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
154	0.008185	0.1845	stm3738	yigC	-11.16	0.433331	228 -- 246	55 -- 74	similar to E. coli orf hypothetical protein (AAC76670.1); Blastp hit to AAC76670.1 (223 aa) 94% identity in aa 19 - 223	_____________227__________________247\n_____________\|____________________\|\n5'-UAA...ACCUC_____________AC_____AAAUG...UUA-3'\n______________GCA__UACAAUAA__CACAA\n______________\|\|\|__:\|\|\|\|:\|\|__\|\|\|\|\|\n______________CGU__GUGUUGUU__GUGUU\n3'-UUU...GUUAA___UU_______________GUAGU...UCA-5'\n_____________\|____________________\|\n_____________75___________________54\n	27 -- 33	78 -- 84	-12.6647 kcal/mol	0.985902 kcal/mol	3.77104 kcal/mol	227 247@LB@ \| \|@LB@5'-UAA...ACCUC AC AAAUG...UUA-3'@LB@ GCA UACAAUAA CACAA@LB@ \|\|\| :\|\|\|\|:\|\| \|\|\|\|\|@LB@ CGU GUGUUGUU GUGUU@LB@3'-UUU...GUUAA UU GUAGU...UCA-5'@LB@ \| \|@LB@ 75 54@LB@@LB@@LB@Energy -11.16 kcal/mol@LB@Hybridization Energy -12.6647 kcal/mol@LB@Unfolding Energy - mRNA 0.985902 kcal/mol@LB@Unfolding Energy - sRNA 3.77104 kcal/mol@LB@@LB@Position - mRNA 228 -- 246@LB@Position - sRNA 55 -- 74@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 78 -- 84@LB@
52	0.001934	0.1324	stm0653	ybeL	-17.18	0.051878	262 -- 299	155 -- 188	similar to E. coli putative alpha helical protein (AAC73744.1); Blastp hit to AAC73744.1 (160 aa) 91% identity in aa 1 - 160	_____________261________________________300\n_____________\|__________________________\|\n5'-AUU...GCGCG________G____G_____G______C-3'\n______________ACAUUGAU_CGCU_GUGGA_CAGGCG\n______________\|\|\|\|\|:\|\|_\|:\|\|_:\|\|\|\|_\|\|\|:\|:\n______________UGUAAUUA_GUGA_UACCU_GUCUGU\n3'-UUU...CACGA__________________________CCCAU...UCA-5'\n_____________\|__________________________\|\n_____________189________________________154\n	275 -- 281	170 -- 176	-23.9532 kcal/mol	9.91713 kcal/mol	4.10825 kcal/mol	261 300@LB@ \| \|@LB@5'-AUU...GCGCG G G G C-3'@LB@ ACAUUGAU CGCU GUGGA CAGGCG@LB@ \|\|\|\|\|:\|\| \|:\|\| :\|\|\|\| \|\|\|:\|:@LB@ UGUAAUUA GUGA UACCU GUCUGU@LB@3'-UUU...CACGA CCCAU...UCA-5'@LB@ \| \|@LB@ 189 154@LB@@LB@@LB@Energy -17.18 kcal/mol@LB@Hybridization Energy -23.9532 kcal/mol@LB@Unfolding Energy - mRNA 9.91713 kcal/mol@LB@Unfolding Energy - sRNA 4.10825 kcal/mol@LB@@LB@Position - mRNA 262 -- 299@LB@Position - sRNA 155 -- 188@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 170 -- 176@LB@
26	0.0006768	0.08814	stm1365	ydiJ	-17.55	0.045121	78 -- 116	57 -- 91	similar to E. coli putative oxidase (AAC74757.1); Blastp hit to AAC74757.1 (1018 aa) 88% identity in aa 1 - 1017	_____________77_________________________117\n_____________\|__________________________\|\n5'-CUA...AAUGU_________AAUA_____________AACGA...CCA-3'\n______________GAUACAACA____ACGCAACA_CGCA\n______________:\|:\|\|\|\|\|\|____\|\|:\|\|\|\|\|_\|:\|\|\n______________UUGUGUUGU____UGUGUUGU_GUGU\n3'-UUU...AACGU_____________________A____UGGCA...UCA-5'\n_____________\|__________________________\|\n_____________92_________________________56\n	95 -- 101	71 -- 77	-21.9961 