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
25	0.0006298	0.08814	stm3161	metC	-13.21	0.223681	190 -- 249	35 -- 90	cystathionine beta-lyase	_____________189__________________250\n_____________\|____________________\|\n5'-CAA...AACUG_________G__________AAAAA...CAC-3'\n______________GUAAACGCA__GACGCAGCA\n______________\|:\|\|\|\|:\|\|__:\|\|:\|\|:\|\|\n______________CGUUUGUGU__UUGUGUUGU\n3'-UUU...GUUAA_________UG_________AGUGU...UCA-5'\n_____________\|____________________\|\n_____________91___________________34\n	243 -- 249	71 -- 77	-21.5854 kcal/mol	5.07977 kcal/mol	3.80671 kcal/mol	189 250@LB@ \| \|@LB@5'-CAA...AACUG G AAAAA...CAC-3'@LB@ GUAAACGCA GACGCAGCA@LB@ \|:\|\|\|\|:\|\| :\|\|:\|\|:\|\|@LB@ CGUUUGUGU UUGUGUUGU@LB@3'-UUU...GUUAA UG AGUGU...UCA-5'@LB@ \| \|@LB@ 91 34@LB@@LB@@LB@Energy -13.21 kcal/mol@LB@Hybridization Energy -21.5854 kcal/mol@LB@Unfolding Energy - mRNA 5.07977 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 190 -- 249@LB@Position - sRNA 35 -- 90@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 71 -- 77@LB@
87	0.004009	0.1596	stm2067	sbcB	-11.70	0.367652	220 -- 292	35 -- 90	exodeoxyribonuclease I	_____________219_____________________293\n_____________\|_______________________\|\n5'-AUU...AUGUA______U________________AUUGG...CCG-3'\n______________CGAACA_UAGCA__ACAAUAUCA\n______________\|:\|\|\|\|_:\|:\|\|__\|\|\|\|:\|\|\|\|\n______________GUUUGU_GUUGU__UGUUGUAGU\n3'-UUU...UUAAC____________UG_________GUUGG...UCA-5'\n_____________\|_______________________\|\n_____________91______________________34\n	110 -- 116	68 -- 74	-17.8808 kcal/mol	2.08887 kcal/mol	5.27986 kcal/mol	219 293@LB@ \| \|@LB@5'-AUU...AUGUA U AUUGG...CCG-3'@LB@ CGAACA UAGCA ACAAUAUCA@LB@ \|:\|\|\|\| :\|:\|\| \|\|\|\|:\|\|\|\|@LB@ GUUUGU GUUGU UGUUGUAGU@LB@3'-UUU...UUAAC UG GUUGG...UCA-5'@LB@ \| \|@LB@ 91 34@LB@@LB@@LB@Energy -11.70 kcal/mol@LB@Hybridization Energy -17.8808 kcal/mol@LB@Unfolding Energy - mRNA 2.08887 kcal/mol@LB@Unfolding Energy - sRNA 5.27986 kcal/mol@LB@@LB@Position - mRNA 220 -- 292@LB@Position - sRNA 35 -- 90@LB@Position Seed - mRNA 110 -- 116@LB@Position Seed - sRNA 68 -- 74@LB@
32	0.001017	0.1132	stm1874	N/A	-30.35	0.000300	5 -- 53	36 -- 83	putative inner membrane protein	_____________4__________________________________________________54\n_____________\|__________________________________________________\|\n_______5'-GGUU___________C______U____CUC________________A_______CCGGC...CCG-3'\n______________CAGCGGCGCAA_CAUUAC_GGCC___AG_CAAGAGCUCAUCA_AACGCGC\n______________\|\|:\|::\|:\|\|\|_\|\|\|:\|\|_::\|\|___\|\|_\|\|\|:\|\|\|:\|\|\|\|\|_\|\|\|:\|\|\|\n______________GUUGUUGUGUU_GUAGUG_UUGG___UC_GUUUUCGGGUAGU_UUGUGCG\n3'-UUU...UUUGU_______________________CAU__G_____________C_______UAAGG...UCA-5'\n_____________\|__________________________________________________\|\n_____________84_________________________________________________35\n	