 174@LB@@LB@@LB@Energy -17.81 kcal/mol@LB@Hybridization Energy -10.1256 kcal/mol@LB@Unfolding Energy - mRNA 0.951731 kcal/mol@LB@Unfolding Energy - sRNA 0.954976 kcal/mol@LB@@LB@Position - mRNA 205 -- 246@LB@Position - sRNA 175 -- 207@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 167 -- 173@LB@
31	0.00657	0.5515	lmo1828	N/A	-18.66	0.019040	211 -- 279	154 -- 211		_____________210__________280\n_____________\|____________\|\n5'-AGU...GAAAA____________UUGGG...AAU-3'\n______________GCAUGACGGGAU\n______________\|\|\|\|:\|\|\|\|\|\|\|\n______________CGUAUUGCCCUA\n3'-GUU...GGAUA____________CUCCG...GGA-5'\n_____________\|____________\|\n_____________212__________153\n	216 -- 222	200 -- 206	-19.8213 kcal/mol	2.93239 kcal/mol	6.43166 kcal/mol	210 280@LB@ \| \|@LB@5'-AGU...GAAAA UUGGG...AAU-3'@LB@ GCAUGACGGGAU@LB@ \|\|\|\|:\|\|\|\|\|\|\|@LB@ CGUAUUGCCCUA@LB@3'-GUU...GGAUA CUCCG...GGA-5'@LB@ \| \|@LB@ 212 153@LB@@LB@@LB@Energy -18.66 kcal/mol@LB@Hybridization Energy -19.8213 kcal/mol@LB@Unfolding Energy - mRNA 2.93239 kcal/mol@LB@Unfolding Energy - sRNA 6.43166 kcal/mol@LB@@LB@Position - mRNA 211 -- 279@LB@Position - sRNA 154 -- 211@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 200 -- 206@LB@
42	0.009182	0.5883	lmo1767	purM	-18.99	0.016282	211 -- 267	155 -- 213	phosphoribosylaminoimidazole synthetase	_____________210__________________________________________________________________________268\n_____________\|____________________________________________________________________________\|\n5'-GGA...ACAAA___AAU___A_AAA_______UA_UAAA_C____________A______________UCA__U_________C___UCAAA...UAG-3'\n______________UCG___GGC_G___AUGCAUA__G____G_AGGCGUGGACGU_GAA__GC_UGGCUA___AG___AGUGGAA_GCA\n______________\|\|\|___\|\|\|_\|___\|\|\|\|\|\|\|__\|____\|_\|\|\|\|:\|:\|\|\|:\|_\|\|\|__:\|_:\|\|\|:\|___\|\|___\|:\|\|:\|\|_:\|\|\n______________AGC___CCG_C___UACGUAU__C____C_UCCGUAUCUGUA_CUU__UG_GCCGGU___UC___UUACUUU_UGU\n3'-GUU...GUACA___________GGA_______UG_CCUA__________________GA__U______UAC__UAC___________UUAUU...GGA-5'\n_____________\|____________________________________________________________________________\|\n_____________214__________________________________________________________________________154\n	257 -- 263	158 -- 164	-45.9009 kcal/mol	14.0255 kcal/mol	22.2914 kcal/mol	210 268@LB@ \| \|@LB@5'-GGA...ACAAA AAU A AAA UA UAAA C A UCA U C UCAAA...UAG-3'@LB@ UCG GGC G AUGCAUA G G AGGCGUGGACGU GAA GC UGGCUA AG AGUGGAA GCA@LB@ \|\|\| \|\|\| \| \|\|\|\|\|\|\| \| \| \|\|\|\|:\|:\|\|\|:\| \|\|\| :\| :\|\|\|:\| \|\| \|:\|\|:\|\| :\|\|@LB@ AGC CCG C UACGUAU C C UCCGUAUCUGUA CUU UG GCCGGU UC UUACUUU UGU@LB@3'-GUU...GUACA GGA UG CCUA GA U UAC UAC UUAUU...GGA-5'@LB@ \| \|@LB@ 214 154@LB@@LB@@LB@Energy -18.99 kcal/mol@LB@Hybridization Energy -45.9009 kcal/mol@LB@Unfolding Energy - mRNA 14.0255 kcal/mol@LB@Unfolding Energy - sRNA 22.2914 kcal/mol@LB@@LB@Position - mRNA 211 -- 267@LB@Position - sRNA 155 -- 213@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 158 -- 164@LB@
