Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
147	0.005701	0.1366	b1622	malY	-7.52	0.364460	44 -- 91	35 -- 85	PLP-dependent beta-cystathionase and maltose regulon regulator	_____________43____________________________________________________92\n_____________\|_____________________________________________________\|\n5'-UCG...GAUAU____C____UAA_______GCACU__________CAAUC___________C__AGUAC...UCA-3'\n______________GUCG_UUGU___UGUGCAG_________GAAGGA_____GGGCAAU_UGG_GU\n______________:\|\|:_\|\|\|\|___\|:\|\|\|\|\|_________:\|\|\|\|\|_____:\|:\|\|\|\|_\|\|\|_\|:\n______________UAGU_AACA___AUACGUC_________UUUCCU_____UCUGUUA_ACC_CG\n3'-UUU...AUGCU____U____CG________AUUAAGUUU______UCAU________U___U__CGUUG...ACG-5'\n_____________\|_____________________________________________________\|\n_____________86____________________________________________________34\n	79 -- 85	42 -- 48	-29.3049 kcal/mol	13.5755 kcal/mol	8.20283 kcal/mol	43 92@LB@ \| \|@LB@5'-UCG...GAUAU C UAA GCACU CAAUC C AGUAC...UCA-3'@LB@ GUCG UUGU UGUGCAG GAAGGA GGGCAAU UGG GU@LB@ :\|\|: \|\|\|\| \|:\|\|\|\|\| :\|\|\|\|\| :\|:\|\|\|\| \|\|\| \|:@LB@ UAGU AACA AUACGUC UUUCCU UCUGUUA ACC CG@LB@3'-UUU...AUGCU U CG AUUAAGUUU UCAU U U CGUUG...ACG-5'@LB@ \| \|@LB@ 86 34@LB@@LB@@LB@Energy -7.52 kcal/mol@LB@Hybridization Energy -29.3049 kcal/mol@LB@Unfolding Energy - mRNA 13.5755 kcal/mol@LB@Unfolding Energy - sRNA 8.20283 kcal/mol@LB@@LB@Position - mRNA 44 -- 91@LB@Position - sRNA 35 -- 85@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 42 -- 48@LB@
148	0.005829	0.1368	b2962	yggX	-8.12	0.280656	21 -- 35	68 -- 81	oxidative damage protective factor for iron-sulfur proteins	_____________20______________36\n_____________\|_______________\|\n5'-UCA...UAGAU______C________CUUCC...AGA-3'\n______________AUUGUG_CUAUGUGG\n______________\|\|\|\|\|\|_\|\|\|\|\|::\|\n______________UAACAC_GAUACGUC\n3'-UUU...UUAGU_______________AUUAA...ACG-5'\n_____________\|_______________\|\n_____________82______________67\n	28 -- 34	69 -- 75	-14.4611 kcal/mol	4.51468 kcal/mol	1.82249 kcal/mol	20 36@LB@ \| \|@LB@5'-UCA...UAGAU C CUUCC...AGA-3'@LB@ AUUGUG CUAUGUGG@LB@ \|\|\|\|\|\| \|\|\|\|\|::\|@LB@ UAACAC GAUACGUC@LB@3'-UUU...UUAGU AUUAA...ACG-5'@LB@ \| \|@LB@ 82 67@LB@@LB@@LB@Energy -8.12 kcal/mol@LB@Hybridization Energy -14.4611 kcal/mol@LB@Unfolding Energy - mRNA 4.51468 kcal/mol@LB@Unfolding Energy - sRNA 1.82249 kcal/mol@LB@@LB@Position - mRNA 21 -- 35@LB@Position - sRNA 68 -- 81@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 69 -- 75@LB@
149	0.005854	0.1368	b2166	psuK	-12.08	0.032688	265 -- 298	54 -- 89	pseudouridine kinase	_____________264___________________________________299\n_____________\|_____________________________________\|\n5'-UUU...UUCAC________UUAAA__________________UCC___UA-3'\n______________AUGAAUCA______UUAUGCGG__AUUCAAA___AGG\n______________\|:\|\|\|\|\|\|______:\|\|\|\|\|:\|__\|\|\|\|\|\|\|___\|\|\|\n______________UGCUUAGU______GAUACGUC__UAAGUUU___UCC\n3'-UUU...CAGCA________UAACAC________AU_______UU____UUCAU...ACG-5'\n_____________\|_____________________________________\|\n_____________90____________________________________53\n	