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
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@
161	0.008343	0.1845	stm3321	yhbH	-14.15	0.160801	194 -- 246	48 -- 88	ribosomal subunit interface protein	_____________193______________________247\n_____________\|________________________\|\n5'-GAU...AAGGA______UAU_____U_________CGGAC...GGA-3'\n______________AGACAC___GCAGC_CAAUAUCAC\n______________\|:\|\|\|\|___:\|\|:\|_\|\|\|:\|\|\|\|\|\n______________UUUGUG___UGUUG_GUUGUAGUG\n3'-UUU...UAACG______U_______U_________UUGGC...UCA-5'\n_____________\|________________________\|\n_____________89_______________________47\n	211 -- 217	67 -- 73	-22.4132 kcal/mol	2.65406 kcal/mol	5.48747 kcal/mol	193 247@LB@ \| \|@LB@5'-GAU...AAGGA UAU U CGGAC...GGA-3'@LB@ AGACAC GCAGC CAAUAUCAC@LB@ \|:\|\|\|\| :\|\|:\| \|\|\|:\|\|\|\|\|@LB@ UUUGUG UGUUG GUUGUAGUG@LB@3'-UUU...UAACG U U UUGGC...UCA-5'@LB@ \| \|@LB@ 89 47@LB@@LB@@LB@Energy -14.15 kcal/mol@LB@Hybridization Energy -22.4132 kcal/mol@LB@Unfolding Energy - mRNA 2.65406 kcal/mol@LB@Unfolding Energy - sRNA 5.48747 kcal/mol@LB@@LB@Position - mRNA 194 -- 246@LB@Position - sRNA 48 -- 88@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 67 -- 73@LB@
162	0.00849	0.1864	stm4221	pgi	-15.16	0.111294	249 -- 289	56 -- 88	glucose-6-phosphate isomerase	_____________248_______________________________________290\n_____________\|_________________________________________\|\n5'-GCU...UCCAG______U_____GAAAUGAAA_____________C______UUUCG...ACG-3'\n______________AAACAC_ACGAU_________GACGUUACGAUCG_UGAGCU\n______________\|\|\|\|\|\|_\|\|:\|:_________:\|\|:\|:\|\|:\|:\|\|_\|:\|\|\|:\n______________UUUGUG_UGUUG_________UUGUAGUGUUGGC_AUUCGG\n3'-UUU...UAACG______U_____UG___________________________UUUUC...UCA-5'\n_____________\|_________________________________________\|\n_____________89________________________________________55\n	272 -- 278	66 -- 72	-30.3131 kcal/mol	6.22888 kcal/mol	11.698 kcal/mol	248 290@LB@ \| \|@LB@5'-GCU...UCCAG U GAAAUGAAA C UUUCG...ACG-3'@LB@ AAACAC ACGAU GACGUUACGAUCG UGAGCU@LB@ \|\|\|\|\|\| \|\|:\|: :\|\|:\|:\|\|:\|:\|\| \|:\|\|\|:@LB@ UUUGUG UGUUG UUGUAGUGUUGGC AUUCGG@LB@3'-UUU...UAACG U UG UUUUC...UCA-5'@LB@ \| \|@LB@ 89 55@LB@@LB@@LB@Energy -15.16 kcal/mol@LB@Hybridization Energy -30.3131 kcal/mol@LB@Unfolding Energy - mRNA 6.22888 kcal/mol@LB@Unfolding Energy - sRNA 11.698 kcal/mol@LB@@LB@Position - mRNA 249 -- 289@LB@Position - sRNA 56 -- 88@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 66 -- 72@LB@
