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
121	0.006021	0.1758	stm3903	ilvE	-13.34	0.214101	130 -- 170	39 -- 78	branched chain amino acid aminotransferase	_____________129__________________171\n_____________\|____________________\|\n5'-GGU...CCAGA___CU___C___U_______AAUCC...GUA-3'\n______________GCG___GC_ACA_CACAACA\n______________\|\|:___:\|_\|\|\|_\|\|\|\|\|\|\|\n______________CGU___UG_UGU_GUGUUGU\n3'-UUU...GUUAA___UUG__U___U_______AGUGU...UCA-5'\n_____________\|____________________\|\n_____________79___________________38\n	164 -- 170	71 -- 77	-14.4922 kcal/mol	2.12049 kcal/mol	3.80671 kcal/mol	129 171@LB@ \| \|@LB@5'-GGU...CCAGA CU C U AAUCC...GUA-3'@LB@ GCG GC ACA CACAACA@LB@ \|\|: :\| \|\|\| \|\|\|\|\|\|\|@LB@ CGU UG UGU GUGUUGU@LB@3'-UUU...GUUAA UUG U U AGUGU...UCA-5'@LB@ \| \|@LB@ 79 38@LB@@LB@@LB@Energy -13.34 kcal/mol@LB@Hybridization Energy -14.4922 kcal/mol@LB@Unfolding Energy - mRNA 2.12049 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 130 -- 170@LB@Position - sRNA 39 -- 78@LB@Position Seed - mRNA 164 -- 170@LB@Position Seed - sRNA 71 -- 77@LB@
140	0.007169	0.182	stm3126	N/A	-18.02	0.037639	66 -- 114	39 -- 91	putative amino acid transporter	_____________65_______________________________115\n_____________\|________________________________\|\n5'-AUU...GCGCA______G______U___________UU_____UAUCC...UGA-3'\n______________UGCGGG_ACGGCG_CACAACGUUAU__ACCGU\n______________\|\|\|:::_\|\|::\|:_\|\|\|\|\|\|:\|:\|:__\|\|\|\|\|\n______________ACGUUU_UGUUGU_GUGUUGUAGUG__UGGCA\n3'-UUU...GGUUA______G______U___________U______UUCGG...UCA-5'\n_____________\|________________________________\|\n_____________92_______________________________38\n	82 -- 88	69 -- 75	-33.8851 kcal/mol	10.4253 kcal/mol	9.42541 kcal/mol	65 115@LB@ \| \|@LB@5'-AUU...GCGCA G U UU UAUCC...UGA-3'@LB@ UGCGGG ACGGCG CACAACGUUAU ACCGU@LB@ \|\|\|::: \|\|::\|: \|\|\|\|\|\|:\|:\|: \|\|\|\|\|@LB@ ACGUUU UGUUGU GUGUUGUAGUG UGGCA@LB@3'-UUU...GGUUA G U U UUCGG...UCA-5'@LB@ \| \|@LB@ 92 38@LB@@LB@@LB@Energy -18.02 kcal/mol@LB@Hybridization Energy -33.8851 kcal/mol@LB@Unfolding Energy - mRNA 10.4253 kcal/mol@LB@Unfolding Energy - sRNA 9.42541 kcal/mol@LB@@LB@Position - mRNA 66 -- 114@LB@Position - sRNA 39 -- 91@LB@Position Seed - mRNA 82 -- 88@LB@Position Seed - sRNA 69 -- 75@LB@
48	0.001762	0.1291	stm4523	yjiW	-20.55	0.014078	157 -- 299	40 -- 186	endoribonuclease SymE	_____________156____________________________________________________________________________________________300\n_____________\|______________________________________________________________________________________________\|\n5'-GUG...AUUUU____AA___CCA__A__A_______CCAUUCU__________CG______UC__GAAGUCUCCC___________C______CUU_________UAUGC...AUU-3'\n______________AGGG__UAG___UC_UG_CUACCGU_______AUUGCAGAUC___UGCGA__CA__________CAACAA_AUAA_CGUCAC___ACCGUGAGU\n______________\|\|\|\|__\|\|\|___\|\|_:\|_\|\|\|\|\|\|\|_______\|\|:\|\|\|\|\|:\|___\|\|\|:\|__\|\|__________\|\|\|\|\|\|_\|:\|\|_\|:\|\|\|\|___\|\|\|\|\|:\|\|:\n______________UCCC__AUC___AG_GC_GAUGGCA_______UAGCGUCUGG___ACGUU__GU__________GUUGUU_UGUU_GUAGUG___UGGCAUUCG\n3'-UUU...CUUUU______________A__________CCAGACU__________UUA_____U___________________G___________U___________GUUUU...UCA-5'\n_____________\|______________________________________________________________________________________________\|\n_____________187____________________________________________________________________________________________39\n	