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
79	0.003723	0.1596	stm1723	trpE	-16.56	0.065817	202 -- 256	41 -- 91	anthranilate synthase subunit I	_____________201__________________257\n_____________\|____________________\|\n5'-UGA...AAAUG__________UU________CGGUU...CGG-3'\n______________GCAGCGACAU__GCAUUACA\n______________:\|\|:\|:\|\|\|:__:\|\|\|:\|\|\|\n______________UGUUGUUGUG__UGUAGUGU\n3'-UUU...GUUUG__________U_________UGGCA...UCA-5'\n_____________\|____________________\|\n_____________92___________________40\n	78 -- 84	66 -- 72	-20.8013 kcal/mol	5.41524 kcal/mol	5.89278 kcal/mol	201 257@LB@ \| \|@LB@5'-UGA...AAAUG UU CGGUU...CGG-3'@LB@ GCAGCGACAU GCAUUACA@LB@ :\|\|:\|:\|\|\|: :\|\|\|:\|\|\|@LB@ UGUUGUUGUG UGUAGUGU@LB@3'-UUU...GUUUG U UGGCA...UCA-5'@LB@ \| \|@LB@ 92 40@LB@@LB@@LB@Energy -16.56 kcal/mol@LB@Hybridization Energy -20.8013 kcal/mol@LB@Unfolding Energy - mRNA 5.41524 kcal/mol@LB@Unfolding Energy - sRNA 5.89278 kcal/mol@LB@@LB@Position - mRNA 202 -- 256@LB@Position - sRNA 41 -- 91@LB@Position Seed - mRNA 78 -- 84@LB@Position Seed - sRNA 66 -- 72@LB@
106	0.005253	0.1728	stm1172	flgM	-15.84	0.086212	196 -- 254	36 -- 82	anti-sigma-28 factor FlgM	_____________195________________255\n_____________\|__________________\|\n5'-GGC...GACGC__G_______________CCGGU...CGU-3'\n______________GC_AAAC_CAGCGACACG\n______________\|\|_\|\|\|\|_\|\|:\|:\|\|\|\|:\n______________CG_UUUG_GUUGUUGUGU\n3'-UUU...GUUAA_______U__________UGUAG...UCA-5'\n_____________\|__________________\|\n_____________83_________________35\n	263 -- 269	74 -- 80	-18.0556 kcal/mol	5.48392 kcal/mol	3.73436 kcal/mol	195 255@LB@ \| \|@LB@5'-GGC...GACGC G CCGGU...CGU-3'@LB@ GC AAAC CAGCGACACG@LB@ \|\| \|\|\|\| \|\|:\|:\|\|\|\|:@LB@ CG UUUG GUUGUUGUGU@LB@3'-UUU...GUUAA U UGUAG...UCA-5'@LB@ \| \|@LB@ 83 35@LB@@LB@@LB@Energy -15.84 kcal/mol@LB@Hybridization Energy -18.0556 kcal/mol@LB@Unfolding Energy - mRNA 5.48392 kcal/mol@LB@Unfolding Energy - sRNA 3.73436 kcal/mol@LB@@LB@Position - mRNA 196 -- 254@LB@Position - sRNA 36 -- 82@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 74 -- 80@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@
55	0.002114	0.1363	stm0887	artJ	-12.89	0.249853	160 -- 177	72 -- 90	arginine ABC transporter substrate-binding protein	_____________159_________________178\n_____________\|___________________\|\n5'-AUG...AUGCC___________________CAUAA...CGU-3'\n______________GCAGACACGGC_GCAUAAU\n______________\|\|\|:\|\|\|\|::\|_:\|\|:\|\|:\n______________CGUUUGUGUUG_UGUGUUG\n3'-UUU...GUUAA___________U_______UAGUG...UCA-5'\n_____________\|___________________\|\n_____________91__________________71\n	171 -- 177	72 -- 78	-21.0424 kcal/mol	4.03353 kcal/mol	3.80362 kcal/mol	159 178@LB@ \| \|@LB@5'-AUG...AUGCC CAUAA...CGU-3'@LB@ GCAGACACGGC GCAUAAU@LB@ \|\|\|:\|\|\|\|::\| :\|\|:\|\|:@LB@ CGUUUGUGUUG UGUGUUG@LB@3'-UUU...GUUAA U UAGUG...UCA-5'@LB@ \| \|@LB@ 91 71@LB@@LB@@LB@Energy -12.89 kcal/mol@LB@Hybridization Energy -21.0424 kcal/mol@LB@Unfolding Energy - mRNA 4.03353 kcal/mol@LB@Unfolding Energy - sRNA 3.80362 kcal/mol@LB@@LB@Position - mRNA 160 -- 177@LB@Position - sRNA 72 -- 90@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 72 -- 78@LB@