163	0.008532	0.1864	stm3093	endA	-16.58	0.065141	135 -- 160	72 -- 101	deoxyribonuclease I	_____________134___________________________________161\n_____________\|_____________________________________\|\n5'-CCA...CUUUC_____________________U_______________UUUCG...CGG-3'\n______________CUGA___GCGGACUGAUUGCA_ACA____GACACAAC\n______________\|\|\|\|___\|\|:\|\|\|::\|\|\|\|\|\|_\|\|\|____:\|\|\|\|\|\|\|\n______________GACU___CGUCUGGUUAACGU_UGU____UUGUGUUG\n3'-UUU...CACCA____UAG______________U___GUUG________UAGUG...UCA-5'\n_____________\|_____________________________________\|\n_____________102___________________________________71\n	154 -- 160	72 -- 78	-36.4155 kcal/mol	5.60666 kcal/mol	13.5432 kcal/mol	134 161@LB@ \| \|@LB@5'-CCA...CUUUC U UUUCG...CGG-3'@LB@ CUGA GCGGACUGAUUGCA ACA GACACAAC@LB@ \|\|\|\| \|\|:\|\|\|::\|\|\|\|\|\| \|\|\| :\|\|\|\|\|\|\|@LB@ GACU CGUCUGGUUAACGU UGU UUGUGUUG@LB@3'-UUU...CACCA UAG U GUUG UAGUG...UCA-5'@LB@ \| \|@LB@ 102 71@LB@@LB@@LB@Energy -16.58 kcal/mol@LB@Hybridization Energy -36.4155 kcal/mol@LB@Unfolding Energy - mRNA 5.60666 kcal/mol@LB@Unfolding Energy - sRNA 13.5432 kcal/mol@LB@@LB@Position - mRNA 135 -- 160@LB@Position - sRNA 72 -- 101@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 72 -- 78@LB@
164	0.008796	0.191	stm2932	ygbE	-13.54	0.199482	240 -- 279	44 -- 82	putative inner membrane protein	_____________239________________280\n_____________\|__________________\|\n5'-CGC...GCGUA__________________UUUCA...CCA-3'\n______________AUAGC__CAUAACAUUAC\n______________\|:\|:\|__\|\|:\|\|\|\|\|:\|\|\n______________UGUUG__GUGUUGUAGUG\n3'-UUU...GUUUG_____UU___________UUGGC...UCA-5'\n_____________\|__________________\|\n_____________83_________________43\n	250 -- 256	67 -- 73	-14.8194 kcal/mol	1.59581 kcal/mol	5.25507 kcal/mol	239 280@LB@ \| \|@LB@5'-CGC...GCGUA UUUCA...CCA-3'@LB@ AUAGC CAUAACAUUAC@LB@ \|:\|:\| \|\|:\|\|\|\|\|:\|\|@LB@ UGUUG GUGUUGUAGUG@LB@3'-UUU...GUUUG UU UUGGC...UCA-5'@LB@ \| \|@LB@ 83 43@LB@@LB@@LB@Energy -13.54 kcal/mol@LB@Hybridization Energy -14.8194 kcal/mol@LB@Unfolding Energy - mRNA 1.59581 kcal/mol@LB@Unfolding Energy - sRNA 5.25507 kcal/mol@LB@@LB@Position - mRNA 240 -- 279@LB@Position - sRNA 44 -- 82@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 67 -- 73@LB@
165	0.008886	0.1918	stm0281	N/A	-13.47	0.204933	267 -- 289	36 -- 56	type VI secretion system-associated protein	_____________266______________________________________________290\n_____________\|________________________________________________\|\n5'-UGA...UAAUU____A_____A______A__UAU___C_____UGACC_C_______G_AGUGA...ACC-3'\n______________ACGG_ACGGG_UAAAUG_AU___GAG_UGGAA_____G_GUAGUCU_G\n______________\|\|:\|_\|\|:\|\|_\|\|\|\|\|\|_\|:___:\|\|_\|\|:\|\|_____\|_\|\|\|\|\|\|\|_\|\n______________UGUC_UGUCC_AUUUAC_UG___UUC_ACUUU_____C_CAUCAGA_C\n3'-UUU...AUACC__________C______A__UCC_________UUC___________G_GAUGG...UCA-5'\n_____________\|________________________________________________\|\n_____________57_______________________________________________35\n	