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	Additional homologs
112	0.005549	0.1728	stm0602	ybdH	-14.01	0.169356	159 -- 193	39 -- 79	oxidoreductase		_____________158_____________194\n_____________\|_______________\|\n5'-GCG...CCCUA_G_____________GAACC...AGC-3'\n______________A_GACAACACAACAU\n______________\|_:\|\|\|\|\|\|\|\|\|\|\|\|\n______________U_UUGUUGUGUUGUA\n3'-UUU...GUUUG_G_____________GUGUU...UCA-5'\n_____________\|_______________\|\n_____________80______________38\n	196 -- 202	70 -- 76	-18.8338 kcal/mol	1.20586 kcal/mol	3.77892 kcal/mol	158 194@LB@ \| \|@LB@5'-GCG...CCCUA G GAACC...AGC-3'@LB@ A GACAACACAACAU@LB@ \| :\|\|\|\|\|\|\|\|\|\|\|\|@LB@ U UUGUUGUGUUGUA@LB@3'-UUU...GUUUG G GUGUU...UCA-5'@LB@ \| \|@LB@ 80 38@LB@@LB@@LB@Energy -14.01 kcal/mol@LB@Hybridization Energy -18.8338 kcal/mol@LB@Unfolding Energy - mRNA 1.20586 kcal/mol@LB@Unfolding Energy - sRNA 3.77892 kcal/mol@LB@@LB@Position - mRNA 159 -- 193@LB@Position - sRNA 39 -- 79@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 70 -- 76@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@
138	0.007086	0.182	stm0624	citC	-16.00	0.081371	136 -- 192	38 -- 93	[citrate (pro-3S)-lyase] ligase	stm0058	_____________135___________________________193\n_____________\|_____________________________\|\n5'-AAA...AUCAA________________________A____GAAAA...AUA-3'\n______________GUUGC_AACACA___GCGCAACAU_UACA\n______________:\|\|\|\|_\|\|\|\|\|\|___:\|:\|\|\|\|\|\|_:\|\|\|\n______________UAACG_UUGUGU___UGUGUUGUA_GUGU\n3'-UUU...CUGGU_____U______UGU______________UGGCA...UCA-5'\n_____________\|_____________________________\|\n_____________94____________________________37\n	149 -- 155	70 -- 76	-24.6588 kcal/mol	7.05918 kcal/mol	6.32558 kcal/mol	135 193@LB@ \| \|@LB@5'-AAA...AUCAA A GAAAA...AUA-3'@LB@ GUUGC AACACA GCGCAACAU UACA@LB@ :\|\|\|\| \|\|\|\|\|\| :\|:\|\|\|\|\|\| :\|\|\|@LB@ UAACG UUGUGU UGUGUUGUA GUGU@LB@3'-UUU...CUGGU U UGU UGGCA...UCA-5'@LB@ \| \|@LB@ 94 37@LB@@LB@@LB@Energy -16.00 kcal/mol@LB@Hybridization Energy -24.6588 kcal/mol@LB@Unfolding Energy - mRNA 7.05918 kcal/mol@LB@Unfolding Energy - sRNA 6.32558 kcal/mol@LB@@LB@Position - mRNA 136 -- 192@LB@Position - sRNA 38 -- 93@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 70 -- 76@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@
47	0.001676	0.127	stm0637	dacA	-17.91	0.039191	14 -- 64	37 -- 92	serine-type D-Ala-D-Ala carboxypeptidase		_____________13____________________65\n_____________\|_____________________\|\n5'-GUU...AACGU_________GA__________UACAG...AUA-3'\n______________UUGCAAACA____AGCACAAU\n______________\|\|\|\|\|\|\|\|\|____\|:\|\|\|\|\|:\n______________AACGUUUGU____UUGUGUUG\n3'-UUU...UGGUU_________GUUG________UAGUG...UCA-5'\n_____________\|_____________________\|\n_____________93____________________36\n	26 -- 32	72 -- 78	-19.7119 kcal/mol	3.03223 kcal/mol	3.80821 kcal/mol	13 65@LB@ \| \|@LB@5'-GUU...AACGU GA UACAG...AUA-3'@LB@ UUGCAAACA AGCACAAU@LB@ \|\|\|\|\|\|\|\|\| \|:\|\|\|\|\|:@LB@ AACGUUUGU UUGUGUUG@LB@3'-UUU...UGGUU GUUG UAGUG...UCA-5'@LB@ \| \|@LB@ 93 36@LB@@LB@@LB@Energy -17.91 kcal/mol@LB@Hybridization Energy -19.7119 kcal/mol@LB@Unfolding Energy - mRNA 3.03223 kcal/mol@LB@Unfolding Energy - sRNA 3.80821 kcal/mol@LB@@LB@Position - mRNA 14 -- 64@LB@Position - sRNA 37 -- 92@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 72 -- 78@LB@