47 -- 53	36 -- 42	-54.7325 kcal/mol	11.1988 kcal/mol	22.0738 kcal/mol	4 54@LB@ \| \|@LB@ 5'-GGUU C U CUC A CCGGC...CCG-3'@LB@ CAGCGGCGCAA CAUUAC GGCC AG CAAGAGCUCAUCA AACGCGC@LB@ \|\|:\|::\|:\|\|\| \|\|\|:\|\| ::\|\| \|\| \|\|\|:\|\|\|:\|\|\|\|\| \|\|\|:\|\|\|@LB@ GUUGUUGUGUU GUAGUG UUGG UC GUUUUCGGGUAGU UUGUGCG@LB@3'-UUU...UUUGU CAU G C UAAGG...UCA-5'@LB@ \| \|@LB@ 84 35@LB@@LB@@LB@Energy -30.35 kcal/mol@LB@Hybridization Energy -54.7325 kcal/mol@LB@Unfolding Energy - mRNA 11.1988 kcal/mol@LB@Unfolding Energy - sRNA 22.0738 kcal/mol@LB@@LB@Position - mRNA 5 -- 53@LB@Position - sRNA 36 -- 83@LB@Position Seed - mRNA 47 -- 53@LB@Position Seed - sRNA 36 -- 42@LB@
156	0.008228	0.1845	stm1715	yciN	-28.69	0.000575	104 -- 163	36 -- 90	similar to E. coli orf hypothetical protein (AAC74355.1); Blastp hit to AAC74355.1 (83 aa) 92% identity in aa 1 - 83	_____________103___________________________________________________________164\n_____________\|_____________________________________________________________\|\n5'-UCG...UGCCA____________UG____AUC_____AUUUC_______AAUAUUU___________G____UCAGC...CCA-3'\n______________GUGAACGCAACA__ACAA___CAUCA_____CUGUGAG_______GCCCAUCAGAA__UGC\n______________\|::\|\|\|:\|\|\|\|\|__\|\|\|\|___\|\|\|\|\|_____\|:\|\|:\|\|_______\|\|\|\|\|\|\|\|\|\|\|__:\|\|\n______________CGUUUGUGUUGU__UGUU___GUAGU_____GGCAUUC_______CGGGUAGUCUU__GCG\n3'-UUU...GUUAA____________UG____________GUU_________GGUUUU____________GU___UAAGG...UCA-5'\n_____________\|_____________________________________________________________\|\n_____________91____________________________________________________________35\n	152 -- 158	42 -- 48	-53.6458 kcal/mol	9.96696 kcal/mol	22.5 kcal/mol	103 164@LB@ \| \|@LB@5'-UCG...UGCCA UG AUC AUUUC AAUAUUU G UCAGC...CCA-3'@LB@ GUGAACGCAACA ACAA CAUCA CUGUGAG GCCCAUCAGAA UGC@LB@ \|::\|\|\|:\|\|\|\|\| \|\|\|\| \|\|\|\|\| \|:\|\|:\|\| \|\|\|\|\|\|\|\|\|\|\| :\|\|@LB@ CGUUUGUGUUGU UGUU GUAGU GGCAUUC CGGGUAGUCUU GCG@LB@3'-UUU...GUUAA UG GUU GGUUUU GU UAAGG...UCA-5'@LB@ \| \|@LB@ 91 35@LB@@LB@@LB@Energy -28.69 kcal/mol@LB@Hybridization Energy -53.6458 kcal/mol@LB@Unfolding Energy - mRNA 9.96696 kcal/mol@LB@Unfolding Energy - sRNA 22.5 kcal/mol@LB@@LB@Position - mRNA 104 -- 163@LB@Position - sRNA 36 -- 90@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 42 -- 48@LB@
