Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
121	0.01216	0.338	b3416	malQ	-13.35	0.020947	179 -- 225	13 -- 54	4-alpha-glucanotransferase (amylomaltase)	_____________178______________________________________________226\n_____________\|________________________________________________\|\n5'-GCG...UGGCA_____AAC__U__GGAA_____________C___C_____________CCGCG...CCA-3'\n______________GGCAA___GC_AA____GCUCGAUGGAAAG_AAA_GUCUG_GAUAAUG\n______________\|\|\|\|\|___\|\|_\|\|____\|\|:\|:\|::\|\|\|\|:_\|\|\|_:\|\|\|\|_\|\|:\|\|\|:\n______________CCGUU___CG_UU____CGGGUUGUCUUUU_UUU_UAGAC_CUGUUAU\n3'-UUU...AGUCA_____A_______AC_______________A_________A_______UUCCG...UUG-5'\n_____________\|________________________________________________\|\n_____________55_______________________________________________12\n	219 -- 225	13 -- 19	-33.3316 kcal/mol	8.88616 kcal/mol	11.0933 kcal/mol	178 226@LB@ \| \|@LB@5'-GCG...UGGCA AAC U GGAA C C CCGCG...CCA-3'@LB@ GGCAA GC AA GCUCGAUGGAAAG AAA GUCUG GAUAAUG@LB@ \|\|\|\|\| \|\| \|\| \|\|:\|:\|::\|\|\|\|: \|\|\| :\|\|\|\| \|\|:\|\|\|:@LB@ CCGUU CG UU CGGGUUGUCUUUU UUU UAGAC CUGUUAU@LB@3'-UUU...AGUCA A AC A A UUCCG...UUG-5'@LB@ \| \|@LB@ 55 12@LB@@LB@@LB@Energy -13.35 kcal/mol@LB@Hybridization Energy -33.3316 kcal/mol@LB@Unfolding Energy - mRNA 8.88616 kcal/mol@LB@Unfolding Energy - sRNA 11.0933 kcal/mol@LB@@LB@Position - mRNA 179 -- 225@LB@Position - sRNA 13 -- 54@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 13 -- 19@LB@
176	0.02144	0.4097	b0948	rlmL	-6.91	0.434425	184 -- 201	13 -- 33	23S rRNA m(2)G2445 and m(7)G2069 methyltransferases SAM-dependent	_____________183___________________202\n_____________\|_____________________\|\n5'-GAC...CUCUU_____________________UGAAU...GUG-3'\n______________AGAGUAAAA___GUGACGAUA\n______________\|:\|:\|\|\|\|\|___\|\|\|\|\|:\|\|\|\n______________UUUUAUUUU___CACUGUUAU\n3'-UUU...UUGUC_________AGA_________UUCCG...UUG-5'\n_____________\|_____________________\|\n_____________34____________________12\n	195 -- 201	13 -- 19	-14.282 kcal/mol	2.4415 kcal/mol	4.9341 kcal/mol	183 202@LB@ \| \|@LB@5'-GAC...CUCUU UGAAU...GUG-3'@LB@ AGAGUAAAA GUGACGAUA@LB@ \|:\|:\|\|\|\|\| \|\|\|\|\|:\|\|\|@LB@ UUUUAUUUU CACUGUUAU@LB@3'-UUU...UUGUC AGA UUCCG...UUG-5'@LB@ \| \|@LB@ 34 12@LB@@LB@@LB@Energy -6.91 kcal/mol@LB@Hybridization Energy -14.282 kcal/mol@LB@Unfolding Energy - mRNA 2.4415 kcal/mol@LB@Unfolding Energy - sRNA 4.9341 kcal/mol@LB@@LB@Position - mRNA 184 -- 201@LB@Position - sRNA 13 -- 33@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 13 -- 19@LB@
