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
171	0.04778	0.7516	lmo0498	N/A	-14.78	0.106331	152 -- 199	154 -- 211	5-phosphate isomerase	_____________151__________________200\n_____________\|____________________\|\n5'-AUC...AUCAA_______AA___________ACAUG...GUU-3'\n______________GGUGAGA__GGA_GAGGAUA\n______________::\|\|\|\|\|__\|:\|_\|\|::\|:\|\n______________UUACUCU__CUU_CUUUUGU\n3'-GUU...GCCGG_______A____A_______UUAUU...GGA-5'\n_____________\|____________________\|\n_____________212__________________153\n	192 -- 198	155 -- 161	-12.5427 kcal/mol	2.39386 kcal/mol	0.954976 kcal/mol	151 200@LB@ \| \|@LB@5'-AUC...AUCAA AA ACAUG...GUU-3'@LB@ GGUGAGA GGA GAGGAUA@LB@ ::\|\|\|\|\| \|:\| \|\|::\|:\|@LB@ UUACUCU CUU CUUUUGU@LB@3'-GUU...GCCGG A A UUAUU...GGA-5'@LB@ \| \|@LB@ 212 153@LB@@LB@@LB@Energy -14.78 kcal/mol@LB@Hybridization Energy -12.5427 kcal/mol@LB@Unfolding Energy - mRNA 2.39386 kcal/mol@LB@Unfolding Energy - sRNA 0.954976 kcal/mol@LB@@LB@Position - mRNA 152 -- 199@LB@Position - sRNA 154 -- 211@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 155 -- 161@LB@
194	0.05602	0.7607	lmo1602	N/A	-15.08	0.094256	153 -- 204	160 -- 207		_____________152_______________________________________205\n_____________\|_________________________________________\|\n5'-UUU...ACUCA_________AAAA___________A_____U____A_____UAGUA...CAA-3'\n______________GGGUAUAGA____GGA__AUAUGG__GGUG_GGAU_GAUGA\n______________:\|\|:\|\|\|\|\|____\|:\|__\|:\|:\|\|__::\|\|_:\|\|\|_:\|\|\|\|\n______________UCCGUAUCU____CUU__UGUGCC__UUAC_UCUA_UUACU\n3'-GUU...CCUAC_________GUA____GA______GG_________C_____UUUGU...GGA-5'\n_____________\|_________________________________________\|\n_____________208_______________________________________159\n	168 -- 174	191 -- 197	-27.2651 kcal/mol	6.9826 kcal/mol	13.8637 kcal/mol	152 205@LB@ \| \|@LB@5'-UUU...ACUCA AAAA A U A UAGUA...CAA-3'@LB@ GGGUAUAGA GGA AUAUGG GGUG GGAU GAUGA@LB@ :\|\|:\|\|\|\|\| \|:\| \|:\|:\|\| ::\|\| :\|\|\| :\|\|\|\|@LB@ UCCGUAUCU CUU UGUGCC UUAC UCUA UUACU@LB@3'-GUU...CCUAC GUA GA GG C UUUGU...GGA-5'@LB@ \| \|@LB@ 208 159@LB@@LB@@LB@Energy -15.08 kcal/mol@LB@Hybridization Energy -27.2651 kcal/mol@LB@Unfolding Energy - mRNA 6.9826 kcal/mol@LB@Unfolding Energy - sRNA 13.8637 kcal/mol@LB@@LB@Position - mRNA 153 -- 204@LB@Position - sRNA 160 -- 207@LB@Position Seed - mRNA 168 -- 174@LB@Position Seed - sRNA 191 -- 197@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@
73	0.0193	0.6733	lmo0405	N/A	-18.50	0.020574	154 -- 209	155 -- 199	phosphate transporter	_____________153____________210\n_____________\|______________\|\n5'-GUG...UUAUG________U_____UACGA...CGA-3'\n______________AUGACGGG_AUGAG\n______________\|\|:\|\|\|\|\|_\|\|\|\|\|\n______________UAUUGCCC_UACUC\n3'-GUU...AUACG______________CGUAU...GGA-5'\n_____________\|______________\|\n_____________200____________154\n	50 -- 56	202 -- 208	-16.311 kcal/mol	2.72131 kcal/mol	0.386761 kcal/mol	153 210@LB@ \| \|@LB@5'-GUG...UUAUG U UACGA...CGA-3'@LB@ AUGACGGG AUGAG@LB@ \|\|:\|\|\|\|\| \|\|\|\|\|@LB@ UAUUGCCC UACUC@LB@3'-GUU...AUACG CGUAU...GGA-5'@LB@ \| \|@LB@ 200 154@LB@@LB@@LB@Energy -18.50 kcal/mol@LB@Hybridization Energy -16.311 kcal/mol@LB@Unfolding Energy - mRNA 2.72131 kcal/mol@LB@Unfolding Energy - sRNA 0.386761 kcal/mol@LB@@LB@Position - mRNA 154 -- 209@LB@Position - sRNA 155 -- 199@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 202 -- 208@LB@
