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: https://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
56	0.002144	0.1363	pslt006	repA	-15.36	0.103288	219 -- 279	36 -- 87	DNA replication	_____________218_____________________280\n_____________\|_______________________\|\n5'-ACU...ACACC_______UGUU____U_______CGACA...CCC-3'\n______________CGAACAC_____CAC__CAUUAC\n______________\|:\|\|\|\|\|_____\|\|\|__\|\|\|:\|\|\n______________GUUUGUG_____GUG__GUAGUG\n3'-UUU...UUAAC_______UUGUU___UU______UUGGC...UCA-5'\n_____________\|_______________________\|\n_____________88______________________35\n	225 -- 231	83 -- 89	-15.7114 kcal/mol	3.78124 kcal/mol	5.66809 kcal/mol	218 280@LB@ \| \|@LB@5'-ACU...ACACC UGUU U CGACA...CCC-3'@LB@ CGAACAC CAC CAUUAC@LB@ \|:\|\|\|\|\| \|\|\| \|\|\|:\|\|@LB@ GUUUGUG GUG GUAGUG@LB@3'-UUU...UUAAC UUGUU UU UUGGC...UCA-5'@LB@ \| \|@LB@ 88 35@LB@@LB@@LB@Energy -15.36 kcal/mol@LB@Hybridization Energy -15.7114 kcal/mol@LB@Unfolding Energy - mRNA 3.78124 kcal/mol@LB@Unfolding Energy - sRNA 5.66809 kcal/mol@LB@@LB@Position - mRNA 219 -- 279@LB@Position - sRNA 36 -- 87@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 83 -- 89@LB@
160	0.008331	0.1845	stm0002	thrA	-15.10	0.113872	18 -- 81	44 -- 90	bifunctional aspartate kinase/homoserine dehydrogenase I	_____________17______________________82\n_____________\|_______________________\|\n5'-CCA...UACAA________AAUAA__________AGUAC...UAG-3'\n______________GACAGACA_____AAAUG_ACAG\n______________\|\|\|\|\|\|\|\|_____\|\|\|\|\|_\|\|\|\|\n______________CUGUCUGU_____UUUAC_UGUC\n3'-UUU...GAUAC________CCCA______A____CUUCA...UCA-5'\n_____________\|_______________________\|\n_____________91______________________43\n	19 -- 25	155 -- 161	-19.4516 kcal/mol	0.236149 kcal/mol	3.68511 kcal/mol	17 82@LB@ \| \|@LB@5'-CCA...UACAA AAUAA AGUAC...UAG-3'@LB@ GACAGACA AAAUG ACAG@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\| \|\|\|\|@LB@ CUGUCUGU UUUAC UGUC@LB@3'-UUU...GAUAC CCCA A CUUCA...UCA-5'@LB@ \| \|@LB@ 91 43@LB@@LB@@LB@Energy -15.10 kcal/mol@LB@Hybridization Energy -19.4516 kcal/mol@LB@Unfolding Energy - mRNA 0.236149 kcal/mol@LB@Unfolding Energy - sRNA 3.68511 kcal/mol@LB@@LB@Position - mRNA 18 -- 81@LB@Position - sRNA 44 -- 90@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 155 -- 161@LB@
177	0.009665	0.1945	stm0079	yaaU	-14.30	0.152587	187 -- 218	40 -- 79	MFS transporter	_____________186___________219\n_____________\|_____________\|\n5'-GAA...GUUGA____G________CAUGC...UGC-3'\n______________AACA_GACAUCAC\n______________\|\|\|\|_:\|\|\|\|\|\|\|\n______________UUGU_UUGUAGUG\n3'-UUU...UGUUG____G________UUGGC...UCA-5'\n_____________\|_____________\|\n_____________80____________39\n	193 -- 199	67 -- 73	-15.1412 kcal/mol	3.61479 kcal/mol	3.57243 kcal/mol	186 219@LB@ \| \|@LB@5'-GAA...GUUGA G CAUGC...UGC-3'@LB@ AACA GACAUCAC@LB@ \|\|\|\| :\|\|\|\|\|\|\|@LB@ UUGU UUGUAGUG@LB@3'-UUU...UGUUG G UUGGC...UCA-5'@LB@ \| \|@LB@ 80 39@LB@@LB@@LB@Energy -14.30 kcal/mol@LB@Hybridization Energy -15.1412 kcal/mol@LB@Unfolding Energy - mRNA 3.61479 kcal/mol@LB@Unfolding Energy - sRNA 3.57243 kcal/mol@LB@@LB@Position - mRNA 187 -- 218@LB@Position - sRNA 40 -- 79@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 67 -- 73@LB@