90	0.02372	0.6733	lmo2712	N/A	-17.76	0.029098	218 -- 285	160 -- 210	gluconate kinase	_____________217________286\n_____________\|__________\|\n5'-AGA...AAAAU__________CUGUU...CGA-3'\n______________GCGGGGUGAG\n______________:\|\|\|\|:\|\|\|\|\n______________UGCCCUACUC\n3'-GUU...CGUAU__________CGUAU...GGA-5'\n_____________\|__________\|\n_____________211________159\n	190 -- 196	197 -- 203	-16.6296 kcal/mol	4.31289 kcal/mol	0.38676 kcal/mol	217 286@LB@ \| \|@LB@5'-AGA...AAAAU CUGUU...CGA-3'@LB@ GCGGGGUGAG@LB@ :\|\|\|\|:\|\|\|\|@LB@ UGCCCUACUC@LB@3'-GUU...CGUAU CGUAU...GGA-5'@LB@ \| \|@LB@ 211 159@LB@@LB@@LB@Energy -17.76 kcal/mol@LB@Hybridization Energy -16.6296 kcal/mol@LB@Unfolding Energy - mRNA 4.31289 kcal/mol@LB@Unfolding Energy - sRNA 0.38676 kcal/mol@LB@@LB@Position - mRNA 218 -- 285@LB@Position - sRNA 160 -- 210@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 197 -- 203@LB@
116	0.03152	0.6968	lmo1963	N/A	-17.16	0.038227	218 -- 258	130 -- 166		_____________217___________________________________________259\n_____________\|_____________________________________________\|\n5'-ACA...CACAU_________AAC________A__GUC___U___________U___GGUGA...UCC-3'\n______________UGAAUGGAA___GCGAAUAA_GA___UGG_UGUUUGGGCAG_UGU\n______________\|\|\|\|\|\|:\|\|___:\|:\|\|\|\|\|_\|\|___\|\|\|_\|\|\|:\|:::\|\|\|_\|\|\|\n______________ACUUACUUU___UGUUUAUU_CU___ACC_ACAGAUUUGUC_ACA\n3'-GUU...ACUCU____________________A__AAA_______________U___GACUG...GGA-5'\n_____________\|_____________________________________________\|\n_____________167___________________________________________129\n	220 -- 226	158 -- 164	-34.7415 kcal/mol	9.15867 kcal/mol	13.701 kcal/mol	217 259@LB@ \| \|@LB@5'-ACA...CACAU AAC A GUC U U GGUGA...UCC-3'@LB@ UGAAUGGAA GCGAAUAA GA UGG UGUUUGGGCAG UGU@LB@ \|\|\|\|\|\|:\|\| :\|:\|\|\|\|\| \|\| \|\|\| \|\|\|:\|:::\|\|\| \|\|\|@LB@ ACUUACUUU UGUUUAUU CU ACC ACAGAUUUGUC ACA@LB@3'-GUU...ACUCU A AAA U GACUG...GGA-5'@LB@ \| \|@LB@ 167 129@LB@@LB@@LB@Energy -17.16 kcal/mol@LB@Hybridization Energy -34.7415 kcal/mol@LB@Unfolding Energy - mRNA 9.15867 kcal/mol@LB@Unfolding Energy - sRNA 13.701 kcal/mol@LB@@LB@Position - mRNA 218 -- 258@LB@Position - sRNA 130 -- 166@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 158 -- 164@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@
33	0.006763	0.5515	lmo1941	N/A	-21.42	0.004845	223 -- 286	154 -- 207		_____________222___________________________________________________________________287\n_____________\|_____________________________________________________________________\|\n5'-UAG...AGAAA_______AUACGAAGAACC___UGAUUAU________UU___AA_________________UC______UGAAC...UGU-3'\n______________AACGGGA____________GGC_______GACAUGAG__CUG___GGCCA___AGAUGAAU___AACAA\n______________\|\|\|\|\|\|\|____________\|\|\|_______\|\|\|\|\|\|\|:__\|\|:___\|\|\|\|\|___\|\|\|\|\|\|\|\|___\|\|\|\|\|\n______________UUGCCCU____________CCG_______CUGUACUU__GAU___CCGGU___UCUACUUA___UUGUU\n3'-GUU...ACGUA_______ACU____________UAU_________________GUG_____UAC________CUU_____UAUUA...GGA-5'\n_____________\|_____________________________________________________________________\|\n_____________208___________________________________________________________________153\n	273 -- 279	