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
154	0.04021	0.7027	lmo2008	N/A	-17.88	0.027453	195 -- 258	157 -- 220	ABC transporter permease	_____________194___________________259\n_____________\|_____________________\|\n5'-CAG...UGAAG____________AU_______GUCCG...UUG-3'\n______________CAGUGAG_UGAA__AGAACAA\n______________\|\|:\|\|\|\|_\|\|\|\|__\|:\|\|\|\|\|\n______________GUUACUC_ACUU__UUUUGUU\n3'-GUU...UGCCG_______U____AC_______UAUUA...GGA-5'\n_____________\|_____________________\|\n_____________221___________________156\n	233 -- 239	154 -- 160	-15.5955 kcal/mol	3.58965 kcal/mol	0.962339 kcal/mol	194 259@LB@ \| \|@LB@5'-CAG...UGAAG AU GUCCG...UUG-3'@LB@ CAGUGAG UGAA AGAACAA@LB@ \|\|:\|\|\|\| \|\|\|\| \|:\|\|\|\|\|@LB@ GUUACUC ACUU UUUUGUU@LB@3'-GUU...UGCCG U AC UAUUA...GGA-5'@LB@ \| \|@LB@ 221 156@LB@@LB@@LB@Energy -17.88 kcal/mol@LB@Hybridization Energy -15.5955 kcal/mol@LB@Unfolding Energy - mRNA 3.58965 kcal/mol@LB@Unfolding Energy - sRNA 0.962339 kcal/mol@LB@@LB@Position - mRNA 195 -- 258@LB@Position - sRNA 157 -- 220@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 154 -- 160@LB@
174	0.04903	0.7583	lmo1615	trmB	-12.39	0.264018	169 -- 243	157 -- 213	tRNA (guanine-N(7)-)-methyltransferase	_____________168________________244\n_____________\|__________________\|\n5'-AAU...AAGAU_________U__A_____AUGCG...AAG-3'\n______________GAUGAGGUG_AA_GAAAG\n______________:\|\|\|\|\|:\|\|_\|\|_\|\|\|\|:\n______________UUACUCUAC_UU_CUUUU\n3'-GUU...GCCGG____________A_____GUUUA...GGA-5'\n_____________\|__________________\|\n_____________214________________156\n	185 -- 191	165 -- 171	-13.3606 kcal/mol	4.29808 kcal/mol	0.930085 kcal/mol	168 244@LB@ \| \|@LB@5'-AAU...AAGAU U A AUGCG...AAG-3'@LB@ GAUGAGGUG AA GAAAG@LB@ :\|\|\|\|\|:\|\| \|\| \|\|\|\|:@LB@ UUACUCUAC UU CUUUU@LB@3'-GUU...GCCGG A GUUUA...GGA-5'@LB@ \| \|@LB@ 214 156@LB@@LB@@LB@Energy -12.39 kcal/mol@LB@Hybridization Energy -13.3606 kcal/mol@LB@Unfolding Energy - mRNA 4.29808 kcal/mol@LB@Unfolding Energy - sRNA 0.930085 kcal/mol@LB@@LB@Position - mRNA 169 -- 243@LB@Position - sRNA 157 -- 213@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 165 -- 171@LB@
180	0.05132	0.7607	lmo1643	N/A	-15.34	0.084306	231 -- 286	157 -- 207	lmo1643	_____________230_______________287\n_____________\|_________________\|\n5'-CGA...UAGUA_______GAU_______AGAAG...CUG-3'\n______________AGUGAGG___AUGAAAA\n______________\|:\|\|\|\|:___\|\|\|\|\|\|\|\n______________UUACUCU___UACUUUU\n3'-GUU...GCCGG_______ACU_______GUUUA...GGA-5'\n_____________\|_________________\|\n_____________208_______________156\n	280 -- 286	157 -- 163	-13.3165 kcal/mol	1.24234 kcal/mol	0.930085 kcal/mol	230 287@LB@ \| \|@LB@5'-CGA...UAGUA GAU AGAAG...CUG-3'@LB@ AGUGAGG AUGAAAA@LB@ \|:\|\|\|\|: \|\|\|\|\|\|\|@LB@ UUACUCU UACUUUU@LB@3'-GUU...GCCGG ACU GUUUA...GGA-5'@LB@ \| \|@LB@ 208 156@LB@@LB@@LB@Energy -15.34 kcal/mol@LB@Hybridization Energy -13.3165 kcal/mol@LB@Unfolding Energy - mRNA 1.24234 kcal/mol@LB@Unfolding Energy - sRNA 0.930085 kcal/mol@LB@@LB@Position - mRNA 231 -- 286@LB@Position - sRNA 157 -- 207@LB@Position Seed - mRNA 280 -- 286@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@