279 -- 285	68 -- 74	-22.7366 kcal/mol	5.9989 kcal/mol	4.66068 kcal/mol	264 299@LB@ \| \|@LB@5'-UUU...UUCAC UUAAA UCC UA-3'@LB@ AUGAAUCA UUAUGCGG AUUCAAA AGG@LB@ \|:\|\|\|\|\|\| :\|\|\|\|\|:\| \|\|\|\|\|\|\| \|\|\|@LB@ UGCUUAGU GAUACGUC UAAGUUU UCC@LB@3'-UUU...CAGCA UAACAC AU UU UUCAU...ACG-5'@LB@ \| \|@LB@ 90 53@LB@@LB@@LB@Energy -12.08 kcal/mol@LB@Hybridization Energy -22.7366 kcal/mol@LB@Unfolding Energy - mRNA 5.9989 kcal/mol@LB@Unfolding Energy - sRNA 4.66068 kcal/mol@LB@@LB@Position - mRNA 265 -- 298@LB@Position - sRNA 54 -- 89@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 68 -- 74@LB@
150	0.005897	0.1368	b0887	cydD	-10.72	0.073556	183 -- 190	1 -- 8	glutathione/cysteine ABC transporter export permease/ATPase	_____________182______191\n_____________\|________\|\n5'-AUU...AUAAC________UAAGC...UGA-3'\n______________UCACCUGC\n______________\|\|\|\|\|\|\|\|\n______________AGUGGACG\n3'-UUU...ACGUA________-5'\n_____________\|_______\|\n_____________9_______1\n	184 -- 190	1 -- 7	-15.001 kcal/mol	1.91816 kcal/mol	2.36381 kcal/mol	182 191@LB@ \| \|@LB@5'-AUU...AUAAC UAAGC...UGA-3'@LB@ UCACCUGC@LB@ \|\|\|\|\|\|\|\|@LB@ AGUGGACG@LB@3'-UUU...ACGUA -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -10.72 kcal/mol@LB@Hybridization Energy -15.001 kcal/mol@LB@Unfolding Energy - mRNA 1.91816 kcal/mol@LB@Unfolding Energy - sRNA 2.36381 kcal/mol@LB@@LB@Position - mRNA 183 -- 190@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 1 -- 7@LB@
151	0.005924	0.1368	b3248	yhdE	-13.35	0.014399	2 -- 41	1 -- 42	dTTP/UTP pyrophosphatase; m(5)UTP/m(5)CTP/pseudo-UTP pyrophosphatase	_____________1___________________________________________42\n_____________\|___________________________________________\|\n__________5'-U_____C___A_______G_____C_________U______G__GGUGG...AGC-3'\n______________UAUGG_AGC__GGCGCU_GUCGU___AUGUUGC_UUCGCU_GU\n______________\|\|\|\|\|_\|\|\|__::\|\|\|:_:\|\|\|:___\|:\|\|\|\|\|_\|\|\|:\|:_\|:\n______________AUACC_UCG__UUGCGG_UAGCG___UGCAACG_AAGUGG_CG\n3'-UUU...CUGUU_________CG______G_____AAC_______U______A__-5'\n_____________\|__________________________________________\|\n_____________43_________________________________________1\n	25 -- 31	11 -- 17	-43.9582 kcal/mol	15.3205 kcal/mol	15.293 kcal/mol	1 42@LB@ \| \|@LB@ 5'-U C A G C U G GGUGG...AGC-3'@LB@ UAUGG AGC GGCGCU GUCGU AUGUUGC UUCGCU GU@LB@ \|\|\|\|\| \|\|\| ::\|\|\|: :\|\|\|: \|:\|\|\|\|\| \|\|\|:\|: \|:@LB@ AUACC UCG UUGCGG UAGCG UGCAACG AAGUGG CG@LB@3'-UUU...CUGUU CG G AAC U A -5'@LB@ \| \|@LB@ 43 1@LB@@LB@@LB@Energy -13.35 kcal/mol@LB@Hybridization Energy -43.9582 kcal/mol@LB@Unfolding Energy - mRNA 15.3205 kcal/mol@LB@Unfolding Energy - sRNA 15.293 kcal/mol@LB@@LB@Position - mRNA 2 -- 41@LB@Position - sRNA 1 -- 42@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 11 -- 17@LB@