kcal/mol	1.97147 kcal/mol	5.98953 kcal/mol	77 117@LB@ \| \|@LB@5'-CUA...AAUGU AAUA AACGA...CCA-3'@LB@ GAUACAACA ACGCAACA CGCA@LB@ :\|:\|\|\|\|\|\| \|\|:\|\|\|\|\| \|:\|\|@LB@ UUGUGUUGU UGUGUUGU GUGU@LB@3'-UUU...AACGU A UGGCA...UCA-5'@LB@ \| \|@LB@ 92 56@LB@@LB@@LB@Energy -17.55 kcal/mol@LB@Hybridization Energy -21.9961 kcal/mol@LB@Unfolding Energy - mRNA 1.97147 kcal/mol@LB@Unfolding Energy - sRNA 5.98953 kcal/mol@LB@@LB@Position - mRNA 78 -- 116@LB@Position - sRNA 57 -- 91@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 71 -- 77@LB@
70	0.003306	0.1596	stm2688	smpB	-12.25	0.308628	191 -- 230	36 -- 77	SsrA-binding protein	_____________190_________________231\n_____________\|___________________\|\n5'-AAU...GCAUA____UUCC__U________AUCGU...GUC-3'\n______________GCAA____CA_CAACAUAA\n______________\|\|\|\|____\|\|_\|\|\|\|\|:\|\|\n______________CGUU____GU_GUUGUGUU\n3'-UUU...GUUAA____UGU___U________GUAGU...UCA-5'\n_____________\|___________________\|\n_____________78__________________35\n	26 -- 32	73 -- 79	-12.551 kcal/mol	1.44298 kcal/mol	3.77104 kcal/mol	190 231@LB@ \| \|@LB@5'-AAU...GCAUA UUCC U AUCGU...GUC-3'@LB@ GCAA CA CAACAUAA@LB@ \|\|\|\| \|\| \|\|\|\|\|:\|\|@LB@ CGUU GU GUUGUGUU@LB@3'-UUU...GUUAA UGU U GUAGU...UCA-5'@LB@ \| \|@LB@ 78 35@LB@@LB@@LB@Energy -12.25 kcal/mol@LB@Hybridization Energy -12.551 kcal/mol@LB@Unfolding Energy - mRNA 1.44298 kcal/mol@LB@Unfolding Energy - sRNA 3.77104 kcal/mol@LB@@LB@Position - mRNA 191 -- 230@LB@Position - sRNA 36 -- 77@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 73 -- 79@LB@
113	0.005549	0.1728	stm2948	cysJ	-13.61	0.194760	269 -- 298	56 -- 85	sulfite reductase [NADPH] flavoprotein subunit alpha	_____________268_______________________299\n_____________\|_________________________\|\n5'-GUU...CCGCU____UUACUG_______________UGACG...UUG-3'\n______________UUGC______GAACAUAACGACGCA\n______________\|\|\|\|______:\|\|\|\|:\|\|\|:\|\|:\|\|\n______________AACG______UUUGUGUUGUUGUGU\n3'-UUU...UGGUU_________________________UGUAG...UCA-5'\n_____________\|_________________________\|\n_____________86________________________55\n	195 -- 201	74 -- 80	-20.7575 kcal/mol	3.67756 kcal/mol	3.73922 kcal/mol	268 299@LB@ \| \|@LB@5'-GUU...CCGCU UUACUG UGACG...UUG-3'@LB@ UUGC GAACAUAACGACGCA@LB@ \|\|\|\| :\|\|\|\|:\|\|\|:\|\|:\|\|@LB@ AACG UUUGUGUUGUUGUGU@LB@3'-UUU...UGGUU UGUAG...UCA-5'@LB@ \| \|@LB@ 86 55@LB@@LB@@LB@Energy -13.61 kcal/mol@LB@Hybridization Energy -20.7575 kcal/mol@LB@Unfolding Energy - mRNA 3.67756 kcal/mol@LB@Unfolding Energy - sRNA 3.73922 kcal/mol@LB@@LB@Position - mRNA 269 -- 298@LB@Position - sRNA 56 -- 85@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 74 -- 80@LB@
