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
153	0.04013	0.7027	lmo0979	N/A	-16.44	0.052648	251 -- 296	172 -- 207	daunorubicin resistance ATP-binding protein	_____________250_____________________________297\n_____________\|_______________________________\|\n5'-AAU...UUGAA__________UU____G_AAA_______G__AUUU-3'\n______________GGGUGUAGAU__UGAA_U___ACAUGGC_AA\n______________:\|\|::\|\|\|\|:__\|\|\|\|_\|___\|\|\|:\|\|\|_\|\|\n______________UCCGUAUCUG__ACUU_A___UGUGCCG_UU\n3'-GUU...CCUAC__________U_____G___________G__ACUCU...GGA-5'\n_____________\|_______________________________\|\n_____________208_____________________________171\n	287 -- 293	175 -- 181	-27.1075 kcal/mol	4.53663 kcal/mol	13.3233 kcal/mol	250 297@LB@ \| \|@LB@5'-AAU...UUGAA UU G AAA G AUUU-3'@LB@ GGGUGUAGAU UGAA U ACAUGGC AA@LB@ :\|\|::\|\|\|\|: \|\|\|\| \| \|\|\|:\|\|\| \|\|@LB@ UCCGUAUCUG ACUU A UGUGCCG UU@LB@3'-GUU...CCUAC U G G ACUCU...GGA-5'@LB@ \| \|@LB@ 208 171@LB@@LB@@LB@Energy -16.44 kcal/mol@LB@Hybridization Energy -27.1075 kcal/mol@LB@Unfolding Energy - mRNA 4.53663 kcal/mol@LB@Unfolding Energy - sRNA 13.3233 kcal/mol@LB@@LB@Position - mRNA 251 -- 296@LB@Position - sRNA 172 -- 207@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 175 -- 181@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@
173	0.04847	0.7539	lmo1143	N/A	-15.38	0.082828	238 -- 287	171 -- 211	PduT protein	_____________237_______________________________288\n_____________\|_________________________________\|\n5'-GUG...GCAUC______GUC____C__U____AAA_________UCGGA...UUU-3'\n______________GAGGCG___GAUA_GA_GCUA___GCGGCCAAU\n______________\|\|\|\|\|:___\|\|:\|_\|\|_:\|\|\|___:\|\|\|\|\|\|\|\|\n______________CUCCGU___CUGU_CU_UGAU___UGCCGGUUA\n3'-GUU...CCCUA______AU_____A_______G___________CUCUA...GGA-5'\n_____________\|_________________________________\|\n_____________212_______________________________170\n	281 -- 287	171 -- 177	-30.6178 kcal/mol	10.0561 kcal/mol	13.341 kcal/mol	237 288@LB@ \| \|@LB@5'-GUG...GCAUC GUC C U AAA UCGGA...UUU-3'@LB@ GAGGCG GAUA GA GCUA GCGGCCAAU@LB@ \|\|\|\|\|: \|\|:\| \|\| :\|\|\| :\|\|\|\|\|\|\|\|@LB@ CUCCGU CUGU CU UGAU UGCCGGUUA@LB@3'-GUU...CCCUA AU A G CUCUA...GGA-5'@LB@ \| \|@LB@ 212 170@LB@@LB@@LB@Energy -15.38 kcal/mol@LB@Hybridization Energy -30.6178 kcal/mol@LB@Unfolding Energy - mRNA 10.0561 kcal/mol@LB@Unfolding Energy - sRNA 13.341 kcal/mol@LB@@LB@Position - mRNA 238 -- 287@LB@Position - sRNA 171 -- 211@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 171 -- 177@LB@
