Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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_000913 Escherichia coli str. K-12 substr. MG1655

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
61	0.006025	0.3261	b4330	yjiH	-10.68	0.204041	214 -- 227	80 -- 92	nucleoside recognition pore and gate family putative inner membrane transporter	_____________213______228\n_____________\|________\|\n5'-ACU...ACAAG________GUAGC...CCG-3'\n______________GGGAUGCU\n______________\|\|\|\|:\|\|\|\n______________CCCUGCGA\n3'-UUU...CAACA________AUUGG...UAG-5'\n_____________\|________\|\n_____________93_______79\n	215 -- 221	85 -- 91	-14.2816 kcal/mol	2.08889 kcal/mol	5.76908 kcal/mol	213 228@LB@ \| \|@LB@5'-ACU...ACAAG GUAGC...CCG-3'@LB@ GGGAUGCU@LB@ \|\|\|\|:\|\|\|@LB@ CCCUGCGA@LB@3'-UUU...CAACA AUUGG...UAG-5'@LB@ \| \|@LB@ 93 79@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -14.2816 kcal/mol@LB@Unfolding Energy - mRNA 2.08889 kcal/mol@LB@Unfolding Energy - sRNA 5.76908 kcal/mol@LB@@LB@Position - mRNA 214 -- 227@LB@Position - sRNA 80 -- 92@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 85 -- 91@LB@
62	0.006126	0.3261	b3824	rhtB	-10.68	0.204362	7 -- 23	171 -- 187	homoserine homoserine lactone and S-methyl-methionine efflux pump	_____________6_________________24\n_____________\|_________________\|\n_____5'-ACGCUG_______AAA_______GCGGU...ACC-3'\n______________ACGCCAG___UCAGUCA\n______________\|\|:\|\|\|:___\|\|\|\|\|\|\|\n______________UGUGGUU___AGUCAGU\n3'-UUU...UAAAA_______AUG_______GUGUA...UAG-5'\n_____________\|_________________\|\n_____________188_______________170\n	17 -- 23	171 -- 177	-18.1223 kcal/mol	1.9449 kcal/mol	4.7016 kcal/mol	6 24@LB@ \| \|@LB@ 5'-ACGCUG AAA GCGGU...ACC-3'@LB@ ACGCCAG UCAGUCA@LB@ \|\|:\|\|\|: \|\|\|\|\|\|\|@LB@ UGUGGUU AGUCAGU@LB@3'-UUU...UAAAA AUG GUGUA...UAG-5'@LB@ \| \|@LB@ 188 170@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -18.1223 kcal/mol@LB@Unfolding Energy - mRNA 1.9449 kcal/mol@LB@Unfolding Energy - sRNA 4.7016 kcal/mol@LB@@LB@Position - mRNA 7 -- 23@LB@Position - sRNA 171 -- 187@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 171 -- 177@LB@
63	0.006154	0.3261	b3750	rbsC	-15.65	0.019915	89 -- 120	139 -- 174	D-ribose ABC transporter permease	_____________88___________________________________121\n_____________\|____________________________________\|\n5'-GAU...UCAUC___________A_______UC_____GG________UACUC...UCU-3'\n______________GUCAUGCAUGA___GGGCA__UCAGC____GGAAUU\n______________\|\|\|\|::\|\|\|\|\|___:\|\|\|\|__\|\|\|:\|____:\|\|\|\|\|\n______________CAGUGUGUACU___UCCGU__AGUUG____UCUUAA\n3'-UUU...UGAGU___________ACG_____UC_____AAAG______CGCCA...UAG-5'\n_____________\|____________________________________\|\n_____________175__________________________________138\n	91 -- 97	166 -- 172	-33.4294 kcal/mol	9.19626 kcal/mol	8.8011 kcal/mol	88 121@LB@ \| \|@LB@5'-GAU...UCAUC A UC GG UACUC...UCU-3'@LB@ GUCAUGCAUGA GGGCA UCAGC GGAAUU@LB@ \|\|\|\|::\|\|\|\|\| :\|\|\|\| \|\|\|:\| :\|\|\|\|\|@LB@ CAGUGUGUACU UCCGU AGUUG UCUUAA@LB@3'-UUU...UGAGU ACG UC AAAG CGCCA...UAG-5'@LB@ \| \|@LB@ 175 138@LB@@LB@@LB@Energy -15.65 kcal/mol@LB@Hybridization Energy -33.4294 kcal/mol@LB@Unfolding Energy - mRNA 9.19626 kcal/mol@LB@Unfolding Energy - sRNA 8.8011 kcal/mol@LB@@LB@Position - mRNA 89 -- 120@LB@Position - sRNA 139 -- 174@LB@Position Seed - mRNA 91 -- 97@LB@Position Seed - sRNA 166 -- 172@LB@