5	6.363e-05	0.04123	stm0399	brnQ	-24.27	0.003272	169 -- 224	36 -- 81	branched-chain amino acid transport system II carrier protein	_____________168_______________________________________________________________225\n_____________\|_________________________________________________________________\|\n5'-AAC...UUUAA___U_________U________C_____G_A_____A__UUAU_A________UUAAAAU_____GAUAU...UCG-3'\n______________UGU___UACAACA_CAC__CAU_CACAG_C_GUAAG_CU____G_CCCAUCAG_______CGCGC\n______________\|\|:___:\|\|\|\|\|\|_\|\|\|__\|\|\|_\|\|\|\|:_\|_\|\|\|\|\|_\|:____\|_\|\|\|\|\|\|\|\|_______\|:\|\|\|\n______________ACG___GUGUUGU_GUG__GUA_GUGUU_G_CAUUC_GG____C_GGGUAGUC_______GUGCG\n3'-UUU...GGUUA___UUU_______U___UU_________G__________UUUU__________UU__________UAAGG...UCA-5'\n_____________\|_________________________________________________________________\|\n_____________82________________________________________________________________35\n	205 -- 211	44 -- 50	-45.9704 kcal/mol	7.09165 kcal/mol	22.503 kcal/mol	168 225@LB@ \| \|@LB@5'-AAC...UUUAA U U C G A A UUAU A UUAAAAU GAUAU...UCG-3'@LB@ UGU UACAACA CAC CAU CACAG C GUAAG CU G CCCAUCAG CGCGC@LB@ \|\|: :\|\|\|\|\|\| \|\|\| \|\|\| \|\|\|\|: \| \|\|\|\|\| \|: \| \|\|\|\|\|\|\|\| \|:\|\|\|@LB@ ACG GUGUUGU GUG GUA GUGUU G CAUUC GG C GGGUAGUC GUGCG@LB@3'-UUU...GGUUA UUU U UU G UUUU UU UAAGG...UCA-5'@LB@ \| \|@LB@ 82 35@LB@@LB@@LB@Energy -24.27 kcal/mol@LB@Hybridization Energy -45.9704 kcal/mol@LB@Unfolding Energy - mRNA 7.09165 kcal/mol@LB@Unfolding Energy - sRNA 22.503 kcal/mol@LB@@LB@Position - mRNA 169 -- 224@LB@Position - sRNA 36 -- 81@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 44 -- 50@LB@
39	0.001399	0.1215	stm4007	glnA	-20.44	0.014679	143 -- 217	36 -- 106	type I glutamate--ammonia ligase	_____________142_____________________________________________________________________________218\n_____________\|_______________________________________________________________________________\|\n5'-CAC...CAGCA______A_____UC____UAC_____________C___G_C___U___GGA____A____UAU_______U________UUUGA...CGA-3'\n______________GAAUUG_AGAUC____GU___CACGACGAC_CGA_CAU_A_CAA_CCG___GAGU_CAAG___GUCCG_C_GAACACGU\n______________\|\|\|\|:\|_\|\|\|:\|____\|:___\|\|\|:\|\|:\|\|_\|:\|_\|\|\|_\|_\|\|\|_\|\|\|___:\|\|:_\|\|\|:___\|:\|\|:_\|_\|\|\|\|\|\|\|:\n______________CUUAGC_UCUGG____CG___GUGUUGUUG_GUU_GUA_U_GUU_GGC___UUCG_GUUU___CGGGU_G_CUUGUGCG\n3'-UUU...CCAGA______G_____UUAA__UUU_________U_______G_________A___________U_______A_U________UAAGG...UCA-5'\n_____________\|_______________________________________________________________________________\|\n_____________107_____________________________________________________________________________35\n	211 -- 217	36 -- 42	-55.3576 kcal/mol	10.964 kcal/mol	31.8708 kcal/mol	142 218@LB@ \| \|@LB@5'-CAC...CAGCA A UC UAC C G C U GGA A UAU U UUUGA...CGA-3'@LB@ GAAUUG AGAUC GU CACGACGAC CGA CAU A CAA CCG GAGU CAAG GUCCG C GAACACGU@LB@ \|\|\|\|:\| \|\|\|:\| \|: \|\|\|:\|\|:\|\| \|:\| \|\|\| \| \|\|\| \|\|\| :\|\|: \|\|\|: \|:\|\|: \| \|\|\|\|\|\|\|:@LB@ CUUAGC UCUGG CG GUGUUGUUG