152	0.005935	0.1368	b2701	mltB	-9.57	0.138424	83 -- 107	69 -- 92	membrane-bound lytic murein transglycosylase B	_____________82________________________108\n_____________\|_________________________\|\n5'-AGA...GAUAG__AG_G____G_____A________AAGUC...GAA-3'\n______________CG__G_GAAU_AGUUG_GUUAUGUA\n______________\|\|__:_\|\|\|\|_\|:\|\|\|_\|:\|\|\|\|:\|\n______________GC__U_CUUA_UUAAC_CGAUACGU\n3'-UUU...CCGCA__A__G____G_____A________CAUUA...ACG-5'\n_____________\|_________________________\|\n_____________93________________________68\n	101 -- 107	69 -- 75	-19.8359 kcal/mol	5.60429 kcal/mol	4.66371 kcal/mol	82 108@LB@ \| \|@LB@5'-AGA...GAUAG AG G G A AAGUC...GAA-3'@LB@ CG G GAAU AGUUG GUUAUGUA@LB@ \|\| : \|\|\|\| \|:\|\|\| \|:\|\|\|\|:\|@LB@ GC U CUUA UUAAC CGAUACGU@LB@3'-UUU...CCGCA A G G A CAUUA...ACG-5'@LB@ \| \|@LB@ 93 68@LB@@LB@@LB@Energy -9.57 kcal/mol@LB@Hybridization Energy -19.8359 kcal/mol@LB@Unfolding Energy - mRNA 5.60429 kcal/mol@LB@Unfolding Energy - sRNA 4.66371 kcal/mol@LB@@LB@Position - mRNA 83 -- 107@LB@Position - sRNA 69 -- 92@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 69 -- 75@LB@
153	0.00596	0.1368	b3892	fdoI	-11.89	0.036676	181 -- 200	31 -- 53	formate dehydrogenase-O cytochrome b556 subunit	_____________180_____________________201\n_____________\|_______________________\|\n5'-CCA...ACGAA___A___________________AUGAA...UGG-3'\n______________GAG_AAGACGA___GGAGCGCAA\n______________:\|\|_\|\|\|\|\|:\|___\|\|\|\|\|\|\|\|\|\n______________UUC_UUCUGUU___CCUCGCGUU\n3'-UUU...UUUCC___A_______AUA_________GCGGG...ACG-5'\n_____________\|_______________________\|\n_____________54______________________30\n	194 -- 200	31 -- 37	-24.6235 kcal/mol	2.95491 kcal/mol	9.77014 kcal/mol	180 201@LB@ \| \|@LB@5'-CCA...ACGAA A AUGAA...UGG-3'@LB@ GAG AAGACGA GGAGCGCAA@LB@ :\|\| \|\|\|\|\|:\| \|\|\|\|\|\|\|\|\|@LB@ UUC UUCUGUU CCUCGCGUU@LB@3'-UUU...UUUCC A AUA GCGGG...ACG-5'@LB@ \| \|@LB@ 54 30@LB@@LB@@LB@Energy -11.89 kcal/mol@LB@Hybridization Energy -24.6235 kcal/mol@LB@Unfolding Energy - mRNA 2.95491 kcal/mol@LB@Unfolding Energy - sRNA 9.77014 kcal/mol@LB@@LB@Position - mRNA 181 -- 200@LB@Position - sRNA 31 -- 53@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 31 -- 37@LB@
154	0.005979	0.1368	b4136	dsbD	-7.81	0.321864	41 -- 58	35 -- 56	thiol:disulfide interchange protein and activator of DsbC	_____________40______________________59\n_____________\|_______________________\|\n5'-UGC...UUACU___A___________________AAGAA...CGG-3'\n______________GGG_AGGUAAG_C____UGGAGC\n______________:\|\|_\|:\|\|\|\|\|_\|____\|\|\|\|\|\|\n______________UCC_UUCAUUC_G____ACCUCG\n3'-UUU...UUUUU___________U_UUAU______CGUUG...ACG-5'\n_____________\|_______________________\|\n_____________57______________________34\n	45 -- 51	47 -- 53	-17.7247 kcal/mol	5.71782 kcal/mol	4.15888 kcal/mol	40 59@LB@ \| \|@LB@5'-UGC...UUACU A AAGAA...CGG-3'@LB@ GGG AGGUAAG C UGGAGC@LB@ :\|\| \|:\|\|\|\|\| \| \|\|\|\|\|\|@LB@ UCC UUCAUUC G ACCUCG@LB@3'-UUU...UUUUU U UUAU CGUUG...ACG-5'@LB@ \| \|@LB@ 57 34@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -17.7247 kcal/mol@LB@Unfolding Energy - mRNA 5.71782 kcal/mol@LB@Unfolding Energy - sRNA 4.15888 kcal/mol@LB@@LB@Position - mRNA 41 -- 58@LB@Position - sRNA 35 -- 56@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 47 -- 53@LB@
