Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
161	0.00773	0.1668	b0945	pyrD	-11.84	0.111523	258 -- 300	33 -- 77	dihydro-orotate oxidase FMN-linked	_____________257____________________________________________300\n_____________\|______________________________________________\|\n5'-UGU...CUCAU___U____UUUU________A__CC__A____A_______ACG____-3'\n______________GAG_UUAC____CAGCAAUU_CG__GU_UUAC_____GGA___CCGU\n______________:\|\|_:\|\|\|____\|\|\|\|\|\|\|\|_\|\|__\|\|_\|:\|\|_____\|\|\|___\|\|:\|\n______________UUC_GAUG____GUCGUUAA_GC__CA_AGUG_____CCU___GGUA\n3'-UUU...CCCGU___U____UGU____________AA__A____AGUCC___AAA____CGAAU...GCA-5'\n_____________\|_______________________________________________\|\n_____________78______________________________________________32\n	271 -- 277	59 -- 65	-22.2972 kcal/mol	5.63827 kcal/mol	4.81602 kcal/mol	257 300@LB@ \| \|@LB@5'-UGU...CUCAU U UUUU A CC A A ACG -3'@LB@ GAG UUAC CAGCAAUU CG GU UUAC GGA CCGU@LB@ :\|\| :\|\|\| \|\|\|\|\|\|\|\| \|\| \|\| \|:\|\| \|\|\| \|\|:\|@LB@ UUC GAUG GUCGUUAA GC CA AGUG CCU GGUA@LB@3'-UUU...CCCGU U UGU AA A AGUCC AAA CGAAU...GCA-5'@LB@ \| \|@LB@ 78 32@LB@@LB@@LB@Energy -11.84 kcal/mol@LB@Hybridization Energy -22.2972 kcal/mol@LB@Unfolding Energy - mRNA 5.63827 kcal/mol@LB@Unfolding Energy - sRNA 4.81602 kcal/mol@LB@@LB@Position - mRNA 258 -- 300@LB@Position - sRNA 33 -- 77@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 59 -- 65@LB@
162	0.007731	0.1668	b4202	rpsR	-9.58	0.287294	60 -- 77	62 -- 76	30S ribosomal subunit protein S18	_____________59_________________78\n_____________\|__________________\|\n5'-CGG...AAACC____CAU___U_______UAACG...UCA-3'\n______________AGGC___UAC_CACAGUA\n______________\|\|:\|___\|\|\|_\|\|\|\|\|:\|\n______________UCUG___AUG_GUGUCGU\n3'-UUU...CCGUU__________U_______UAAGC...GCA-5'\n_____________\|__________________\|\n_____________77_________________61\n	71 -- 77	62 -- 68	-14.2281 kcal/mol	1.39912 kcal/mol	3.25371 kcal/mol	59 78@LB@ \| \|@LB@5'-CGG...AAACC CAU U UAACG...UCA-3'@LB@ AGGC UAC CACAGUA@LB@ \|\|:\| \|\|\| \|\|\|\|\|:\|@LB@ UCUG AUG GUGUCGU@LB@3'-UUU...CCGUU U UAAGC...GCA-5'@LB@ \| \|@LB@ 77 61@LB@@LB@@LB@Energy -9.58 kcal/mol@LB@Hybridization Energy -14.2281 kcal/mol@LB@Unfolding Energy - mRNA 1.39912 kcal/mol@LB@Unfolding Energy - sRNA 3.25371 kcal/mol@LB@@LB@Position - mRNA 60 -- 77@LB@Position - sRNA 62 -- 76@LB@Position Seed - mRNA 71 -- 77@LB@Position Seed - sRNA 62 -- 68@LB@