64	0.006252	0.3261	b3195	mlaF	-10.58	0.212925	52 -- 62	81 -- 91	ABC transporter maintaining OM lipid asymmetry ATP-binding protein	_____________51____________________________________63\n_____________\|_____________________________________\|\n5'-UUU...UUCAA___UAA___GA______________AAAA__A_____AGACG...GAG-3'\n______________GGU___AUU__GCGCC_AUGCUUAG____UC_ACGCA\n______________\|\|\|___\|\|\|__:\|:\|\|_\|\|:\|\|:\|\|____\|\|_\|\|:\|\|\n______________CCA___UAA__UGUGG_UAUGAGUC____AG_UGUGU\n3'-UUU...ACCGC___C_____AA_____U____________________ACUAC...UAG-5'\n_____________\|_____________________________________\|\n_____________92____________________________________80\n	166 -- 172	174 -- 180	-23.2269 kcal/mol	9.4943 kcal/mol	5.22711 kcal/mol	51 63@LB@ \| \|@LB@5'-UUU...UUCAA UAA GA AAAA A AGACG...GAG-3'@LB@ GGU AUU GCGCC AUGCUUAG UC ACGCA@LB@ \|\|\| \|\|\| :\|:\|\| \|\|:\|\|:\|\| \|\| \|\|:\|\|@LB@ CCA UAA UGUGG UAUGAGUC AG UGUGU@LB@3'-UUU...ACCGC C AA U ACUAC...UAG-5'@LB@ \| \|@LB@ 92 80@LB@@LB@@LB@Energy -10.58 kcal/mol@LB@Hybridization Energy -23.2269 kcal/mol@LB@Unfolding Energy - mRNA 9.4943 kcal/mol@LB@Unfolding Energy - sRNA 5.22711 kcal/mol@LB@@LB@Position - mRNA 52 -- 62@LB@Position - sRNA 81 -- 91@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 174 -- 180@LB@
65	0.006332	0.3261	b3857	mobA	-11.59	0.134663	143 -- 181	126 -- 173	molybdopterin-guanine dinucleotide synthase	_____________142________________________________________________________182\n_____________\|__________________________________________________________\|\n5'-UCC...AUAGU_______C_____U_U___GA___A__C______AG______________A_______AAUAA...AAC-3'\n______________GAUGCUC__UUAC_C_UGA__CAG_CA_GUUAGC____________GGUC_AUCCCAC\n______________:\|\|:\|\|\|__\|:\|\|_\|_\|\|\|__\|\|\|_\|\|_\|\|:\|:\|____________\|\|\|\|_\|\|\|\|\|\|\|\n______________UUAUGAG__AGUG_G_ACU__GUC_GU_CAGUUG____________CCAG_UAGGGUG\n3'-UUU...UGUGG_______UC____U_U___AC___C__U______AAAGUCUUAACG____________ACGUA...UAG-5'\n_____________\|__________________________________________________________\|\n_____________174________________________________________________________125\n	175 -- 181	126 -- 132	-38.7055 kcal/mol	10.57 kcal/mol	15.6637 kcal/mol	142 182@LB@ \| \|@LB@5'-UCC...AUAGU C U U GA A C AG A AAUAA...AAC-3'@LB@ GAUGCUC UUAC C UGA CAG CA GUUAGC GGUC AUCCCAC@LB@ :\|\|:\|\|\| \|:\|\| \| \|\|\| \|\|\| \|\| \|\|:\|:\| \|\|\|\| \|\|\|\|\|\|\|@LB@ UUAUGAG AGUG G ACU GUC GU CAGUUG CCAG UAGGGUG@LB@3'-UUU...UGUGG UC U U AC C U AAAGUCUUAACG ACGUA...UAG-5'@LB@ \| \|@LB@ 174 125@LB@@LB@@LB@Energy -11.59 kcal/mol@LB@Hybridization Energy -38.7055 kcal/mol@LB@Unfolding Energy - mRNA 10.57 kcal/mol@LB@Unfolding Energy - sRNA 15.6637 kcal/mol@LB@@LB@Position - mRNA 143 -- 181@LB@Position - sRNA 126 -- 173@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 126 -- 132@LB@