80	0.02141	0.6733	lmo1147	N/A	-19.90	0.010431	143 -- 214	146 -- 207	cobalamin biosynthesis protein CopB	_____________142____________________________________________________________________215\n_____________\|______________________________________________________________________\|\n5'-UAU...AUUUG_______AUUUUUA________A____AUC____UGU_______A_______GAAUGGAC__________UGAUG...CAA-3'\n______________AGCGGGA_______GGGGC_UA_ACGU___GGAU___UACGCGG__AAUGAG________AUGAGUGAAA\n______________\|:\|\|\|\|\|_______\|:\|\|\|_\|\|_\|\|:\|___\|:\|:___\|\|\|:\|\|\|__\|\|\|\|\|\|________\|\|\|\|:\|\|\|\|\|\n______________UUGCCCU_______CUCCG_AU_UGUA___CUUG___AUGUGCC__UUACUC________UACUUACUUU\n3'-GUU...ACGUA_______A___________U__C_____________________GG________________________UGUUU...GGA-5'\n_____________\|______________________________________________________________________\|\n_____________208____________________________________________________________________145\n	204 -- 210	158 -- 164	-42.8674 kcal/mol	12.3523 kcal/mol	18.5828 kcal/mol	142 215@LB@ \| \|@LB@5'-UAU...AUUUG AUUUUUA A AUC UGU A GAAUGGAC UGAUG...CAA-3'@LB@ AGCGGGA GGGGC UA ACGU GGAU UACGCGG AAUGAG AUGAGUGAAA@LB@ \|:\|\|\|\|\| \|:\|\|\| \|\| \|\|:\| \|:\|: \|\|\|:\|\|\| \|\|\|\|\|\| \|\|\|\|:\|\|\|\|\|@LB@ UUGCCCU CUCCG AU UGUA CUUG AUGUGCC UUACUC UACUUACUUU@LB@3'-GUU...ACGUA A U C GG UGUUU...GGA-5'@LB@ \| \|@LB@ 208 145@LB@@LB@@LB@Energy -19.90 kcal/mol@LB@Hybridization Energy -42.8674 kcal/mol@LB@Unfolding Energy - mRNA 12.3523 kcal/mol@LB@Unfolding Energy - sRNA 18.5828 kcal/mol@LB@@LB@Position - mRNA 143 -- 214@LB@Position - sRNA 146 -- 207@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 158 -- 164@LB@
166	0.04633	0.7403	lmo1152	N/A	-16.33	0.055198	97 -- 188	95 -- 169	PduB protein	_____________96_______________189\n_____________\|________________\|\n5'-GGC...AAGUC________________AAUAA...AAG-3'\n______________AGAUGAGUGA__GCAA\n______________\|\|\|\|\|\|:\|\|\|__:\|\|\|\n______________UCUACUUACU__UGUU\n3'-GUU...GUUAC__________UU____UAUUA...GGA-5'\n_____________\|________________\|\n_____________170______________94\n	100 -- 106	160 -- 166	-13.7881 kcal/mol	2.27776 kcal/mol	0.924402 kcal/mol	96 189@LB@ \| \|@LB@5'-GGC...AAGUC AAUAA...AAG-3'@LB@ AGAUGAGUGA GCAA@LB@ \|\|\|\|\|\|:\|\|\| :\|\|\|@LB@ UCUACUUACU UGUU@LB@3'-GUU...GUUAC UU UAUUA...GGA-5'@LB@ \| \|@LB@ 170 94@LB@@LB@@LB@Energy -16.33 kcal/mol@LB@Hybridization Energy -13.7881 kcal/mol@LB@Unfolding Energy - mRNA 2.27776 kcal/mol@LB@Unfolding Energy - sRNA 0.924402 kcal/mol@LB@@LB@Position - mRNA 97 -- 188@LB@Position - sRNA 95 -- 169@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 160 -- 166@LB@
189	0.05497	0.7607	lmo1156	N/A	-15.46	0.080118	37 -- 70	155 -- 186	diol dehydratase-reactivating factor large subunit	_____________36________________71\n_____________\|_________________\|\n5'-UAU...AAAUG______A__________UAUAU...CUA-3'\n______________CGGUGA_AUGAAUGAAG\n______________\|::\|\|\|_\|\|\|\|\|\|\|\|\|:\n______________GUUACU_UACUUACUUU\n3'-GUU...UGCCG______C__________UGUUU...GGA-5'\n_____________\|_________________\|\n_____________187_______________154\n	200 -- 206	158 -- 164	-15.35 kcal/mol	3.5534 kcal/mol	0.871719 kcal/mol	36 71@LB@ \| \|@LB@5'-UAU...AAAUG A