219 -- 225	121 -- 127	-29.4304 kcal/mol	8.43831 kcal/mol	11.9516 kcal/mol	266 290@LB@ \| \|@LB@5'-UGA...UAAUU A A A UAU C UGACC C G AGUGA...ACC-3'@LB@ ACGG ACGGG UAAAUG AU GAG UGGAA G GUAGUCU G@LB@ \|\|:\| \|\|:\|\| \|\|\|\|\|\| \|: :\|\| \|\|:\|\| \| \|\|\|\|\|\|\| \|@LB@ UGUC UGUCC AUUUAC UG UUC ACUUU C CAUCAGA C@LB@3'-UUU...AUACC C A UCC UUC G GAUGG...UCA-5'@LB@ \| \|@LB@ 57 35@LB@@LB@@LB@Energy -13.47 kcal/mol@LB@Hybridization Energy -29.4304 kcal/mol@LB@Unfolding Energy - mRNA 8.43831 kcal/mol@LB@Unfolding Energy - sRNA 11.9516 kcal/mol@LB@@LB@Position - mRNA 267 -- 289@LB@Position - sRNA 36 -- 56@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 121 -- 127@LB@
166	0.009028	0.1932	stm1173	flgA	-14.00	0.169768	53 -- 102	33 -- 85	flagella basal body P-ring formation protein FlgA	_____________52__________________103\n_____________\|___________________\|\n5'-GCU...CCCUG___________GG______ACGCC...CCC-3'\n______________ACAAUGGCGCA__ACAUCA\n______________\|\|\|\|:::\|:\|\|__\|\|\|\|\|\|\n______________UGUUGUUGUGU__UGUAGU\n3'-UUU...GUUUG___________________GUUGG...UCA-5'\n_____________\|___________________\|\n_____________86__________________32\n	259 -- 265	74 -- 80	-16.6955 kcal/mol	2.54166 kcal/mol	4.84988 kcal/mol	52 103@LB@ \| \|@LB@5'-GCU...CCCUG GG ACGCC...CCC-3'@LB@ ACAAUGGCGCA ACAUCA@LB@ \|\|\|\|:::\|:\|\| \|\|\|\|\|\|@LB@ UGUUGUUGUGU UGUAGU@LB@3'-UUU...GUUUG GUUGG...UCA-5'@LB@ \| \|@LB@ 86 32@LB@@LB@@LB@Energy -14.00 kcal/mol@LB@Hybridization Energy -16.6955 kcal/mol@LB@Unfolding Energy - mRNA 2.54166 kcal/mol@LB@Unfolding Energy - sRNA 4.84988 kcal/mol@LB@@LB@Position - mRNA 53 -- 102@LB@Position - sRNA 33 -- 85@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 74 -- 80@LB@
167	0.009062	0.1932	stm2673	rplS	-14.99	0.118272	119 -- 180	38 -- 88	50S ribosomal protein L19	_____________118_________________181\n_____________\|___________________\|\n5'-GAU...GUUCA_____G____C________GCAGC...UUG-3'\n______________AAACA_AACA_GCACAACA\n______________\|\|\|\|\|_\|\|\|\|_:\|\|\|\|\|\|\|\n______________UUUGU_UUGU_UGUGUUGU\n3'-UUU...UAACG_____G_____________AGUGU...UCA-5'\n_____________\|___________________\|\n_____________89__________________37\n	126 -- 132	71 -- 77	-18.964 kcal/mol	3.18358 kcal/mol	3.68874 kcal/mol	118 181@LB@ \| \|@LB@5'-GAU...GUUCA G C GCAGC...UUG-3'@LB@ AAACA AACA GCACAACA@LB@ \|\|\|\|\| \|\|\|\| :\|\|\|\|\|\|\|@LB@ UUUGU UUGU UGUGUUGU@LB@3'-UUU...UAACG G AGUGU...UCA-5'@LB@ \| \|@LB@ 89 37@LB@@LB@@LB@Energy -14.99 kcal/mol@LB@Hybridization Energy -18.964 kcal/mol@LB@Unfolding Energy - mRNA 3.18358 kcal/mol@LB@Unfolding Energy - sRNA 3.68874 kcal/mol@LB@@LB@Position - mRNA 119 -- 180@LB@Position - sRNA 38 -- 88@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 71 -- 77@LB@