163	0.007762	0.1668	b0394	mak	-14.23	0.032787	242 -- 265	40 -- 75	manno(fructo)kinase	_____________241__________________________________266\n_____________\|____________________________________\|\n5'-GUU...GAAGU________UG______G___________________GCAGU...GUG-3'\n______________GAUUGCAC__GGCGAU_____________CAGGGGA\n______________\|\|:\|:\|\|\|__:\|\|:\|\|_____________\|\|\|\|\|\|\|\n______________CUGAUGUG__UCGUUA_____________GUCCCCU\n3'-UUU...CGUUU________UG______AGCAACAAAGUGA_______AAAGG...GCA-5'\n_____________\|____________________________________\|\n_____________76___________________________________39\n	259 -- 265	40 -- 46	-27.5886 kcal/mol	8.58508 kcal/mol	4.77786 kcal/mol	241 266@LB@ \| \|@LB@5'-GUU...GAAGU UG G GCAGU...GUG-3'@LB@ GAUUGCAC GGCGAU CAGGGGA@LB@ \|\|:\|:\|\|\| :\|\|:\|\| \|\|\|\|\|\|\|@LB@ CUGAUGUG UCGUUA GUCCCCU@LB@3'-UUU...CGUUU UG AGCAACAAAGUGA AAAGG...GCA-5'@LB@ \| \|@LB@ 76 39@LB@@LB@@LB@Energy -14.23 kcal/mol@LB@Hybridization Energy -27.5886 kcal/mol@LB@Unfolding Energy - mRNA 8.58508 kcal/mol@LB@Unfolding Energy - sRNA 4.77786 kcal/mol@LB@@LB@Position - mRNA 242 -- 265@LB@Position - sRNA 40 -- 75@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 40 -- 46@LB@
164	0.007775	0.1668	b2097	fbaB	-9.67	0.277966	247 -- 265	48 -- 68	fructose-bisphosphate aldolase class I	_____________246___________________266\n_____________\|_____________________\|\n5'-AAU...CCUUU_______C________A_G__AAUUC...AUG-3'\n______________UACAGCA___CGUUGU_U_AC\n______________:\|\|\|\|\|\|___\|\|\|\|\|\|_\|_\|\|\n______________GUGUCGU___GCAACA_A_UG\n3'-UUU...GAUGU_______UAA______A_G__AGUCC...GCA-5'\n_____________\|_____________________\|\n_____________69____________________47\n	247 -- 253	62 -- 68	-18.0796 kcal/mol	4.78239 kcal/mol	3.63277 kcal/mol	246 266@LB@ \| \|@LB@5'-AAU...CCUUU C A G AAUUC...AUG-3'@LB@ UACAGCA CGUUGU U AC@LB@ :\|\|\|\|\|\| \|\|\|\|\|\| \| \|\|@LB@ GUGUCGU GCAACA A UG@LB@3'-UUU...GAUGU UAA A G AGUCC...GCA-5'@LB@ \| \|@LB@ 69 47@LB@@LB@@LB@Energy -9.67 kcal/mol@LB@Hybridization Energy -18.0796 kcal/mol@LB@Unfolding Energy - mRNA 4.78239 kcal/mol@LB@Unfolding Energy - sRNA 3.63277 kcal/mol@LB@@LB@Position - mRNA 247 -- 265@LB@Position - sRNA 48 -- 68@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 62 -- 68@LB@
165	0.007934	0.1692	b3355	prkB	-7.13	0.603515	287 -- 294	63 -- 70	putative phosphoribulokinase	_____________286______295\n_____________\|________\|\n5'-GGC...AUAUU________UAAAUC-3'\n______________CGCGCAGU\n______________\|:\|:\|\|\|:\n______________GUGUGUCG\n3'-UUU...CUGAU________UUAAG...GCA-5'\n_____________\|________\|\n_____________71_______62\n	288 -- 294	63 -- 69	-11.0055 kcal/mol	0.741841 kcal/mol	3.13161 kcal/mol	286 295@LB@ \| \|@LB@5'-GGC...AUAUU UAAAUC-3'@LB@ CGCGCAGU@LB@ \|:\|:\|\|\|:@LB@ GUGUGUCG@LB@3'-UUU...CUGAU UUAAG...GCA-5'@LB@ \| \|@LB@ 71 62@LB@@LB@@LB@Energy -7.13 kcal/mol@LB@Hybridization Energy -11.0055 kcal/mol@LB@Unfolding Energy - mRNA 0.741841 kcal/mol@LB@Unfolding Energy - sRNA 3.13161 kcal/mol@LB@@LB@Position - mRNA 287 -- 294@LB@Position - sRNA 63 -- 70@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 63 -- 69@LB@