35	0.002227	0.2088	b1482	osmC	-7.15	0.399399	183 -- 208	14 -- 42	lipoyl-dependent Cys-based peroxidase hydroperoxide resistance; salt-shock inducible membrane protein; peroxiredoxin	_____________182___________________________209\n_____________\|_____________________________\|\n5'-UAG...UUUAA_____________GCAACAA_________CCAUA...CGU-3'\n______________GCCC_ACAGGAGA_________UGACAAU\n______________\|\|\|\|_\|\|\|\|:\|:\|_________\|\|\|\|\|\|\|\n______________CGGG_UGUCUUUU_________ACUGUUA\n3'-UUU...GUUAC____U________AUUUUAGAC_______UUUCC...UUG-5'\n_____________\|_____________________________\|\n_____________43____________________________13\n	202 -- 208	14 -- 20	-22.1887 kcal/mol	4.46968 kcal/mol	10.5676 kcal/mol	182 209@LB@ \| \|@LB@5'-UAG...UUUAA GCAACAA CCAUA...CGU-3'@LB@ GCCC ACAGGAGA UGACAAU@LB@ \|\|\|\| \|\|\|\|:\|:\| \|\|\|\|\|\|\|@LB@ CGGG UGUCUUUU ACUGUUA@LB@3'-UUU...GUUAC U AUUUUAGAC UUUCC...UUG-5'@LB@ \| \|@LB@ 43 13@LB@@LB@@LB@Energy -7.15 kcal/mol@LB@Hybridization Energy -22.1887 kcal/mol@LB@Unfolding Energy - mRNA 4.46968 kcal/mol@LB@Unfolding Energy - sRNA 10.5676 kcal/mol@LB@@LB@Position - mRNA 183 -- 208@LB@Position - sRNA 14 -- 42@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 14 -- 20@LB@
107	0.009921	0.3118	b0836	bssR	-14.44	0.011050	12 -- 65	14 -- 65	repressor of biofilm formation by indole transport regulation	_____________11____________________________________________________________66\n_____________\|_____________________________________________________________\|\n5'-AUU...UUACA_____G___________________A___U______UUCUG____________AUC_____CUCAU...ACA-3'\n______________GGAAA_GUCAG_GGCAG______GG_UUC_ACAGAG_____GAUAAAAUUUGU___GCAAU\n______________\|\|\|\|\|_:\|\|\|\|_\|\|\|\|:______\|\|_::\|_\|\|\|\|\|:_____:\|\|\|\|\|\|\|:\|\|\|___:\|\|\|\|\n______________CCUUU_UAGUC_CCGUU______CC_GGG_UGUCUU_____UUAUUUUAGACA___UGUUA\n3'-UUU...UACAA___________A_____ACGUUA______U_______________________C_______UUUCC...UUG-5'\n_____________\|_____________________________________________________________\|\n_____________66____________________________________________________________13\n	46 -- 52	25 -- 31	-37.4064 kcal/mol	11.8508 kcal/mol	11.1173 kcal/mol	11 66@LB@ \| \|@LB@5'-AUU...UUACA G A U UUCUG AUC CUCAU...ACA-3'@LB@ GGAAA GUCAG GGCAG GG UUC ACAGAG GAUAAAAUUUGU GCAAU@LB@ \|\|\|\|\| :\|\|\|\| \|\|\|\|: \|\| ::\| \|\|\|\|\|: :\|\|\|\|\|\|\|:\|\|\| :\|\|\|\|@LB@ CCUUU UAGUC CCGUU CC GGG UGUCUU UUAUUUUAGACA UGUUA@LB@3'-UUU...UACAA A ACGUUA U C UUUCC...UUG-5'@LB@ \| \|@LB@ 66 13@LB@@LB@@LB@Energy -14.44 kcal/mol@LB@Hybridization Energy -37.4064 kcal/mol@LB@Unfolding Energy - mRNA 11.8508 kcal/mol@LB@Unfolding Energy - sRNA 11.1173 kcal/mol@LB@@LB@Position - mRNA 12 -- 65@LB@Position - sRNA 14 -- 65@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 25 -- 31@LB@
