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
61	0.01458	0.6412	lmo2589	N/A	-18.59	0.019740	180 -- 258	153 -- 210	TetR family transcriptional regulator	_____________179__________259\n_____________\|____________\|\n5'-ACU...AACAG____________UGUUU...CUG-3'\n______________AAC_GGGUGGGG\n______________\|\|\|_\|\|:\|\|:\|\|\n______________UUG_CCUACUCC\n3'-GUU...ACGUA___C________GUAUC...GGA-5'\n_____________\|____________\|\n_____________211__________152\n	186 -- 192	197 -- 203	-13.3669 kcal/mol	1.19489 kcal/mol	3.58567 kcal/mol	179 259@LB@ \| \|@LB@5'-ACU...AACAG UGUUU...CUG-3'@LB@ AAC GGGUGGGG@LB@ \|\|\| \|\|:\|\|:\|\|@LB@ UUG CCUACUCC@LB@3'-GUU...ACGUA C GUAUC...GGA-5'@LB@ \| \|@LB@ 211 152@LB@@LB@@LB@Energy -18.59 kcal/mol@LB@Hybridization Energy -13.3669 kcal/mol@LB@Unfolding Energy - mRNA 1.19489 kcal/mol@LB@Unfolding Energy - sRNA 3.58567 kcal/mol@LB@@LB@Position - mRNA 180 -- 258@LB@Position - sRNA 153 -- 210@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 197 -- 203@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@
63	0.01551	0.6624	lmo2613	rplO	-17.63	0.030853	185 -- 213	177 -- 203	50S ribosomal protein L15	_____________184______214\n_____________\|________\|\n5'-AAU...AUUCG________UCACU...GCG-3'\n______________UGGGAUGA\n______________:\|\|\|\|\|\|\|\n______________GCCCUACU\n3'-GUU...GUAUU________CCGUA...GGA-5'\n_____________\|________\|\n_____________204______176\n	98 -- 104	198 -- 204	-11.9514 kcal/mol	5.35707 kcal/mol	0.374397 kcal/mol	184 214@LB@ \| \|@LB@5'-AAU...AUUCG UCACU...GCG-3'@LB@ UGGGAUGA@LB@ :\|\|\|\|\|\|\|@LB@ GCCCUACU@LB@3'-GUU...GUAUU CCGUA...GGA-5'@LB@ \| \|@LB@ 204 176@LB@@LB@@LB@Energy -17.63 kcal/mol@LB@Hybridization Energy -11.9514 kcal/mol@LB@Unfolding Energy - mRNA 5.35707 kcal/mol@LB@Unfolding Energy - sRNA 0.374397 kcal/mol@LB@@LB@Position - mRNA 185 -- 213@LB@Position - sRNA 177 -- 203@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 198 -- 204@LB@
64	0.01603	0.6733	lmo0131	N/A	-19.25	0.014339	193 -- 248	149 -- 204		_____________192____________________________________________________249\n_____________\|______________________________________________________\|\n5'-UGU...AAAAG____G_____G______AUCUCGA______AAAU________C___UAG_____AUAGU...UCG-3'\n______________GAGG_AUA_A_AUGGAU_______GCACGG____AUGGGAUG_GAU___GAGAA\n______________\|\|\|\|_\|\|\|_\|_\|\|\|:\|:_______:\|\|\|\|\|____\|\|\|:\|\|\|\|_:\|\|___\|\|:\|\|\n______________CUCC_UAU_U_UACUUG_______UGUGCC____UACUCUAC_UUA___CUUUU\n3'-GUU...CCCUA____G___C_G______A____________GGU_____________________GUUUA...GGA-5'\n_____________\|______________________________________________________\|\n_____________205____________________________________________________148\n	225 -- 231	165 -- 171	-32.0138 kcal/mol	8.31689 kcal/mol	13.9574 kcal/mol	192 249@LB@ \| \|@LB@5'-UGU...AAAAG G G AUCUCGA AAAU C UAG AUAGU...UCG-3'@LB@ GAGG AUA A AUGGAU GCACGG AUGGGAUG GAU GAGAA@LB@ \|\|\|\| \|\|\| \| \|\|\|:\|: :\|\|\|\|\| \|\|\|:\|\|\|\| :\|\| \|\|:\|\|@LB@ CUCC UAU U UACUUG UGUGCC UACUCUAC UUA CUUUU@LB@3'-GUU...CCCUA G C G A GGU GUUUA...GGA-5'@LB@ \| \|@LB@ 205 148@LB@@LB@@LB@Energy -19.25 kcal/mol@LB@Hybridization Energy -32.0138 kcal/mol@LB@Unfolding Energy - mRNA 8.31689 kcal/mol@LB@Unfolding Energy - sRNA 13.9574 kcal/mol@LB@@LB@Position - mRNA 193 -- 248@LB@Position - sRNA 149 -- 204@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 165 -- 171@LB@
