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
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@
102	0.005164	0.1728	stm0668	ybeY	-18.23	0.034693	146 -- 193	37 -- 81	rRNA maturation RNase YbeY	_____________145__________________________________________194\n_____________\|____________________________________________\|\n5'-UCC...AAAAC____________UUG____________G_______GU_______AGGAG...CGC-3'\n______________GCAAA_GCGGCG___GCGGCA____GA_CGUAAGC__GAAGCCC\n______________\|\|\|\|\|_:\|::\|:___:\|::\|\|____:\|_\|\|\|\|\|\|\|__:\|\|\|\|\|\|\n______________CGUUU_UGUUGU___UGUUGU____UU_GCAUUCG__UUUCGGG\n3'-UUU...GUUAA_____G______UG_______AGUG__G_______GU_______UAGUC...UCA-5'\n_____________\|____________________________________________\|\n_____________82___________________________________________36\n	178 -- 184	48 -- 54	-38.2699 kcal/mol	15.4401 kcal/mol	16.4278 kcal/mol	145 194@LB@ \| \|@LB@5'-UCC...AAAAC UUG G GU AGGAG...CGC-3'@LB@ GCAAA GCGGCG GCGGCA GA CGUAAGC GAAGCCC@LB@ \|\|\|\|\| :\|::\|: :\|::\|\| :\| \|\|\|\|\|\|\| :\|\|\|\|\|\|@LB@ CGUUU UGUUGU UGUUGU UU GCAUUCG UUUCGGG@LB@3'-UUU...GUUAA G UG AGUG G GU UAGUC...UCA-5'@LB@ \| \|@LB@ 82 36@LB@@LB@@LB@Energy -18.23 kcal/mol@LB@Hybridization Energy -38.2699 kcal/mol@LB@Unfolding Energy - mRNA 15.4401 kcal/mol@LB@Unfolding Energy - sRNA 16.4278 kcal/mol@LB@@LB@Position - mRNA 146 -- 193@LB@Position - sRNA 37 -- 81@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 48 -- 54@LB@
103	0.005167	0.1728	stm2670	aroF	-17.31	0.049328	173 -- 242	25 -- 90	3-deoxy-7-phosphoheptulonate synthase	_____________172______________________________________________________________________243\n_____________\|________________________________________________________________________\|\n5'-CUU...CUAUC_______AGAA__G____G_____C___AU____A_____A_G____U___UAACG_______CA_______ACAGG...AGG-3'\n______________GCAAACA____AA_ACAG_AUCGC_AUC____GC_AAAAG_C_CG_C_GAA_____UACGUAU__CCGAUGA\n______________\|\|\|\|\|\|\|____\|\|_\|\|\|:_\|\|\|:\|_\|:\|____\|\|_\|\|\|\|\|_\|_\|:_\|_\|\|\|_____:\|\|\|:\|\|__\|\|\|\|\|:\|\n______________CGUUUGU____UU_UGUU_UAGUG_UGG____CG_UUUUC_G_GU_G_CUU_____GUGCGUA__GGCUAUU\n3'-UUU...GUUAA_______GUUG__G____G_____U___CAUU__G_______G__A_U_______________A________UUGAA...UCA-5'\n_____________\|________________________________________________________________________\|\n_____________91_______________________________________________________________________24\n	226 -- 232	34 -- 40	-46.7665 kcal/mol	10.372 kcal/mol	24.1795 kcal/mol	172 243@LB@ \| \|@LB@5'-CUU...CUAUC AGAA G G C AU A A G U UAACG CA ACAGG...AGG-3'@LB@ GCAAACA AA ACAG AUCGC AUC GC AAAAG C CG C GAA UACGUAU CCGAUGA@LB@ \|\|\|\|\|\|\| \|\| \|\|\|: \|\|\|:\| \|:\| \|\| \|\|\|\|\| \| \|: \| \|\|\| :\|\|\|:\|\| \|\|\|\|\|:\|@LB@ CGUUUGU UU UGUU UAGUG UGG CG UUUUC G GU G CUU GUGCGUA GGCUAUU@LB@3'-UUU...GUUAA GUUG G G U CAUU G G A U A UUGAA...UCA-5'@LB@ \| \|@LB@ 91 24@LB@@LB@@LB@Energy -17.31 kcal/mol@LB@Hybridization Energy -46.7665 kcal/mol@LB@Unfolding Energy - mRNA 10.372 kcal/mol@LB@Unfolding Energy - sRNA 24.1795 kcal/mol@LB@@LB@Position - mRNA 173 -- 242@LB@Position - sRNA 25 -- 90@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 34 -- 40@LB@
