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
44	0.003817	0.292	b0967	rlmI	-10.41	0.230051	81 -- 118	128 -- 161	23S rRNA m(5)C1962 methyltransferase SAM-dependent	_____________80_________________________________119\n_____________\|__________________________________\|\n5'-CGU...UGAAC____C___AAACC_______UUAU_CA_______GACAU...AAG-3'\n______________UCGC_CGU_____CAGGCAA____G__GACUUUC\n______________\|\|:\|_\|:\|_____\|\|\|\|\|\|\|____\|__:\|\|\|\|\|\|\n______________AGUG_GUA_____GUCCGUU____C__UUGAAAG\n3'-UUU...GAGUC____U___CUAC_____________AG_______UCUUA...UAG-5'\n_____________\|__________________________________\|\n_____________162________________________________127\n	95 -- 101	145 -- 151	-21.0542 kcal/mol	5.99356 kcal/mol	7.97203 kcal/mol	80 119@LB@ \| \|@LB@5'-CGU...UGAAC C AAACC UUAU CA GACAU...AAG-3'@LB@ UCGC CGU CAGGCAA G GACUUUC@LB@ \|\|:\| \|:\| \|\|\|\|\|\|\| \| :\|\|\|\|\|\|@LB@ AGUG GUA GUCCGUU C UUGAAAG@LB@3'-UUU...GAGUC U CUAC AG UCUUA...UAG-5'@LB@ \| \|@LB@ 162 127@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -21.0542 kcal/mol@LB@Unfolding Energy - mRNA 5.99356 kcal/mol@LB@Unfolding Energy - sRNA 7.97203 kcal/mol@LB@@LB@Position - mRNA 81 -- 118@LB@Position - sRNA 128 -- 161@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 145 -- 151@LB@
117	0.01283	0.3575	b3096	mzrA	-10.41	0.230387	15 -- 55	168 -- 208	modulator of EnvZ/OmpR regulon	_____________14________________________________________________________56\n_____________\|_________________________________________________________\|\n_____5'-UCAACU____G____________________________GAUCCUGA___CU__G________GCUCG...AGC-3'\n______________GGAU_AGCGG______UCUGCU_GUGGGU_AUU________CAA__CU_GGUUACAU\n______________::\|:_\|\|\|:\|______\|\|\|\|\|\|_\|:\|\|\|\|_\|\|\|________\|\|\|__\|\|_:\|\|:\|\|\|:\n______________UUUG_UCGUC______AGACGA_CGCCCA_UAA________GUU__GA_UCAGUGUG\n______3'-UUUUU____G_____CAUAUU______C______C___AAUGUG_____AU__G________UACUA...UAG-5'\n_____________\|_________________________________________________________\|\n_____________209_______________________________________________________167\n	49 -- 55	168 -- 174	-40.4023 kcal/mol	11.8856 kcal/mol	18.3074 kcal/mol	14 56@LB@ \| \|@LB@ 5'-UCAACU G GAUCCUGA CU G GCUCG...AGC-3'@LB@ GGAU AGCGG UCUGCU GUGGGU AUU CAA CU GGUUACAU@LB@ ::\|: \|\|\|:\| \|\|\|\|\|\| \|:\|\|\|\| \|\|\| \|\|\| \|\| :\|\|:\|\|\|:@LB@ UUUG UCGUC AGACGA CGCCCA UAA GUU GA UCAGUGUG@LB@ 3'-UUUUU G CAUAUU C C AAUGUG AU G UACUA...UAG-5'@LB@ \| \|@LB@ 209 167@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -40.4023 kcal/mol@LB@Unfolding Energy - mRNA 11.8856 kcal/mol@LB@Unfolding Energy - sRNA 18.3074 kcal/mol@LB@@LB@Position - mRNA 15 -- 55@LB@Position - sRNA 168 -- 208@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 168 -- 174@LB@
108	0.01175	0.3575	b0723	sdhA	-10.39	0.232370	178 -- 209	28 -- 62	succinate dehydrogenase flavoprotein subunit	_____________177_______________________210\n_____________\|_________________________\|\n5'-GGU...GAAAU__________G_G_AUU________UUGUG...GUG-3'\n______________UGC_CAGUCA_A_A___UGAUGCAG\n______________\|:\|_\|\|\|\|\|\|_\|_\|___\|\|\|\|\|\|\|\|\n______________AUG_GUCAGU_U_U___ACUACGUC\n3'-UUU...UGGUU___A______G_G____________CGUUC...UAG-5'\n_____________\|_________________________\|\n_____________63________________________27\n	225 -- 231	159 -- 165	-22.5908 kcal/mol	8.24888 kcal/mol	4.81331 kcal/mol	177 210@LB@ \| \|@LB@5'-GGU...GAAAU G G AUU UUGUG...GUG-3'@LB@ UGC CAGUCA A A UGAUGCAG@LB@ \|:\| \|\|\|\|\|\| \| \| \|\|\|\|\|\|\|\|@LB@ AUG GUCAGU U U ACUACGUC@LB@3'-UUU...UGGUU A G G CGUUC...UAG-5'@LB@ \| \|@LB@ 63 27@LB@@LB@@LB@Energy -10.39 kcal/mol@LB@Hybridization Energy -22.5908 kcal/mol@LB@Unfolding Energy - mRNA 8.24888 kcal/mol@LB@Unfolding Energy - sRNA 4.81331 kcal/mol@LB@@LB@Position - mRNA 178 -- 209@LB@Position - sRNA 28 -- 62@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 159 -- 165@LB@