71	0.003339	0.1596	stm0105	yabI	-14.10	0.163814	151 -- 168	141 -- 162	similar to E. coli orf hypothetical protein (AAC73176.1); Blastp hit to AAC73176.1 (254 aa) 89% identity in aa 1 - 253	_____________150____________________169\n_____________\|______________________\|\n5'-UGA...ACGAA__G___________________AAUCC...GGU-3'\n______________GG_GGACGGGGUAA____GCAG\n______________\|:_:\|\|\|:\|\|\|\|\|\|____:\|\|\|\n______________CU_UCUGUCCCAUU____UGUC\n3'-UUU...GAUAC__G___________UACA____CUUCA...UCA-5'\n_____________\|______________________\|\n_____________163____________________140\n	158 -- 164	149 -- 155	-23.8591 kcal/mol	5.26969 kcal/mol	3.68511 kcal/mol	150 169@LB@ \| \|@LB@5'-UGA...ACGAA G AAUCC...GGU-3'@LB@ GG GGACGGGGUAA GCAG@LB@ \|: :\|\|\|:\|\|\|\|\|\| :\|\|\|@LB@ CU UCUGUCCCAUU UGUC@LB@3'-UUU...GAUAC G UACA CUUCA...UCA-5'@LB@ \| \|@LB@ 163 140@LB@@LB@@LB@Energy -14.10 kcal/mol@LB@Hybridization Energy -23.8591 kcal/mol@LB@Unfolding Energy - mRNA 5.26969 kcal/mol@LB@Unfolding Energy - sRNA 3.68511 kcal/mol@LB@@LB@Position - mRNA 151 -- 168@LB@Position - sRNA 141 -- 162@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 149 -- 155@LB@
18	0.0003131	0.06194	stm0112	leuB	-16.29	0.072835	153 -- 217	44 -- 93	3-isopropylmalate dehydrogenase	_____________152___________218\n_____________\|_____________\|\n5'-AAA...AAAGA_____________AGCUC...GUU-3'\n______________AUUGC_AACGCAA\n______________\|\|\|\|\|_\|\|\|:\|\|\|\n______________UAACG_UUGUGUU\n3'-UUU...CUGGU_____U_______GUUGU...UCA-5'\n_____________\|_____________\|\n_____________94____________43\n	158 -- 164	81 -- 87	-11.6192 kcal/mol	1.90811 kcal/mol	3.57619 kcal/mol	152 218@LB@ \| \|@LB@5'-AAA...AAAGA AGCUC...GUU-3'@LB@ AUUGC AACGCAA@LB@ \|\|\|\|\| \|\|\|:\|\|\|@LB@ UAACG UUGUGUU@LB@3'-UUU...CUGGU U GUUGU...UCA-5'@LB@ \| \|@LB@ 94 43@LB@@LB@@LB@Energy -16.29 kcal/mol@LB@Hybridization Energy -11.6192 kcal/mol@LB@Unfolding Energy - mRNA 1.90811 kcal/mol@LB@Unfolding Energy - sRNA 3.57619 kcal/mol@LB@@LB@Position - mRNA 153 -- 217@LB@Position - sRNA 44 -- 93@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 81 -- 87@LB@
101	0.005112	0.1728	stm0113	leuA	-13.72	0.187230	187 -- 230	37 -- 84	2-isopropylmalate synthase	_____________186_____________________231\n_____________\|_______________________\|\n5'-AUA...UGGAG____G_____________G____AGCAA...UGG-3'\n______________ACAA_GAC_C_ACAUCAU_AGCC\n______________\|\|\|\|_:\|\|_\|_\|\|\|\|\|\|:_\|:\|\|\n______________UGUU_UUG_G_UGUAGUG_UUGG\n3'-UUU...GUUUG____G___U_U____________CAUUC...UCA-5'\n_____________\|_______________________\|\n_____________85______________________36\n	196 -- 202	67 -- 73	-19.8594 kcal/mol	2.76514 kcal/mol	8.15907 kcal/mol	186 231@LB@ \| \|@LB@5'-AUA...UGGAG G G AGCAA...UGG-3'@LB@ ACAA GAC C ACAUCAU AGCC@LB@ \|\|\|\| :\|\| \| \|\|\|\|\|\|: \|:\|\|@LB@ UGUU UUG G UGUAGUG UUGG@LB@3'-UUU...GUUUG G U U CAUUC...UCA-5'@LB@ \| \|@LB@ 85 36@LB@@LB@@LB@Energy -13.72 kcal/mol@LB@Hybridization Energy -19.8594 kcal/mol@LB@Unfolding Energy - mRNA 2.76514 kcal/mol@LB@Unfolding Energy - sRNA 8.15907 kcal/mol@LB@@LB@Position - mRNA 187 -- 230@LB@Position - sRNA 37 -- 84@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 67 -- 73@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@
