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
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@
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@
53	0.0118	0.599	lmo2394	N/A	-15.56	0.076801	20 -- 80	100 -- 170		_____________19_____________________________________81\n_____________\|______________________________________\|\n5'-GGA...UUUUC________GUG___GG____________A_________AUAGU...AAA-3'\n______________GAUAGAUG___GAU________AUUUUG_UGGAGGAUG\n______________:\|:\|\|\|\|\|___\|\|:________\|\|\|:\|:_\|\|\|\|:\|\|\|\|\n______________UUGUCUAC___CUG________UAAGAU_ACCUUCUAC\n3'-GUU...CAGAU________AGA___AUCAACGG______A_________CUAUG...GGA-5'\n_____________\|______________________________________\|\n_____________171____________________________________99\n	189 -- 195	97 -- 103	-26.5698 kcal/mol	4.81204 kcal/mol	9.44565 kcal/mol	19 81@LB@ \| \|@LB@5'-GGA...UUUUC GUG GG A AUAGU...AAA-3'@LB@ GAUAGAUG GAU AUUUUG UGGAGGAUG@LB@ :\|:\|\|\|\|\| \|\|: \|\|\|:\|: \|\|\|\|:\|\|\|\|@LB@ UUGUCUAC CUG UAAGAU ACCUUCUAC@LB@3'-GUU...CAGAU AGA AUCAACGG A CUAUG...GGA-5'@LB@ \| \|@LB@ 171 99@LB@@LB@@LB@Energy -15.56 kcal/mol@LB@Hybridization Energy -26.5698 kcal/mol@LB@Unfolding Energy - mRNA 4.81204 kcal/mol@LB@Unfolding Energy - sRNA 9.44565 kcal/mol@LB@@LB@Position - mRNA 20 -- 80@LB@Position - sRNA 100 -- 170@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 97 -- 103@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@
55	0.01256	0.6043	lmo1725	N/A	-17.74	0.029271	269 -- 300	152 -- 185	GntR family tramscriptional regulator	_____________268______________________________301\n_____________\|________________________________\|\n5'-CAG...CAAAU___________G_______A___A________GU-3'\n______________GAUUACA_GGC_AAUG_GA_GGG_GAGGAUAA\n______________:\|:\|\|\|\|_\|\|\|_\|\|\|\|_\|\|_\|::_\|\|::\|:\|\|\n______________UUGAUGU_CCG_UUAC_CU_CUU_CUUUUGUU\n3'-GUU...UGUAC_______G___G____U__A___A________UAUUA...GGA-5'\n_____________\|________________________________\|\n_____________186______________________________151\n	291 -- 297	155 -- 161	-25.158 kcal/mol	5.52494 kcal/mol	9.66022 kcal/mol	268 301@LB@ \| \|@LB@5'-CAG...CAAAU G A A GU-3'@LB@ GAUUACA GGC AAUG GA GGG GAGGAUAA@LB@ :\|:\|\|\|\| \|\|\| \|\|\|\| \|\| \|:: \|\|::\|:\|\|@LB@ UUGAUGU CCG UUAC CU CUU CUUUUGUU@LB@3'-GUU...UGUAC G G U A A UAUUA...GGA-5'@LB@ \| \|@LB@ 186 151@LB@@LB@@LB@Energy -17.74 kcal/mol@LB@Hybridization Energy -25.158 kcal/mol@LB@Unfolding Energy - mRNA 5.52494 kcal/mol@LB@Unfolding Energy - sRNA 9.66022 kcal/mol@LB@@LB@Position - mRNA 269 -- 300@LB@Position - sRNA 152 -- 185@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 155 -- 161@LB@
56	0.01257	0.6043	lmo2205	N/A	-16.72	0.046467	190 -- 249	147 -- 203	phosphoglyceromutase	_____________189_____________________250\n_____________\|_______________________\|\n5'-AUG...GCGAA____GAA________________AAUUA...UGG-3'\n______________AAUG___GGAUGAG_GAAGAUGA\n______________\|\|\|\|___:\|\|\|\|\|:_\|\|\|:\|::\|\n______________UUAC___UCUACUU_CUUUUGUU\n3'-GUU...GCCGG______________A________UAUUA...GGA-5'\n_____________\|_______________________\|\n_____________204_____________________146\n	197 -- 203	155 -- 161	-13.1674 kcal/mol	1.25432 kcal/mol	0.959215 kcal/mol	189 250@LB@ \| \|@LB@5'-AUG...GCGAA GAA AAUUA...UGG-3'@LB@ AAUG GGAUGAG GAAGAUGA@LB@ \|\|\|\| :\|\|\|\|\|: \|\|\|:\|::\|@LB@ UUAC UCUACUU CUUUUGUU@LB@3'-GUU...GCCGG A UAUUA...GGA-5'@LB@ \| \|@LB@ 204 146@LB@@LB@@LB@Energy -16.72 kcal/mol@LB@Hybridization Energy -13.1674 kcal/mol@LB@Unfolding Energy - mRNA 1.25432 kcal/mol@LB@Unfolding Energy - sRNA 0.959215 kcal/mol@LB@@LB@Position - mRNA 190 -- 249@LB@Position - sRNA 147 -- 203@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 155 -- 161@LB@
