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
134	0.006725	0.1774	stm0546	fimD	-17.45	0.046766	176 -- 200	37 -- 60	outer membrane usher protein	stm0301 stm0175 stm4593 stm3638 stm0023	_____________175_____________201\n_____________\|_______________\|\n5'-UCA...AAGCC______G________GAAGA...CGA-3'\n______________ACACGA_AACACGAU\n______________\|\|\|\|:\|_\|\|\|\|\|:\|:\n______________UGUGUU_UUGUGUUG\n3'-UUU...ACGUU______G________UAGUG...UCA-5'\n_____________\|_______________\|\n_____________61______________36\n	196 -- 202	72 -- 78	-17.1314 kcal/mol	2.16166 kcal/mol	3.50587 kcal/mol	175 201@LB@ \| \|@LB@5'-UCA...AAGCC G GAAGA...CGA-3'@LB@ ACACGA AACACGAU@LB@ \|\|\|\|:\| \|\|\|\|\|:\|:@LB@ UGUGUU UUGUGUUG@LB@3'-UUU...ACGUU G UAGUG...UCA-5'@LB@ \| \|@LB@ 61 36@LB@@LB@@LB@Energy -17.45 kcal/mol@LB@Hybridization Energy -17.1314 kcal/mol@LB@Unfolding Energy - mRNA 2.16166 kcal/mol@LB@Unfolding Energy - sRNA 3.50587 kcal/mol@LB@@LB@Position - mRNA 176 -- 200@LB@Position - sRNA 37 -- 60@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 72 -- 78@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@
130	0.00652	0.1774	stm4228	malF	-14.47	0.143021	162 -- 175	1 -- 15	maltose ABC transporter permease MalF		_____________161_____________176\n_____________\|_______________\|\n5'-AAC...ACAUC_______________UUCAA...UAA-3'\n______________UCCGGC_CAGGAAGU\n______________\|\|\|\|\|\|_\|\|\|\|\|\|\|\|\n______________AGGCCG_GUCCUUCA\n3'-UUU...AAGCA______A________-5'\n_____________\|______________\|\n_____________16_____________1\n	169 -- 175	1 -- 7	-25.2779 kcal/mol	6.67863 kcal/mol	4.81264 kcal/mol	161 176@LB@ \| \|@LB@5'-AAC...ACAUC UUCAA...UAA-3'@LB@ UCCGGC CAGGAAGU@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ AGGCCG GUCCUUCA@LB@3'-UUU...AAGCA A -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -14.47 kcal/mol@LB@Hybridization Energy -25.2779 kcal/mol@LB@Unfolding Energy - mRNA 6.67863 kcal/mol@LB@Unfolding Energy - sRNA 4.81264 kcal/mol@LB@@LB@Position - mRNA 162 -- 175@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 1 -- 7@LB@
136	0.006805	0.1774	stm2812	N/A	-16.76	0.060981	84 -- 153	36 -- 90	MFS transporter		_____________83_____________________________________________154\n_____________\|______________________________________________\|\n5'-GGC...AUCCG__C________CUCUCCUCAAAGC______UU_______UC_____UCCCC...UGC-3'\n______________GC_AACGCAAU_____________GCACGA__CAUCACG__ACCGU\n______________\|\|_\|\|\|:\|\|\|:_____________:\|\|\|:\|__\|\|\|\|\|\|:__\|\|\|\|\|\n______________CG_UUGUGUUG_____________UGUGUU__GUAGUGU__UGGCA\n3'-UUU...GUUAA__U________U__________________________________UUCGG...UCA-5'\n_____________\|______________________________________________\|\n_____________91_____________________________________________35\n	116 -- 122	66 -- 72	-26.7431 kcal/mol	6.46375 kcal/mol	9.42239 kcal/mol	83 154@LB@ \| \|@LB@5'-GGC...AUCCG C CUCUCCUCAAAGC UU UC UCCCC...UGC-3'@LB@ GC AACGCAAU GCACGA CAUCACG ACCGU@LB@ \|\| \|\|\|:\|\|\|: :\|\|\|:\| \|\|\|\|\|\|: \|\|\|\|\|@LB@ CG UUGUGUUG UGUGUU GUAGUGU UGGCA@LB@3'-UUU...GUUAA U U UUCGG...UCA-5'@LB@ \| \|@LB@ 91 35@LB@@LB@@LB@Energy -16.76 kcal/mol@LB@Hybridization Energy -26.7431 kcal/mol@LB@Unfolding Energy - mRNA 6.46375 kcal/mol@LB@Unfolding Energy - sRNA 9.42239 kcal/mol@LB@@LB@Position - mRNA 84 -- 153@LB@Position - sRNA 36 -- 90@LB@Position Seed - mRNA 116 -- 122@LB@Position Seed - sRNA 66 -- 72@LB@