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@
93	0.02416	0.6733	lmo2042	N/A	-17.13	0.038629	149 -- 196	158 -- 206	cell division protein MraZ	_____________148_____________________________________________197\n_____________\|_______________________________________________\|\n5'-UUU...GCGAA_________________UAAAG_____AUGU____AA__________UCUAA...CCC-3'\n______________GUGGGG___AGAUGUGG______UGGU____AUGA__GUGGGUGAAG\n______________:\|\|:\|\|___\|\|\|::\|\|:______:\|\|:____\|\|\|\|__:\|\|::\|\|\|\|:\n______________UACUCC___UCUGUACU______GCCG____UACU__UACUUACUUU\n3'-GUU...UGCCC______GUA________UGAUGU____GU______C___________UGUUU...GGA-5'\n_____________\|_______________________________________________\|\n_____________207_____________________________________________157\n	190 -- 196	158 -- 164	-27.738 kcal/mol	5.20754 kcal/mol	13.9391 kcal/mol	148 197@LB@ \| \|@LB@5'-UUU...GCGAA UAAAG AUGU AA UCUAA...CCC-3'@LB@ GUGGGG AGAUGUGG UGGU AUGA GUGGGUGAAG@LB@ :\|\|:\|\| \|\|\|::\|\|: :\|\|: \|\|\|\| :\|\|::\|\|\|\|:@LB@ UACUCC UCUGUACU GCCG UACU UACUUACUUU@LB@3'-GUU...UGCCC GUA UGAUGU GU C UGUUU...GGA-5'@LB@ \| \|@LB@ 207 157@LB@@LB@@LB@Energy -17.13 kcal/mol@LB@Hybridization Energy -27.738 kcal/mol@LB@Unfolding Energy - mRNA 5.20754 kcal/mol@LB@Unfolding Energy - sRNA 13.9391 kcal/mol@LB@@LB@Position - mRNA 149 -- 196@LB@Position - sRNA 158 -- 206@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 158 -- 164@LB@
151	0.03914	0.6976	lmo1466	N/A	-16.64	0.048271	185 -- 226	158 -- 202		_____________184_______________________________________________227\n_____________\|_________________________________________________\|\n5'-UGA...UUAGA____AGA__A_______A_____________________________G_UUGGU...UUC-3'\n______________GAGG___CA_AGAUGUG_AACUA____GCCAA_GA____AAUGGAGA_A\n______________\|\|\|\|___\|\|_\|\|\|::\|\|_\|\|\|\|\|____\|\|\|\|\|_\|\|____\|\|\|\|:\|:\|_\|\n______________CUCC___GU_UCUGUAC_UUGAU____CGGUU_CU____UUACUUUU_U\n3'-GUU...CCCUA_________A_____________GUGC_____A__CUAC________G_UUAUU...GGA-5'\n_____________\|_________________________________________________\|\n_____________203_______________________________________________157\n	218 -- 224	157 -- 163	-27.6675 kcal/mol	5.9878 kcal/mol	13.9822 kcal/mol	184 227@LB@ \| \|@LB@5'-UGA...UUAGA AGA A A G UUGGU...UUC-3'@LB@ GAGG CA AGAUGUG AACUA GCCAA GA AAUGGAGA A@LB@ \|\|\|\| \|\| \|\|\|::\|\| \|\|\|\|\| \|\|\|\|\| \|\| \|\|\|\|:\|:\| \|@LB@ CUCC GU UCUGUAC UUGAU CGGUU CU UUACUUUU U@LB@3'-GUU...CCCUA A GUGC A CUAC G UUAUU...GGA-5'@LB@ \| \|@LB@ 203 157@LB@@LB@@LB@Energy -16.64 kcal/mol@LB@Hybridization Energy -27.6675 kcal/mol@LB@Unfolding Energy - mRNA 5.9878 kcal/mol@LB@Unfolding Energy - sRNA 13.9822 kcal/mol@LB@@LB@Position - mRNA 185 -- 226@LB@Position - sRNA 158 -- 202@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 157 -- 163@LB@
