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
82	0.02188	0.6733	lmo0200	prfA	-17.77	0.028863	191 -- 222	162 -- 204	listeriolysin positive regulatory protein	_____________190______223\n_____________\|________\|\n5'-UCA...AUUGG________ACAUG...AUC-3'\n______________GGGAUGAG\n______________\|\|\|\|\|\|\|\|\n______________CCCUACUC\n3'-GUU...UAUUG________CGUAU...GGA-5'\n_____________\|________\|\n_____________205______161\n	192 -- 198	197 -- 203	-14.1607 kcal/mol	1.90446 kcal/mol	0.386531 kcal/mol	190 223@LB@ \| \|@LB@5'-UCA...AUUGG ACAUG...AUC-3'@LB@ GGGAUGAG@LB@ \|\|\|\|\|\|\|\|@LB@ CCCUACUC@LB@3'-GUU...UAUUG CGUAU...GGA-5'@LB@ \| \|@LB@ 205 161@LB@@LB@@LB@Energy -17.77 kcal/mol@LB@Hybridization Energy -14.1607 kcal/mol@LB@Unfolding Energy - mRNA 1.90446 kcal/mol@LB@Unfolding Energy - sRNA 0.386531 kcal/mol@LB@@LB@Position - mRNA 191 -- 222@LB@Position - sRNA 162 -- 204@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 197 -- 203@LB@
54	0.01218	0.6043	lmo0065	N/A	-17.22	0.037093	77 -- 100	146 -- 171	lmo0065	_____________76_________________________101\n_____________\|__________________________\|\n5'-GUA...GCAUU____________________U_____UGGUA...CUA-3'\n______________UGAGAUG___GAAGACAAAU_AAUGA\n______________\|\|\|\|\|\|\|___\|\|\|:\|\|\|\|\|\|_\|\|\|\|\|\n______________ACUCUAC___CUUUUGUUUA_UUACU\n3'-GUU...CGGUU_______UUA________________AAAAC...GGA-5'\n_____________\|__________________________\|\n_____________172________________________145\n	87 -- 93	152 -- 158	-20.9762 kcal/mol	2.94176 kcal/mol	5.93625 kcal/mol	76 101@LB@ \| \|@LB@5'-GUA...GCAUU U UGGUA...CUA-3'@LB@ UGAGAUG GAAGACAAAU AAUGA@LB@ \|\|\|\|\|\|\| \|\|\|:\|\|\|\|\|\| \|\|\|\|\|@LB@ ACUCUAC CUUUUGUUUA UUACU@LB@3'-GUU...CGGUU UUA AAAAC...GGA-5'@LB@ \| \|@LB@ 172 145@LB@@LB@@LB@Energy -17.22 kcal/mol@LB@Hybridization Energy -20.9762 kcal/mol@LB@Unfolding Energy - mRNA 2.94176 kcal/mol@LB@Unfolding Energy - sRNA 5.93625 kcal/mol@LB@@LB@Position - mRNA 77 -- 100@LB@Position - sRNA 146 -- 171@LB@Position Seed - mRNA 87 -- 93@LB@Position Seed - sRNA 152 -- 158@LB@
117	0.03157	0.6968	lmo0079	N/A	-15.68	0.073126	244 -- 277	156 -- 185	lmo0079	_____________243________________________________278\n_____________\|__________________________________\|\n5'-UCG...AUACC_________CAA_______ACCAG___G______UAUCC...CCG-3'\n______________AGCUACGUG___CCAAUGA_____GAA_GAAAAC\n______________\|:\|\|\|\|::\|___\|\|\|\|\|\|\|_____\|\|\|_\|\|\|\|\|\|\n______________UUGAUGUGC___GGUUACU_____CUU_CUUUUG\n3'-GUU...UGUAC_________C_________CUA_____A______UUUAU...GGA-5'\n_____________\|__________________________________\|\n_____________186________________________________155\n	256 -- 262	169 -- 175	-22.638 kcal/mol	3.99376 kcal/mol	9.64492 kcal/mol	243 278@LB@ \| \|@LB@5'-UCG...AUACC CAA ACCAG G UAUCC...CCG-3'@LB@ AGCUACGUG CCAAUGA GAA GAAAAC@LB@ \|:\|\|\|\|::\| \|\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|@LB@ UUGAUGUGC GGUUACU CUU CUUUUG@LB@3'-GUU...UGUAC C CUA A UUUAU...GGA-5'@LB@ \| \|@LB@ 186 155@LB@@LB@@LB@Energy -15.68 kcal/mol@LB@Hybridization Energy -22.638 kcal/mol@LB@Unfolding Energy - mRNA 3.99376 kcal/mol@LB@Unfolding Energy - sRNA 9.64492 kcal/mol@LB@@LB@Position - mRNA 244 -- 277@LB@Position - sRNA 156 -- 185@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 169 -- 175@LB@