82	0.006986	0.2822	b3128	garD	-14.80	0.008847	185 -- 224	15 -- 66	D-galactarate dehydrogenase	_____________184__________________________________________________225\n_____________\|____________________________________________________\|\n5'-AUA...CUGGC________AUU_____________________UC__________A_______GAAAC...UGA-3'\n______________UGGAGAAU_____GCA___CAAUGGCC_AACA______GAAAUC___GACAA\n______________\|\|\|\|:\|\|\|_____\|\|\|___\|\|\|\|\|\|\|\|_\|\|\|\|______:\|\|\|\|\|___\|\|\|\|\|\n______________ACCUUUUA_____CGU___GUUACCGG_UUGU______UUUUAG___CUGUU\n3'-UUU...AUACA________GUCAC___UAC________G____CUUUUA______ACA_____AUUUC...UUG-5'\n_____________\|____________________________________________________\|\n_____________67___________________________________________________14\n	200 -- 206	40 -- 46	-31.4715 kcal/mol	5.54782 kcal/mol	11.1209 kcal/mol	184 225@LB@ \| \|@LB@5'-AUA...CUGGC AUU UC A GAAAC...UGA-3'@LB@ UGGAGAAU GCA CAAUGGCC AACA GAAAUC GACAA@LB@ \|\|\|\|:\|\|\| \|\|\| \|\|\|\|\|\|\|\| \|\|\|\| :\|\|\|\|\| \|\|\|\|\|@LB@ ACCUUUUA CGU GUUACCGG UUGU UUUUAG CUGUU@LB@3'-UUU...AUACA GUCAC UAC G CUUUUA ACA AUUUC...UUG-5'@LB@ \| \|@LB@ 67 14@LB@@LB@@LB@Energy -14.80 kcal/mol@LB@Hybridization Energy -31.4715 kcal/mol@LB@Unfolding Energy - mRNA 5.54782 kcal/mol@LB@Unfolding Energy - sRNA 11.1209 kcal/mol@LB@@LB@Position - mRNA 185 -- 224@LB@Position - sRNA 15 -- 66@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 40 -- 46@LB@
137	0.01537	0.3774	b0952	pqiC	-8.31	0.257066	203 -- 237	17 -- 64	DUF330 family putative lipoprotein	_____________202________________________________________________238\n_____________\|__________________________________________________\|\n5'-ACG...ACAAU_____________U____A_______G_______________________UGGCC...GCG-3'\n______________GAAAA__AGUGGC_AGUG_CGAU__U_CAGCA___________CUGUGGC\n______________\|\|\|\|\|__\|\|\|\|\|\|_\|:\|\|_\|:\|\|__:_\|\|:\|\|___________\|\|\|\|\|:\|\n______________CUUUU__UCACCG_UUAC_GUUA__G_GUUGU___________GACACUG\n3'-UUU...ACAAC_____AG________________CC_G_____CUUUUAUUUUA_______UUAUU...UUG-5'\n_____________\|__________________________________________________\|\n_____________65_________________________________________________16\n	231 -- 237	17 -- 23	-29.1693 kcal/mol	9.7543 kcal/mol	11.1047 kcal/mol	202 238@LB@ \| \|@LB@5'-ACG...ACAAU U A G UGGCC...GCG-3'@LB@ GAAAA AGUGGC AGUG CGAU U CAGCA CUGUGGC@LB@ \|\|\|\|\| \|\|\|\|\|\| \|:\|\| \|:\|\| : \|\|:\|\| \|\|\|\|\|:\|@LB@ CUUUU UCACCG UUAC GUUA G GUUGU GACACUG@LB@3'-UUU...ACAAC AG CC G CUUUUAUUUUA UUAUU...UUG-5'@LB@ \| \|@LB@ 65 16@LB@@LB@@LB@Energy -8.31 kcal/mol@LB@Hybridization Energy -29.1693 kcal/mol@LB@Unfolding Energy - mRNA 9.7543 kcal/mol@LB@Unfolding Energy - sRNA 11.1047 kcal/mol@LB@@LB@Position - mRNA 203 -- 237@LB@Position - sRNA 17 -- 64@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 17 -- 23@LB@
