Input and runtime details for job 3202356 (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 3202356 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:02 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:35 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:03:47 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:03:55 CET 2018
	Job Completed		@ Sat Feb 17 02:04:28 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

Description of the job

GcvB

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_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

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
19	0.0004167	0.0781	stm0475	acrB	-19.12	0.024591	69 -- 114	139 -- 185	aminoglycoside/multidrug transporter permease	_____________68_______________________115\n_____________\|________________________\|\n5'-AAG...GUCCU____C_____U_____________AAUUA...CGC-3'\n______________GGCG_ACAGG_UAAA_GUACAGGA\n______________\|:\|:_\|\|\|\|\|_\|\|\|\|_\|\|\|\|\|\|\|\|\n______________CUGU_UGUCC_AUUU_CAUGUCCU\n3'-UUU...GAUAC____C_____C____A________UCACU...UCA-5'\n_____________\|________________________\|\n_____________186______________________138\n	108 -- 114	139 -- 145	-25.274 kcal/mol	6.90525 kcal/mol	3.69132 kcal/mol	68 115@LB@ \| \|@LB@5'-AAG...GUCCU C U AAUUA...CGC-3'@LB@ GGCG ACAGG UAAA GUACAGGA@LB@ \|:\|: \|\|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\|@LB@ CUGU UGUCC AUUU CAUGUCCU@LB@3'-UUU...GAUAC C C A UCACU...UCA-5'@LB@ \| \|@LB@ 186 138@LB@@LB@@LB@Energy -19.12 kcal/mol@LB@Hybridization Energy -25.274 kcal/mol@LB@Unfolding Energy - mRNA 6.90525 kcal/mol@LB@Unfolding Energy - sRNA 3.69132 kcal/mol@LB@@LB@Position - mRNA 69 -- 114@LB@Position - sRNA 139 -- 185@LB@Position Seed - mRNA 108 -- 114@LB@Position Seed - sRNA 139 -- 145@LB@
86	0.004005	0.1596	stm1961	fliS	-19.11	0.024619	1 -- 77	23 -- 90	flagellar export chaperone FliS	______________1__________________________________________________________________________________78\n______________\|__________________________________________________________________________________\|\n___________5'-_______G_______UU____C________AA_____UGACAAAACAGUACCU_________C____________________CGUUG...AUG-3'\n______________GC__GCA_GACAACG__AACG_CAC_GCUG__AAGCC________________GUCCGUUAG_AACA_GCAU__CGAUGAAAC\n______________\|\|__:\|\|_:\|\|\|\|\|:__\|\|\|:_\|\|\|_:\|:\|__\|\|\|\|\|________________\|:\|\|:\|:\|\|_\|\|\|\|_\|\|\|\|__\|\|\|\|:\|\|\|\|\n______________CG__UGU_UUGUUGU__UUGU_GUG_UGGC__UUCGG________________CGGGUAGUC_UUGU_CGUA__GCUAUUUUG\n3'-UUU...GUUAA__UU___G_______G_____A___U____A______UUUU__________________________G____AG_________AAAAG...UCA-5'\n_____________\|___________________________________________________________________________________\|\n_____________91__________________________________________________________________________________22\n	7 -- 13	76 -- 82	-54.7378 kcal/mol	16.9215 kcal/mol	25.0607 kcal/mol	1 78@LB@ \| \|@LB@ 5'- G UU C AA UGACAAAACAGUACCU C CGUUG...AUG-3'@LB@ GC GCA GACAACG AACG CAC GCUG AAGCC GUCCGUUAG AACA GCAU CGAUGAAAC@LB@ \|\| :\|\| :\|\|\|\|\|: \|\|\|: \|\|\| :\|:\| \|\|\|\|\| \|:\|\|:\|:\|\| \|\|\|\| \|\|\|\| \|\|\|\|:\|\|\|\|@LB@ CG UGU UUGUUGU UUGU GUG UGGC UUCGG CGGGUAGUC UUGU CGUA GCUAUUUUG@LB@3'-UUU...GUUAA UU G G A U A UUUU G AG AAAAG...UCA-5'@LB@ \| \|@LB@ 91 22@LB@@LB@@LB@Energy -19.11 kcal/mol@LB@Hybridization Energy -54.7378 kcal/mol@LB@Unfolding Energy - mRNA 16.9215 kcal/mol@LB@Unfolding Energy - sRNA 25.0607 kcal/mol@LB@@LB@Position - mRNA 1 -- 77@LB@Position - sRNA 23 -- 90@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 76 -- 82@LB@