168	0.009144	0.1938	stm3609	yhjE	-18.08	0.036777	202 -- 261	35 -- 91	MFS transporter	_____________201__________________________________262\n_____________\|____________________________________\|\n5'-UAA...UAGUA_______A__C_____________U_____A_____AGGAA...UUG-3'\n______________UGCAAGC_AC_GC__CACAACA_C_CGACC_UGAGC\n______________\|\|\|\|\|:\|_\|\|_:\|__\|\|\|\|\|\|\|_\|_\|:\|\|\|_\|:\|\|\|\n______________ACGUUUG_UG_UG__GUGUUGU_G_GUUGG_AUUCG\n3'-UUU...GGUUA__________U__UU_______A_U_____C_____GUUUU...UCA-5'\n_____________\|____________________________________\|\n_____________92___________________________________34\n	215 -- 221	71 -- 77	-32.2191 kcal/mol	4.27941 kcal/mol	11.5198 kcal/mol	201 262@LB@ \| \|@LB@5'-UAA...UAGUA A C U A AGGAA...UUG-3'@LB@ UGCAAGC AC GC CACAACA C CGACC UGAGC@LB@ \|\|\|\|\|:\| \|\| :\| \|\|\|\|\|\|\| \| \|:\|\|\| \|:\|\|\|@LB@ ACGUUUG UG UG GUGUUGU G GUUGG AUUCG@LB@3'-UUU...GGUUA U UU A U C GUUUU...UCA-5'@LB@ \| \|@LB@ 92 34@LB@@LB@@LB@Energy -18.08 kcal/mol@LB@Hybridization Energy -32.2191 kcal/mol@LB@Unfolding Energy - mRNA 4.27941 kcal/mol@LB@Unfolding Energy - sRNA 11.5198 kcal/mol@LB@@LB@Position - mRNA 202 -- 261@LB@Position - sRNA 35 -- 91@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 71 -- 77@LB@
169	0.009276	0.1945	stm0495	ybaK	-13.73	0.186840	16 -- 30	44 -- 58	aminoacyl-tRNA deacylase	_____________15_________________31\n_____________\|__________________\|\n5'-AAA...CAUUC____CU__G_________CGAAU...UGG-3'\n______________ACAC__AC_AUCACGAUC\n______________\|\|\|\|__\|\|_\|\|\|\|\|:\|:\|\n______________UGUG__UG_UAGUGUUGG\n3'-UUU...GUUGU____U_____________CAUUC...UCA-5'\n_____________\|__________________\|\n_____________59_________________43\n	264 -- 270	63 -- 69	-14.6876 kcal/mol	0.727125 kcal/mol	6.44907 kcal/mol	15 31@LB@ \| \|@LB@5'-AAA...CAUUC CU G CGAAU...UGG-3'@LB@ ACAC AC AUCACGAUC@LB@ \|\|\|\| \|\| \|\|\|\|\|:\|:\|@LB@ UGUG UG UAGUGUUGG@LB@3'-UUU...GUUGU U CAUUC...UCA-5'@LB@ \| \|@LB@ 59 43@LB@@LB@@LB@Energy -13.73 kcal/mol@LB@Hybridization Energy -14.6876 kcal/mol@LB@Unfolding Energy - mRNA 0.727125 kcal/mol@LB@Unfolding Energy - sRNA 6.44907 kcal/mol@LB@@LB@Position - mRNA 16 -- 30@LB@Position - sRNA 44 -- 58@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 63 -- 69@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

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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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