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
71	0.003339	0.1596	stm0105	yabI	-14.10	0.163814	151 -- 168	141 -- 162	similar to E. coli orf hypothetical protein (AAC73176.1); Blastp hit to AAC73176.1 (254 aa) 89% identity in aa 1 - 253		_____________150____________________169\n_____________\|______________________\|\n5'-UGA...ACGAA__G___________________AAUCC...GGU-3'\n______________GG_GGACGGGGUAA____GCAG\n______________\|:_:\|\|\|:\|\|\|\|\|\|____:\|\|\|\n______________CU_UCUGUCCCAUU____UGUC\n3'-UUU...GAUAC__G___________UACA____CUUCA...UCA-5'\n_____________\|______________________\|\n_____________163____________________140\n	158 -- 164	149 -- 155	-23.8591 kcal/mol	5.26969 kcal/mol	3.68511 kcal/mol	150 169@LB@ \| \|@LB@5'-UGA...ACGAA G AAUCC...GGU-3'@LB@ GG GGACGGGGUAA GCAG@LB@ \|: :\|\|\|:\|\|\|\|\|\| :\|\|\|@LB@ CU UCUGUCCCAUU UGUC@LB@3'-UUU...GAUAC G UACA CUUCA...UCA-5'@LB@ \| \|@LB@ 163 140@LB@@LB@@LB@Energy -14.10 kcal/mol@LB@Hybridization Energy -23.8591 kcal/mol@LB@Unfolding Energy - mRNA 5.26969 kcal/mol@LB@Unfolding Energy - sRNA 3.68511 kcal/mol@LB@@LB@Position - mRNA 151 -- 168@LB@Position - sRNA 141 -- 162@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 149 -- 155@LB@
72	0.003348	0.1596	stm0849	yliB	-19.23	0.023527	175 -- 193	139 -- 162	glutathione ABC transporter substrate-binding protein GsiB		_____________174______________________194\n_____________\|________________________\|\n5'-GUU...AUUCA____________UU__________GAACA...CGG-3'\n______________GACAGGCAGGGU_______CAGGA\n______________\|\|\|\|\|:\|\|\|\|\|\|_______\|\|\|\|\|\n______________CUGUCUGUCCCA_______GUCCU\n3'-UUU...GAUAC____________UUUACAU_____UCACU...UCA-5'\n_____________\|________________________\|\n_____________163______________________138\n	180 -- 186	151 -- 157	-27.2027 kcal/mol	3.52422 kcal/mol	3.69132 kcal/mol	174 194@LB@ \| \|@LB@5'-GUU...AUUCA UU GAACA...CGG-3'@LB@ GACAGGCAGGGU CAGGA@LB@ \|\|\|\|\|:\|\|\|\|\|\| \|\|\|\|\|@LB@ CUGUCUGUCCCA GUCCU@LB@3'-UUU...GAUAC UUUACAU UCACU...UCA-5'@LB@ \| \|@LB@ 163 138@LB@@LB@@LB@Energy -19.23 kcal/mol@LB@Hybridization Energy -27.2027 kcal/mol@LB@Unfolding Energy - mRNA 3.52422 kcal/mol@LB@Unfolding Energy - sRNA 3.69132 kcal/mol@LB@@LB@Position - mRNA 175 -- 193@LB@Position - sRNA 139 -- 162@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 151 -- 157@LB@
73	0.003444	0.1596	stm1437	ydhM	-18.33	0.033340	6 -- 47	35 -- 81	TetR family transcriptional regulator		_____________5_______________________48\n_____________\|_______________________\|\n5'-CGG...CAAAC___________CC___G______UGCUG...AGU-3'\n______________CGAACACGAUA__CGC_AACAUC\n______________\|:\|\|\|\|\|:\|:\|__\|:\|_\|\|\|\|\|\|\n______________GUUUGUGUUGU__GUG_UUGUAG\n3'-UUU...UUAAC___________U___________UGUUG...UCA-5'\n_____________\|_______________________\|\n_____________82______________________34\n	219 -- 225	79 -- 85	-19.8292 kcal/mol	2.08213 kcal/mol	4.32311 kcal/mol	5 48@LB@ \| \|@LB@5'-CGG...CAAAC CC G UGCUG...AGU-3'@LB@ CGAACACGAUA CGC AACAUC@LB@ \|:\|\|\|\|\|:\|:\| \|:\| \|\|\|\|\|\|@LB@ GUUUGUGUUGU GUG UUGUAG@LB@3'-UUU...UUAAC U UGUUG...UCA-5'@LB@ \| \|@LB@ 82 34@LB@@LB@@LB@Energy -18.33 kcal/mol@LB@Hybridization Energy -19.8292 kcal/mol@LB@Unfolding Energy - mRNA 2.08213 kcal/mol@LB@Unfolding Energy - sRNA 4.32311 kcal/mol@LB@@LB@Position - mRNA 6 -- 47@LB@Position - sRNA 35 -- 81@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 79 -- 85@LB@