104	0.005232	0.1728	stm0744	ybgC	-16.85	0.058772	132 -- 175	54 -- 90	tol-pal system-associated acyl-CoA thioesterase	_____________131_____________________________176\n_____________\|_______________________________\|\n5'-CUU...ACAAG____U____________UCUUGA________GGCGG...AAA-3'\n______________GCGA_AUACAACGGCAU______GGCAUUAC\n______________\|\|:\|_\|:\|\|\|\|\|::\|\|:______::\|\|\|:\|\|\n______________CGUU_UGUGUUGUUGUG______UUGUAGUG\n3'-UUU...GUUAA_______________________________UUGGC...UCA-5'\n_____________\|_______________________________\|\n_____________91______________________________53\n	156 -- 162	67 -- 73	-23.8418 kcal/mol	6.2547 kcal/mol	5.68203 kcal/mol	131 176@LB@ \| \|@LB@5'-CUU...ACAAG U UCUUGA GGCGG...AAA-3'@LB@ GCGA AUACAACGGCAU GGCAUUAC@LB@ \|\|:\| \|:\|\|\|\|\|::\|\|: ::\|\|\|:\|\|@LB@ CGUU UGUGUUGUUGUG UUGUAGUG@LB@3'-UUU...GUUAA UUGGC...UCA-5'@LB@ \| \|@LB@ 91 53@LB@@LB@@LB@Energy -16.85 kcal/mol@LB@Hybridization Energy -23.8418 kcal/mol@LB@Unfolding Energy - mRNA 6.2547 kcal/mol@LB@Unfolding Energy - sRNA 5.68203 kcal/mol@LB@@LB@Position - mRNA 132 -- 175@LB@Position - sRNA 54 -- 90@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 67 -- 73@LB@
105	0.005236	0.1728	stm4566	yjjI	-12.28	0.305832	96 -- 137	40 -- 77	YjjI family glycine radical enzyme	_____________95________________138\n_____________\|_________________\|\n5'-ACA...UUUUC____________U____CCGGC...UGG-3'\n______________UACAAUAGCGCA_CGUC\n______________:\|\|\|\|:\|:\|:\|\|_\|:\|\|\n______________GUGUUGUUGUGU_GUAG\n3'-UUU...CGUUU____________U____UGUUG...UCA-5'\n_____________\|_________________\|\n_____________78________________39\n	167 -- 173	74 -- 80	-18.3997 kcal/mol	3.44142 kcal/mol	3.92987 kcal/mol	95 138@LB@ \| \|@LB@5'-ACA...UUUUC U CCGGC...UGG-3'@LB@ UACAAUAGCGCA CGUC@LB@ :\|\|\|\|:\|:\|:\|\| \|:\|\|@LB@ GUGUUGUUGUGU GUAG@LB@3'-UUU...CGUUU U UGUUG...UCA-5'@LB@ \| \|@LB@ 78 39@LB@@LB@@LB@Energy -12.28 kcal/mol@LB@Hybridization Energy -18.3997 kcal/mol@LB@Unfolding Energy - mRNA 3.44142 kcal/mol@LB@Unfolding Energy - sRNA 3.92987 kcal/mol@LB@@LB@Position - mRNA 96 -- 137@LB@Position - sRNA 40 -- 77@LB@Position Seed - mRNA 167 -- 173@LB@Position Seed - sRNA 74 -- 80@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@
107	0.00529	0.1728	stm0994	mukB	-11.10	0.440174	5 -- 20	154 -- 167	cell division protein MukB	_____________4_________________________21\n_____________\|_________________________\|\n5'-UGG...UCAGC_______U__________G______AAUAA...CCG-3'\n______________CGGACAG_GG_______A_AGGAAG\n______________\|:\|\|\|\|\|_\|\|_______\|_\|\|\|\|\|\|\n______________GUCUGUC_CC_______U_UCCUUC\n3'-UUU...UACCU__________AUUUACA_G______ACUUU...UCA-5'\n_____________\|_________________________\|\n_____________168_______________________153\n	179 -- 185	154 -- 160	-19.4251 kcal/mol	3.58038 kcal/mol	5.99227 kcal/mol	4 21@LB@ \| \|@LB@5'-UGG...UCAGC U G AAUAA...CCG-3'@LB@ CGGACAG GG A AGGAAG@LB@ \|:\|\|\|\|\| \|\| \| \|\|\|\|\|\|@LB@ GUCUGUC CC U UCCUUC@LB@3'-UUU...UACCU AUUUACA G ACUUU...UCA-5'@LB@ \| \|@LB@ 168 153@LB@@LB@@LB@Energy -11.10 kcal/mol@LB@Hybridization Energy -19.4251 kcal/mol@LB@Unfolding Energy - mRNA 3.58038 kcal/mol@LB@Unfolding Energy - sRNA 5.99227 kcal/mol@LB@@LB@Position - mRNA 5 -- 20@LB@Position - sRNA 154 -- 167@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 154 -- 160@LB@