21	0.000482	0.08173	stm1057	pepN	-18.92	0.026522	201 -- 244	36 -- 81	aminopeptidase N	_____________200______________245\n_____________\|________________\|\n5'-CUU...UUUAU___________C____GCCAA...AAA-3'\n______________GACACAACAGC_ACAA\n______________:\|\|\|\|\|\|\|\|:\|_\|\|\|\|\n______________UUGUGUUGUUG_UGUU\n3'-UUU...AACGU________________GUAGU...UCA-5'\n_____________\|________________\|\n_____________82_______________35\n	207 -- 213	77 -- 83	-17.6161 kcal/mol	1.99149 kcal/mol	3.56182 kcal/mol	200 245@LB@ \| \|@LB@5'-CUU...UUUAU C GCCAA...AAA-3'@LB@ GACACAACAGC ACAA@LB@ :\|\|\|\|\|\|\|\|:\| \|\|\|\|@LB@ UUGUGUUGUUG UGUU@LB@3'-UUU...AACGU GUAGU...UCA-5'@LB@ \| \|@LB@ 82 35@LB@@LB@@LB@Energy -18.92 kcal/mol@LB@Hybridization Energy -17.6161 kcal/mol@LB@Unfolding Energy - mRNA 1.99149 kcal/mol@LB@Unfolding Energy - sRNA 3.56182 kcal/mol@LB@@LB@Position - mRNA 201 -- 244@LB@Position - sRNA 36 -- 81@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 77 -- 83@LB@
191	0.01055	0.1967	stm0634	ybeF	-18.83	0.027435	210 -- 262	35 -- 82	putative LysR family transcriptional regulator	_____________209____________________________________________________________263\n_____________\|______________________________________________________________\|\n5'-GCU...CGUGA____UA_____C_G____AAAG_______________UCAACA____________AAC____AAUUU...UGU-3'\n______________GUGA__AUAAU_A_GCAG____ACAACCG___GCCGA______CCUA_CAGGACA___CGCA\n______________\|::\|__\|:\|\|:_\|_:\|\|:____\|\|\|\|\|\|\|___\|\|\|:\|______\|\|:\|_\|\|\|:\|\|\|___\|\|\|\|\n______________CGUU__UGUUG_U_UGUU____UGUUGGC___CGGUU______GGGU_GUCUUGU___GCGU\n3'-UUU...GUUAA____UG_____U_G____GUAG_______AUU_____UUC_______A______________AAGGC...UCA-5'\n_____________\|______________________________________________________________\|\n_____________83_____________________________________________________________34\n	227 -- 233	62 -- 68	-42.1612 kcal/mol	9.04443 kcal/mol	22.5095 kcal/mol	209 263@LB@ \| \|@LB@5'-GCU...CGUGA UA C G AAAG UCAACA AAC AAUUU...UGU-3'@LB@ GUGA AUAAU A GCAG ACAACCG GCCGA CCUA CAGGACA CGCA@LB@ \|::\| \|:\|\|: \| :\|\|: \|\|\|\|\|\|\| \|\|\|:\| \|\|:\| \|\|\|:\|\|\| \|\|\|\|@LB@ CGUU UGUUG U UGUU UGUUGGC CGGUU GGGU GUCUUGU GCGU@LB@3'-UUU...GUUAA UG U G GUAG AUU UUC A AAGGC...UCA-5'@LB@ \| \|@LB@ 83 34@LB@@LB@@LB@Energy -18.83 kcal/mol@LB@Hybridization Energy -42.1612 kcal/mol@LB@Unfolding Energy - mRNA 9.04443 kcal/mol@LB@Unfolding Energy - sRNA 22.5095 kcal/mol@LB@@LB@Position - mRNA 210 -- 262@LB@Position - sRNA 35 -- 82@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 62 -- 68@LB@