UAUAU...CUA-3'@LB@ CGGUGA AUGAAUGAAG@LB@ \|::\|\|\| \|\|\|\|\|\|\|\|\|:@LB@ GUUACU UACUUACUUU@LB@3'-GUU...UGCCG C UGUUU...GGA-5'@LB@ \| \|@LB@ 187 154@LB@@LB@@LB@Energy -15.46 kcal/mol@LB@Hybridization Energy -15.35 kcal/mol@LB@Unfolding Energy - mRNA 3.5534 kcal/mol@LB@Unfolding Energy - sRNA 0.871719 kcal/mol@LB@@LB@Position - mRNA 37 -- 70@LB@Position - sRNA 155 -- 186@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 158 -- 164@LB@
17	0.003248	0.4469	lmo1161	N/A	-22.54	0.002685	189 -- 238	155 -- 204	ethanolamine utilization protein EutJ	_____________188___________________________________________________239\n_____________\|_____________________________________________________\|\n5'-GGU...GUAAG_____GGAAAA________U_______AACA________AC____________GCUUG...AAG-3'\n______________GAGGU______AUGGAUAU___UUACA____GCCAAUGA___GAAUGGAA_CA\n______________\|\|\|\|:______\|\|:\|\|:\|\|___:\|\|\|\|____\|\|\|\|\|\|\|\|___\|\|\|\|\|:\|\|_\|\|\n______________CUCCG______UAUCUGUA___GAUGU____CGGUUACU___CUUACUUU_GU\n3'-GUU...CCCUA___________________CUU_____GC__________CUA________U__UUAUU...GGA-5'\n_____________\|_____________________________________________________\|\n_____________205___________________________________________________154\n	230 -- 236	158 -- 164	-34.4634 kcal/mol	5.85583 kcal/mol	13.9822 kcal/mol	188 239@LB@ \| \|@LB@5'-GGU...GUAAG GGAAAA U AACA AC GCUUG...AAG-3'@LB@ GAGGU AUGGAUAU UUACA GCCAAUGA GAAUGGAA CA@LB@ \|\|\|\|: \|\|:\|\|:\|\| :\|\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|:\|\| \|\|@LB@ CUCCG UAUCUGUA GAUGU CGGUUACU CUUACUUU GU@LB@3'-GUU...CCCUA CUU GC CUA U UUAUU...GGA-5'@LB@ \| \|@LB@ 205 154@LB@@LB@@LB@Energy -22.54 kcal/mol@LB@Hybridization Energy -34.4634 kcal/mol@LB@Unfolding Energy - mRNA 5.85583 kcal/mol@LB@Unfolding Energy - sRNA 13.9822 kcal/mol@LB@@LB@Position - mRNA 189 -- 238@LB@Position - sRNA 155 -- 204@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 158 -- 164@LB@
62	0.01477	0.6412	lmo1163	N/A	-15.96	0.064740	175 -- 219	154 -- 212	carbon dioxide concentrating mechanism protein	_____________174_________________________________________________________220\n_____________\|___________________________________________________________\|\n5'-UAG...AAUAU____GU______A______GU_____UAUGUU______A____________________CAGGA...AUG-3'\n______________UGCA__GCGGGA__AGGCA__GACGU______UAUGGC______________AAAAUAA\n______________\|\|\|\|__:\|\|\|\|\|__\|\|\|\|\|__\|\|\|:\|______:\|:\|\|\|______________\|\|\|\|:\|\|\n______________ACGU__UGCCCU__UCCGU__CUGUA______GUGCCG______________UUUUGUU\n3'-GUU...CGGAU____AU______AC_____AU_____CUUGAU______GUUACUCUACUUAC_______UAUUA...GGA-5'\n_____________\|___________________________________________________________\|\n_____________213_________________________________________________________153\n	213 -- 219	154 -- 160	-36.6169 kcal/mol	12.1656 kcal/mol	19.5998 