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
91	0.004202	0.1596	stm0387	yaiI	-16.26	0.073758	5 -- 45	23 -- 58	similar to E. coli orf hypothetical protein (AAC73490.1); Blastp hit to AAC73490.1 (192 aa) 89% identity in aa 41 - 191		_____________4____________________________________________46\n_____________\|____________________________________________\|\n_______5'-GUCC_______AUAGCCUU______AUU________G___A_______CGAUU...CCA-3'\n______________GCCAAGA________GCCCAU____AC_CGCA__CC_AUAAAAC\n______________\|\|\|\|\|:\|________\|\|\|\|\|\|____\|\|_\|\|\|\|__\|\|_\|\|\|\|\|\|\|\n______________CGGUUUU________CGGGUA____UG_GCGU__GG_UAUUUUG\n3'-UUU...GCAUU_____________________GUCU__U____AA__C_______AAAAG...UCA-5'\n_____________\|____________________________________________\|\n_____________59___________________________________________22\n	5 -- 11	52 -- 58	-32.2087 kcal/mol	3.21436 kcal/mol	17.1718 kcal/mol	4 46@LB@ \| \|@LB@ 5'-GUCC AUAGCCUU AUU G A CGAUU...CCA-3'@LB@ GCCAAGA GCCCAU AC CGCA CC AUAAAAC@LB@ \|\|\|\|\|:\| \|\|\|\|\|\| \|\| \|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ CGGUUUU CGGGUA UG GCGU GG UAUUUUG@LB@3'-UUU...GCAUU GUCU U AA C AAAAG...UCA-5'@LB@ \| \|@LB@ 59 22@LB@@LB@@LB@Energy -16.26 kcal/mol@LB@Hybridization Energy -32.2087 kcal/mol@LB@Unfolding Energy - mRNA 3.21436 kcal/mol@LB@Unfolding Energy - sRNA 17.1718 kcal/mol@LB@@LB@Position - mRNA 5 -- 45@LB@Position - sRNA 23 -- 58@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 52 -- 58@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@
93	0.004254	0.1596	stm0408	secF	-18.22	0.034847	7 -- 64	39 -- 91	protein-export membrane protein SecF		_____________6______________________________________65\n_____________\|______________________________________\|\n5'-CUU...GCACA_G__U____UGUUG______UA________________AGUCU...UGC-3'\n______________G_AA_ACAC_____AACAAC__AAC__CACGGCCGUAA\n______________\|_\|\|_\|\|\|\|_____\|\|\|\|\|\|__\|\|\|__\|\|\|::\|\|\|\|\|\|\n______________C_UU_UGUG_____UUGUUG__UUG__GUGUUGGCAUU\n3'-UUU...GUUAA_G__________________UG___UA___________CGGUU...UCA-5'\n_____________\|______________________________________\|\n_____________92_____________________________________38\n	238 -- 244	59 -- 65	-26.2573 kcal/mol	3.95572 kcal/mol	10.1648 kcal/mol	6 65@LB@ \| \|@LB@5'-CUU...GCACA G U UGUUG UA AGUCU...UGC-3'@LB@ G AA ACAC AACAAC AAC CACGGCCGUAA@LB@ \| \|\| \|\|\|\| \|\|\|\|\|\| \|\|\| \|\|\|::\|\|\|\|\|\|@LB@ C UU UGUG UUGUUG UUG GUGUUGGCAUU@LB@3'-UUU...GUUAA G UG UA CGGUU...UCA-5'@LB@ \| \|@LB@ 92 38@LB@@LB@@LB@Energy -18.22 kcal/mol@LB@Hybridization Energy -26.2573 kcal/mol@LB@Unfolding Energy - mRNA 3.95572 kcal/mol@LB@Unfolding Energy - sRNA 10.1648 kcal/mol@LB@@LB@Position - mRNA 7 -- 64@LB@Position - sRNA 39 -- 91@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 59 -- 65@LB@
94	0.0043	0.1596	stm3866	atpG	-16.85	0.058909	206 -- 253	35 -- 80	F0F1 ATP synthase subunit gamma		_____________205______________________254\n_____________\|________________________\|\n5'-GGU...CAAAA________AA_C______G_U___CGCCG...GUA-3'\n______________GAUCACUA__G_GAUGGA_A_GGU\n______________:\|\|\|\|\|\|\|__\|_\|\|::\|\|_\|_\|\|\|\n______________UUAGUGAU__C_CUGUCU_U_CCA\n3'-UUU...UGUAA________A_________G_C___UUUAC...UCA-5'\n_____________\|________________________\|\n_____________81_______________________34\n	258 -- 