52	0.001934	0.1324	stm0653	ybeL	-17.18	0.051878	262 -- 299	155 -- 188	similar to E. coli putative alpha helical protein (AAC73744.1); Blastp hit to AAC73744.1 (160 aa) 91% identity in aa 1 - 160		_____________261________________________300\n_____________\|__________________________\|\n5'-AUU...GCGCG________G____G_____G______C-3'\n______________ACAUUGAU_CGCU_GUGGA_CAGGCG\n______________\|\|\|\|\|:\|\|_\|:\|\|_:\|\|\|\|_\|\|\|:\|:\n______________UGUAAUUA_GUGA_UACCU_GUCUGU\n3'-UUU...CACGA__________________________CCCAU...UCA-5'\n_____________\|__________________________\|\n_____________189________________________154\n	275 -- 281	170 -- 176	-23.9532 kcal/mol	9.91713 kcal/mol	4.10825 kcal/mol	261 300@LB@ \| \|@LB@5'-AUU...GCGCG G G G C-3'@LB@ ACAUUGAU CGCU GUGGA CAGGCG@LB@ \|\|\|\|\|:\|\| \|:\|\| :\|\|\|\| \|\|\|:\|:@LB@ UGUAAUUA GUGA UACCU GUCUGU@LB@3'-UUU...CACGA CCCAU...UCA-5'@LB@ \| \|@LB@ 189 154@LB@@LB@@LB@Energy -17.18 kcal/mol@LB@Hybridization Energy -23.9532 kcal/mol@LB@Unfolding Energy - mRNA 9.91713 kcal/mol@LB@Unfolding Energy - sRNA 4.10825 kcal/mol@LB@@LB@Position - mRNA 262 -- 299@LB@Position - sRNA 155 -- 188@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 170 -- 176@LB@
6	7.515e-05	0.04123	stm0665	gltI	-17.87	0.039793	157 -- 199	35 -- 81	glutamate/aspartate transporter		_____________156__________________200\n_____________\|____________________\|\n5'-CGA...UGCAG____UA______U_______GCUAU...CUG-3'\n______________GCAA__ACAACA_CACAAUA\n______________\|\|\|\|__\|\|\|\|\|\|_\|\|\|\|\|:\|\n______________CGUU__UGUUGU_GUGUUGU\n3'-UUU...GUUAA____UG______U_______AGUGU...UCA-5'\n_____________\|____________________\|\n_____________82___________________34\n	170 -- 176	71 -- 77	-19.9204 kcal/mol	1.29616 kcal/mol	3.80671 kcal/mol	156 200@LB@ \| \|@LB@5'-CGA...UGCAG UA U GCUAU...CUG-3'@LB@ GCAA ACAACA CACAAUA@LB@ \|\|\|\| \|\|\|\|\|\| \|\|\|\|\|:\|@LB@ CGUU UGUUGU GUGUUGU@LB@3'-UUU...GUUAA UG U AGUGU...UCA-5'@LB@ \| \|@LB@ 82 34@LB@@LB@@LB@Energy -17.87 kcal/mol@LB@Hybridization Energy -19.9204 kcal/mol@LB@Unfolding Energy - mRNA 1.29616 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 157 -- 199@LB@Position - sRNA 35 -- 81@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 71 -- 77@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@
92	0.004229	0.1596	stm0669	phoL	-19.39	0.022083	221 -- 286	36 -- 89	putative phosphate starvation-inducible protein ATP-binding		_____________220__________________________________________________________________287\n_____________\|____________________________________________________________________\|\n5'-AAA...CGAUA_________G__GAACAGUUUGAAUAUA____C______AAUUAC___UU____________CA____CCGUC...GCC-3'\n______________CAGACACAA_AG________________GACA_UCGCGA_______CC__GAGCCCG_CAGA__ACGC\n______________\|\|:\|\|\|\|\|\|_\|:________________:\|\|\|_\|\|:\|:\|_______\|\|__:\|\|\|\|\|:_\|\|\|\|__\|\|\|\|\n______________GUUUGUGUU_UU________________UUGU_AGUGUU_______GG__UUCGGGU_GUCU__UGCG\n3'-UUU...UUAAC_________G__GUG________________________GGCAUUC__UU_______A____UG____UAAGG...UCA-5'\n_____________\|____________________________________________________________________\|\n_____________90___________________________________________________________________35\n	270 -- 276	47 -- 53	-43.5648 kcal/mol	9.30805 kcal/mol	22.4875 kcal/mol	220 287@LB@ \| \|@LB@5'-AAA...CGAUA G GAACAGUUUGAAUAUA C AAUUAC UU CA CCGUC...GCC-3'@LB@ CAGACACAA AG GACA UCGCGA CC GAGCCCG CAGA ACGC@LB@ \|\|:\|\|\|\|\|\| \|: :\|\|\| \|\|:\|:\| \|\| :\|\|\|\|\|: \|\|\|\| \|\|\|\|@LB@ GUUUGUGUU UU UUGU AGUGUU GG UUCGGGU GUCU UGCG@LB@3'-UUU...UUAAC G GUG GGCAUUC UU A UG UAAGG...UCA-5'@LB@ \| \|@LB@ 90 35@LB@@LB@@LB@Energy -19.39 kcal/mol@LB@Hybridization Energy -43.5648 kcal/mol@LB@Unfolding Energy - mRNA 9.30805 kcal/mol@LB@Unfolding Energy - sRNA 22.4875 kcal/mol@LB@@LB@Position - mRNA 221 -- 286@LB@Position - sRNA 36 -- 89@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 47 -- 53@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@

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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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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