222 -- 228	95 -- 101	-59.8396 kcal/mol	18.2388 kcal/mol	27.0823 kcal/mol	156 300@LB@ \| \|@LB@5'-GUG...AUUUU AA CCA A A CCAUUCU CG UC GAAGUCUCCC C CUU UAUGC...AUU-3'@LB@ AGGG UAG UC UG CUACCGU AUUGCAGAUC UGCGA CA CAACAA AUAA CGUCAC ACCGUGAGU@LB@ \|\|\|\| \|\|\| \|\| :\| \|\|\|\|\|\|\| \|\|:\|\|\|\|\|:\| \|\|\|:\| \|\| \|\|\|\|\|\| \|:\|\| \|:\|\|\|\| \|\|\|\|\|:\|\|:@LB@ UCCC AUC AG GC GAUGGCA UAGCGUCUGG ACGUU GU GUUGUU UGUU GUAGUG UGGCAUUCG@LB@3'-UUU...CUUUU A CCAGACU UUA U G U GUUUU...UCA-5'@LB@ \| \|@LB@ 187 39@LB@@LB@@LB@Energy -20.55 kcal/mol@LB@Hybridization Energy -59.8396 kcal/mol@LB@Unfolding Energy - mRNA 18.2388 kcal/mol@LB@Unfolding Energy - sRNA 27.0823 kcal/mol@LB@@LB@Position - mRNA 157 -- 299@LB@Position - sRNA 40 -- 186@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 95 -- 101@LB@
59	0.00232	0.14	stm4105	metF	-16.51	0.066936	223 -- 245	40 -- 59	methylenetetrahydrofolate reductase [NAD(P)H]	_____________222__________________246\n_____________\|____________________\|\n5'-AAG...UUUAC__________AUA_______GCGAU...GCA-3'\n______________AACACAACAA___AUAACAU\n______________\|\|\|\|\|\|\|\|\|\|___\|:\|\|\|\|\|\n______________UUGUGUUGUU___UGUUGUA\n3'-UUU...AACGU__________G_________GUGUU...UCA-5'\n_____________\|____________________\|\n_____________60___________________39\n	175 -- 181	70 -- 76	-16.6304 kcal/mol	0.675865 kcal/mol	3.87174 kcal/mol	222 246@LB@ \| \|@LB@5'-AAG...UUUAC AUA GCGAU...GCA-3'@LB@ AACACAACAA AUAACAU@LB@ \|\|\|\|\|\|\|\|\|\| \|:\|\|\|\|\|@LB@ UUGUGUUGUU UGUUGUA@LB@3'-UUU...AACGU G GUGUU...UCA-5'@LB@ \| \|@LB@ 60 39@LB@@LB@@LB@Energy -16.51 kcal/mol@LB@Hybridization Energy -16.6304 kcal/mol@LB@Unfolding Energy - mRNA 0.675865 kcal/mol@LB@Unfolding Energy - sRNA 3.87174 kcal/mol@LB@@LB@Position - mRNA 223 -- 245@LB@Position - sRNA 40 -- 59@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 70 -- 76@LB@
61	0.002902	0.1596	stm3567	livJ	-18.03	0.037474	150 -- 196	40 -- 87	high-affinity branched-chain amino acid transporter	_____________149_______________________197\n_____________\|_________________________\|\n5'-CGG...ACAAU_____C____________A______AGAAU...CCG-3'\n______________AACAC_ACAACACA_CGU_ACAACC\n______________\|\|\|\|\|_\|\|\|\|\|\|\|\|_\|:\|_\|\|\|\|\|\|\n______________UUGUG_UGUUGUGU_GUA_UGUUGG\n3'-UUU...AACGU_____U________U___G______CAUUC...UCA-5'\n_____________\|_________________________\|\n_____________88________________________39\n	157 -- 163	74 -- 80	-27.1738 kcal/mol	3.63117 kcal/mol	8.28637 kcal/mol	149 197@LB@ \| \|@LB@5'-CGG...ACAAU C A AGAAU...CCG-3'@LB@ AACAC ACAACACA CGU ACAACC@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\| \|:\| \|\|\|\|\|\|@LB@ UUGUG UGUUGUGU GUA UGUUGG@LB@3'-UUU...AACGU U U G CAUUC...UCA-5'@LB@ \| \|@LB@ 88 39@LB@@LB@@LB@Energy -18.03 kcal/mol@LB@Hybridization Energy -27.1738 kcal/mol@LB@Unfolding Energy - mRNA 3.63117 kcal/mol@LB@Unfolding Energy - sRNA 8.28637 kcal/mol@LB@@LB@Position - mRNA 150 -- 196@LB@Position - sRNA 40 -- 87@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 74 -- 80@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@