74	0.003449	0.1596	stm1129	N/A	-19.64	0.020096	190 -- 238	139 -- 186	N-acetylmannosamine-6-phosphate 2-epimerase	stm3337	_____________189__________________________________239\n_____________\|____________________________________\|\n5'-AUA...UGGAU________UAGC_____U__AACA_________C__AAACG...AAA-3'\n______________GUCACUAU____CAGGC_GG____AAGUGUACA_GA\n______________:\|\|\|\|\|\|\|____\|\|\|:\|_\|\|____\|\|:\|\|\|\|\|\|_\|\|\n______________UAGUGAUA____GUCUG_CC____UUUACAUGU_CU\n3'-UUU...GUAAU________CCU______U__CA___________C__UCACU...UCA-5'\n_____________\|____________________________________\|\n_____________187__________________________________138\n	229 -- 235	142 -- 148	-26.4502 kcal/mol	8.56913 kcal/mol	5.67007 kcal/mol	189 239@LB@ \| \|@LB@5'-AUA...UGGAU UAGC U AACA C AAACG...AAA-3'@LB@ GUCACUAU CAGGC GG AAGUGUACA GA@LB@ :\|\|\|\|\|\|\| \|\|\|:\| \|\| \|\|:\|\|\|\|\|\| \|\|@LB@ UAGUGAUA GUCUG CC UUUACAUGU CU@LB@3'-UUU...GUAAU CCU U CA C UCACU...UCA-5'@LB@ \| \|@LB@ 187 138@LB@@LB@@LB@Energy -19.64 kcal/mol@LB@Hybridization Energy -26.4502 kcal/mol@LB@Unfolding Energy - mRNA 8.56913 kcal/mol@LB@Unfolding Energy - sRNA 5.67007 kcal/mol@LB@@LB@Position - mRNA 190 -- 238@LB@Position - sRNA 139 -- 186@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 142 -- 148@LB@
75	0.003517	0.1596	stm1214	ycfR	-14.36	0.148951	168 -- 212	35 -- 81	multiple stress resistance protein BhsA	stm0823	_____________167______________213\n_____________\|________________\|\n5'-AAA...ACCAC_________CA_____AUUCA...AAC-3'\n______________UUCUGGCUC___GAGU\n______________\|\|\|:\|\|\|\|\|___:\|\|\|\n______________AAGGCCGAG___UUCA\n3'-UUU...AAAGC_________UCC____-5'\n_____________\|_______________\|\n_____________82______________35\n	15 -- 21	8 -- 14	-15.9373 kcal/mol	4.12962 kcal/mol	4.82557 kcal/mol	167 213@LB@ \| \|@LB@5'-AAA...ACCAC CA AUUCA...AAC-3'@LB@ UUCUGGCUC GAGU@LB@ \|\|\|:\|\|\|\|\| :\|\|\|@LB@ AAGGCCGAG UUCA@LB@3'-UUU...AAAGC UCC -5'@LB@ \| \|@LB@ 82 35@LB@@LB@@LB@Energy -14.36 kcal/mol@LB@Hybridization Energy -15.9373 kcal/mol@LB@Unfolding Energy - mRNA 4.12962 kcal/mol@LB@Unfolding Energy - sRNA 4.82557 kcal/mol@LB@@LB@Position - mRNA 168 -- 212@LB@Position - sRNA 35 -- 81@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 8 -- 14@LB@
76	0.003538	0.1596	stm3058	pepP	-14.75	0.129287	129 -- 167	36 -- 78	Xaa-Pro aminopeptidase		_____________128_________________168\n_____________\|___________________\|\n5'-CGA...CUGGC___________CCG_____GCCGC...GCA-3'\n______________GCAAAUGCAGC___GCAGC\n______________\|\|\|\|\|::\|\|:\|___:\|\|:\|\n______________CGUUUGUGUUG___UGUUG\n3'-UUU...GUUAA___________UUG_____UAGUG...UCA-5'\n_____________\|___________________\|\n_____________79__________________35\n	249 -- 255	80 -- 86	-18.5262 kcal/mol	6.77337 kcal/mol	3.80362 kcal/mol	128 168@LB@ \| \|@LB@5'-CGA...CUGGC CCG GCCGC...GCA-3'@LB@ GCAAAUGCAGC GCAGC@LB@ \|\|\|\|\|::\|\|:\| :\|\|:\|@LB@ CGUUUGUGUUG UGUUG@LB@3'-UUU...GUUAA UUG UAGUG...UCA-5'@LB@ \| \|@LB@ 79 35@LB@@LB@@LB@Energy -14.75 kcal/mol@LB@Hybridization Energy -18.5262 kcal/mol@LB@Unfolding Energy - mRNA 6.77337 kcal/mol@LB@Unfolding Energy - sRNA 3.80362 kcal/mol@LB@@LB@Position - mRNA 129 -- 167@LB@Position - sRNA 36 -- 78@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 80 -- 86@LB@