81	0.02179	0.6733	lmo0087	N/A	-17.84	0.027970	185 -- 226	166 -- 207	lmo0087	_____________184____________________227\n_____________\|______________________\|\n5'-ACU...AUUAU___AU____G____________AACCU...AUC-3'\n______________UGA__UGGA_GAGAGCAAAUGA\n______________\|\|\|__\|\|:\|_\|\|:\|:\|\|\|\|\|:\|\n______________ACU__ACUU_CUUUUGUUUAUU\n3'-GUU...CGGUU___CU____A____________ACUAA...GGA-5'\n_____________\|______________________\|\n_____________208____________________165\n	195 -- 201	153 -- 159	-17.3998 kcal/mol	2.37482 kcal/mol	5.01319 kcal/mol	184 227@LB@ \| \|@LB@5'-ACU...AUUAU AU G AACCU...AUC-3'@LB@ UGA UGGA GAGAGCAAAUGA@LB@ \|\|\| \|\|:\| \|\|:\|:\|\|\|\|\|:\|@LB@ ACU ACUU CUUUUGUUUAUU@LB@3'-GUU...CGGUU CU A ACUAA...GGA-5'@LB@ \| \|@LB@ 208 165@LB@@LB@@LB@Energy -17.84 kcal/mol@LB@Hybridization Energy -17.3998 kcal/mol@LB@Unfolding Energy - mRNA 2.37482 kcal/mol@LB@Unfolding Energy - sRNA 5.01319 kcal/mol@LB@@LB@Position - mRNA 185 -- 226@LB@Position - sRNA 166 -- 207@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 153 -- 159@LB@
172	0.04804	0.7516	lmo0111	N/A	-17.34	0.035270	180 -- 204	147 -- 170	lmo0111	_____________179______________________205\n_____________\|________________________\|\n5'-AAU...AUAGA____A_A________G________GGACU...CAG-3'\n______________GAGG_G_AAUGAGAA_GGAUGAUG\n______________\|\|\|:_\|_\|\|\|\|\|:\|\|_::\|\|:\|\|\|\n______________CUCU_C_UUACUUUU_UUUAUUAC\n3'-GUU...GGUUA____A__________G________UAAAA...GGA-5'\n_____________\|________________________\|\n_____________171______________________146\n	188 -- 194	157 -- 163	-20.9699 kcal/mol	2.01501 kcal/mol	5.93381 kcal/mol	179 205@LB@ \| \|@LB@5'-AAU...AUAGA A A G GGACU...CAG-3'@LB@ GAGG G AAUGAGAA GGAUGAUG@LB@ \|\|\|: \| \|\|\|\|\|:\|\| ::\|\|:\|\|\|@LB@ CUCU C UUACUUUU UUUAUUAC@LB@3'-GUU...GGUUA A G UAAAA...GGA-5'@LB@ \| \|@LB@ 171 146@LB@@LB@@LB@Energy -17.34 kcal/mol@LB@Hybridization Energy -20.9699 kcal/mol@LB@Unfolding Energy - mRNA 2.01501 kcal/mol@LB@Unfolding Energy - sRNA 5.93381 kcal/mol@LB@@LB@Position - mRNA 180 -- 204@LB@Position - sRNA 147 -- 170@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 157 -- 163@LB@
47	0.01063	0.599	lmo0138	N/A	-20.04	0.009767	146 -- 210	158 -- 213	lmo0138	_____________145_________________________________________________________________________211\n_____________\|___________________________________________________________________________\|\n5'-AAA...AAUGC____G_____U_____UAA_____A____UUCAUUAUU________________A___GCA___A__________UAAAA...GCA-3'\n______________GUGC__AUGC_AUAAU___GGGAU_AGGU_________AUAGACA_GAG__AUG_GGC____GA_AUGAGUGAAA\n______________\|:\|\|__\|\|\|\|_\|\|\|\|:___\|\|\|\|\|_\|\|\|:_________\|\|\|\|\|\|\|_\|\|:__\|::_\|\|\|____\|\|_\|\|\|\|:\|\|\|\|\|\n______________CGCG__UACG_UAUUG___CCCUA_UCCG_________UAUCUGU_CUU__UGU_CCG____CU_UACUUACUUU\n3'-GUU...AAGCC____GA__________________C____________________A___GA___G___GUUA__C__________UGUUU...GGA-5'\n_____________\|___________________________________________________________________________\|\n_____________214_________________________________________________________________________157\n	204 -- 210	158 -- 164	-47.7003 kcal/mol	15.2802 kcal/mol	21.9717 