57	0.01283	0.6057	lmo2379	N/A	-18.13	0.024463	194 -- 217	150 -- 173	monovalent cation/H+ antiporter subunit B	_____________193__________________218\n_____________\|____________________\|\n5'-GUA...AACGA_______AU___________AUGAC...AUA-3'\n______________GGUGAGA__GAUGAAAACGA\n______________::\|\|\|\|\|__:\|\|\|\|\|\|\|\|:\|\n______________UUACUCU__UUACUUUUGUU\n3'-GUU...GCCGG_______AC___________UAUUA...GGA-5'\n_____________\|____________________\|\n_____________174__________________149\n	207 -- 213	154 -- 160	-18.1864 kcal/mol	2.62553 kcal/mol	0.959215 kcal/mol	193 218@LB@ \| \|@LB@5'-GUA...AACGA AU AUGAC...AUA-3'@LB@ GGUGAGA GAUGAAAACGA@LB@ ::\|\|\|\|\| :\|\|\|\|\|\|\|\|:\|@LB@ UUACUCU UUACUUUUGUU@LB@3'-GUU...GCCGG AC UAUUA...GGA-5'@LB@ \| \|@LB@ 174 149@LB@@LB@@LB@Energy -18.13 kcal/mol@LB@Hybridization Energy -18.1864 kcal/mol@LB@Unfolding Energy - mRNA 2.62553 kcal/mol@LB@Unfolding Energy - sRNA 0.959215 kcal/mol@LB@@LB@Position - mRNA 194 -- 217@LB@Position - sRNA 150 -- 173@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 154 -- 160@LB@
58	0.0137	0.6248	lmo1724	N/A	-17.96	0.026530	144 -- 212	156 -- 211	ABC transporter ATP-binding protein	_____________143__________213\n_____________\|____________\|\n5'-UUA...CAACC____________CUGAU...UCA-3'\n______________AUGAAUGAAAAC\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________UACUUACUUUUG\n3'-GUU...UACUC____________UUUAU...GGA-5'\n_____________\|____________\|\n_____________212__________155\n	206 -- 212	156 -- 162	-13.4321 kcal/mol	1.37849 kcal/mol	0.849227 kcal/mol	143 213@LB@ \| \|@LB@5'-UUA...CAACC CUGAU...UCA-3'@LB@ AUGAAUGAAAAC@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ UACUUACUUUUG@LB@3'-GUU...UACUC UUUAU...GGA-5'@LB@ \| \|@LB@ 212 155@LB@@LB@@LB@Energy -17.96 kcal/mol@LB@Hybridization Energy -13.4321 kcal/mol@LB@Unfolding Energy - mRNA 1.37849 kcal/mol@LB@Unfolding Energy - sRNA 0.849227 kcal/mol@LB@@LB@Position - mRNA 144 -- 212@LB@Position - sRNA 156 -- 211@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 156 -- 162@LB@
59	0.0137	0.6248	lmo0642	N/A	-14.84	0.103863	179 -- 256	168 -- 213	lmo0642	_____________178________257\n_____________\|__________\|\n5'-UUC...GAUUG__________CAUGA...CAA-3'\n______________GAGAUGAGUG\n______________\|\|\|\|\|\|\|:\|\|\n______________CUCUACUUAC\n3'-GUU...GGUUA__________UUUUG...GGA-5'\n_____________\|__________\|\n_____________214________167\n	193 -- 199	161 -- 167	-14.0942 kcal/mol	3.54513 kcal/mol	0.812237 kcal/mol	178 257@LB@ \| \|@LB@5'-UUC...GAUUG CAUGA...CAA-3'@LB@ GAGAUGAGUG@LB@ \|\|\|\|\|\|\|:\|\|@LB@ CUCUACUUAC@LB@3'-GUU...GGUUA UUUUG...GGA-5'@LB@ \| \|@LB@ 214 167@LB@@LB@@LB@Energy -14.84 kcal/mol@LB@Hybridization Energy -14.0942 kcal/mol@LB@Unfolding Energy - mRNA 3.54513 kcal/mol@LB@Unfolding Energy - sRNA 0.812237 kcal/mol@LB@@LB@Position - mRNA 179 -- 256@LB@Position - sRNA 168 -- 213@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 161 -- 167@LB@
60	0.01449	0.6412	lmo0835	N/A	-17.67	0.030280	187 -- 229	146 -- 187	peptidoglycan binding protein	_____________186______________________________________________230\n_____________\|________________________________________________\|\n5'-UUU...UAUGA_____UUGGAGGA____________UAAA____U____A_________UAACU...CAG-3'\n______________GAACU________AUGGUCAGUGAG____AAUG_AAAA_AAAUAGUGA\n______________\|\|\|\|\|________\|:\|\|:\|\|:\|\|\|\|____\|\|\|\|_\|\|\|\|_\|\|\|\|\|:\|\|\|\n______________CUUGA________UGCCGGUUACUC____UUAC_UUUU_UUUAUUACU\n3'-GUU...CUGUA_____UG__________________UAC__________G_________AAAAC...GGA-5'\n_____________\|________________________________________________\|\n_____________188______________________________________________145\n	199 -- 205	168 -- 174	-31.6389 kcal/mol	7.07372 kcal/mol	14.4129 kcal/mol	186 230@LB@ \| \|@LB@5'-UUU...UAUGA UUGGAGGA UAAA U A UAACU...CAG-3'@LB@ GAACU AUGGUCAGUGAG AAUG AAAA AAAUAGUGA@LB@ \|\|\|\|\| \|:\|\|:\|\|:\|\|\|\| \|\|\|\| \|\|\|\| \|\|\|\|\|:\|\|\|@LB@ CUUGA UGCCGGUUACUC UUAC UUUU UUUAUUACU@LB@3'-GUU...CUGUA UG UAC G AAAAC...GGA-5'@LB@ \| \|@LB@ 188 145@LB@@LB@@LB@Energy -17.67 kcal/mol@LB@Hybridization Energy -31.6389 kcal/mol@LB@Unfolding Energy - mRNA 7.07372 kcal/mol@LB@Unfolding Energy - sRNA 14.4129 kcal/mol@LB@@LB@Position - mRNA 187 -- 229@LB@Position - sRNA 146 -- 187@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 168 -- 174@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)

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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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