128	0.006467	0.1774	stm3907	N/A	-18.55	0.030594	118 -- 173	37 -- 89			_____________117__________________________174\n_____________\|____________________________\|\n5'-UCA...AAAAA____________ACCAGU______G___AAAAC...UUU-3'\n______________CAGACGCAACAA______CAGCAU_AUA\n______________\|\|:\|\|:\|\|\|\|\|\|______\|\|:\|\|\|_\|:\|\n______________GUUUGUGUUGUU______GUUGUA_UGU\n3'-UUU...UUAAC____________GU__________G___UGGCA...UCA-5'\n_____________\|____________________________\|\n_____________90___________________________36\n	123 -- 129	78 -- 84	-22.8944 kcal/mol	3.16008 kcal/mol	6.30461 kcal/mol	117 174@LB@ \| \|@LB@5'-UCA...AAAAA ACCAGU G AAAAC...UUU-3'@LB@ CAGACGCAACAA CAGCAU AUA@LB@ \|\|:\|\|:\|\|\|\|\|\| \|\|:\|\|\| \|:\|@LB@ GUUUGUGUUGUU GUUGUA UGU@LB@3'-UUU...UUAAC GU G UGGCA...UCA-5'@LB@ \| \|@LB@ 90 36@LB@@LB@@LB@Energy -18.55 kcal/mol@LB@Hybridization Energy -22.8944 kcal/mol@LB@Unfolding Energy - mRNA 3.16008 kcal/mol@LB@Unfolding Energy - sRNA 6.30461 kcal/mol@LB@@LB@Position - mRNA 118 -- 173@LB@Position - sRNA 37 -- 89@LB@Position Seed - mRNA 123 -- 129@LB@Position Seed - sRNA 78 -- 84@LB@
135	0.006796	0.1774	stm1044	sodC	-14.39	0.147293	208 -- 244	43 -- 78	Gifsy-2 prophage superoxide dismutase precursor (Cu-Zn)	stm1440 stm0924	_____________207__________245\n_____________\|____________\|\n5'-GAA...GCUUU____________CAGGG...CCA-3'\n______________GGUGGUCUCGCU\n______________\|\|\|:\|\|\|\|\|\|\|\|\n______________CCAUCAGAGCGA\n3'-UUU...UUUUC____________UGGCA...UCA-5'\n_____________\|____________\|\n_____________79___________42\n	78 -- 84	117 -- 123	-21.9622 kcal/mol	4.44224 kcal/mol	6.55795 kcal/mol	207 245@LB@ \| \|@LB@5'-GAA...GCUUU CAGGG...CCA-3'@LB@ GGUGGUCUCGCU@LB@ \|\|\|:\|\|\|\|\|\|\|\|@LB@ CCAUCAGAGCGA@LB@3'-UUU...UUUUC UGGCA...UCA-5'@LB@ \| \|@LB@ 79 42@LB@@LB@@LB@Energy -14.39 kcal/mol@LB@Hybridization Energy -21.9622 kcal/mol@LB@Unfolding Energy - mRNA 4.44224 kcal/mol@LB@Unfolding Energy - sRNA 6.55795 kcal/mol@LB@@LB@Position - mRNA 208 -- 244@LB@Position - sRNA 43 -- 78@LB@Position Seed - mRNA 78 -- 84@LB@Position Seed - sRNA 117 -- 123@LB@
125	0.006333	0.1774	stm3094	yggJ	-12.37	0.297521	35 -- 55	69 -- 89	putative cytoplasmic protein		_____________34____________________56\n_____________\|_____________________\|\n5'-GCG...GCCAA__________UUUU_______UGGGA...AGA-3'\n______________CAAACGCAGC____UAACGUC\n______________\|\|\|\|\|:\|\|:\|____:\|\|\|:\|\|\n______________GUUUGUGUUG____GUUGUAG\n3'-UUU...UUAAC__________UUGU_______UGUUG...UCA-5'\n_____________\|_____________________\|\n_____________90____________________68\n	49 -- 55	69 -- 75	-19.7914 