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
142	0.03693	0.6968	lmo2586	N/A	-16.96	0.041696	196 -- 266	151 -- 227	formate dehydrogenase subunit alpha	_____________195______267\n_____________\|________\|\n5'-UUU...GUGGC________UGGUG...AUC-3'\n______________GCGGGAUG\n______________:\|\|\|\|\|\|\|\n______________UGCCCUAC\n3'-GUU...CGUAU________UCCGU...GGA-5'\n_____________\|________\|\n_____________228______150\n	240 -- 246	199 -- 205	-13.0644 kcal/mol	3.68871 kcal/mol	0.331032 kcal/mol	195 267@LB@ \| \|@LB@5'-UUU...GUGGC UGGUG...AUC-3'@LB@ GCGGGAUG@LB@ :\|\|\|\|\|\|\|@LB@ UGCCCUAC@LB@3'-GUU...CGUAU UCCGU...GGA-5'@LB@ \| \|@LB@ 228 150@LB@@LB@@LB@Energy -16.96 kcal/mol@LB@Hybridization Energy -13.0644 kcal/mol@LB@Unfolding Energy - mRNA 3.68871 kcal/mol@LB@Unfolding Energy - sRNA 0.331032 kcal/mol@LB@@LB@Position - mRNA 196 -- 266@LB@Position - sRNA 151 -- 227@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 199 -- 205@LB@
156	0.04133	0.7058	lmo1481	holA	-16.45	0.052293	189 -- 224	151 -- 199	DNA polymerase III subunit delta	_____________188_________225\n_____________\|___________\|\n5'-CAA...UGCCA___________GAUAC...UUU-3'\n______________GAAUGGAAACA\n______________\|\|\|\|\|:\|\|\|\|\|\n______________CUUACUUUUGU\n3'-GUU...CUCUA___________UUAUU...GGA-5'\n_____________\|___________\|\n_____________200_________150\n	213 -- 219	156 -- 162	-12.8572 kcal/mol	1.78423 kcal/mol	0.853601 kcal/mol	188 225@LB@ \| \|@LB@5'-CAA...UGCCA GAUAC...UUU-3'@LB@ GAAUGGAAACA@LB@ \|\|\|\|\|:\|\|\|\|\|@LB@ CUUACUUUUGU@LB@3'-GUU...CUCUA UUAUU...GGA-5'@LB@ \| \|@LB@ 200 150@LB@@LB@@LB@Energy -16.45 kcal/mol@LB@Hybridization Energy -12.8572 kcal/mol@LB@Unfolding Energy - mRNA 1.78423 kcal/mol@LB@Unfolding Energy - sRNA 0.853601 kcal/mol@LB@@LB@Position - mRNA 189 -- 224@LB@Position - sRNA 151 -- 199@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 156 -- 162@LB@
176	0.04979	0.7607	lmo1340	N/A	-16.63	0.048446	193 -- 216	151 -- 177		_____________192_____________217\n_____________\|_______________\|\n5'-UGC...UUGGA_______________AAAAU...CUG-3'\n______________GGCCA__GAGAUGAA\n______________\|\|\|\|\|__\|\|\|\|\|\|\|\|\n______________CCGGU__CUCUACUU\n3'-GUU...AUGUG_____UA________ACUUU...GGA-5'\n_____________\|_______________\|\n_____________178_____________150\n	199 -- 205	163 -- 169	-19.0992 kcal/mol	1.80937 kcal/mol	7.44208 kcal/mol	192 217@LB@ \| \|@LB@5'-UGC...UUGGA AAAAU...CUG-3'@LB@ GGCCA GAGAUGAA@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ CCGGU CUCUACUU@LB@3'-GUU...AUGUG UA ACUUU...GGA-5'@LB@ \| \|@LB@ 178 150@LB@@LB@@LB@Energy -16.63 kcal/mol@LB@Hybridization Energy -19.0992 kcal/mol@LB@Unfolding Energy - mRNA 1.80937 kcal/mol@LB@Unfolding Energy - sRNA 7.44208 kcal/mol@LB@@LB@Position - mRNA 193 -- 216@LB@Position - sRNA 151 -- 177@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 163 -- 169@LB@