kcal/mol	145 211@LB@ \| \|@LB@5'-AAA...AAUGC G U UAA A UUCAUUAUU A GCA A UAAAA...GCA-3'@LB@ GUGC AUGC AUAAU GGGAU AGGU AUAGACA GAG AUG GGC GA AUGAGUGAAA@LB@ \|:\|\| \|\|\|\| \|\|\|\|: \|\|\|\|\| \|\|\|: \|\|\|\|\|\|\| \|\|: \|:: \|\|\| \|\| \|\|\|\|:\|\|\|\|\|@LB@ CGCG UACG UAUUG CCCUA UCCG UAUCUGU CUU UGU CCG CU UACUUACUUU@LB@3'-GUU...AAGCC GA C A GA G GUUA C UGUUU...GGA-5'@LB@ \| \|@LB@ 214 157@LB@@LB@@LB@Energy -20.04 kcal/mol@LB@Hybridization Energy -47.7003 kcal/mol@LB@Unfolding Energy - mRNA 15.2802 kcal/mol@LB@Unfolding Energy - sRNA 21.9717 kcal/mol@LB@@LB@Position - mRNA 146 -- 210@LB@Position - sRNA 158 -- 213@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 158 -- 164@LB@
52	0.01176	0.599	lmo0302	N/A	-19.32	0.013869	143 -- 287	107 -- 220	lmo0302	_____________142________________288\n_____________\|__________________\|\n5'-CGA...CAUAG_________A__U_____AAAAA...AUA-3'\n______________GAGAUGAAU_GA_GAUGA\n______________\|\|\|\|\|\|\|\|\|_\|\|_:\|::\|\n______________CUCUACUUA_CU_UUGUU\n3'-GUU...GGUUA____________U_____UAUUA...GGA-5'\n_____________\|__________________\|\n_____________221________________106\n	189 -- 195	162 -- 168	-14.2485 kcal/mol	1.08239 kcal/mol	0.933796 kcal/mol	142 288@LB@ \| \|@LB@5'-CGA...CAUAG A U AAAAA...AUA-3'@LB@ GAGAUGAAU GA GAUGA@LB@ \|\|\|\|\|\|\|\|\| \|\| :\|::\|@LB@ CUCUACUUA CU UUGUU@LB@3'-GUU...GGUUA U UAUUA...GGA-5'@LB@ \| \|@LB@ 221 106@LB@@LB@@LB@Energy -19.32 kcal/mol@LB@Hybridization Energy -14.2485 kcal/mol@LB@Unfolding Energy - mRNA 1.08239 kcal/mol@LB@Unfolding Energy - sRNA 0.933796 kcal/mol@LB@@LB@Position - mRNA 143 -- 287@LB@Position - sRNA 107 -- 220@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 162 -- 168@LB@
67	0.01689	0.6733	lmo0335	N/A	-16.81	0.044620	154 -- 214	153 -- 220	lmo0335	_____________153_____________________________________________________________215\n_____________\|_______________________________________________________________\|\n5'-AAA...CUACC______AUA______G____A____AUAUA______G_G____________A___________AUAAA...AUA-3'\n______________GGUGCU_____AUGA_GGGG__AGG_____CAUAGA_A_GAA__GCAU_GC_GAUGAGA_GAA\n______________\|\|:\|\|:_____\|\|:\|_\|\|\|:__\|\|\|_____\|\|\|\|\|\|_\|_\|\|\|__:\|\|:_\|\|_:\|\|\|\|\|\|_\|\|\|\n______________CCGCGG_____UAUU_CCCU__UCC_____GUAUCU_U_CUU__UGUG_CG_UUACUCU_CUU\n3'-GUU...CAAGC______AUACG____G____AC______________G_A___GA____C__G_______A___ACUUU...GGA-5'\n_____________\|_______________________________________________________________\|\n_____________221_____________________________________________________________152\n	200 -- 206	167 -- 173	-43.0643 kcal/mol	10.4394 kcal/mol	21.4092 kcal/mol	153 215@LB@ \| \|@LB@5'-AAA...CUACC AUA G A AUAUA G G A AUAAA...AUA-3'@LB@ GGUGCU AUGA GGGG AGG CAUAGA A GAA GCAU GC GAUGAGA GAA@LB@ \|\|:\|\|: \|\|:\| \|\|\|: \|\|\| \|\|\|\|\|\| \| \|\|\| :\|\|: \|\| :\|\|\|\|\|\| \|\|\|@LB@ CCGCGG UAUU CCCU UCC GUAUCU U CUU UGUG CG UUACUCU CUU@LB@3'-GUU...CAAGC AUACG G AC G A GA C G A ACUUU...GGA-5'@LB@ \| \|@LB@ 221 152@LB@@LB@@LB@Energy -16.81 kcal/mol@LB@Hybridization Energy -43.0643 kcal/mol@LB@Unfolding Energy - mRNA 10.4394 kcal/mol@LB@Unfolding Energy - sRNA 21.4092 kcal/mol@LB@@LB@Position - mRNA 154 -- 214@LB@Position - sRNA 153 -- 220@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 167 -- 173@LB@