10	0.0001468	0.05229	stm0680	asnB	-17.15	0.052408	158 -- 224	32 -- 90	asparagine synthetase B	_____________157________________________225\n_____________\|__________________________\|\n5'-CAU...GUCAA_________AAAAGU___________GAUUA...CGG-3'\n______________GCAAAUACA______ACGACGCAACA\n______________\|\|\|\|\|:\|\|\|______\|\|:\|\|:\|\|\|\|\|\n______________CGUUUGUGU______UGUUGUGUUGU\n3'-UUU...GUUAA__________________________AGUGU...UCA-5'\n_____________\|__________________________\|\n_____________91_________________________31\n	177 -- 183	71 -- 77	-23.872 kcal/mol	3.8402 kcal/mol	3.80671 kcal/mol	157 225@LB@ \| \|@LB@5'-CAU...GUCAA AAAAGU GAUUA...CGG-3'@LB@ GCAAAUACA ACGACGCAACA@LB@ \|\|\|\|\|:\|\|\| \|\|:\|\|:\|\|\|\|\|@LB@ CGUUUGUGU UGUUGUGUUGU@LB@3'-UUU...GUUAA AGUGU...UCA-5'@LB@ \| \|@LB@ 91 31@LB@@LB@@LB@Energy -17.15 kcal/mol@LB@Hybridization Energy -23.872 kcal/mol@LB@Unfolding Energy - mRNA 3.8402 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 158 -- 224@LB@Position - sRNA 32 -- 90@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 71 -- 77@LB@
149	0.007892	0.1845	stm2071	hisG	-15.61	0.094042	166 -- 245	36 -- 100	ATP phosphoribosyltransferase	_____________165________________________246\n_____________\|__________________________\|\n5'-UUU...AGACC__UU________A________G____ACGCA...AUU-3'\n______________GG__CAGACAGG_UAA____A_AGGA\n______________\|\|__\|\|\|\|\|\|\|\|_\|\|\|____\|_\|\|\|\|\n______________CC__GUCUGUCC_AUU____U_UCCU\n3'-UUU...UGAUA__U_________C___UACA_G____UCACU...UCA-5'\n_____________\|__________________________\|\n_____________101________________________35\n	177 -- 183	153 -- 159	-19.7047 kcal/mol	3.01127 kcal/mol	3.70983 kcal/mol	165 246@LB@ \| \|@LB@5'-UUU...AGACC UU A G ACGCA...AUU-3'@LB@ GG CAGACAGG UAA A AGGA@LB@ \|\| \|\|\|\|\|\|\|\| \|\|\| \| \|\|\|\|@LB@ CC GUCUGUCC AUU U UCCU@LB@3'-UUU...UGAUA U C UACA G UCACU...UCA-5'@LB@ \| \|@LB@ 101 35@LB@@LB@@LB@Energy -15.61 kcal/mol@LB@Hybridization Energy -19.7047 kcal/mol@LB@Unfolding Energy - mRNA 3.01127 kcal/mol@LB@Unfolding Energy - sRNA 3.70983 kcal/mol@LB@@LB@Position - mRNA 166 -- 245@LB@Position - sRNA 36 -- 100@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 153 -- 159@LB@