46	0.004081	0.2985	b2466	ypfG	-10.37	0.233995	256 -- 280	68 -- 95	DUF1176 family protein	_____________255_____281\n_____________\|_______\|\n5'-AAA...CAAAC_______UUAAU...UCA-3'\n______________GUCACAU\n______________\|\|\|\|\|\|:\n______________CAGUGUG\n3'-UUU...UGAGU_______UACUA...UAG-5'\n_____________\|_______\|\n_____________96______67\n	57 -- 63	168 -- 174	-9.42181 kcal/mol	2.13246 kcal/mol	0.260649 kcal/mol	255 281@LB@ \| \|@LB@5'-AAA...CAAAC UUAAU...UCA-3'@LB@ GUCACAU@LB@ \|\|\|\|\|\|:@LB@ CAGUGUG@LB@3'-UUU...UGAGU UACUA...UAG-5'@LB@ \| \|@LB@ 96 67@LB@@LB@@LB@Energy -10.37 kcal/mol@LB@Hybridization Energy -9.42181 kcal/mol@LB@Unfolding Energy - mRNA 2.13246 kcal/mol@LB@Unfolding Energy - sRNA 0.260649 kcal/mol@LB@@LB@Position - mRNA 256 -- 280@LB@Position - sRNA 68 -- 95@LB@Position Seed - mRNA 57 -- 63@LB@Position Seed - sRNA 168 -- 174@LB@
85	0.009065	0.3575	b3155	yhbQ	-10.34	0.236900	54 -- 88	123 -- 160	GIY-YIG nuclease superfamily protein	_____________53______________________89\n_____________\|_______________________\|\n5'-UUU...GAUCC_____G__GACAAUAA_______ACCGG...GCG-3'\n______________GUACC_CC________GCUUUAU\n______________\|:\|\|\|_\|\|________\|\|\|\|:\|\|\n______________CGUGG_GG________CGAAGUA\n3'-UUU...UACCC_____G__AA_____________G-5'\n_____________\|_______________________\|\n_____________161_____________________122\n	245 -- 251	2 -- 8	-16.2438 kcal/mol	1.2562 kcal/mol	7.2187 kcal/mol	53 89@LB@ \| \|@LB@5'-UUU...GAUCC G GACAAUAA ACCGG...GCG-3'@LB@ GUACC CC GCUUUAU@LB@ \|:\|\|\| \|\| \|\|\|\|:\|\|@LB@ CGUGG GG CGAAGUA@LB@3'-UUU...UACCC G AA G-5'@LB@ \| \|@LB@ 161 122@LB@@LB@@LB@Energy -10.34 kcal/mol@LB@Hybridization Energy -16.2438 kcal/mol@LB@Unfolding Energy - mRNA 1.2562 kcal/mol@LB@Unfolding Energy - sRNA 7.2187 kcal/mol@LB@@LB@Position - mRNA 54 -- 88@LB@Position - sRNA 123 -- 160@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 2 -- 8@LB@
190	0.02217	0.3833	b2754	ygbF	-10.33	0.238061	176 -- 225	124 -- 165	CRISPR adaptation ssRNA endonuclease	_____________175____________226\n_____________\|______________\|\n5'-UGG...AAAAU________GC____ACGAG...GUG-3'\n______________GUACCUCC__GCUU\n______________\|:\|\|\|:\|\|__\|\|\|\|\n______________CGUGGGGG__CGAA\n3'-UUU...UACCC________AA____GUAG-5'\n_____________\|______________\|\n_____________166____________123\n	232 -- 238	11 -- 17	-17.8256 kcal/mol	3.33543 kcal/mol	6.90657 kcal/mol	175 226@LB@ \| \|@LB@5'-UGG...AAAAU GC ACGAG...GUG-3'@LB@ GUACCUCC GCUU@LB@ \|:\|\|\|:\|\| \|\|\|\|@LB@ CGUGGGGG CGAA@LB@3'-UUU...UACCC AA GUAG-5'@LB@ \| \|@LB@ 166 123@LB@@LB@@LB@Energy -10.33 kcal/mol@LB@Hybridization Energy -17.8256 kcal/mol@LB@Unfolding Energy - mRNA 3.33543 kcal/mol@LB@Unfolding Energy - sRNA 6.90657 kcal/mol@LB@@LB@Position - mRNA 176 -- 225@LB@Position - sRNA 124 -- 165@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 11 -- 17@LB@