264	165 -- 171	-17.4899 kcal/mol	5.94142 kcal/mol	3.53572 kcal/mol	205 254@LB@ \| \|@LB@5'-GGU...CAAAA AA C G U CGCCG...GUA-3'@LB@ GAUCACUA G GAUGGA A GGU@LB@ :\|\|\|\|\|\|\| \| \|\|::\|\| \| \|\|\|@LB@ UUAGUGAU C CUGUCU U CCA@LB@3'-UUU...UGUAA A G C UUUAC...UCA-5'@LB@ \| \|@LB@ 81 34@LB@@LB@@LB@Energy -16.85 kcal/mol@LB@Hybridization Energy -17.4899 kcal/mol@LB@Unfolding Energy - mRNA 5.94142 kcal/mol@LB@Unfolding Energy - sRNA 3.53572 kcal/mol@LB@@LB@Position - mRNA 206 -- 253@LB@Position - sRNA 35 -- 80@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 165 -- 171@LB@
95	0.004301	0.1596	stm4114	pflD	-11.77	0.360092	46 -- 100	34 -- 88	formate C-acetyltransferase	stm0843	_____________45_____________________101\n_____________\|______________________\|\n5'-UUU...CGGUA_______C______________GAACA...AGA-3'\n______________AAACGCG_CGACGC__CAUUAU\n______________\|\|\|\|:\|:_\|:\|\|:\|__\|\|\|:\|:\n______________UUUGUGU_GUUGUG__GUAGUG\n3'-UUU...UAACG_______U______UU______UUGGC...UCA-5'\n_____________\|______________________\|\n_____________89_____________________33\n	46 -- 52	82 -- 88	-16.7675 kcal/mol	5.49067 kcal/mol	5.48747 kcal/mol	45 101@LB@ \| \|@LB@5'-UUU...CGGUA C GAACA...AGA-3'@LB@ AAACGCG CGACGC CAUUAU@LB@ \|\|\|\|:\|: \|:\|\|:\| \|\|\|:\|:@LB@ UUUGUGU GUUGUG GUAGUG@LB@3'-UUU...UAACG U UU UUGGC...UCA-5'@LB@ \| \|@LB@ 89 33@LB@@LB@@LB@Energy -11.77 kcal/mol@LB@Hybridization Energy -16.7675 kcal/mol@LB@Unfolding Energy - mRNA 5.49067 kcal/mol@LB@Unfolding Energy - sRNA 5.48747 kcal/mol@LB@@LB@Position - mRNA 46 -- 100@LB@Position - sRNA 34 -- 88@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 82 -- 88@LB@
96	0.004303	0.1596	stm4243	yjbN	-11.74	0.363864	272 -- 280	155 -- 163	tRNA dihydrouridine(20/20a) synthase DusA		_____________271______________________________281\n_____________\|________________________________\|\n5'-UUA...UUAAU___AC_________C____A_____CCU____GGCAG...GUU-3'\n______________GGG____UGUACGG_GAAG_UGAAA___GGGG\n______________\|\|\|____\|\|\|\|\|:\|_\|\|\|\|_\|\|\|\|\|___:\|\|\|\n______________CCC____ACAUGUC_CUUC_ACUUU___UCCC\n3'-UUU...UCUGU___AUUU__________________U______AUCAG...UCA-5'\n_____________\|________________________________\|\n_____________164______________________________154\n	58 -- 64	141 -- 147	-26.0653 kcal/mol	8.12251 kcal/mol	7.07058 kcal/mol	271 281@LB@ \| \|@LB@5'-UUA...UUAAU AC C A CCU GGCAG...GUU-3'@LB@ GGG UGUACGG GAAG UGAAA GGGG@LB@ \|\|\| \|\|\|\|\|:\| \|\|\|\| \|\|\|\|\| :\|\|\|@LB@ CCC ACAUGUC CUUC ACUUU UCCC@LB@3'-UUU...UCUGU AUUU U AUCAG...UCA-5'@LB@ \| \|@LB@ 164 154@LB@@LB@@LB@Energy -11.74 kcal/mol@LB@Hybridization Energy -26.0653 kcal/mol@LB@Unfolding Energy - mRNA 8.12251 kcal/mol@LB@Unfolding Energy - sRNA 7.07058 kcal/mol@LB@@LB@Position - mRNA 272 -- 280@LB@Position - sRNA 155 -- 163@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 141 -- 147@LB@
