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
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@
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@
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@
122	0.00604	0.1758	stm2353	hisQ	-14.65	0.134227	190 -- 212	140 -- 163	amino acid ABC transporter permease		_____________189______________________213\n_____________\|________________________\|\n5'-GAU...CAACA________UGCAUGU_________UUUUC...UCG-3'\n______________GGACAGGC________UGUACGGG\n______________\|\|\|\|\|\|:\|________\|\|\|\|\|:\|\|\n______________CCUGUCUG________ACAUGUCC\n3'-UUU...UGAUA________UCCCAUUU________UUCAC...UCA-5'\n_____________\|________________________\|\n_____________164______________________139\n	206 -- 212	140 -- 146	-25.7393 kcal/mol	6.65037 kcal/mol	3.70771 kcal/mol	189 213@LB@ \| \|@LB@5'-GAU...CAACA UGCAUGU UUUUC...UCG-3'@LB@ GGACAGGC UGUACGGG@LB@ \|\|\|\|\|\|:\| \|\|\|\|\|:\|\|@LB@ CCUGUCUG ACAUGUCC@LB@3'-UUU...UGAUA UCCCAUUU UUCAC...UCA-5'@LB@ \| \|@LB@ 164 139@LB@@LB@@LB@Energy -14.65 kcal/mol@LB@Hybridization Energy -25.7393 kcal/mol@LB@Unfolding Energy - mRNA 6.65037 kcal/mol@LB@Unfolding Energy - sRNA 3.70771 kcal/mol@LB@@LB@Position - mRNA 190 -- 212@LB@Position - sRNA 140 -- 163@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 140 -- 146@LB@
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@
114	0.005594	0.1728	stm4557	holD	-13.75	0.185681	35 -- 94	141 -- 186	DNA polymerase III subunit psi		_____________34_____________________________________________95\n_____________\|______________________________________________\|\n5'-AGG...AAAUC__________C____CAAGACUUCACUUGC_________A______ACAUG...UUC-3'\n______________AUCACUGUGG_GCAG_______________CGGGGUAAA___GCAG\n______________\|\|\|\|\|\|:\|\|\|_:\|\|\|_______________\|:\|\|\|\|\|\|\|___:\|\|\|\n______________UAGUGAUACC_UGUC_______________GUCCCAUUU___UGUC\n3'-UUU...GUAAU_______________U_______________________ACA____CUUCA...UCA-5'\n_____________\|______________________________________________\|\n_____________187____________________________________________140\n	83 -- 89	148 -- 154	-31.7183 kcal/mol	12.8981 kcal/mol	5.60568 kcal/mol	34 95@LB@ \| \|@LB@5'-AGG...AAAUC C CAAGACUUCACUUGC A ACAUG...UUC-3'@LB@ AUCACUGUGG GCAG CGGGGUAAA GCAG@LB@ \|\|\|\|\|\|:\|\|\| :\|\|\| \|:\|\|\|\|\|\|\| :\|\|\|@LB@ UAGUGAUACC UGUC GUCCCAUUU UGUC@LB@3'-UUU...GUAAU U ACA CUUCA...UCA-5'@LB@ \| \|@LB@ 187 140@LB@@LB@@LB@Energy -13.75 kcal/mol@LB@Hybridization Energy -31.7183 kcal/mol@LB@Unfolding Energy - mRNA 12.8981 kcal/mol@LB@Unfolding Energy - sRNA 5.60568 kcal/mol@LB@@LB@Position - mRNA 35 -- 94@LB@Position - sRNA 141 -- 186@LB@Position Seed - mRNA 83 -- 89@LB@Position Seed - sRNA 148 -- 154@LB@
127	0.006343	0.1774	stm1751	hns	-12.42	0.292757	1 -- 14	147 -- 162	transcriptional regulator		______________1_______________15\n______________\|_______________\|\n___________5'-________________AUCCC...UAG-3'\n______________GACAGAC__GGUGAGU\n______________\|\|\|\|\|\|\|__\|\|\|:\|:\|\n______________CUGUCUG__CCAUUUA\n3'-UUU...GAUAC_______UC_______CAUGU...UCA-5'\n_____________\|________________\|\n_____________163______________146\n	8 -- 14	147 -- 153	-17.2475 kcal/mol	3.56352 kcal/mol	3.32093 kcal/mol	1 15@LB@ \| \|@LB@ 5'- AUCCC...UAG-3'@LB@ GACAGAC GGUGAGU@LB@ \|\|\|\|\|\|\| \|\|\|:\|:\|@LB@ CUGUCUG CCAUUUA@LB@3'-UUU...GAUAC UC CAUGU...UCA-5'@LB@ \| \|@LB@ 163 146@LB@@LB@@LB@Energy -12.42 kcal/mol@LB@Hybridization Energy -17.2475 kcal/mol@LB@Unfolding Energy - mRNA 3.56352 kcal/mol@LB@Unfolding Energy - sRNA 3.32093 kcal/mol@LB@@LB@Position - mRNA 1 -- 14@LB@Position - sRNA 147 -- 162@LB@Position Seed - mRNA 8 -- 14@LB@Position Seed - sRNA 147 -- 153@LB@