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@
177	0.009665	0.1945	stm0079	yaaU	-14.30	0.152587	187 -- 218	40 -- 79	MFS transporter	_____________186___________219\n_____________\|_____________\|\n5'-GAA...GUUGA____G________CAUGC...UGC-3'\n______________AACA_GACAUCAC\n______________\|\|\|\|_:\|\|\|\|\|\|\|\n______________UUGU_UUGUAGUG\n3'-UUU...UGUUG____G________UUGGC...UCA-5'\n_____________\|_____________\|\n_____________80____________39\n	193 -- 199	67 -- 73	-15.1412 kcal/mol	3.61479 kcal/mol	3.57243 kcal/mol	186 219@LB@ \| \|@LB@5'-GAA...GUUGA G CAUGC...UGC-3'@LB@ AACA GACAUCAC@LB@ \|\|\|\| :\|\|\|\|\|\|\|@LB@ UUGU UUGUAGUG@LB@3'-UUU...UGUUG G UUGGC...UCA-5'@LB@ \| \|@LB@ 80 39@LB@@LB@@LB@Energy -14.30 kcal/mol@LB@Hybridization Energy -15.1412 kcal/mol@LB@Unfolding Energy - mRNA 3.61479 kcal/mol@LB@Unfolding Energy - sRNA 3.57243 kcal/mol@LB@@LB@Position - mRNA 187 -- 218@LB@Position - sRNA 40 -- 79@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 67 -- 73@LB@
31	0.0007673	0.08814	stm0403	yajB	-17.88	0.039643	23 -- 70	41 -- 90	ACP phosphodiesterase	_____________22_____________71\n_____________\|______________\|\n5'-CCC...GGGUA_______AU_____AUUCG...AUU-3'\n______________GUGGGCA__CAGGG\n______________:\|\|\|:\|\|__\|\|\|\|\|\n______________UACCUGU__GUCCC\n3'-UUU...AGUGA_______CU_____AUUUA...UCA-5'\n_____________\|______________\|\n_____________91_____________40\n	57 -- 63	159 -- 165	-19.6891 kcal/mol	4.4153 kcal/mol	3.13232 kcal/mol	22 71@LB@ \| \|@LB@5'-CCC...GGGUA AU AUUCG...AUU-3'@LB@ GUGGGCA CAGGG@LB@ :\|\|\|:\|\| \|\|\|\|\|@LB@ UACCUGU GUCCC@LB@3'-UUU...AGUGA CU AUUUA...UCA-5'@LB@ \| \|@LB@ 91 40@LB@@LB@@LB@Energy -17.88 kcal/mol@LB@Hybridization Energy -19.6891 kcal/mol@LB@Unfolding Energy - mRNA 4.4153 kcal/mol@LB@Unfolding Energy - sRNA 3.13232 kcal/mol@LB@@LB@Position - mRNA 23 -- 70@LB@Position - sRNA 41 -- 90@LB@Position Seed - mRNA 57 -- 63@LB@Position Seed - sRNA 159 -- 165@LB@
79	0.003723	0.1596	stm1723	trpE	-16.56	0.065817	202 -- 256	41 -- 91	anthranilate synthase subunit I	_____________201__________________257\n_____________\|____________________\|\n5'-UGA...AAAUG__________UU________CGGUU...CGG-3'\n______________GCAGCGACAU__GCAUUACA\n______________:\|\|:\|:\|\|\|:__:\|\|\|:\|\|\|\n______________UGUUGUUGUG__UGUAGUGU\n3'-UUU...GUUUG__________U_________UGGCA...UCA-5'\n_____________\|____________________\|\n_____________92___________________40\n	78 -- 84	66 -- 72	-20.8013 kcal/mol	5.41524 kcal/mol	5.89278 kcal/mol	201 257@LB@ \| \|@LB@5'-UGA...AAAUG UU CGGUU...CGG-3'@LB@ GCAGCGACAU GCAUUACA@LB@ :\|\|:\|:\|\|\|: :\|\|\|:\|\|\|@LB@ UGUUGUUGUG UGUAGUGU@LB@3'-UUU...GUUUG U UGGCA...UCA-5'@LB@ \| \|@LB@ 92 40@LB@@LB@@LB@Energy -16.56 kcal/mol@LB@Hybridization Energy -20.8013 kcal/mol@LB@Unfolding Energy - mRNA 5.41524 kcal/mol@LB@Unfolding Energy - sRNA 5.89278 kcal/mol@LB@@LB@Position - mRNA 202 -- 256@LB@Position - sRNA 41 -- 91@LB@Position Seed - mRNA 78 -- 84@LB@Position Seed - sRNA 66 -- 72@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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