99	0.004942	0.1728	stm0604	ybdM	-18.77	0.028138	203 -- 249	36 -- 81	similar to E. coli orf hypothetical protein (AAC73702.1); Blastp hit to AAC73702.1 (209 aa) 77% identity in aa 5 - 209	_____________202___________________250\n_____________\|_____________________\|\n5'-AAA...CUUAU______C______________AAAUA...AUA-3'\n______________GCAACA_CGAC_UCACAACCG\n______________:\|\|\|\|\|_\|:\|\|_\|\|\|\|\|\|\|\|\|\n______________UGUUGU_GUUG_AGUGUUGGC\n3'-UUU...UGUGU___________U_________AUUCG...UCA-5'\n_____________\|_____________________\|\n_____________82____________________35\n	216 -- 222	62 -- 68	-25.0091 kcal/mol	1.37283 kcal/mol	7.72388 kcal/mol	202 250@LB@ \| \|@LB@5'-AAA...CUUAU C AAAUA...AUA-3'@LB@ GCAACA CGAC UCACAACCG@LB@ :\|\|\|\|\| \|:\|\| \|\|\|\|\|\|\|\|\|@LB@ UGUUGU GUUG AGUGUUGGC@LB@3'-UUU...UGUGU U AUUCG...UCA-5'@LB@ \| \|@LB@ 82 35@LB@@LB@@LB@Energy -18.77 kcal/mol@LB@Hybridization Energy -25.0091 kcal/mol@LB@Unfolding Energy - mRNA 1.37283 kcal/mol@LB@Unfolding Energy - sRNA 7.72388 kcal/mol@LB@@LB@Position - mRNA 203 -- 249@LB@Position - sRNA 36 -- 81@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 62 -- 68@LB@
139	0.007115	0.182	stm0826	ybiN	-18.61	0.029895	232 -- 282	36 -- 90	23S rRNA (adenine(1618)-N(6))-methyltransferase	_____________231___________________283\n_____________\|_____________________\|\n5'-CUC...GAGCC_____AACGAGCG________AAUUC...UUC-3'\n______________GAUCA________AGGCAGGG\n______________:\|\|\|\|________\|\|:\|\|\|\|\|\n______________UUAGU________UCUGUCCC\n3'-UUU...UGUAA_____GAUACCUG________AUUUA...UCA-5'\n_____________\|_____________________\|\n_____________91____________________35\n	124 -- 130	152 -- 158	-17.5433 kcal/mol	4.82059 kcal/mol	3.53427 kcal/mol	231 283@LB@ \| \|@LB@5'-CUC...GAGCC AACGAGCG AAUUC...UUC-3'@LB@ GAUCA AGGCAGGG@LB@ :\|\|\|\| \|\|:\|\|\|\|\|@LB@ UUAGU UCUGUCCC@LB@3'-UUU...UGUAA GAUACCUG AUUUA...UCA-5'@LB@ \| \|@LB@ 91 35@LB@@LB@@LB@Energy -18.61 kcal/mol@LB@Hybridization Energy -17.5433 kcal/mol@LB@Unfolding Energy - mRNA 4.82059 kcal/mol@LB@Unfolding Energy - sRNA 3.53427 kcal/mol@LB@@LB@Position - mRNA 232 -- 282@LB@Position - sRNA 36 -- 90@LB@Position Seed - mRNA 124 -- 130@LB@Position Seed - sRNA 152 -- 158@LB@
128	0.006467	0.1774	stm3907	N/A	-18.55	0.030594	118 -- 173	37 -- 89		_____________117__________________________174\n_____________\|____________________________\|\n5'-UCA...AAAAA____________ACCAGU______G___AAAAC...UUU-3'\n______________CAGACGCAACAA______CAGCAU_AUA\n______________\|\|:\|\|:\|\|\|\|\|\|______\|\|:\|\|\|_\|:\|\n______________GUUUGUGUUGUU______GUUGUA_UGU\n3'-UUU...UUAAC____________GU__________G___UGGCA...UCA-5'\n_____________\|____________________________\|\n_____________90___________________________36\n	123 -- 129	78 -- 84	-22.8944 kcal/mol	3.16008 kcal/mol	6.30461 kcal/mol	117 174@LB@ \| \|@LB@5'-UCA...AAAAA ACCAGU G AAAAC...UUU-3'@LB@ CAGACGCAACAA CAGCAU AUA@LB@ \|\|:\|\|:\|\|\|\|\|\| \|\|:\|\|\| \|:\|@LB@ GUUUGUGUUGUU GUUGUA UGU@LB@3'-UUU...UUAAC GU G UGGCA...UCA-5'@LB@ \| \|@LB@ 90 36@LB@@LB@@LB@Energy -18.55 kcal/mol@LB@Hybridization Energy -22.8944 kcal/mol@LB@Unfolding Energy - mRNA 3.16008 kcal/mol@LB@Unfolding Energy - sRNA 6.30461 kcal/mol@LB@@LB@Position - mRNA 118 -- 173@LB@Position - sRNA 37 -- 89@LB@Position Seed - mRNA 123 -- 129@LB@Position Seed - sRNA 78 -- 84@LB@