97	0.004849	0.1728	stm0832	ybiF	-11.58	0.382043	25 -- 72	45 -- 91	threonine/homoserine exporter RhtA		_____________24______________________73\n_____________\|_______________________\|\n5'-GGC...GCGCG_________________U_____CAGAU...CGU-3'\n______________UGC_GGCGCGAUA_CAU__CAUC\n______________\|\|\|_::\|:\|:\|:\|_\|\|:__\|\|\|\|\n______________ACG_UUGUGUUGU_GUG__GUAG\n3'-UUU...GGUUA___U_________U___UU____UGUUG...UCA-5'\n_____________\|_______________________\|\n_____________92______________________44\n	30 -- 36	79 -- 85	-16.3644 kcal/mol	3.58897 kcal/mol	4.34303 kcal/mol	24 73@LB@ \| \|@LB@5'-GGC...GCGCG U CAGAU...CGU-3'@LB@ UGC GGCGCGAUA CAU CAUC@LB@ \|\|\| ::\|:\|:\|:\| \|\|: \|\|\|\|@LB@ ACG UUGUGUUGU GUG GUAG@LB@3'-UUU...GGUUA U U UU UGUUG...UCA-5'@LB@ \| \|@LB@ 92 44@LB@@LB@@LB@Energy -11.58 kcal/mol@LB@Hybridization Energy -16.3644 kcal/mol@LB@Unfolding Energy - mRNA 3.58897 kcal/mol@LB@Unfolding Energy - sRNA 4.34303 kcal/mol@LB@@LB@Position - mRNA 25 -- 72@LB@Position - sRNA 45 -- 91@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 79 -- 85@LB@
98	0.004857	0.1728	stm2811	proX	-15.53	0.097032	195 -- 224	56 -- 84	glycine betaine ABC transporter substrate-binding protein		_____________194________________________225\n_____________\|__________________________\|\n5'-GCA...AAGGA__________________________UAUUU...CUA-3'\n______________ACAACGAUGCGACAU____ACCGUGA\n______________\|\|\|\|\|:\|::\|:\|\|\|\|____\|\|\|\|\|:\|\n______________UGUUGUUGUGUUGUA____UGGCAUU\n3'-UUU...GUUUG_______________GUGU_______CGGUU...UCA-5'\n_____________\|__________________________\|\n_____________85_________________________55\n	210 -- 216	59 -- 65	-26.0076 kcal/mol	3.5169 kcal/mol	9.80321 kcal/mol	194 225@LB@ \| \|@LB@5'-GCA...AAGGA UAUUU...CUA-3'@LB@ ACAACGAUGCGACAU ACCGUGA@LB@ \|\|\|\|\|:\|::\|:\|\|\|\| \|\|\|\|\|:\|@LB@ UGUUGUUGUGUUGUA UGGCAUU@LB@3'-UUU...GUUUG GUGU CGGUU...UCA-5'@LB@ \| \|@LB@ 85 55@LB@@LB@@LB@Energy -15.53 kcal/mol@LB@Hybridization Energy -26.0076 kcal/mol@LB@Unfolding Energy - mRNA 3.5169 kcal/mol@LB@Unfolding Energy - sRNA 9.80321 kcal/mol@LB@@LB@Position - mRNA 195 -- 224@LB@Position - sRNA 56 -- 84@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 59 -- 65@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@
100	0.00495	0.1728	stm1879	ptrB	-19.83	0.018631	144 -- 223	40 -- 120	oligopeptidase B		_____________143____________________________________________224\n_____________\|______________________________________________\|\n5'-AAG...UAUAA_________________AAGAAAAA_____A___U___________AAUCG...AGC-3'\n______________CAAAUAU__UAACGCAA________ACGAC_UGU__GCCAAAAGCC\n______________\|\|\|\|:\|:__:\|\|\|:\|\|\|________\|\|:\|\|_:\|\|__\|\|\|\|\|\|\|\|\|\|\n______________GUUUGUG__GUUGUGUU________UGUUG_GCA__CGGUUUUCGG\n3'-UUU...UUAAC_______UU________GUAG_____________UU__________GUAGU...UCA-5'\n_____________\|______________________________________________\|\n_____________121____________________________________________39\n	209 -- 215	49 -- 55	-34.4525 kcal/mol	3.62291 kcal/mol	15.2208 kcal/mol	143 224@LB@ \| \|@LB@5'-AAG...UAUAA AAGAAAAA A U AAUCG...AGC-3'@LB@ CAAAUAU UAACGCAA ACGAC UGU GCCAAAAGCC@LB@ \|\|\|\|:\|: :\|\|\|:\|\|\| \|\|:\|\| :\|\| \|\|\|\|\|\|\|\|\|\|@LB@ GUUUGUG GUUGUGUU UGUUG GCA CGGUUUUCGG@LB@3'-UUU...UUAAC UU GUAG UU GUAGU...UCA-5'@LB@ \| \|@LB@ 121 39@LB@@LB@@LB@Energy -19.83 kcal/mol@LB@Hybridization Energy -34.4525 kcal/mol@LB@Unfolding Energy - mRNA 3.62291 kcal/mol@LB@Unfolding Energy - sRNA 15.2208 kcal/mol@LB@@LB@Position - mRNA 144 -- 223@LB@Position - sRNA 40 -- 120@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 49 -- 55@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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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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