166	0.008074	0.1711	b2158	yeiH	-9.26	0.321503	233 -- 257	41 -- 72	UPF0324 family inner membrane protein	_____________232_______________________________258\n_____________\|_________________________________\|\n5'-CAC...CAUCG_____UG_____________________C____UUAGC...GUG-3'\n______________UACAC__UGGCA________UUUUAUUC_GGGG\n______________\|\|\|\|\|__::\|\|\|________\|\|\|:\|:\|\|_\|\|\|\|\n______________AUGUG__GUCGU________AAAGUGAG_CCCC\n3'-UUU...UUCUG_____U______UAAGCAAC________U____UAAAG...GCA-5'\n_____________\|_________________________________\|\n_____________73________________________________40\n	246 -- 252	46 -- 52	-21.8619 kcal/mol	7.84401 kcal/mol	4.75632 kcal/mol	232 258@LB@ \| \|@LB@5'-CAC...CAUCG UG C UUAGC...GUG-3'@LB@ UACAC UGGCA UUUUAUUC GGGG@LB@ \|\|\|\|\| ::\|\|\| \|\|\|:\|:\|\| \|\|\|\|@LB@ AUGUG GUCGU AAAGUGAG CCCC@LB@3'-UUU...UUCUG U UAAGCAAC U UAAAG...GCA-5'@LB@ \| \|@LB@ 73 40@LB@@LB@@LB@Energy -9.26 kcal/mol@LB@Hybridization Energy -21.8619 kcal/mol@LB@Unfolding Energy - mRNA 7.84401 kcal/mol@LB@Unfolding Energy - sRNA 4.75632 kcal/mol@LB@@LB@Position - mRNA 233 -- 257@LB@Position - sRNA 41 -- 72@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 46 -- 52@LB@
167	0.008121	0.1711	b2603	yfiR	-9.52	0.293133	262 -- 278	35 -- 51	putative periplasmic inhibitor of YfiN activity	_____________261_______________279\n_____________\|_________________\|\n5'-GUA...AAUAC_________A_CC____GACGU...GUA-3'\n______________UCGCUCAGG_G__UUCU\n______________\|\|:\|\|\|\|\|\|_\|__\|\|\|:\n______________AGUGAGUCC_C__AAGG\n3'-UUU...AACAA_________C_UA____UACGA...GCA-5'\n_____________\|_________________\|\n_____________52________________34\n	264 -- 270	43 -- 49	-18.1931 kcal/mol	6.80204 kcal/mol	1.87111 kcal/mol	261 279@LB@ \| \|@LB@5'-GUA...AAUAC A CC GACGU...GUA-3'@LB@ UCGCUCAGG G UUCU@LB@ \|\|:\|\|\|\|\|\| \| \|\|\|:@LB@ AGUGAGUCC C AAGG@LB@3'-UUU...AACAA C UA UACGA...GCA-5'@LB@ \| \|@LB@ 52 34@LB@@LB@@LB@Energy -9.52 kcal/mol@LB@Hybridization Energy -18.1931 kcal/mol@LB@Unfolding Energy - mRNA 6.80204 kcal/mol@LB@Unfolding Energy - sRNA 1.87111 kcal/mol@LB@@LB@Position - mRNA 262 -- 278@LB@Position - sRNA 35 -- 51@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 43 -- 49@LB@
168	0.008282	0.1723	b3822	recQ	-12.50	0.081546	124 -- 155	43 -- 77	ATP-dependent DNA helicase	_____________123___________________________________156\n_____________\|_____________________________________\|\n5'-CGC...UCUCA_______AAA____U_______C_________G____CGCUG...UUA-3'\n______________GAGACUA___GCAU_GCAGUUU______UCGC_CAGG\n______________:\|\|\|\|\|\|___:\|\|:_\|\|\|:\|\|:______\|\|:\|_\|\|\|\|\n______________UUCUGAU___UGUG_CGUUAAG______AGUG_GUCC\n3'-UUU...CCCGU_______G______U_______CAACAA____A____CCUAA...GCA-5'\n_____________\|_____________________________________\|\n_____________78____________________________________42\n	139 -- 145	58 -- 64	-25.7534 kcal/mol	8.90299 kcal/mol	4.3531 