108	0.005311	0.1728	stm2183	cdd	-16.35	0.071230	31 -- 68	151 -- 187	cytidine deaminase		_____________30_________________69\n_____________\|__________________\|\n5'-UGG...AGAUC_____UUAA_________GGCCC...UGA-3'\n______________ACAUA____GACAUAGCA\n______________\|\|\|:\|____:\|\|\|:\|:\|\|\n______________UGUGU____UUGUGUUGU\n3'-UUU...ACGUU_____UG___________AGUGU...UCA-5'\n_____________\|__________________\|\n_____________188________________150\n	150 -- 156	71 -- 77	-12.389 kcal/mol	1.12571 kcal/mol	3.50787 kcal/mol	30 69@LB@ \| \|@LB@5'-UGG...AGAUC UUAA GGCCC...UGA-3'@LB@ ACAUA GACAUAGCA@LB@ \|\|\|:\| :\|\|\|:\|:\|\|@LB@ UGUGU UUGUGUUGU@LB@3'-UUU...ACGUU UG AGUGU...UCA-5'@LB@ \| \|@LB@ 188 150@LB@@LB@@LB@Energy -16.35 kcal/mol@LB@Hybridization Energy -12.389 kcal/mol@LB@Unfolding Energy - mRNA 1.12571 kcal/mol@LB@Unfolding Energy - sRNA 3.50787 kcal/mol@LB@@LB@Position - mRNA 31 -- 68@LB@Position - sRNA 151 -- 187@LB@Position Seed - mRNA 150 -- 156@LB@Position Seed - sRNA 71 -- 77@LB@
65	0.003171	0.1596	stm0830	glnH	-11.06	0.446113	180 -- 193	153 -- 165	glutamine ABC transporter substrate-binding protein GlnH		_____________179____________194\n_____________\|______________\|\n5'-AGA...GCCCC_________AA___AAAUG...CGG-3'\n______________GUGGAUAGA__AGG\n______________:\|\|\|\|:\|\|\|__\|\|\|\n______________UACCUGUCU__UCC\n3'-UUU...AGUGA_________G____CAUUU...UCA-5'\n_____________\|______________\|\n_____________166____________152\n	182 -- 188	157 -- 163	-15.2236 kcal/mol	3.11192 kcal/mol	2.82582 kcal/mol	179 194@LB@ \| \|@LB@5'-AGA...GCCCC AA AAAUG...CGG-3'@LB@ GUGGAUAGA AGG@LB@ :\|\|\|\|:\|\|\| \|\|\|@LB@ UACCUGUCU UCC@LB@3'-UUU...AGUGA G CAUUU...UCA-5'@LB@ \| \|@LB@ 166 152@LB@@LB@@LB@Energy -11.06 kcal/mol@LB@Hybridization Energy -15.2236 kcal/mol@LB@Unfolding Energy - mRNA 3.11192 kcal/mol@LB@Unfolding Energy - sRNA 2.82582 kcal/mol@LB@@LB@Position - mRNA 180 -- 193@LB@Position - sRNA 153 -- 165@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 157 -- 163@LB@
118	0.005761	0.1738	stm1840	yobG	-17.14	0.052758	234 -- 267	153 -- 188	PhoP regulon feedback inhibition protein MgrB		_____________233____________________________________________________________________________________268\n_____________\|______________________________________________________________________________________\|\n5'-ACA...AGAGU___________AUUUCGAU____C_U_____GC________GGUA______U___U_____UGU________GUGUU_________GUGCG...AAU-3'\n______________GGAGUGAAAAA________GGGU_G_UCUCG__AUCGUGGU_______GUA_GCC_GUUGC___GGGCGCAG_____UAAUAUCAU\n______________\|:\|\|\|\|\|\|\|\|\|________\|\|\|\|_\|_\|\|\|\|\|__\|:\|\|\|\|\|\|_______\|:\|_:\|\|_:\|\|\|\|___:::\|:\|\|:_____:\|\|:\|\|\|\|:\n______________CUUCACUUUUU________CCCA_C_AGAGC__UGGCACCA_______CGU_UGG_UAACG___UUUGUGUU_____GUUGUAGUG\n3'-UUU...AUGUC_______________________U_______GA________GACUUAG___C___U________________GUUGU_________UUGGC...UCA-5'\n_____________\|______________________________________________________________________________________\|\n_____________189____________________________________________________________________________________152\n	274 -- 280	67 -- 73	-62.0847 kcal/mol	28.922 kcal/mol	22.0106 kcal/mol	233 268@LB@ \| \|@LB@5'-ACA...AGAGU AUUUCGAU C U GC GGUA U U UGU GUGUU GUGCG...AAU-3'@LB@ GGAGUGAAAAA GGGU G UCUCG AUCGUGGU GUA GCC GUUGC GGGCGCAG UAAUAUCAU@LB@ \|:\|\|\|\|\|\|\|\|\| \|\|\|\| \| \|\|\|\|\| \|:\|\|\|\|\|\| \|:\| :\|\| :\|\|\|\| :::\|:\|\|: :\|\|:\|\|\|\|:@LB@ CUUCACUUUUU CCCA C AGAGC UGGCACCA CGU UGG UAACG UUUGUGUU GUUGUAGUG@LB@3'-UUU...AUGUC U GA GACUUAG C U GUUGU UUGGC...UCA-5'@LB@ \| \|@LB@ 189 152@LB@@LB@@LB@Energy -17.14 kcal/mol@LB@Hybridization Energy -62.0847 kcal/mol@LB@Unfolding Energy - mRNA 28.922 kcal/mol@LB@Unfolding Energy - sRNA 22.0106 kcal/mol@LB@@LB@Position - mRNA 234 -- 267@LB@Position - sRNA 153 -- 188@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 67 -- 73@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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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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