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	Additional homologs
171	0.006844	0.141	b4537	yecJ	-11.04	0.061373	25 -- 77	39 -- 91	DUF2766 family protein		_____________24_______________________________________________________78\n_____________\|________________________________________________________\|\n5'-UGA...GAAAA_____U______AA_____U___A__AC_________CGUACCGCC__________UUCCG...CGC-3'\n______________GUAUG__UCAAU____CUA_UGC_AG__GUUCAAAGA_________AGGCAAUAUG\n______________\|\|\|:\|__\|\|\|\|\|____\|\|\|_\|\|\|_\|\|__:\|\|\|\|\|\|:\|_________\|\|:\|\|\|\|\|\|\|\n______________CAUGC__AGUUA____GAU_ACG_UC__UAAGUUUUU_________UCUGUUAUAC\n3'-UUU...CGCAG_____UU_____ACAC__________AU_________UCCUUCAU___________CUCGC...ACG-5'\n_____________\|________________________________________________________\|\n_____________92_______________________________________________________38\n	71 -- 77	39 -- 45	-28.4449 kcal/mol	10.572 kcal/mol	6.83352 kcal/mol	24 78@LB@ \| \|@LB@5'-UGA...GAAAA U AA U A AC CGUACCGCC UUCCG...CGC-3'@LB@ GUAUG UCAAU CUA UGC AG GUUCAAAGA AGGCAAUAUG@LB@ \|\|\|:\| \|\|\|\|\| \|\|\| \|\|\| \|\| :\|\|\|\|\|\|:\| \|\|:\|\|\|\|\|\|\|@LB@ CAUGC AGUUA GAU ACG UC UAAGUUUUU UCUGUUAUAC@LB@3'-UUU...CGCAG UU ACAC AU UCCUUCAU CUCGC...ACG-5'@LB@ \| \|@LB@ 92 38@LB@@LB@@LB@Energy -11.04 kcal/mol@LB@Hybridization Energy -28.4449 kcal/mol@LB@Unfolding Energy - mRNA 10.572 kcal/mol@LB@Unfolding Energy - sRNA 6.83352 kcal/mol@LB@@LB@Position - mRNA 25 -- 77@LB@Position - sRNA 39 -- 91@LB@Position Seed - mRNA 71 -- 77@LB@Position Seed - sRNA 39 -- 45@LB@
77	0.00185	0.08273	b2325	yfcL	-11.04	0.061434	190 -- 213	35 -- 57	uncharacterized protein		_____________189______________________214\n_____________\|________________________\|\n5'-AAC...ACAAU______AG________CGC_____UUGAA...GCC-3'\n______________GAGGAA__AAGAUGAU___GGAGU\n______________:\|\|\|\|\|__\|\|\|\|::\|\|___\|\|\|\|:\n______________UUCCUU__UUCUGUUA___CCUCG\n3'-UUU...GUUUU______CA________UA______CGUUG...ACG-5'\n_____________\|________________________\|\n_____________58_______________________34\n	199 -- 205	42 -- 48	-19.5886 kcal/mol	4.3321 kcal/mol	4.1846 kcal/mol	189 214@LB@ \| \|@LB@5'-AAC...ACAAU AG CGC UUGAA...GCC-3'@LB@ GAGGAA AAGAUGAU GGAGU@LB@ :\|\|\|\|\| \|\|\|\|::\|\| \|\|\|\|:@LB@ UUCCUU UUCUGUUA CCUCG@LB@3'-UUU...GUUUU CA UA CGUUG...ACG-5'@LB@ \| \|@LB@ 58 34@LB@@LB@@LB@Energy -11.04 kcal/mol@LB@Hybridization Energy -19.5886 kcal/mol@LB@Unfolding Energy - mRNA 4.3321 kcal/mol@LB@Unfolding Energy - sRNA 4.1846 kcal/mol@LB@@LB@Position - mRNA 190 -- 213@LB@Position - sRNA 35 -- 57@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 42 -- 48@LB@
126	0.004539	0.1258	b0546	ybcM	-11.00	0.062763	188 -- 220	45 -- 91	DLP12 prophage; putative DNA-binding transcriptional regulator	b1499 b0564 b3515 b4116 b0566 b3516	_____________187_____________________________________________221\n_____________\|_______________________________________________\|\n5'-GCU...AUAAA___G__UGA__GUA_________A_______________________UAACU...GUC-3'\n______________GUA_GG___GA___UGCUG_GCA______________GAGGUAAGAC\n______________\|\|\|_\|:___:\|___\|\|\|\|:_\|\|\|______________\|\|:\|\|\|\|\|\|\|\n______________CAU_CU___UU___ACGAU_CGU______________CUUCAUUCUG\n3'-UUU...CGCAG___G__UAG__AAC_____A___CAUUAAGUUUUUUC__________UUAUA...ACG-5'\n_____________\|_______________________________________________\|\n_____________92______________________________________________44\n	214 -- 220	45 -- 51	-23.4531 kcal/mol	6.72952 kcal/mol	5.72765 kcal/mol	187 221@LB@ \| \|@LB@5'-GCU...AUAAA G UGA GUA A UAACU...GUC-3'@LB@ GUA GG GA UGCUG GCA GAGGUAAGAC@LB@ \|\|\| \|: :\| \|\|\|\|: \|\|\| \|\|:\|\|\|\|\|\|\|@LB@ CAU CU UU ACGAU CGU CUUCAUUCUG@LB@3'-UUU...CGCAG G UAG AAC A CAUUAAGUUUUUUC UUAUA...ACG-5'@LB@ \| \|@LB@ 92 44@LB@@LB@@LB@Energy -11.00 kcal/mol@LB@Hybridization Energy -23.4531 kcal/mol@LB@Unfolding Energy - mRNA 6.72952 kcal/mol@LB@Unfolding Energy - sRNA 5.72765 kcal/mol@LB@@LB@Position - mRNA 188 -- 220@LB@Position - sRNA 45 -- 91@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 45 -- 51@LB@