kcal/mol	1.34113 kcal/mol	4.32311 kcal/mol	34 56@LB@ \| \|@LB@5'-GCG...GCCAA UUUU UGGGA...AGA-3'@LB@ CAAACGCAGC UAACGUC@LB@ \|\|\|\|\|:\|\|:\| :\|\|\|:\|\|@LB@ GUUUGUGUUG GUUGUAG@LB@3'-UUU...UUAAC UUGU UGUUG...UCA-5'@LB@ \| \|@LB@ 90 68@LB@@LB@@LB@Energy -12.37 kcal/mol@LB@Hybridization Energy -19.7914 kcal/mol@LB@Unfolding Energy - mRNA 1.34113 kcal/mol@LB@Unfolding Energy - sRNA 4.32311 kcal/mol@LB@@LB@Position - mRNA 35 -- 55@LB@Position - sRNA 69 -- 89@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 69 -- 75@LB@
138	0.007086	0.182	stm0624	citC	-16.00	0.081371	136 -- 192	38 -- 93	[citrate (pro-3S)-lyase] ligase	stm0058	_____________135___________________________193\n_____________\|_____________________________\|\n5'-AAA...AUCAA________________________A____GAAAA...AUA-3'\n______________GUUGC_AACACA___GCGCAACAU_UACA\n______________:\|\|\|\|_\|\|\|\|\|\|___:\|:\|\|\|\|\|\|_:\|\|\|\n______________UAACG_UUGUGU___UGUGUUGUA_GUGU\n3'-UUU...CUGGU_____U______UGU______________UGGCA...UCA-5'\n_____________\|_____________________________\|\n_____________94____________________________37\n	149 -- 155	70 -- 76	-24.6588 kcal/mol	7.05918 kcal/mol	6.32558 kcal/mol	135 193@LB@ \| \|@LB@5'-AAA...AUCAA A GAAAA...AUA-3'@LB@ GUUGC AACACA GCGCAACAU UACA@LB@ :\|\|\|\| \|\|\|\|\|\| :\|:\|\|\|\|\|\| :\|\|\|@LB@ UAACG UUGUGU UGUGUUGUA GUGU@LB@3'-UUU...CUGGU U UGU UGGCA...UCA-5'@LB@ \| \|@LB@ 94 37@LB@@LB@@LB@Energy -16.00 kcal/mol@LB@Hybridization Energy -24.6588 kcal/mol@LB@Unfolding Energy - mRNA 7.05918 kcal/mol@LB@Unfolding Energy - sRNA 6.32558 kcal/mol@LB@@LB@Position - mRNA 136 -- 192@LB@Position - sRNA 38 -- 93@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 70 -- 76@LB@
142	0.007269	0.182	stm4341	frdC	-12.15	0.319206	131 -- 234	54 -- 160	fumarate reductase subunit C		_____________130__________________235\n_____________\|____________________\|\n5'-AGA...AGGAG_______________UA___GCAAA...CGG-3'\n______________UGC_AACAUGACGAC__AAC\n______________\|\|\|_\|\|\|\|::\|\|:\|\|__\|\|\|\n______________ACG_UUGUGUUGUUG__UUG\n3'-UUU...GGUUA___U___________UG___UAGUG...UCA-5'\n_____________\|____________________\|\n_____________161__________________53\n	202 -- 208	77 -- 83	-18.8897 kcal/mol	4.02107 kcal/mol	3.80548 kcal/mol	130 235@LB@ \| \|@LB@5'-AGA...AGGAG UA GCAAA...CGG-3'@LB@ UGC AACAUGACGAC AAC@LB@ \|\|\| \|\|\|\|::\|\|:\|\| \|\|\|@LB@ ACG UUGUGUUGUUG UUG@LB@3'-UUU...GGUUA U UG UAGUG...UCA-5'@LB@ \| \|@LB@ 161 53@LB@@LB@@LB@Energy -12.15 kcal/mol@LB@Hybridization Energy -18.8897 kcal/mol@LB@Unfolding Energy - mRNA 4.02107 kcal/mol@LB@Unfolding Energy - sRNA 3.80548 kcal/mol@LB@@LB@Position - mRNA 131 -- 234@LB@Position - sRNA 54 -- 160@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 77 -- 83@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@

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)

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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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