kcal/mol	123 156@LB@ \| \|@LB@5'-CGC...UCUCA AAA U C G CGCUG...UUA-3'@LB@ GAGACUA GCAU GCAGUUU UCGC CAGG@LB@ :\|\|\|\|\|\| :\|\|: \|\|\|:\|\|: \|\|:\| \|\|\|\|@LB@ UUCUGAU UGUG CGUUAAG AGUG GUCC@LB@3'-UUU...CCCGU G U CAACAA A CCUAA...GCA-5'@LB@ \| \|@LB@ 78 42@LB@@LB@@LB@Energy -12.50 kcal/mol@LB@Hybridization Energy -25.7534 kcal/mol@LB@Unfolding Energy - mRNA 8.90299 kcal/mol@LB@Unfolding Energy - sRNA 4.3531 kcal/mol@LB@@LB@Position - mRNA 124 -- 155@LB@Position - sRNA 43 -- 77@LB@Position Seed - mRNA 139 -- 145@LB@Position Seed - sRNA 58 -- 64@LB@
169	0.008352	0.1723	b1222	narX	-15.18	0.018797	58 -- 74	61 -- 75	sensory histidine kinase in two-component regulatory system with NarL	_____________57________________75\n_____________\|_________________\|\n5'-AAA...AAAGC_____AC__________AUAAG...CUG-3'\n______________GACUA__CACACGGCAA\n______________\|\|\|\|\|__\|\|\|\|\|:\|\|\|\|\n______________CUGAU__GUGUGUCGUU\n3'-UUU...CGUUU_________________AAGCA...GCA-5'\n_____________\|_________________\|\n_____________76________________60\n	68 -- 74	61 -- 67	-20.5903 kcal/mol	2.1582 kcal/mol	3.25399 kcal/mol	57 75@LB@ \| \|@LB@5'-AAA...AAAGC AC AUAAG...CUG-3'@LB@ GACUA CACACGGCAA@LB@ \|\|\|\|\| \|\|\|\|\|:\|\|\|\|@LB@ CUGAU GUGUGUCGUU@LB@3'-UUU...CGUUU AAGCA...GCA-5'@LB@ \| \|@LB@ 76 60@LB@@LB@@LB@Energy -15.18 kcal/mol@LB@Hybridization Energy -20.5903 kcal/mol@LB@Unfolding Energy - mRNA 2.1582 kcal/mol@LB@Unfolding Energy - sRNA 3.25399 kcal/mol@LB@@LB@Position - mRNA 58 -- 74@LB@Position - sRNA 61 -- 75@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 61 -- 67@LB@
170	0.008354	0.1723	b3294	rplQ	-12.86	0.068031	178 -- 204	31 -- 54	50S ribosomal subunit protein L17	_____________177_________________________205\n_____________\|___________________________\|\n5'-UAU...UUAAG________G__AA____AAGG______GCCAU...UCA-3'\n______________GUUUUACU_AG__GGAU____UCAUGC\n______________\|\|\|\|:\|\|\|_\|\|__\|\|\|\|____:\|\|\|\|\|\n______________CAAAGUGA_UC__CCUA____GGUACG\n3'-UUU...AGCAA________G__C_____AA________AAUAU...GCA-5'\n_____________\|___________________________\|\n_____________55__________________________30\n	179 -- 185	47 -- 53	-21.6424 kcal/mol	4.376 kcal/mol	4.40484 kcal/mol	177 205@LB@ \| \|@LB@5'-UAU...UUAAG G AA AAGG GCCAU...UCA-3'@LB@ GUUUUACU AG GGAU UCAUGC@LB@ \|\|\|\|:\|\|\| \|\| \|\|\|\| :\|\|\|\|\|@LB@ CAAAGUGA UC CCUA GGUACG@LB@3'-UUU...AGCAA G C AA AAUAU...GCA-5'@LB@ \| \|@LB@ 55 30@LB@@LB@@LB@Energy -12.86 kcal/mol@LB@Hybridization Energy -21.6424 kcal/mol@LB@Unfolding Energy - mRNA 4.376 kcal/mol@LB@Unfolding Energy - sRNA 4.40484 kcal/mol@LB@@LB@Position - mRNA 178 -- 204@LB@Position - sRNA 31 -- 54@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 47 -- 53@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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