183	0.0534	0.7607	lmo2583	N/A	-16.44	0.052604	178 -- 212	151 -- 181	DNA-binding response regulator	_____________177___________________________213\n_____________\|_____________________________\|\n5'-UAA...AAAUA_G_____AA______C_____________AACAA...AUG-3'\n______________A_ACGGU__GGUGAG___GGUGAAAAUGA\n______________\|_\|\|\|\|:__::\|\|\|\|___::\|\|\|\|\|\|::\|\n______________U_UGCCG__UUACUC___UUACUUUUGUU\n3'-GUU...CUUGA_G_____G_______UAC___________UAUUA...GGA-5'\n_____________\|_____________________________\|\n_____________182___________________________150\n	197 -- 203	155 -- 161	-21.6156 kcal/mol	3.93053 kcal/mol	8.33518 kcal/mol	177 213@LB@ \| \|@LB@5'-UAA...AAAUA G AA C AACAA...AUG-3'@LB@ A ACGGU GGUGAG GGUGAAAAUGA@LB@ \| \|\|\|\|: ::\|\|\|\| ::\|\|\|\|\|\|::\|@LB@ U UGCCG UUACUC UUACUUUUGUU@LB@3'-GUU...CUUGA G G UAC UAUUA...GGA-5'@LB@ \| \|@LB@ 182 150@LB@@LB@@LB@Energy -16.44 kcal/mol@LB@Hybridization Energy -21.6156 kcal/mol@LB@Unfolding Energy - mRNA 3.93053 kcal/mol@LB@Unfolding Energy - sRNA 8.33518 kcal/mol@LB@@LB@Position - mRNA 178 -- 212@LB@Position - sRNA 151 -- 181@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 155 -- 161@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@
55	0.01256	0.6043	lmo1725	N/A	-17.74	0.029271	269 -- 300	152 -- 185	GntR family tramscriptional regulator	_____________268______________________________301\n_____________\|________________________________\|\n5'-CAG...CAAAU___________G_______A___A________GU-3'\n______________GAUUACA_GGC_AAUG_GA_GGG_GAGGAUAA\n______________:\|:\|\|\|\|_\|\|\|_\|\|\|\|_\|\|_\|::_\|\|::\|:\|\|\n______________UUGAUGU_CCG_UUAC_CU_CUU_CUUUUGUU\n3'-GUU...UGUAC_______G___G____U__A___A________UAUUA...GGA-5'\n_____________\|________________________________\|\n_____________186______________________________151\n	291 -- 297	155 -- 161	-25.158 kcal/mol	5.52494 kcal/mol	9.66022 kcal/mol	268 301@LB@ \| \|@LB@5'-CAG...CAAAU G A A GU-3'@LB@ GAUUACA GGC AAUG GA GGG GAGGAUAA@LB@ :\|:\|\|\|\| \|\|\| \|\|\|\| \|\| \|:: \|\|::\|:\|\|@LB@ UUGAUGU CCG UUAC CU CUU CUUUUGUU@LB@3'-GUU...UGUAC G G U A A UAUUA...GGA-5'@LB@ \| \|@LB@ 186 151@LB@@LB@@LB@Energy -17.74 kcal/mol@LB@Hybridization Energy -25.158 kcal/mol@LB@Unfolding Energy - mRNA 5.52494 kcal/mol@LB@Unfolding Energy - sRNA 9.66022 kcal/mol@LB@@LB@Position - mRNA 269 -- 300@LB@Position - sRNA 152 -- 185@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 155 -- 161@LB@
111	0.02805	0.6801	lmo2841	N/A	-15.50	0.078879	184 -- 209	152 -- 178	sucrose phosphorylase	_____________183_______________________210\n_____________\|_________________________\|\n5'-UUU...AGGUA_____U__C____UUAA________CUUUC...AAC-3'\n______________AAUGA_GA_GAAU____GAAAACGA\n______________\|\|\|\|\|_\|\|_\|\|\|\|____\|\|\|\|\|\|:\|\n______________UUACU_CU_CUUA____CUUUUGUU\n3'-GUU...GCCGG________A________________UAUUA...GGA-5'\n_____________\|_________________________\|\n_____________179_______________________151\n	215 -- 221	154 -- 160	-12.3618 kcal/mol	2.60591 kcal/mol	0.959215 kcal/mol	183 210@LB@ \| \|@LB@5'-UUU...AGGUA U C UUAA CUUUC...AAC-3'@LB@ AAUGA GA GAAU GAAAACGA@LB@ \|\|\|\|\| \|\| \|\|\|\| \|\|\|\|\|\|:\|@LB@ UUACU CU CUUA CUUUUGUU@LB@3'-GUU...GCCGG A UAUUA...GGA-5'@LB@ \| \|@LB@ 179 151@LB@@LB@@LB@Energy -15.50 kcal/mol@LB@Hybridization Energy -12.3618 kcal/mol@LB@Unfolding Energy - mRNA 2.60591 kcal/mol@LB@Unfolding Energy - sRNA 0.959215 kcal/mol@LB@@LB@Position - mRNA 184 -- 209@LB@Position - sRNA 152 -- 178@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 154 -- 160@LB@