37	0.007696	0.5562	lmo0551	N/A	-17.72	0.029617	133 -- 210	151 -- 204	lmo0551	_____________132____________211\n_____________\|______________\|\n5'-AGA...UUAAG________G_____AAUUC...CUU-3'\n______________GAGGUGAG_GAAGA\n______________\|\|\|:\|\|\|:_\|\|\|:\|\n______________CUCUACUU_CUUUU\n3'-GUU...GGUUA________A_____GUUUA...GGA-5'\n_____________\|______________\|\n_____________205____________150\n	135 -- 141	163 -- 169	-13.8898 kcal/mol	2.56868 kcal/mol	0.904482 kcal/mol	132 211@LB@ \| \|@LB@5'-AGA...UUAAG G AAUUC...CUU-3'@LB@ GAGGUGAG GAAGA@LB@ \|\|\|:\|\|\|: \|\|\|:\|@LB@ CUCUACUU CUUUU@LB@3'-GUU...GGUUA A GUUUA...GGA-5'@LB@ \| \|@LB@ 205 150@LB@@LB@@LB@Energy -17.72 kcal/mol@LB@Hybridization Energy -13.8898 kcal/mol@LB@Unfolding Energy - mRNA 2.56868 kcal/mol@LB@Unfolding Energy - sRNA 0.904482 kcal/mol@LB@@LB@Position - mRNA 133 -- 210@LB@Position - sRNA 151 -- 204@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 163 -- 169@LB@
30	0.00607	0.5445	lmo0619	N/A	-20.15	0.009257	186 -- 283	154 -- 223	lmo0619	_____________185_____________________________________________________________________________________________________284\n_____________\|_______________________________________________________________________________________________________\|\n5'-UAU...AACAG_____G__GC____CUU___________AAAAAG_____AGUAAAUUACUUCA_______AAAAAAGCGACCAAUU_________GUAUUA____________GGCGG...CAA-3'\n______________UCGGG_GU____GC___AU_GGAUGGGG______AGACA______________UGAAUUA________________UAC_GCCAA_______GAUGAAAACGA\n______________\|\|\|\|\|_\|:____\|\|___\|:_\|\|\|\|\|:\|\|______\|\|\|\|\|______________\|\|\|\|:\|\|________________:\|\|_\|\|\|\|\|_______:\|\|\|\|\|\|\|\|:\|\n______________AGCCC_CG____CG___UG_CCUACUCC______UCUGU______________ACUUGAU________________GUG_CGGUU_______UUACUUUUGUU\n3'-GUU...GUACA_____G__GAUA__UAU__C________GUA________________________________________________C_____ACUCUAC___________UAUUA...GGA-5'\n_____________\|_______________________________________________________________________________________________________\|\n_____________224_____________________________________________________________________________________________________153\n	277 -- 283	154 -- 160	-48.8019 kcal/mol	13.571 kcal/mol	22.2956 kcal/mol	185 284@LB@ \| \|@LB@5'-UAU...AACAG G GC CUU AAAAAG AGUAAAUUACUUCA AAAAAAGCGACCAAUU GUAUUA GGCGG...CAA-3'@LB@ UCGGG GU GC AU GGAUGGGG AGACA UGAAUUA UAC GCCAA GAUGAAAACGA@LB@ \|\|\|\|\| \|: \|\| \|: \|\|\|\|\|:\|\| \|\|\|\|\| \|\|\|\|:\|\| :\|\| \|\|\|\|\| :\|\|\|\|\|\|\|\|:\|@LB@ AGCCC CG CG UG CCUACUCC UCUGU ACUUGAU GUG CGGUU UUACUUUUGUU@LB@3'-GUU...GUACA G GAUA UAU C GUA C ACUCUAC UAUUA...GGA-5'@LB@ \| \|@LB@ 224 153@LB@@LB@@LB@Energy -20.15 kcal/mol@LB@Hybridization Energy -48.8019 kcal/mol@LB@Unfolding Energy - mRNA 13.571 kcal/mol@LB@Unfolding Energy - sRNA 22.2956 kcal/mol@LB@@LB@Position - mRNA 186 -- 283@LB@Position - sRNA 154 -- 223@LB@Position Seed - mRNA 277 -- 283@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)

Job resubmission

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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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