162 -- 168	-39.5283 kcal/mol	10.6608 kcal/mol	18.6655 kcal/mol	222 287@LB@ \| \|@LB@5'-UAG...AGAAA AUACGAAGAACC UGAUUAU UU AA UC UGAAC...UGU-3'@LB@ AACGGGA GGC GACAUGAG CUG GGCCA AGAUGAAU AACAA@LB@ \|\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|\|: \|\|: \|\|\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ UUGCCCU CCG CUGUACUU GAU CCGGU UCUACUUA UUGUU@LB@3'-GUU...ACGUA ACU UAU GUG UAC CUU UAUUA...GGA-5'@LB@ \| \|@LB@ 208 153@LB@@LB@@LB@Energy -21.42 kcal/mol@LB@Hybridization Energy -39.5283 kcal/mol@LB@Unfolding Energy - mRNA 10.6608 kcal/mol@LB@Unfolding Energy - sRNA 18.6655 kcal/mol@LB@@LB@Position - mRNA 223 -- 286@LB@Position - sRNA 154 -- 207@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 162 -- 168@LB@
75	0.01961	0.6733	lmo0383	N/A	-20.23	0.008871	224 -- 265	150 -- 186	methylmalonate-semialdehyde dehydrogenase	_____________223________________________________________266\n_____________\|__________________________________________\|\n5'-UUC...UUAAA_______AUUG_____G______UC___A_U___________AUAUG...AAG-3'\n______________GAAUUAU____ACGGC_AAUGGG__GAG_G_AAGACAGAUAA\n______________\|\|\|:\|\|:____\|\|\|\|\|_\|\|\|\|:\|__\|\|:_\|_\|\|:\|\|\|:\|\|\|\|\n______________CUUGAUG____UGCCG_UUACUC__CUU_C_UUUUGUUUAUU\n3'-GUU...CUGUA________________G______UA___A_____________ACUAA...GGA-5'\n_____________\|__________________________________________\|\n_____________187________________________________________149\n	257 -- 263	152 -- 158	-34.2826 kcal/mol	8.25616 kcal/mol	13.66 kcal/mol	223 266@LB@ \| \|@LB@5'-UUC...UUAAA AUUG G UC A U AUAUG...AAG-3'@LB@ GAAUUAU ACGGC AAUGGG GAG G AAGACAGAUAA@LB@ \|\|\|:\|\|: \|\|\|\|\| \|\|\|\|:\| \|\|: \| \|\|:\|\|\|:\|\|\|\|@LB@ CUUGAUG UGCCG UUACUC CUU C UUUUGUUUAUU@LB@3'-GUU...CUGUA G UA A ACUAA...GGA-5'@LB@ \| \|@LB@ 187 149@LB@@LB@@LB@Energy -20.23 kcal/mol@LB@Hybridization Energy -34.2826 kcal/mol@LB@Unfolding Energy - mRNA 8.25616 kcal/mol@LB@Unfolding Energy - sRNA 13.66 kcal/mol@LB@@LB@Position - mRNA 224 -- 265@LB@Position - sRNA 150 -- 186@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 152 -- 158@LB@
147	0.03815	0.6968	lmo0655	N/A	-15.78	0.070044	227 -- 290	154 -- 212	phosphoprotein phosphatase	_____________226_____________291\n_____________\|_______________\|\n______5'-AACAA______UU_______CCACA...UUG-3'\n______________GAGA_G__UGAAGAC\n______________\|\|\|\|_\|__\|\|\|\|:\|\|\n______________CUCU_C__ACUUUUG\n3'-GUU...GGUUA____A_UU_______UUUAU...GGA-5'\n_____________\|_______________\|\n_____________213_____________153\n	13 -- 19	156 -- 162	-12.8457 kcal/mol	3.32795 kcal/mol	0.916023 kcal/mol	226 291@LB@ \| \|@LB@ 5'-AACAA UU CCACA...UUG-3'@LB@ GAGA G UGAAGAC@LB@ \|\|\|\| \| \|\|\|\|:\|\|@LB@ CUCU C ACUUUUG@LB@3'-GUU...GGUUA A UU UUUAU...GGA-5'@LB@ \| \|@LB@ 213 153@LB@@LB@@LB@Energy -15.78 kcal/mol@LB@Hybridization Energy -12.8457 kcal/mol@LB@Unfolding Energy - mRNA 3.32795 kcal/mol@LB@Unfolding Energy - sRNA 0.916023 kcal/mol@LB@@LB@Position - mRNA 227 -- 290@LB@Position - sRNA 154 -- 212@LB@Position Seed - mRNA 13 -- 19@LB@Position Seed - sRNA 156 -- 162@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