92	0.01029	0.3575	b3360	pabA	-10.28	0.244097	93 -- 100	16 -- 23	aminodeoxychorismate synthase subunit II	_____________92__________101\n_____________\|___________\|\n5'-GCG...ACCUC___________UUGUG...CGU-3'\n______________UACCAGUACUU\n______________:\|\|\|\|:\|\|\|\|:\n______________GUGGUUAUGAG\n3'-UUU...AAAAU___________UCAGU...UAG-5'\n_____________\|___________\|\n_____________24__________15\n	250 -- 256	176 -- 182	-13.2399 kcal/mol	3.06354 kcal/mol	3.38772 kcal/mol	92 101@LB@ \| \|@LB@5'-GCG...ACCUC UUGUG...CGU-3'@LB@ UACCAGUACUU@LB@ :\|\|\|\|:\|\|\|\|:@LB@ GUGGUUAUGAG@LB@3'-UUU...AAAAU UCAGU...UAG-5'@LB@ \| \|@LB@ 24 15@LB@@LB@@LB@Energy -10.28 kcal/mol@LB@Hybridization Energy -13.2399 kcal/mol@LB@Unfolding Energy - mRNA 3.06354 kcal/mol@LB@Unfolding Energy - sRNA 3.38772 kcal/mol@LB@@LB@Position - mRNA 93 -- 100@LB@Position - sRNA 16 -- 23@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 176 -- 182@LB@
152	0.0171	0.3749	b3605	lldD	-10.23	0.248595	212 -- 221	68 -- 77	L-lactate dehydrogenase FMN-linked	_____________211_______222\n_____________\|_________\|\n5'-UUU...GAAAA_________UAUUU...ACA-3'\n______________ACGCAUGAU\n______________\|\|:\|\|\|\|\|\|\n______________UGUGUACUA\n3'-UUU...GUCAG_________CGUCC...UAG-5'\n_____________\|_________\|\n_____________78________67\n	199 -- 205	163 -- 169	-11.1438 kcal/mol	1.00002 kcal/mol	4.14962 kcal/mol	211 222@LB@ \| \|@LB@5'-UUU...GAAAA UAUUU...ACA-3'@LB@ ACGCAUGAU@LB@ \|\|:\|\|\|\|\|\|@LB@ UGUGUACUA@LB@3'-UUU...GUCAG CGUCC...UAG-5'@LB@ \| \|@LB@ 78 67@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -11.1438 kcal/mol@LB@Unfolding Energy - mRNA 1.00002 kcal/mol@LB@Unfolding Energy - sRNA 4.14962 kcal/mol@LB@@LB@Position - mRNA 212 -- 221@LB@Position - sRNA 68 -- 77@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 163 -- 169@LB@
186	0.02152	0.3833	b3581	sgbH	-10.17	0.255482	135 -- 158	123 -- 153	3-keto-L-gulonate 6-phosphate decarboxylase	_____________134________159\n_____________\|__________\|\n5'-UUU...UAAGG__________UAUGA...AAG-3'\n______________AG_CACACAU\n______________\|\|_\|\|\|\|\|\|\|\n______________UC_GUGUGUA\n3'-UUU...AUGAG__A_______CUACG...UAG-5'\n_____________\|__________\|\n_____________154________122\n	193 -- 199	166 -- 172	-9.15702 kcal/mol	1.98532 kcal/mol	0.591348 kcal/mol	134 159@LB@ \| \|@LB@5'-UUU...UAAGG UAUGA...AAG-3'@LB@ AG CACACAU@LB@ \|\| \|\|\|\|\|\|\|@LB@ UC GUGUGUA@LB@3'-UUU...AUGAG A CUACG...UAG-5'@LB@ \| \|@LB@ 154 122@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -9.15702 kcal/mol@LB@Unfolding Energy - mRNA 1.98532 kcal/mol@LB@Unfolding Energy - sRNA 0.591348 kcal/mol@LB@@LB@Position - mRNA 135 -- 158@LB@Position - sRNA 123 -- 153@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 166 -- 172@LB@
197	0.02355	0.3833	b2764	cysJ	-10.17	0.255883	3 -- 30	98 -- 123	sulfite reductase alpha subunit flavoprotein	_____________2________31\n_____________\|________\|\n5'-UUC...AACAG________ACUGG...UUG-3'\n______________CUUUGCUU\n______________\|:\|\|\|\|\|\|\n______________GGAACGAA\n3'-UUU...GUGGG________GUAG-5'\n_____________\|________\|\n_____________124______97\n	176 -- 182	5 -- 11	-8.59037 kcal/mol	0.881795 kcal/mol	1.04254 kcal/mol	2 31@LB@ \| \|@LB@5'-UUC...AACAG ACUGG...UUG-3'@LB@ CUUUGCUU@LB@ \|:\|\|\|\|\|\|@LB@ GGAACGAA@LB@3'-UUU...GUGGG GUAG-5'@LB@ \| \|@LB@ 124 97@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -8.59037 kcal/mol@LB@Unfolding Energy - mRNA 0.881795 kcal/mol@LB@Unfolding Energy - sRNA 1.04254 kcal/mol@LB@@LB@Position - mRNA 3 -- 30@LB@Position - sRNA 98 -- 123@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 5 -- 11@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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