GUU GUA U GUU GGC UUCG GUUU CGGGU G CUUGUGCG@LB@3'-UUU...CCAGA G UUAA UUU U G A U A U UAAGG...UCA-5'@LB@ \| \|@LB@ 107 35@LB@@LB@@LB@Energy -20.44 kcal/mol@LB@Hybridization Energy -55.3576 kcal/mol@LB@Unfolding Energy - mRNA 10.964 kcal/mol@LB@Unfolding Energy - sRNA 31.8708 kcal/mol@LB@@LB@Position - mRNA 143 -- 217@LB@Position - sRNA 36 -- 106@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 36 -- 42@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@
21	0.000482	0.08173	stm1057	pepN	-18.92	0.026522	201 -- 244	36 -- 81	aminopeptidase N	_____________200______________245\n_____________\|________________\|\n5'-CUU...UUUAU___________C____GCCAA...AAA-3'\n______________GACACAACAGC_ACAA\n______________:\|\|\|\|\|\|\|\|:\|_\|\|\|\|\n______________UUGUGUUGUUG_UGUU\n3'-UUU...AACGU________________GUAGU...UCA-5'\n_____________\|________________\|\n_____________82_______________35\n	207 -- 213	77 -- 83	-17.6161 kcal/mol	1.99149 kcal/mol	3.56182 kcal/mol	200 245@LB@ \| \|@LB@5'-CUU...UUUAU C GCCAA...AAA-3'@LB@ GACACAACAGC ACAA@LB@ :\|\|\|\|\|\|\|\|:\| \|\|\|\|@LB@ UUGUGUUGUUG UGUU@LB@3'-UUU...AACGU GUAGU...UCA-5'@LB@ \| \|@LB@ 82 35@LB@@LB@@LB@Energy -18.92 kcal/mol@LB@Hybridization Energy -17.6161 kcal/mol@LB@Unfolding Energy - mRNA 1.99149 kcal/mol@LB@Unfolding Energy - sRNA 3.56182 kcal/mol@LB@@LB@Position - mRNA 201 -- 244@LB@Position - sRNA 36 -- 81@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 77 -- 83@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@
139	0.007115	0.182	stm0826	ybiN	-18.61	0.029895	232 -- 282	36 -- 90	23S rRNA (adenine(1618)-N(6))-methyltransferase	_____________231___________________283\n_____________\|_____________________\|\n5'-CUC...GAGCC_____AACGAGCG________AAUUC...UUC-3'\n______________GAUCA________AGGCAGGG\n______________:\|\|\|\|________\|\|:\|\|\|\|\|\n______________UUAGU________UCUGUCCC\n3'-UUU...UGUAA_____GAUACCUG________AUUUA...UCA-5'\n_____________\|_____________________\|\n_____________91____________________35\n	124 -- 130	152 -- 158	-17.5433 kcal/mol	4.82059 kcal/mol	3.53427 kcal/mol	231 283@LB@ \| \|@LB@5'-CUC...GAGCC AACGAGCG AAUUC...UUC-3'@LB@ GAUCA AGGCAGGG@LB@ :\|\|\|\| \|\|:\|\|\|\|\|@LB@ UUAGU UCUGUCCC@LB@3'-UUU...UGUAA GAUACCUG AUUUA...UCA-5'@LB@ \| \|@LB@ 91 35@LB@@LB@@LB@Energy -18.61 kcal/mol@LB@Hybridization Energy -17.5433 kcal/mol@LB@Unfolding Energy - mRNA 4.82059 kcal/mol@LB@Unfolding Energy - sRNA 3.53427 kcal/mol@LB@@LB@Position - mRNA 232 -- 282@LB@Position - sRNA 36 -- 90@LB@Position Seed - mRNA 124 -- 130@LB@Position Seed - sRNA 152 -- 158@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:

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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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