77	0.003608	0.1596	stm4473	yjgM	-11.12	0.437983	252 -- 285	42 -- 82	GNAT family N-acetyltransferase		_____________251________________286\n_____________\|__________________\|\n5'-AUU...CGCCG________CC___C____AUGCC...ACG-3'\n______________AAUCACUA___GC_GACA\n______________\|\|\|\|\|\|\|\|___:\|_\|\|\|\|\n______________UUAGUGAU___UG_CUGU\n3'-UUU...UGUAA________ACC__U____CCCAU...UCA-5'\n_____________\|__________________\|\n_____________83_________________41\n	240 -- 246	165 -- 171	-13.0222 kcal/mol	3.39479 kcal/mol	3.49149 kcal/mol	251 286@LB@ \| \|@LB@5'-AUU...CGCCG CC C AUGCC...ACG-3'@LB@ AAUCACUA GC GACA@LB@ \|\|\|\|\|\|\|\| :\| \|\|\|\|@LB@ UUAGUGAU UG CUGU@LB@3'-UUU...UGUAA ACC U CCCAU...UCA-5'@LB@ \| \|@LB@ 83 41@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -13.0222 kcal/mol@LB@Unfolding Energy - mRNA 3.39479 kcal/mol@LB@Unfolding Energy - sRNA 3.49149 kcal/mol@LB@@LB@Position - mRNA 252 -- 285@LB@Position - sRNA 42 -- 82@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 165 -- 171@LB@
78	0.003685	0.1596	stm0423	ispA	-20.49	0.014403	269 -- 289	38 -- 58	(2E 6E)-farnesyl diphosphate synthase		_____________268____________________290\n_____________\|______________________\|\n5'-UGA...AUCGC____CU_____UU_________UCCCG...UCG-3'\n______________GCCA___GCCC__UCAGAACAC\n______________\|\|\|\|___\|\|\|\|__\|\|\|\|\|\|\|\|\|\n______________CGGU___CGGG__AGUCUUGUG\n3'-UUU...GCAUU____UUU____U__________CGUAA...UCA-5'\n_____________\|______________________\|\n_____________59_____________________37\n	281 -- 287	40 -- 46	-28.5082 kcal/mol	2.40221 kcal/mol	13.7699 kcal/mol	268 290@LB@ \| \|@LB@5'-UGA...AUCGC CU UU UCCCG...UCG-3'@LB@ GCCA GCCC UCAGAACAC@LB@ \|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ CGGU CGGG AGUCUUGUG@LB@3'-UUU...GCAUU UUU U CGUAA...UCA-5'@LB@ \| \|@LB@ 59 37@LB@@LB@@LB@Energy -20.49 kcal/mol@LB@Hybridization Energy -28.5082 kcal/mol@LB@Unfolding Energy - mRNA 2.40221 kcal/mol@LB@Unfolding Energy - sRNA 13.7699 kcal/mol@LB@@LB@Position - mRNA 269 -- 289@LB@Position - sRNA 38 -- 58@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 40 -- 46@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@
80	0.003756	0.1596	stm0132	ftsA	-17.45	0.046754	189 -- 236	139 -- 186	cell division protein FtsA		_____________188_______________________________________237\n_____________\|_________________________________________\|\n5'-AAU...GAACA___A______AG___C_________AAAACUG___G_____CUGGA...UCA-3'\n______________ACA_UGAUCA____G_GACGGACAG_______GUA_UAGGA\n______________\|\|\|_\|:\|\|\|\|____\|_\|\|\|:\|\|\|\|\|_______\|\|\|_:\|\|\|\|\n______________UGU_AUUAGU____C_CUGUCUGUC_______CAU_GUCCU\n3'-UUU...CACGA___A______GAUA___________CCAUUUA_________UCACU...UCA-5'\n_____________\|_________________________________________\|\n_____________187_______________________________________138\n	214 -- 220	154 -- 160	-27.6527 kcal/mol	5.88434 kcal/mol	5.72652 kcal/mol	188 237@LB@ \| \|@LB@5'-AAU...GAACA A AG C AAAACUG G CUGGA...UCA-3'@LB@ ACA UGAUCA G GACGGACAG GUA UAGGA@LB@ \|\|\| \|:\|\|\|\| \| \|\|\|:\|\|\|\|\| \|\|\| :\|\|\|\|@LB@ UGU AUUAGU C CUGUCUGUC CAU GUCCU@LB@3'-UUU...CACGA A GAUA CCAUUUA UCACU...UCA-5'@LB@ \| \|@LB@ 187 138@LB@@LB@@LB@Energy -17.45 kcal/mol@LB@Hybridization Energy -27.6527 kcal/mol@LB@Unfolding Energy - mRNA 5.88434 kcal/mol@LB@Unfolding Energy - sRNA 5.72652 kcal/mol@LB@@LB@Position - mRNA 189 -- 236@LB@Position - sRNA 139 -- 186@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 154 -- 160@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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