177	0.05015	0.7607	lmo1905	cca	-16.43	0.052746	154 -- 208	160 -- 211	tRNA CCA-pyrophosphorylase	_____________153_______________209\n_____________\|_________________\|\n5'-UUA...AGGAG______CA_________CGUUU...UGC-3'\n______________CGAUGA__GAUGAAUGA\n______________\|:\|\|\|\|__\|\|\|\|\|\|\|\|\|\n______________GUUACU__CUACUUACU\n3'-GUU...UGCCG_________________UUUGU...GGA-5'\n_____________\|_________________\|\n_____________212_______________159\n	202 -- 208	160 -- 166	-15.3935 kcal/mol	2.32419 kcal/mol	0.846187 kcal/mol	153 209@LB@ \| \|@LB@5'-UUA...AGGAG CA CGUUU...UGC-3'@LB@ CGAUGA GAUGAAUGA@LB@ \|:\|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ GUUACU CUACUUACU@LB@3'-GUU...UGCCG UUUGU...GGA-5'@LB@ \| \|@LB@ 212 159@LB@@LB@@LB@Energy -16.43 kcal/mol@LB@Hybridization Energy -15.3935 kcal/mol@LB@Unfolding Energy - mRNA 2.32419 kcal/mol@LB@Unfolding Energy - sRNA 0.846187 kcal/mol@LB@@LB@Position - mRNA 154 -- 208@LB@Position - sRNA 160 -- 211@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 160 -- 166@LB@
51	0.01168	0.599	lmo0105	N/A	-17.88	0.027496	155 -- 205	153 -- 201	chitinase B	_____________154_________________206\n_____________\|___________________\|\n5'-ACC...GUGAA_________AA________AAAAG...AAA-3'\n______________GAGAUGAAU__GAAGAUGA\n______________\|\|\|\|\|\|\|\|\|__\|\|\|:\|::\|\n______________CUCUACUUA__CUUUUGUU\n3'-GUU...GGUUA___________________UAUUA...GGA-5'\n_____________\|___________________\|\n_____________202_________________152\n	197 -- 203	155 -- 161	-15.8376 kcal/mol	2.73398 kcal/mol	0.933796 kcal/mol	154 206@LB@ \| \|@LB@5'-ACC...GUGAA AA AAAAG...AAA-3'@LB@ GAGAUGAAU GAAGAUGA@LB@ \|\|\|\|\|\|\|\|\| \|\|\|:\|::\|@LB@ CUCUACUUA CUUUUGUU@LB@3'-GUU...GGUUA UAUUA...GGA-5'@LB@ \| \|@LB@ 202 152@LB@@LB@@LB@Energy -17.88 kcal/mol@LB@Hybridization Energy -15.8376 kcal/mol@LB@Unfolding Energy - mRNA 2.73398 kcal/mol@LB@Unfolding Energy - sRNA 0.933796 kcal/mol@LB@@LB@Position - mRNA 155 -- 205@LB@Position - sRNA 153 -- 201@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 155 -- 161@LB@
70	0.01838	0.6733	lmo0265	N/A	-16.33	0.055331	156 -- 199	158 -- 207	succinyl-diaminopimelate desuccinylase	_____________155_____200\n_____________\|_______\|\n5'-UUU...UAGAG_______AAACA...UGU-3'\n______________AACGGGA\n______________\|\|\|\|\|\|\|\n______________UUGCCCU\n3'-GUU...ACGUA_______ACUCC...GGA-5'\n_____________\|_______\|\n_____________208_____157\n	156 -- 162	201 -- 207	-11.1784 kcal/mol	0.573427 kcal/mol	0.326294 kcal/mol	155 200@LB@ \| \|@LB@5'-UUU...UAGAG AAACA...UGU-3'@LB@ AACGGGA@LB@ \|\|\|\|\|\|\|@LB@ UUGCCCU@LB@3'-GUU...ACGUA ACUCC...GGA-5'@LB@ \| \|@LB@ 208 157@LB@@LB@@LB@Energy -16.33 kcal/mol@LB@Hybridization Energy -11.1784 kcal/mol@LB@Unfolding Energy - mRNA 0.573427 kcal/mol@LB@Unfolding Energy - sRNA 0.326294 kcal/mol@LB@@LB@Position - mRNA 156 -- 199@LB@Position - sRNA 158 -- 207@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 201 -- 207@LB@