66	0.006473	0.3261	b0712	ybgK	-17.58	0.008094	217 -- 255	130 -- 164	putative allophanate hydrolase subunit 2	_____________216________________________________________________________256\n_____________\|__________________________________________________________\|\n5'-CGC...GGAGU_____GA__A____U_____________U__AUACC___GUG______G_________ACGGU...AUA-3'\n______________AUGCU__AG_UUAU_C___GUGCGGGCA_GU_____ACU___CAGGAU_GCGGUCGUC\n______________\|\|:\|\|__\|\|_\|:\|:_\|___:\|\|\|:\|\|\|\|_\|\|_____\|\|\|___\|\|\|:\|\|_\|\|\|\|\|\|:\|\|\n______________UAUGA__UC_AGUG_G___UACGUCCGU_CA_____UGA___GUCUUA_CGCCAGUAG\n3'-UUU...GUGGU_____G________U_UAC_________U__GU______AA_______A_________GGUGA...UAG-5'\n_____________\|__________________________________________________________\|\n_____________165________________________________________________________129\n	249 -- 255	130 -- 136	-44.2735 kcal/mol	15.0195 kcal/mol	15.1988 kcal/mol	216 256@LB@ \| \|@LB@5'-CGC...GGAGU GA A U U AUACC GUG G ACGGU...AUA-3'@LB@ AUGCU AG UUAU C GUGCGGGCA GU ACU CAGGAU GCGGUCGUC@LB@ \|\|:\|\| \|\| \|:\|: \| :\|\|\|:\|\|\|\| \|\| \|\|\| \|\|\|:\|\| \|\|\|\|\|\|:\|\|@LB@ UAUGA UC AGUG G UACGUCCGU CA UGA GUCUUA CGCCAGUAG@LB@3'-UUU...GUGGU G U UAC U GU AA A GGUGA...UAG-5'@LB@ \| \|@LB@ 165 129@LB@@LB@@LB@Energy -17.58 kcal/mol@LB@Hybridization Energy -44.2735 kcal/mol@LB@Unfolding Energy - mRNA 15.0195 kcal/mol@LB@Unfolding Energy - sRNA 15.1988 kcal/mol@LB@@LB@Position - mRNA 217 -- 255@LB@Position - sRNA 130 -- 164@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 130 -- 136@LB@
67	0.006568	0.3261	b1927	amyA	-8.95	0.423898	77 -- 95	58 -- 76	cytoplasmic alpha-amylase	_____________76_____________________96\n_____________\|______________________\|\n5'-UUA...GAAAC__G_______GU___C______AAAAU...AUA-3'\n______________UG_UCGGUCA__CAU_GGUGCA\n______________\|:_\|\|:\|\|\|\|__\|\|\|_\|:\|\|\|\|\n______________AU_AGUCAGU__GUA_CUACGU\n3'-UUU...UGGUU__G_______GU__________CCGUU...UAG-5'\n_____________\|______________________\|\n_____________77_____________________57\n	35 -- 41	171 -- 177	-21.7732 kcal/mol	10.1812 kcal/mol	4.80336 kcal/mol	76 96@LB@ \| \|@LB@5'-UUA...GAAAC G GU C AAAAU...AUA-3'@LB@ UG UCGGUCA CAU GGUGCA@LB@ \|: \|\|:\|\|\|\| \|\|\| \|:\|\|\|\|@LB@ AU AGUCAGU GUA CUACGU@LB@3'-UUU...UGGUU G GU CCGUU...UAG-5'@LB@ \| \|@LB@ 77 57@LB@@LB@@LB@Energy -8.95 kcal/mol@LB@Hybridization Energy -21.7732 kcal/mol@LB@Unfolding Energy - mRNA 10.1812 kcal/mol@LB@Unfolding Energy - sRNA 4.80336 kcal/mol@LB@@LB@Position - mRNA 77 -- 95@LB@Position - sRNA 58 -- 76@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 171 -- 177@LB@