108	0.005311	0.1728	stm2183	cdd	-16.35	0.071230	31 -- 68	151 -- 187	cytidine deaminase	_____________30_________________69\n_____________\|__________________\|\n5'-UGG...AGAUC_____UUAA_________GGCCC...UGA-3'\n______________ACAUA____GACAUAGCA\n______________\|\|\|:\|____:\|\|\|:\|:\|\|\n______________UGUGU____UUGUGUUGU\n3'-UUU...ACGUU_____UG___________AGUGU...UCA-5'\n_____________\|__________________\|\n_____________188________________150\n	150 -- 156	71 -- 77	-12.389 kcal/mol	1.12571 kcal/mol	3.50787 kcal/mol	30 69@LB@ \| \|@LB@5'-UGG...AGAUC UUAA GGCCC...UGA-3'@LB@ ACAUA GACAUAGCA@LB@ \|\|\|:\| :\|\|\|:\|:\|\|@LB@ UGUGU UUGUGUUGU@LB@3'-UUU...ACGUU UG AGUGU...UCA-5'@LB@ \| \|@LB@ 188 150@LB@@LB@@LB@Energy -16.35 kcal/mol@LB@Hybridization Energy -12.389 kcal/mol@LB@Unfolding Energy - mRNA 1.12571 kcal/mol@LB@Unfolding Energy - sRNA 3.50787 kcal/mol@LB@@LB@Position - mRNA 31 -- 68@LB@Position - sRNA 151 -- 187@LB@Position Seed - mRNA 150 -- 156@LB@Position Seed - sRNA 71 -- 77@LB@
109	0.005328	0.1728	stm3082	N/A	-12.60	0.275269	106 -- 154	38 -- 90	galactonate oxidoreductase	_____________105________________________155\n_____________\|__________________________\|\n5'-AAU...ACAAC______UUUUUA_______UU_____GGCCU...CGG-3'\n______________GCAGAC______AACAACA__CAGCA\n______________\|\|\|:\|\|______\|\|\|\|\|\|\|__\|\|:\|\|\n______________CGUUUG______UUGUUGU__GUUGU\n3'-UUU...GUUAA______UG__________________AGUGU...UCA-5'\n_____________\|__________________________\|\n_____________91_________________________37\n	118 -- 124	76 -- 82	-16.9817 kcal/mol	2.50135 kcal/mol	3.80671 kcal/mol	105 155@LB@ \| \|@LB@5'-AAU...ACAAC UUUUUA UU GGCCU...CGG-3'@LB@ GCAGAC AACAACA CAGCA@LB@ \|\|\|:\|\| \|\|\|\|\|\|\| \|\|:\|\|@LB@ CGUUUG UUGUUGU GUUGU@LB@3'-UUU...GUUAA UG AGUGU...UCA-5'@LB@ \| \|@LB@ 91 37@LB@@LB@@LB@Energy -12.60 kcal/mol@LB@Hybridization Energy -16.9817 kcal/mol@LB@Unfolding Energy - mRNA 2.50135 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 106 -- 154@LB@Position - sRNA 38 -- 90@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 76 -- 82@LB@
110	0.005337	0.1728	stm1920	cheW	-12.58	0.277263	149 -- 192	51 -- 90	chemotaxis protein CheW	_____________148__________193\n_____________\|____________\|\n5'-GUC...UGAUU____________AAUAA...UCC-3'\n______________GAGUGAGAAGGG\n______________:\|\|\|\|\|:\|\|:\|\|\n______________UUCACUUUUUCC\n3'-UUU...UGUCC____________CAUCA...UCA-5'\n_____________\|____________\|\n_____________91___________50\n	188 -- 194	128 -- 134	-15.4894 kcal/mol	2.64754 kcal/mol	3.77328 kcal/mol	148 193@LB@ \| \|@LB@5'-GUC...UGAUU AAUAA...UCC-3'@LB@ GAGUGAGAAGGG@LB@ :\|\|\|\|\|:\|\|:\|\|@LB@ UUCACUUUUUCC@LB@3'-UUU...UGUCC CAUCA...UCA-5'@LB@ \| \|@LB@ 91 50@LB@@LB@@LB@Energy -12.58 kcal/mol@LB@Hybridization Energy -15.4894 kcal/mol@LB@Unfolding Energy - mRNA 2.64754 kcal/mol@LB@Unfolding Energy - sRNA 3.77328 kcal/mol@LB@@LB@Position - mRNA 149 -- 192@LB@Position - sRNA 51 -- 90@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 128 -- 134@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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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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