kcal/mol	174 220@LB@ \| \|@LB@5'-UAG...AAUAU GU A GU UAUGUU A CAGGA...AUG-3'@LB@ UGCA GCGGGA AGGCA GACGU UAUGGC AAAAUAA@LB@ \|\|\|\| :\|\|\|\|\| \|\|\|\|\| \|\|\|:\| :\|:\|\|\| \|\|\|\|:\|\|@LB@ ACGU UGCCCU UCCGU CUGUA GUGCCG UUUUGUU@LB@3'-GUU...CGGAU AU AC AU CUUGAU GUUACUCUACUUAC UAUUA...GGA-5'@LB@ \| \|@LB@ 213 153@LB@@LB@@LB@Energy -15.96 kcal/mol@LB@Hybridization Energy -36.6169 kcal/mol@LB@Unfolding Energy - mRNA 12.1656 kcal/mol@LB@Unfolding Energy - sRNA 19.5998 kcal/mol@LB@@LB@Position - mRNA 175 -- 219@LB@Position - sRNA 154 -- 212@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 154 -- 160@LB@
155	0.04112	0.7058	lmo1165	N/A	-16.89	0.043077	88 -- 150	155 -- 206	ethanolamine utilization protein EutE	_____________87_______________________________151\n_____________\|________________________________\|\n5'-AAG...AAUGG____________G___C_______G_______UCCAC...CAA-3'\n______________GGAUUA_GCGGC_GAU_AG_UGGA_GAAGAUA\n______________\|:\|:\|\|_:\|\|\|\|_:\|\|_\|\|_\|\|:\|_\|\|\|:\|:\|\n______________CUUGAU_UGCCG_UUA_UC_ACUU_CUUUUGU\n3'-GUU...CUGUA______G_____G___C__U____A_______UUAUU...GGA-5'\n_____________\|________________________________\|\n_____________207______________________________154\n	144 -- 150	155 -- 161	-24.1777 kcal/mol	5.41964 kcal/mol	9.66922 kcal/mol	87 151@LB@ \| \|@LB@5'-AAG...AAUGG G C G UCCAC...CAA-3'@LB@ GGAUUA GCGGC GAU AG UGGA GAAGAUA@LB@ \|:\|:\|\| :\|\|\|\| :\|\| \|\| \|\|:\| \|\|\|:\|:\|@LB@ CUUGAU UGCCG UUA UC ACUU CUUUUGU@LB@3'-GUU...CUGUA G G C U A UUAUU...GGA-5'@LB@ \| \|@LB@ 207 154@LB@@LB@@LB@Energy -16.89 kcal/mol@LB@Hybridization Energy -24.1777 kcal/mol@LB@Unfolding Energy - mRNA 5.41964 kcal/mol@LB@Unfolding Energy - sRNA 9.66922 kcal/mol@LB@@LB@Position - mRNA 88 -- 150@LB@Position - sRNA 155 -- 206@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 155 -- 161@LB@
79	0.02126	0.6733	lmo1172	N/A	-17.83	0.028138	200 -- 242	163 -- 210	two-component response regulator	_____________199_________243\n_____________\|___________\|\n5'-CAC...CAGGA___________AAUUG...UAG-3'\n______________AUGAAUGGAAG\n______________\|\|\|\|\|\|\|:\|\|:\n______________UACUUACUUUU\n3'-GUU...UACUC___________GUUUA...GGA-5'\n_____________\|___________\|\n_____________211_________162\n	214 -- 220	157 -- 163	-10.013 kcal/mol	1.15656 kcal/mol	0.82573 kcal/mol	199 243@LB@ \| \|@LB@5'-CAC...CAGGA AAUUG...UAG-3'@LB@ AUGAAUGGAAG@LB@ \|\|\|\|\|\|\|:\|\|:@LB@ UACUUACUUUU@LB@3'-GUU...UACUC GUUUA...GGA-5'@LB@ \| \|@LB@ 211 162@LB@@LB@@LB@Energy -17.83 kcal/mol@LB@Hybridization Energy -10.013 kcal/mol@LB@Unfolding Energy - mRNA 1.15656 kcal/mol@LB@Unfolding Energy - sRNA 0.82573 kcal/mol@LB@@LB@Position - mRNA 200 -- 242@LB@Position - sRNA 163 -- 210@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 157 -- 163@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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