30	0.001842	0.2065	b3574	yiaJ	-8.97	0.194276	228 -- 279	20 -- 64	transcriptional repressor for the yiaKLMNO-lyxK-sgbHUE operon	_____________227_____________________________________________________280\n_____________\|_______________________________________________________\|\n5'-CCC...AAAAA_____CG__A___________GAAAAAGAGC______C______CC_________UUCGC...UUG-3'\n______________GAGAA__AG_UGGC___GCAG__________GUCCAG_CGGAAG__AGAGUCUGU\n______________\|\|:\|\|__\|\|_\|\|\|\|___\|\|\|:__________\|:\|\|\|:_\|:\|\|\|:__\|:\|:\|\|\|\|\|\n______________CUUUU__UC_ACCG___CGUU__________CGGGUU_GUCUUU__UUUUAGACA\n3'-UUU...ACAAC_____AG_______UUA____AC_____________________UA_________CUGUU...UUG-5'\n_____________\|_______________________________________________________\|\n_____________65______________________________________________________19\n	273 -- 279	20 -- 26	-33.3994 kcal/mol	13.3805 kcal/mol	11.0456 kcal/mol	227 280@LB@ \| \|@LB@5'-CCC...AAAAA CG A GAAAAAGAGC C CC UUCGC...UUG-3'@LB@ GAGAA AG UGGC GCAG GUCCAG CGGAAG AGAGUCUGU@LB@ \|\|:\|\| \|\| \|\|\|\| \|\|\|: \|:\|\|\|: \|:\|\|\|: \|:\|:\|\|\|\|\|@LB@ CUUUU UC ACCG CGUU CGGGUU GUCUUU UUUUAGACA@LB@3'-UUU...ACAAC AG UUA AC UA CUGUU...UUG-5'@LB@ \| \|@LB@ 65 19@LB@@LB@@LB@Energy -8.97 kcal/mol@LB@Hybridization Energy -33.3994 kcal/mol@LB@Unfolding Energy - mRNA 13.3805 kcal/mol@LB@Unfolding Energy - sRNA 11.0456 kcal/mol@LB@@LB@Position - mRNA 228 -- 279@LB@Position - sRNA 20 -- 64@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 20 -- 26@LB@
18	0.0007704	0.1438	b4526	ydaE	-7.35	0.372707	186 -- 222	21 -- 54	conserved protein Rac prophage	_____________185___________________________________223\n_____________\|_____________________________________\|\n5'-ACU...GUAAA_____A__C_____GA____UA____________G__CUUAC...UAU-3'\n______________GGCGG_GU_AUGGU__UGAC__AGAAAAUAAAAU_UG\n______________\|\|\|::_\|:_\|\|\|\|:__::\|\|__\|\|\|\|\|\|\|\|\|\|\|\|_\|\|\n______________CCGUU_CG_UACCG__GUUG__UCUUUUAUUUUA_AC\n3'-UUU...AGUCA_____A__U_____G___________________G__ACUGU...UUG-5'\n_____________\|_____________________________________\|\n_____________55____________________________________20\n	212 -- 218	25 -- 31	-28.7009 kcal/mol	12.2907 kcal/mol	9.06413 kcal/mol	185 223@LB@ \| \|@LB@5'-ACU...GUAAA A C GA UA G CUUAC...UAU-3'@LB@ GGCGG GU AUGGU UGAC AGAAAAUAAAAU UG@LB@ \|\|\|:: \|: \|\|\|\|: ::\|\| \|\|\|\|\|\|\|\|\|\|\|\| \|\|@LB@ CCGUU CG UACCG GUUG UCUUUUAUUUUA AC@LB@3'-UUU...AGUCA A U G G ACUGU...UUG-5'@LB@ \| \|@LB@ 55 20@LB@@LB@@LB@Energy -7.35 kcal/mol@LB@Hybridization Energy -28.7009 kcal/mol@LB@Unfolding Energy - mRNA 12.2907 kcal/mol@LB@Unfolding Energy - sRNA 9.06413 kcal/mol@LB@@LB@Position - mRNA 186 -- 222@LB@Position - sRNA 21 -- 54@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 25 -- 31@LB@