155	0.006038	0.137	b4374	yjjG	-10.88	0.067155	203 -- 266	1 -- 54	dUMP phosphatase	_____________202_____________________________________________________________________267\n_____________\|_______________________________________________________________________\|\n5'-CUG...AUAAU__________________UUUUCUUU______G__GAAA____GUUUACCUU____U___________G__CUGCA...CCU-3'\n______________GAAGUGGGAC____UGGA________GAUGCC_AU____CGCU_________UGAC____CAUUCACC_GC\n______________\|\|\|\|\|::\|\|\|____\|\|\|\|________:\|:\|\|\|_\|\|____\|\|\|\|_________\|\|\|\|____\|\|\|\|\|\|\|\|_\|\|\n______________CUUCAUUCUG____ACCU________UUGCGG_UA____GCGA_________ACUG____GUAAGUGG_CG\n3'-UUU...UUUUC__________UUAU____CGCG__________G_______________________CAAC________A__-5'\n_____________\|______________________________________________________________________\|\n_____________55_____________________________________________________________________1\n	257 -- 263	4 -- 10	-41.6423 kcal/mol	13.9643 kcal/mol	16.8 kcal/mol	202 267@LB@ \| \|@LB@5'-CUG...AUAAU UUUUCUUU G GAAA GUUUACCUU U G CUGCA...CCU-3'@LB@ GAAGUGGGAC UGGA GAUGCC AU CGCU UGAC CAUUCACC GC@LB@ \|\|\|\|\|::\|\|\| \|\|\|\| :\|:\|\|\| \|\| \|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\| \|\|@LB@ CUUCAUUCUG ACCU UUGCGG UA GCGA ACUG GUAAGUGG CG@LB@3'-UUU...UUUUC UUAU CGCG G CAAC A -5'@LB@ \| \|@LB@ 55 1@LB@@LB@@LB@Energy -10.88 kcal/mol@LB@Hybridization Energy -41.6423 kcal/mol@LB@Unfolding Energy - mRNA 13.9643 kcal/mol@LB@Unfolding Energy - sRNA 16.8 kcal/mol@LB@@LB@Position - mRNA 203 -- 266@LB@Position - sRNA 1 -- 54@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 4 -- 10@LB@
157	0.006139	0.1377	b2347	yfdC	-9.29	0.160067	171 -- 205	37 -- 76	putative inner membrane protein	_____________170________________________________________206\n_____________\|__________________________________________\|\n5'-GCA...CUUUA_____AC___C_______________________C_______CAACG...UCC-3'\n______________GCUAU__GUG_UAAUUCAAGA___GAAG__AGAC___AUGGA\n______________\|\|\|\|\|__\|::_\|\|\|\|\|\|\|\|:\|___\|\|\|\|__\|\|\|\|___\|\|\|\|\|\n______________CGAUA__CGU_AUUAAGUUUU___CUUC__UCUG___UACCU\n3'-UUU...UAACA__________C__________UUC____AU____UUA_____CGCGU...ACG-5'\n_____________\|__________________________________________\|\n_____________77_________________________________________36\n	185 -- 191	58 -- 64	-24.5838 kcal/mol	7.63937 kcal/mol	7.64142 kcal/mol	170 206@LB@ \| \|@LB@5'-GCA...CUUUA AC C C CAACG...UCC-3'@LB@ GCUAU GUG UAAUUCAAGA GAAG AGAC AUGGA@LB@ \|\|\|\|\| \|:: \|\|\|\|\|\|\|\|:\| \|\|\|\| \|\|\|\| \|\|\|\|\|@LB@ CGAUA CGU AUUAAGUUUU CUUC UCUG UACCU@LB@3'-UUU...UAACA C UUC AU UUA CGCGU...ACG-5'@LB@ \| \|@LB@ 77 36@LB@@LB@@LB@Energy -9.29 kcal/mol@LB@Hybridization Energy -24.5838 kcal/mol@LB@Unfolding Energy - mRNA 7.63937 kcal/mol@LB@Unfolding Energy - sRNA 7.64142 kcal/mol@LB@@LB@Position - mRNA 171 -- 205@LB@Position - sRNA 37 -- 76@LB@Position Seed - mRNA 185 -- 191@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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