182	0.05242	0.7607	lmo2028	N/A	-14.74	0.108099	169 -- 210	158 -- 185		_____________168_________211\n_____________\|___________\|\n5'-CUU...AUUAU___________UUUAU...AAC-3'\n______________GAUGGAUGGAA\n______________\|\|\|\|:\|\|\|:\|\|\n______________CUACUUACUUU\n3'-GUU...UUACU___________UGUUU...GGA-5'\n_____________\|___________\|\n_____________186_________157\n	204 -- 210	158 -- 164	-12.4441 kcal/mol	2.18802 kcal/mol	0.806249 kcal/mol	168 211@LB@ \| \|@LB@5'-CUU...AUUAU UUUAU...AAC-3'@LB@ GAUGGAUGGAA@LB@ \|\|\|\|:\|\|\|:\|\|@LB@ CUACUUACUUU@LB@3'-GUU...UUACU UGUUU...GGA-5'@LB@ \| \|@LB@ 186 157@LB@@LB@@LB@Energy -14.74 kcal/mol@LB@Hybridization Energy -12.4441 kcal/mol@LB@Unfolding Energy - mRNA 2.18802 kcal/mol@LB@Unfolding Energy - sRNA 0.806249 kcal/mol@LB@@LB@Position - mRNA 169 -- 210@LB@Position - sRNA 158 -- 185@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 158 -- 164@LB@
10	0.002311	0.4469	lmo2106	N/A	-20.89	0.006356	172 -- 222	159 -- 207		_____________171__________________________________________________223\n_____________\|____________________________________________________\|\n5'-AGU...UAAUA_______AC__CAA______G_____AAA____U__UUAA_______G____UUAUA...AUG-3'\n______________AAUGGGA__AG___CAUAGA_GUGAA____AUG_CU____AGAUGAA_UGGA\n______________\|\|:\|\|\|\|__\|\|___\|\|\|\|\|\|_:\|\|\|\|____\|:\|_\|:____\|\|\|\|\|\|\|_\|\|:\|\n______________UUGCCCU__UC___GUAUCU_UACUU____UGC_GG____UCUACUU_ACUU\n3'-GUU...ACGUA_______AC__C________G_____GAUG___C__UUAC____________UUGUU...GGA-5'\n_____________\|____________________________________________________\|\n_____________208__________________________________________________158\n	211 -- 217	163 -- 169	-34.9864 kcal/mol	6.68059 kcal/mol	18.5724 kcal/mol	171 223@LB@ \| \|@LB@5'-AGU...UAAUA AC CAA G AAA U UUAA G UUAUA...AUG-3'@LB@ AAUGGGA AG CAUAGA GUGAA AUG CU AGAUGAA UGGA@LB@ \|\|:\|\|\|\| \|\| \|\|\|\|\|\| :\|\|\|\| \|:\| \|: \|\|\|\|\|\|\| \|\|:\|@LB@ UUGCCCU UC GUAUCU UACUU UGC GG UCUACUU ACUU@LB@3'-GUU...ACGUA AC C G GAUG C UUAC UUGUU...GGA-5'@LB@ \| \|@LB@ 208 158@LB@@LB@@LB@Energy -20.89 kcal/mol@LB@Hybridization Energy -34.9864 kcal/mol@LB@Unfolding Energy - mRNA 6.68059 kcal/mol@LB@Unfolding Energy - sRNA 18.5724 kcal/mol@LB@@LB@Position - mRNA 172 -- 222@LB@Position - sRNA 159 -- 207@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 163 -- 169@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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