124	0.006123	0.1758	stm0794	bioB	-18.46	0.031660	1 -- 37	38 -- 79	biotin synthase	______________1________________38\n______________\|________________\|\n___________5'-_________________UUCGG...AGC-3'\n______________AAC_CAGC_UCGCAGCC\n______________\|\|\|_\|\|:\|_\|\|:\|\|:\|\|\n______________UUG_GUUG_AGUGUUGG\n3'-UUU...UGUUG___U____U________CAUUC...UCA-5'\n_____________\|_________________\|\n_____________80________________37\n	9 -- 15	63 -- 69	-17.7754 kcal/mol	2.27351 kcal/mol	6.48115 kcal/mol	1 38@LB@ \| \|@LB@ 5'- UUCGG...AGC-3'@LB@ AAC CAGC UCGCAGCC@LB@ \|\|\| \|\|:\| \|\|:\|\|:\|\|@LB@ UUG GUUG AGUGUUGG@LB@3'-UUU...UGUUG U U CAUUC...UCA-5'@LB@ \| \|@LB@ 80 37@LB@@LB@@LB@Energy -18.46 kcal/mol@LB@Hybridization Energy -17.7754 kcal/mol@LB@Unfolding Energy - mRNA 2.27351 kcal/mol@LB@Unfolding Energy - sRNA 6.48115 kcal/mol@LB@@LB@Position - mRNA 1 -- 37@LB@Position - sRNA 38 -- 79@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 63 -- 69@LB@
81	0.003764	0.1596	stm0121	ftsL	-18.45	0.031843	91 -- 225	48 -- 186	cell division protein FtsL	_____________90__________________226\n_____________\|___________________\|\n5'-CGU...UGCCG__________A________GAAAA...UGC-3'\n______________GGUGAAAAAG_GGUAG_CU\n______________:\|\|\|\|\|\|\|\|\|_\|\|\|\|\|_\|\|\n______________UCACUUUUUC_CCAUC_GA\n3'-UUU...GUCCU________________A__GCGAU...UCA-5'\n_____________\|___________________\|\n_____________187_________________47\n	133 -- 139	129 -- 135	-20.6582 kcal/mol	4.19087 kcal/mol	6.37024 kcal/mol	90 226@LB@ \| \|@LB@5'-CGU...UGCCG A GAAAA...UGC-3'@LB@ GGUGAAAAAG GGUAG CU@LB@ :\|\|\|\|\|\|\|\|\| \|\|\|\|\| \|\|@LB@ UCACUUUUUC CCAUC GA@LB@3'-UUU...GUCCU A GCGAU...UCA-5'@LB@ \| \|@LB@ 187 47@LB@@LB@@LB@Energy -18.45 kcal/mol@LB@Hybridization Energy -20.6582 kcal/mol@LB@Unfolding Energy - mRNA 4.19087 kcal/mol@LB@Unfolding Energy - sRNA 6.37024 kcal/mol@LB@@LB@Position - mRNA 91 -- 225@LB@Position - sRNA 48 -- 186@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 129 -- 135@LB@
183	0.01015	0.1966	stm0813	ybhP	-18.40	0.032407	2 -- 54	36 -- 90	similar to E. coli orf hypothetical protein (AAC73877.1); Blastp hit to AAC73877.1 (253 aa) 86% identity in aa 1 - 253	_____________1____________________________________55\n_____________\|____________________________________\|\n__________5'-A____________UA__CU__CA______________GGUUG...UGC-3'\n______________GUAAAUGCAACA__AU__GC___ACAACCG_AGGCC\n______________\|:\|\|\|::\|\|\|\|\|__\|:__:\|___\|\|\|\|\|\|\|_\|:\|\|\|\n______________CGUUUGUGUUGU__UG__UG___UGUUGGC_UUCGG\n3'-UUU...GUUAA____________UG__U___UAG_______A_____UUUUC...UCA-5'\n_____________\|____________________________________\|\n_____________91___________________________________35\n	24 -- 30	62 -- 68	-32.6929 kcal/mol	6.87264 kcal/mol	11.8287 kcal/mol	1 55@LB@ \| \|@LB@ 5'-A UA CU CA GGUUG...UGC-3'@LB@ GUAAAUGCAACA AU GC ACAACCG AGGCC@LB@ \|:\|\|\|::\|\|\|\|\| \|: :\| \|\|\|\|\|\|\| \|:\|\|\|@LB@ CGUUUGUGUUGU UG UG UGUUGGC UUCGG@LB@3'-UUU...GUUAA UG U UAG A UUUUC...UCA-5'@LB@ \| \|@LB@ 91 35@LB@@LB@@LB@Energy -18.40 kcal/mol@LB@Hybridization Energy -32.6929 kcal/mol@LB@Unfolding Energy - mRNA 6.87264 kcal/mol@LB@Unfolding Energy - sRNA 11.8287 kcal/mol@LB@@LB@Position - mRNA 2 -- 54@LB@Position - sRNA 36 -- 90@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 62 -- 68@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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