179	0.009806	0.1951	stm3912	rep	-13.00	0.240883	219 -- 287	22 -- 83	ATP-dependent DNA helicase Rep	_____________218__________________________288\n_____________\|____________________________\|\n5'-AGU...UCCCA____UUUAAAUCCC______________CUGUC...CCA-3'\n______________UGCG__________GGC_CAACAACACG\n______________\|\|\|:__________::\|_\|\|\|\|\|\|\|\|\|:\n______________ACGU__________UUG_GUUGUUGUGU\n3'-UUU...GGUUA_________________U__________UGUAG...UCA-5'\n_____________\|____________________________\|\n_____________84___________________________21\n	222 -- 228	74 -- 80	-15.5311 kcal/mol	3.54327 kcal/mol	3.73631 kcal/mol	218 288@LB@ \| \|@LB@5'-AGU...UCCCA UUUAAAUCCC CUGUC...CCA-3'@LB@ UGCG GGC CAACAACACG@LB@ \|\|\|: ::\| \|\|\|\|\|\|\|\|\|:@LB@ ACGU UUG GUUGUUGUGU@LB@3'-UUU...GGUUA U UGUAG...UCA-5'@LB@ \| \|@LB@ 84 21@LB@@LB@@LB@Energy -13.00 kcal/mol@LB@Hybridization Energy -15.5311 kcal/mol@LB@Unfolding Energy - mRNA 3.54327 kcal/mol@LB@Unfolding Energy - sRNA 3.73631 kcal/mol@LB@@LB@Position - mRNA 219 -- 287@LB@Position - sRNA 22 -- 83@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 74 -- 80@LB@
129	0.006472	0.1774	stm0158	acnB	-11.80	0.356459	140 -- 172	33 -- 60	bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase	_____________139________________173\n_____________\|__________________\|\n5'-AUU...CUUUU_________G_U______UUAAA...UGC-3'\n______________UUGUAAACA_A_UAACAC\n______________\|\|\|:\|\|\|\|\|_\|_:\|\|\|\|\|\n______________AACGUUUGU_U_GUUGUG\n3'-UUU...UGGUU_________G_U______UUGUA...UCA-5'\n_____________\|__________________\|\n_____________61_________________32\n	48 -- 54	84 -- 90	-17.8051 kcal/mol	3.41045 kcal/mol	3.73018 kcal/mol	139 173@LB@ \| \|@LB@5'-AUU...CUUUU G U UUAAA...UGC-3'@LB@ UUGUAAACA A UAACAC@LB@ \|\|\|:\|\|\|\|\| \| :\|\|\|\|\|@LB@ AACGUUUGU U GUUGUG@LB@3'-UUU...UGGUU G U UUGUA...UCA-5'@LB@ \| \|@LB@ 61 32@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -17.8051 kcal/mol@LB@Unfolding Energy - mRNA 3.41045 kcal/mol@LB@Unfolding Energy - sRNA 3.73018 kcal/mol@LB@@LB@Position - mRNA 140 -- 172@LB@Position - sRNA 33 -- 60@LB@Position Seed - mRNA 48 -- 54@LB@Position Seed - sRNA 84 -- 90@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@
186	0.01044	0.1967	stm1725	trpC	-12.00	0.335236	146 -- 174	55 -- 86	bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase	_____________145_______________175\n_____________\|_________________\|\n5'-AAA...GUUCU____________C____AUGAC...AGC-3'\n______________GCGCAACGGCAC_GCAU\n______________:\|:\|\|\|\|::\|\|\|_:\|\|\|\n______________UGUGUUGUUGUG_UGUA\n3'-UUU...ACGUU____________U____GUGUU...UCA-5'\n_____________\|_________________\|\n_____________87________________54\n	151 -- 157	75 -- 81	-20.8979 kcal/mol	6.12922 kcal/mol	3.85824 kcal/mol	145 175@LB@ \| \|@LB@5'-AAA...GUUCU C AUGAC...AGC-3'@LB@ GCGCAACGGCAC GCAU@LB@ :\|:\|\|\|\|::\|\|\| :\|\|\|@LB@ UGUGUUGUUGUG UGUA@LB@3'-UUU...ACGUU U GUGUU...UCA-5'@LB@ \| \|@LB@ 87 54@LB@@LB@@LB@Energy -12.00 kcal/mol@LB@Hybridization Energy -20.8979 kcal/mol@LB@Unfolding Energy - mRNA 6.12922 kcal/mol@LB@Unfolding Energy - sRNA 3.85824 kcal/mol@LB@@LB@Position - mRNA 146 -- 174@LB@Position - sRNA 55 -- 86@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 75 -- 81@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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