125	0.03321	0.6968	lmo2357	N/A	-16.59	0.049158	2 -- 27	152 -- 176		_____________1_____________________28\n_____________\|_____________________\|\n_______5'-AGCU___AU________C_______AUCUU...CAC-3'\n______________GAU__GAUGGAUG_AAAACAA\n______________:\|\|__\|\|\|\|:\|\|\|_\|\|\|\|\|\|\|\n______________UUA__CUACUUAC_UUUUGUU\n3'-GUU...GCCGG___CU________________UAUUA...GGA-5'\n_____________\|_____________________\|\n_____________177___________________151\n	19 -- 25	154 -- 160	-15.1634 kcal/mol	3.68151 kcal/mol	0.959215 kcal/mol	1 28@LB@ \| \|@LB@ 5'-AGCU AU C AUCUU...CAC-3'@LB@ GAU GAUGGAUG AAAACAA@LB@ :\|\| \|\|\|\|:\|\|\| \|\|\|\|\|\|\|@LB@ UUA CUACUUAC UUUUGUU@LB@3'-GUU...GCCGG CU UAUUA...GGA-5'@LB@ \| \|@LB@ 177 151@LB@@LB@@LB@Energy -16.59 kcal/mol@LB@Hybridization Energy -15.1634 kcal/mol@LB@Unfolding Energy - mRNA 3.68151 kcal/mol@LB@Unfolding Energy - sRNA 0.959215 kcal/mol@LB@@LB@Position - mRNA 2 -- 27@LB@Position - sRNA 152 -- 176@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 154 -- 160@LB@
179	0.05074	0.7607	lmo1598	tyrS	-15.93	0.065557	245 -- 292	152 -- 211	tyrosyl-tRNA synthetase	_____________244_______________293\n_____________\|_________________\|\n5'-UAG...AAAAG____AU___________AUAUU...UGU-3'\n______________GAGA__GAUGAAAAUGA\n______________\|\|\|\|__:\|\|\|\|\|\|\|::\|\n______________CUCU__UUACUUUUGUU\n3'-GUU...GGUUA____AC___________UAUUA...GGA-5'\n_____________\|_________________\|\n_____________212_______________151\n	197 -- 203	155 -- 161	-12.3519 kcal/mol	1.69495 kcal/mol	0.933796 kcal/mol	244 293@LB@ \| \|@LB@5'-UAG...AAAAG AU AUAUU...UGU-3'@LB@ GAGA GAUGAAAAUGA@LB@ \|\|\|\| :\|\|\|\|\|\|\|::\|@LB@ CUCU UUACUUUUGUU@LB@3'-GUU...GGUUA AC UAUUA...GGA-5'@LB@ \| \|@LB@ 212 151@LB@@LB@@LB@Energy -15.93 kcal/mol@LB@Hybridization Energy -12.3519 kcal/mol@LB@Unfolding Energy - mRNA 1.69495 kcal/mol@LB@Unfolding Energy - sRNA 0.933796 kcal/mol@LB@@LB@Position - mRNA 245 -- 292@LB@Position - sRNA 152 -- 211@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 155 -- 161@LB@
14	0.00304	0.4469	lmo1187	N/A	-19.26	0.014311	139 -- 172	153 -- 183	ethanolamine utilization protein EutQ	_____________138_______________________________173\n_____________\|_________________________________\|\n5'-UAA...GGUAU____________CC__AU______GA_______AGCAA...UUU-3'\n______________CUAUAUGGCUAA__GA__GAUGAA__AAAAUAA\n______________\|\|\|:\|:\|\|\|:\|\|__\|\|__\|\|\|\|\|\|__\|\|\|\|:\|\|\n______________GAUGUGCCGGUU__CU__CUACUU__UUUUGUU\n3'-GUU...UACUU____________A___________AC_______UAUUA...GGA-5'\n_____________\|_________________________________\|\n_____________184_______________________________152\n	165 -- 171	154 -- 160	-25.2263 kcal/mol	3.98561 kcal/mol	9.539 kcal/mol	138 173@LB@ \| \|@LB@5'-UAA...GGUAU CC AU GA AGCAA...UUU-3'@LB@ CUAUAUGGCUAA GA GAUGAA AAAAUAA@LB@ \|\|\|:\|:\|\|\|:\|\| \|\| \|\|\|\|\|\| \|\|\|\|:\|\|@LB@ GAUGUGCCGGUU CU CUACUU UUUUGUU@LB@3'-GUU...UACUU A AC UAUUA...GGA-5'@LB@ \| \|@LB@ 184 152@LB@@LB@@LB@Energy -19.26 kcal/mol@LB@Hybridization Energy -25.2263 kcal/mol@LB@Unfolding Energy - mRNA 3.98561 kcal/mol@LB@Unfolding Energy - sRNA 9.539 kcal/mol@LB@@LB@Position - mRNA 139 -- 172@LB@Position - sRNA 153 -- 183@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 154 -- 160@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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