65	0.01641	0.6733	lmo0040	N/A	-17.01	0.040772	52 -- 100	171 -- 220	agmatine deiminase	_____________51______________101\n_____________\|_______________\|\n5'-GUC...AAUAG____A__________GGGAC...CUG-3'\n______________GAGG_GAAUGAGGAU\n______________\|\|\|:_\|\|\|\|\|\|::\|:\n______________CUCU_CUUACUUUUG\n3'-GUU...GGUUA____A__________UUUAU...GGA-5'\n_____________\|_______________\|\n_____________221_____________170\n	196 -- 202	156 -- 162	-15.5399 kcal/mol	0.994344 kcal/mol	0.916023 kcal/mol	51 101@LB@ \| \|@LB@5'-GUC...AAUAG A GGGAC...CUG-3'@LB@ GAGG GAAUGAGGAU@LB@ \|\|\|: \|\|\|\|\|\|::\|:@LB@ CUCU CUUACUUUUG@LB@3'-GUU...GGUUA A UUUAU...GGA-5'@LB@ \| \|@LB@ 221 170@LB@@LB@@LB@Energy -17.01 kcal/mol@LB@Hybridization Energy -15.5399 kcal/mol@LB@Unfolding Energy - mRNA 0.994344 kcal/mol@LB@Unfolding Energy - sRNA 0.916023 kcal/mol@LB@@LB@Position - mRNA 52 -- 100@LB@Position - sRNA 171 -- 220@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 156 -- 162@LB@
66	0.01668	0.6733	lmo0959	N/A	-18.16	0.024105	185 -- 212	177 -- 206	undacaprenyl-phosphate N-acetylglucosaminyltransferase	_____________184________________213\n_____________\|__________________\|\n5'-GAA...AAGUA_____________A____AUUUG...CAG-3'\n______________UAAUGAGAUGAGU_AAAA\n______________:\|\|\|\|\|\|\|\|\|\|:\|_\|\|\|\|\n______________GUUACUCUACUUA_UUUU\n3'-GUU...UGCCG_____________C____GUUUA...GGA-5'\n_____________\|__________________\|\n_____________207________________176\n	169 -- 175	162 -- 168	-15.497 kcal/mol	1.5517 kcal/mol	0.933292 kcal/mol	184 213@LB@ \| \|@LB@5'-GAA...AAGUA A AUUUG...CAG-3'@LB@ UAAUGAGAUGAGU AAAA@LB@ :\|\|\|\|\|\|\|\|\|\|:\| \|\|\|\|@LB@ GUUACUCUACUUA UUUU@LB@3'-GUU...UGCCG C GUUUA...GGA-5'@LB@ \| \|@LB@ 207 176@LB@@LB@@LB@Energy -18.16 kcal/mol@LB@Hybridization Energy -15.497 kcal/mol@LB@Unfolding Energy - mRNA 1.5517 kcal/mol@LB@Unfolding Energy - sRNA 0.933292 kcal/mol@LB@@LB@Position - mRNA 185 -- 212@LB@Position - sRNA 177 -- 206@LB@Position Seed - mRNA 169 -- 175@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@
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@
69	0.01791	0.6733	lmo0011	N/A	-18.87	0.017267	48 -- 93	161 -- 209	mevalonate diphosphate decarboxylase	_____________47_________94\n_____________\|__________\|\n5'-AGU...CGGUA__________CAUUA...CCU-3'\n______________GAGGUGGAUG\n______________\|\|\|:\|\|:\|\|\|\n______________CUCUACUUAC\n3'-GUU...GGUUA__________UUUUG...GGA-5'\n_____________\|__________\|\n_____________210________160\n	87 -- 93	161 -- 167	-12.2828 kcal/mol	3.75931 kcal/mol	0.812237 kcal/mol	47 94@LB@ \| \|@LB@5'-AGU...CGGUA CAUUA...CCU-3'@LB@ GAGGUGGAUG@LB@ \|\|\|:\|\|:\|\|\|@LB@ CUCUACUUAC@LB@3'-GUU...GGUUA UUUUG...GGA-5'@LB@ \| \|@LB@ 210 160@LB@@LB@@LB@Energy -18.87 kcal/mol@LB@Hybridization Energy -12.2828 kcal/mol@LB@Unfolding Energy - mRNA 3.75931 kcal/mol@LB@Unfolding Energy - sRNA 0.812237 kcal/mol@LB@@LB@Position - mRNA 48 -- 93@LB@Position - sRNA 161 -- 209@LB@Position Seed - mRNA 87 -- 93@LB@Position Seed - sRNA 161 -- 167@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@

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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