176	0.009613	0.1945	stm3378	N/A	-14.56	0.138793	155 -- 243	45 -- 125	sulfoxide reductase heme-binding subunit YedZ	_____________154_______________________________________________________________________________________244\n_____________\|_________________________________________________________________________________________\|\n5'-UGU...AAUGA____GCU_____GU____C_____CAAU_______AGAAUUU____G____U___________A____G_______U____________UUGUC...GUG-3'\n______________AGUC___UCGCU__AUCG_GGUCU____UUGCGGG_______UUAA_UGCG__C_UGACAGCA_AACA__AUAACC___GGCUAAAAGU\n______________\|\|\|\|___\|\|\|\|\|__\|:\|\|_\|\|\|\|\|____\|:\|\|:\|:_______::\|\|_\|\|\|:__\|_::\|\|\|:\|\|_\|\|\|\|__\|:\|\|\|\|___:\|\|:\|\|\|\|\|:\n______________UCAG___AGCGA__UGGC_CCAGA____AGCGUCU_______GGUU_ACGU__G_GUUGUUGU_UUGU__UGUUGG___UCGGUUUUCG\n3'-UUU...UCCCA__________________A_____CUU___________________A____UU_U________G____AG______CAU__________GGUAG...UCA-5'\n_____________\|_________________________________________________________________________________________\|\n_____________126_______________________________________________________________________________________44\n	209 -- 215	76 -- 82	-59.1156 kcal/mol	19.0244 kcal/mol	31.7466 kcal/mol	154 244@LB@ \| \|@LB@5'-UGU...AAUGA GCU GU C CAAU AGAAUUU G U A G U UUGUC...GUG-3'@LB@ AGUC UCGCU AUCG GGUCU UUGCGGG UUAA UGCG C UGACAGCA AACA AUAACC GGCUAAAAGU@LB@ \|\|\|\| \|\|\|\|\| \|:\|\| \|\|\|\|\| \|:\|\|:\|: ::\|\| \|\|\|: \| ::\|\|\|:\|\| \|\|\|\| \|:\|\|\|\| :\|\|:\|\|\|\|\|:@LB@ UCAG AGCGA UGGC CCAGA AGCGUCU GGUU ACGU G GUUGUUGU UUGU UGUUGG UCGGUUUUCG@LB@3'-UUU...UCCCA A CUU A UU U G AG CAU GGUAG...UCA-5'@LB@ \| \|@LB@ 126 44@LB@@LB@@LB@Energy -14.56 kcal/mol@LB@Hybridization Energy -59.1156 kcal/mol@LB@Unfolding Energy - mRNA 19.0244 kcal/mol@LB@Unfolding Energy - sRNA 31.7466 kcal/mol@LB@@LB@Position - mRNA 155 -- 243@LB@Position - sRNA 45 -- 125@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 76 -- 82@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@
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@
104	0.005232	0.1728	stm0744	ybgC	-16.85	0.058772	132 -- 175	54 -- 90	tol-pal system-associated acyl-CoA thioesterase	_____________131_____________________________176\n_____________\|_______________________________\|\n5'-CUU...ACAAG____U____________UCUUGA________GGCGG...AAA-3'\n______________GCGA_AUACAACGGCAU______GGCAUUAC\n______________\|\|:\|_\|:\|\|\|\|\|::\|\|:______::\|\|\|:\|\|\n______________CGUU_UGUGUUGUUGUG______UUGUAGUG\n3'-UUU...GUUAA_______________________________UUGGC...UCA-5'\n_____________\|_______________________________\|\n_____________91______________________________53\n	156 -- 162	67 -- 73	-23.8418 kcal/mol	6.2547 kcal/mol	5.68203 kcal/mol	131 176@LB@ \| \|@LB@5'-CUU...ACAAG U UCUUGA GGCGG...AAA-3'@LB@ GCGA AUACAACGGCAU GGCAUUAC@LB@ \|\|:\| \|:\|\|\|\|\|::\|\|: ::\|\|\|:\|\|@LB@ CGUU UGUGUUGUUGUG UUGUAGUG@LB@3'-UUU...GUUAA UUGGC...UCA-5'@LB@ \| \|@LB@ 91 53@LB@@LB@@LB@Energy -16.85 kcal/mol@LB@Hybridization Energy -23.8418 kcal/mol@LB@Unfolding Energy - mRNA 6.2547 kcal/mol@LB@Unfolding Energy - sRNA 5.68203 kcal/mol@LB@@LB@Position - mRNA 132 -- 175@LB@Position - sRNA 54 -- 90@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 67 -- 73@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@

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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