68	0.00659	0.3261	b4080	mdtP	-14.15	0.040423	195 -- 221	144 -- 172	outer membrane factor of efflux pump	_____________194_______________________________222\n_____________\|_________________________________\|\n5'-CUG...CAAGG__C_____A________AUC_____________CGUCU...CUC-3'\n______________AG_CACGC_AUGAU_CA_____GUCAACUUUCA\n______________\|\|_\|\|\|:\|_\|\|\|\|\|_\|\|_____\|\|\|\|\|\|\|\|\|\|\|\n______________UC_GUGUG_UACUA_GU_____CAGUUGAAAGU\n3'-UUU...AUGAG__A___________C__CCGUU___________CUUAA...UAG-5'\n_____________\|_________________________________\|\n_____________173_______________________________143\n	215 -- 221	144 -- 150	-24.8993 kcal/mol	3.71866 kcal/mol	8.07675 kcal/mol	194 222@LB@ \| \|@LB@5'-CUG...CAAGG C A AUC CGUCU...CUC-3'@LB@ AG CACGC AUGAU CA GUCAACUUUCA@LB@ \|\| \|\|\|:\| \|\|\|\|\| \|\| \|\|\|\|\|\|\|\|\|\|\|@LB@ UC GUGUG UACUA GU CAGUUGAAAGU@LB@3'-UUU...AUGAG A C CCGUU CUUAA...UAG-5'@LB@ \| \|@LB@ 173 143@LB@@LB@@LB@Energy -14.15 kcal/mol@LB@Hybridization Energy -24.8993 kcal/mol@LB@Unfolding Energy - mRNA 3.71866 kcal/mol@LB@Unfolding Energy - sRNA 8.07675 kcal/mol@LB@@LB@Position - mRNA 195 -- 221@LB@Position - sRNA 144 -- 172@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 144 -- 150@LB@
69	0.006739	0.3286	b2265	menF	-9.03	0.410924	65 -- 108	52 -- 101	isochorismate synthase 2	_____________64__________109\n_____________\|___________\|\n5'-ACU...CGGGU___________CUUUC...CUC-3'\n______________UAUCGAUAUUC\n______________:\|:\|:\|\|\|:\|\|\n______________GUGGUUAUGAG\n3'-UUU...AAAAU___________UCAGU...UAG-5'\n_____________\|___________\|\n_____________102_________51\n	285 -- 291	176 -- 182	-9.38108 kcal/mol	0.14396 kcal/mol	3.38772 kcal/mol	64 109@LB@ \| \|@LB@5'-ACU...CGGGU CUUUC...CUC-3'@LB@ UAUCGAUAUUC@LB@ :\|:\|:\|\|\|:\|\|@LB@ GUGGUUAUGAG@LB@3'-UUU...AAAAU UCAGU...UAG-5'@LB@ \| \|@LB@ 102 51@LB@@LB@@LB@Energy -9.03 kcal/mol@LB@Hybridization Energy -9.38108 kcal/mol@LB@Unfolding Energy - mRNA 0.14396 kcal/mol@LB@Unfolding Energy - sRNA 3.38772 kcal/mol@LB@@LB@Position - mRNA 65 -- 108@LB@Position - sRNA 52 -- 101@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 176 -- 182@LB@
70	0.00686	0.3298	b0761	modE	-10.05	0.269682	248 -- 271	57 -- 77	transcriptional repressor for the molybdenum transport operon modABC	_____________247______272\n_____________\|________\|\n5'-ACC...GAAAA________CUUUU...CCA-3'\n______________GCACUCCC\n______________\|\|\|\|:\|\|\|\n______________CGUGGGGG\n3'-UUU...UACCC________AACGA...UAG-5'\n_____________\|________\|\n_____________78_______56\n	126 -- 132	11 -- 17	-14.7879 kcal/mol	0.633098 kcal/mol	5.13224 kcal/mol	247 272@LB@ \| \|@LB@5'-ACC...GAAAA CUUUU...CCA-3'@LB@ GCACUCCC@LB@ \|\|\|\|:\|\|\|@LB@ CGUGGGGG@LB@3'-UUU...UACCC AACGA...UAG-5'@LB@ \| \|@LB@ 78 56@LB@@LB@@LB@Energy -10.05 kcal/mol@LB@Hybridization Energy -14.7879 kcal/mol@LB@Unfolding Energy - mRNA 0.633098 kcal/mol@LB@Unfolding Energy - sRNA 5.13224 kcal/mol@LB@@LB@Position - mRNA 248 -- 271@LB@Position - sRNA 57 -- 77@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 11 -- 17@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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