78	0.02097	0.6733	lmo1196	N/A	-18.80	0.017871	157 -- 213	158 -- 203	cobalt-precorrin-6Y C(15)-methyltransferase	_____________156_________________________________________________________214\n_____________\|___________________________________________________________\|\n5'-CCU...AACCA____AA___GCAAAAAAAUAC_________GUAG____G_U__U_______AGA_____UAUUU...AAA-3'\n______________GAGG__GUA____________GAUAUGAAU____UGGU_A_UG_AGAUGAA___UGAAG\n______________\|\|\|\|__:\|\|____________\|\|:\|\|\|\|\|:____:\|\|:_\|_\|\|_\|\|\|\|\|\|\|___\|\|\|\|:\n______________CUCC__UAU____________CUGUACUUG____GCCG_U_AC_UCUACUU___ACUUU\n3'-GUU...CCCUA____G_________________________AUGU____G_U__________________UGUUU...GGA-5'\n_____________\|___________________________________________________________\|\n_____________204_________________________________________________________157\n	199 -- 205	163 -- 169	-30.6214 kcal/mol	5.96601 kcal/mol	13.8965 kcal/mol	156 214@LB@ \| \|@LB@5'-CCU...AACCA AA GCAAAAAAAUAC GUAG G U U AGA UAUUU...AAA-3'@LB@ GAGG GUA GAUAUGAAU UGGU A UG AGAUGAA UGAAG@LB@ \|\|\|\| :\|\| \|\|:\|\|\|\|\|: :\|\|: \| \|\| \|\|\|\|\|\|\| \|\|\|\|:@LB@ CUCC UAU CUGUACUUG GCCG U AC UCUACUU ACUUU@LB@3'-GUU...CCCUA G AUGU G U UGUUU...GGA-5'@LB@ \| \|@LB@ 204 157@LB@@LB@@LB@Energy -18.80 kcal/mol@LB@Hybridization Energy -30.6214 kcal/mol@LB@Unfolding Energy - mRNA 5.96601 kcal/mol@LB@Unfolding Energy - sRNA 13.8965 kcal/mol@LB@@LB@Position - mRNA 157 -- 213@LB@Position - sRNA 158 -- 203@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 163 -- 169@LB@
48	0.01096	0.599	lmo0184	N/A	-18.00	0.026009	159 -- 211	157 -- 203	oligo-1 6-glucosidase	_____________158_____212\n_____________\|_______\|\n5'-ACG...ACAAG_______AUUUA...GAA-3'\n______________GGCGGGA\n______________::\|\|\|\|\|\n______________UUGCCCU\n3'-GUU...ACGUA_______ACUCC...GGA-5'\n_____________\|_______\|\n_____________204_____156\n	185 -- 191	201 -- 207	-10.9952 kcal/mol	1.94403 kcal/mol	0.326294 kcal/mol	158 212@LB@ \| \|@LB@5'-ACG...ACAAG AUUUA...GAA-3'@LB@ GGCGGGA@LB@ ::\|\|\|\|\|@LB@ UUGCCCU@LB@3'-GUU...ACGUA ACUCC...GGA-5'@LB@ \| \|@LB@ 204 156@LB@@LB@@LB@Energy -18.00 kcal/mol@LB@Hybridization Energy -10.9952 kcal/mol@LB@Unfolding Energy - mRNA 1.94403 kcal/mol@LB@Unfolding Energy - sRNA 0.326294 kcal/mol@LB@@LB@Position - mRNA 159 -- 211@LB@Position - sRNA 157 -- 203@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 201 -- 207@LB@
129	0.03464	0.6968	lmo0756	N/A	-20.18	0.009099	160 -- 214	175 -- 223	ABC transporter ATP-binding protein	_____________159__________215\n_____________\|____________\|\n5'-AGU...AUAGA_______G____AGAAG...UUU-3'\n______________GACGGGA_GGGG\n______________:\|\|\|\|\|\|_\|:\|\|\n______________UUGCCCU_CUCC\n3'-GUU...ACGUA_______A____GUAUC...GGA-5'\n_____________\|____________\|\n_____________224__________174\n	181 -- 187	201 -- 207	-16.8336 kcal/mol	1.76926 kcal/mol	3.58567 kcal/mol	159 215@LB@ \| \|@LB@5'-AGU...AUAGA G AGAAG...UUU-3'@LB@ GACGGGA GGGG@LB@ :\|\|\|\|\|\| \|:\|\|@LB@ UUGCCCU CUCC@LB@3'-GUU...ACGUA A GUAUC...GGA-5'@LB@ \| \|@LB@ 224 174@LB@@LB@@LB@Energy -20.18 kcal/mol@LB@Hybridization Energy -16.8336 kcal/mol@LB@Unfolding Energy - mRNA 1.76926 kcal/mol@LB@Unfolding Energy - sRNA 3.58567 kcal/mol@LB@@LB@Position - mRNA 160 -- 214@LB@Position - sRNA 175 -- 223@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 201 -- 207@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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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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