67	0.003193	0.1596	stm0122	ftsI	-11.87	0.349270	199 -- 241	52 -- 90	peptidoglycan glycosyltransferase FtsI	_____________198_______________________242\n_____________\|_________________________\|\n5'-GUU...CGCGA____UUG_____UG___________CUGAU...UGG-3'\n______________UGCA___GACAU__AAUGGCGCAAC\n______________\|\|\|\|___:\|\|\|:__\|\|:::\|:\|\|\|\|\n______________ACGU___UUGUG__UUGUUGUGUUG\n3'-UUU...GGUUA_________________________UAGUG...UCA-5'\n_____________\|_________________________\|\n_____________91________________________51\n	62 -- 68	72 -- 78	-17.673 kcal/mol	4.85802 kcal/mol	3.80548 kcal/mol	198 242@LB@ \| \|@LB@5'-GUU...CGCGA UUG UG CUGAU...UGG-3'@LB@ UGCA GACAU AAUGGCGCAAC@LB@ \|\|\|\| :\|\|\|: \|\|:::\|:\|\|\|\|@LB@ ACGU UUGUG UUGUUGUGUUG@LB@3'-UUU...GGUUA UAGUG...UCA-5'@LB@ \| \|@LB@ 91 51@LB@@LB@@LB@Energy -11.87 kcal/mol@LB@Hybridization Energy -17.673 kcal/mol@LB@Unfolding Energy - mRNA 4.85802 kcal/mol@LB@Unfolding Energy - sRNA 3.80548 kcal/mol@LB@@LB@Position - mRNA 199 -- 241@LB@Position - sRNA 52 -- 90@LB@Position Seed - mRNA 62 -- 68@LB@Position Seed - sRNA 72 -- 78@LB@
80	0.003756	0.1596	stm0132	ftsA	-17.45	0.046754	189 -- 236	139 -- 186	cell division protein FtsA	_____________188_______________________________________237\n_____________\|_________________________________________\|\n5'-AAU...GAACA___A______AG___C_________AAAACUG___G_____CUGGA...UCA-3'\n______________ACA_UGAUCA____G_GACGGACAG_______GUA_UAGGA\n______________\|\|\|_\|:\|\|\|\|____\|_\|\|\|:\|\|\|\|\|_______\|\|\|_:\|\|\|\|\n______________UGU_AUUAGU____C_CUGUCUGUC_______CAU_GUCCU\n3'-UUU...CACGA___A______GAUA___________CCAUUUA_________UCACU...UCA-5'\n_____________\|_________________________________________\|\n_____________187_______________________________________138\n	214 -- 220	154 -- 160	-27.6527 kcal/mol	5.88434 kcal/mol	5.72652 kcal/mol	188 237@LB@ \| \|@LB@5'-AAU...GAACA A AG C AAAACUG G CUGGA...UCA-3'@LB@ ACA UGAUCA G GACGGACAG GUA UAGGA@LB@ \|\|\| \|:\|\|\|\| \| \|\|\|:\|\|\|\|\| \|\|\| :\|\|\|\|@LB@ UGU AUUAGU C CUGUCUGUC CAU GUCCU@LB@3'-UUU...CACGA A GAUA CCAUUUA UCACU...UCA-5'@LB@ \| \|@LB@ 187 138@LB@@LB@@LB@Energy -17.45 kcal/mol@LB@Hybridization Energy -27.6527 kcal/mol@LB@Unfolding Energy - mRNA 5.88434 kcal/mol@LB@Unfolding Energy - sRNA 5.72652 kcal/mol@LB@@LB@Position - mRNA 189 -- 236@LB@Position - sRNA 139 -- 186@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 154 -- 160@LB@
38	0.001379	0.1215	stm0150	aroP	-12.21	0.313123	213 -- 232	63 -- 83	APC family aromatic amino acid transporter	_____________212_________________________233\n_____________\|___________________________\|\n5'-CAU...UGAUG____GU_____________A_______CAAGC...UGU-3'\n______________GACA__CAGCAGCACGGCG__GCAGCU\n______________:\|\|\|__\|\|:\|\|:\|\|\|::\|:__:\|\|:\|:\n______________UUGU__GUUGUUGUGUUGU__UGUUGG\n3'-UUU...AACGU___________________AG______CAUUC...UCA-5'\n_____________\|___________________________\|\n_____________84__________________________62\n	219 -- 225	71 -- 77	-26.8853 kcal/mol	7.73214 kcal/mol	8.28637 kcal/mol	212 233@LB@ \| \|@LB@5'-CAU...UGAUG GU A CAAGC...UGU-3'@LB@ GACA CAGCAGCACGGCG GCAGCU@LB@ :\|\|\| \|\|:\|\|:\|\|\|::\|: :\|\|:\|:@LB@ UUGU GUUGUUGUGUUGU UGUUGG@LB@3'-UUU...AACGU AG CAUUC...UCA-5'@LB@ \| \|@LB@ 84 62@LB@@LB@@LB@Energy -12.21 kcal/mol@LB@Hybridization Energy -26.8853 kcal/mol@LB@Unfolding Energy - mRNA 7.73214 kcal/mol@LB@Unfolding Energy - sRNA 8.28637 kcal/mol@LB@@LB@Position - mRNA 213 -- 232@LB@Position - sRNA 63 -- 83@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 71 -- 77@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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