140	0.01599	0.3828	b0119	yacL	-11.32	0.063485	266 -- 299	25 -- 57	UPF0231 family protein	_____________265_________________________________300\n_____________\|___________________________________\|\n5'-GGU...CAUGA______CGG___C_________GA___________G-3'\n______________AGUGGU___GCA_UGGUUUAAU__AGA_GGUGAAA\n______________\|\|\|\|\|:___\|\|\|_\|\|\|:::\|\|:__\|\|\|_::\|:\|\|\|\n______________UCACCG___CGU_ACCGGGUUG__UCU_UUAUUUU\n3'-UUU...UUUAG______UUA___U______________U_______AGACA...UUG-5'\n_____________\|___________________________________\|\n_____________58__________________________________24\n	293 -- 299	25 -- 31	-25.5028 kcal/mol	4.248 kcal/mol	9.93955 kcal/mol	265 300@LB@ \| \|@LB@5'-GGU...CAUGA CGG C GA G-3'@LB@ AGUGGU GCA UGGUUUAAU AGA GGUGAAA@LB@ \|\|\|\|\|: \|\|\| \|\|\|:::\|\|: \|\|\| ::\|:\|\|\|@LB@ UCACCG CGU ACCGGGUUG UCU UUAUUUU@LB@3'-UUU...UUUAG UUA U U AGACA...UUG-5'@LB@ \| \|@LB@ 58 24@LB@@LB@@LB@Energy -11.32 kcal/mol@LB@Hybridization Energy -25.5028 kcal/mol@LB@Unfolding Energy - mRNA 4.248 kcal/mol@LB@Unfolding Energy - sRNA 9.93955 kcal/mol@LB@@LB@Position - mRNA 266 -- 299@LB@Position - sRNA 25 -- 57@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 25 -- 31@LB@
69	0.005697	0.2777	b0829	gsiA	-9.42	0.158982	246 -- 287	28 -- 64	glutathione ABC transporter ATPase	_____________245__________________________________________288\n_____________\|____________________________________________\|\n5'-CGG...CGGUU_______UGAAUAUU__CUUU_________A_____________GCUGC...GCA-3'\n______________GAAAAUC________GC____AUGCA__GG_CCAGCAGAAAAUA\n______________\|\|\|\|\|\|\|________\|\|____\|\|\|\|\|__\|\|_\|\|\|:\|\|\|\|\|\|\|\|\|\n______________CUUUUAG________CG____UACGU__CC_GGUUGUCUUUUAU\n3'-UUU...ACAAC_______UCAC______U________UA__G_____________UUUAG...UUG-5'\n_____________\|____________________________________________\|\n_____________65___________________________________________27\n	246 -- 252	58 -- 64	-27.8415 kcal/mol	7.44564 kcal/mol	10.972 kcal/mol	245 288@LB@ \| \|@LB@5'-CGG...CGGUU UGAAUAUU CUUU A GCUGC...GCA-3'@LB@ GAAAAUC GC AUGCA GG CCAGCAGAAAAUA@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\|\| \|\| \|\|\|:\|\|\|\|\|\|\|\|\|@LB@ CUUUUAG CG UACGU CC GGUUGUCUUUUAU@LB@3'-UUU...ACAAC UCAC U UA G UUUAG...UUG-5'@LB@ \| \|@LB@ 65 27@LB@@LB@@LB@Energy -9.42 kcal/mol@LB@Hybridization Energy -27.8415 kcal/mol@LB@Unfolding Energy - mRNA 7.44564 kcal/mol@LB@Unfolding Energy - sRNA 10.972 kcal/mol@LB@@LB@Position - mRNA 246 -- 287@LB@Position - sRNA 28 -- 64@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 58 -- 64@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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service.

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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