142	0.005444	0.1351	b3950	frwB	-10.99	0.063119	13 -- 50	47 -- 86	putative enzyme IIB component of PTS	b3899	_____________12__________________________________________51\n_____________\|___________________________________________\|\n5'-GCA...GGGGU____U__________C__________________C___C____UUAUA...GGG-3'\n______________GGUC_GAUUGUGCUG__CGGUGGUU____GAAGG_AAG_UGGG\n______________::\|\|_:\|\|\|\|\|\|\|\|:__\|:\|\|::\|\|____:\|\|\|\|_\|\|\|_\|::\|\n______________UUAG_UUAACACGAU__GUCAUUAA____UUUCC_UUC_AUUC\n3'-UUU...CAUGC_______________AC________GUUU______________UGUUA...ACG-5'\n_____________\|___________________________________________\|\n_____________87__________________________________________46\n	30 -- 36	63 -- 69	-27.1662 kcal/mol	11.4404 kcal/mol	4.74035 kcal/mol	12 51@LB@ \| \|@LB@5'-GCA...GGGGU U C C C UUAUA...GGG-3'@LB@ GGUC GAUUGUGCUG CGGUGGUU GAAGG AAG UGGG@LB@ ::\|\| :\|\|\|\|\|\|\|\|: \|:\|\|::\|\| :\|\|\|\| \|\|\| \|::\|@LB@ UUAG UUAACACGAU GUCAUUAA UUUCC UUC AUUC@LB@3'-UUU...CAUGC AC GUUU UGUUA...ACG-5'@LB@ \| \|@LB@ 87 46@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -27.1662 kcal/mol@LB@Unfolding Energy - mRNA 11.4404 kcal/mol@LB@Unfolding Energy - sRNA 4.74035 kcal/mol@LB@@LB@Position - mRNA 13 -- 50@LB@Position - sRNA 47 -- 86@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 63 -- 69@LB@
173	0.007186	0.145	b3554	yiaF	-10.99	0.063148	166 -- 198	46 -- 94	barrier effect co-colonization resistance factor; DUF3053 family lipoprotein		_____________165_______________________________________________199\n_____________\|_________________________________________________\|\n5'-AAU...GUGUC________CU__UU___G_______________________________AAAUG...AGC-3'\n______________GUUGUGCG__UU__UUG_GU_______________GAAAGG_AGUAAGA\n______________\|\|:\|\|:\|\|__\|:__\|\|\|_\|:_______________:\|\|\|\|\|_\|\|\|\|\|\|\|\n______________CAGCAUGC__AG__AAC_CG_______________UUUUCC_UCAUUCU\n3'-UUU...AGCCG________UU__UU___A__AUACGUCAUUAAGUU______U_______GUUAU...ACG-5'\n_____________\|_________________________________________________\|\n_____________95________________________________________________45\n	192 -- 198	46 -- 52	-24.2986 kcal/mol	7.73667 kcal/mol	5.5768 kcal/mol	165 199@LB@ \| \|@LB@5'-AAU...GUGUC CU UU G AAAUG...AGC-3'@LB@ GUUGUGCG UU UUG GU GAAAGG AGUAAGA@LB@ \|\|:\|\|:\|\| \|: \|\|\| \|: :\|\|\|\|\| \|\|\|\|\|\|\|@LB@ CAGCAUGC AG AAC CG UUUUCC UCAUUCU@LB@3'-UUU...AGCCG UU UU A AUACGUCAUUAAGUU U GUUAU...ACG-5'@LB@ \| \|@LB@ 95 45@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -24.2986 kcal/mol@LB@Unfolding Energy - mRNA 7.73667 kcal/mol@LB@Unfolding Energy - sRNA 5.5768 kcal/mol@LB@@LB@Position - mRNA 166 -- 198@LB@Position - sRNA 46 -- 94@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 46 -- 52@LB@
89	0.002455	0.09689	b0466	ybaM	-10.99	0.063193	248 -- 263	68 -- 82	DUF2496 family protein		_____________247______________264\n_____________\|________________\|\n5'-GCA...GAUUU__________C__G__GAAAA...CGC-3'\n______________GAUUGUGCUG_UG_AG\n______________:\|\|\|\|\|\|\|\|:_\|\|_\|\|\n______________UUAACACGAU_AC_UC\n3'-UUU...CUUAG_____________G__AUUAA...ACG-5'\n_____________\|________________\|\n_____________83_______________67\n	251 -- 257	73 -- 79	-16.1643 kcal/mol	2.45269 kcal/mol	2.72435 kcal/mol	247 264@LB@ \| \|@LB@5'-GCA...GAUUU C G GAAAA...CGC-3'@LB@ GAUUGUGCUG UG AG@LB@ :\|\|\|\|\|\|\|\|: \|\| \|\|@LB@ UUAACACGAU AC UC@LB@3'-UUU...CUUAG G AUUAA...ACG-5'@LB@ \| \|@LB@ 83 67@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -16.1643 kcal/mol@LB@Unfolding Energy - mRNA 2.45269 kcal/mol@LB@Unfolding Energy - sRNA 2.72435 kcal/mol@LB@@LB@Position - mRNA 248 -- 263@LB@Position - sRNA 68 -- 82@LB@Position Seed - mRNA 251 -- 257@LB@Position Seed - sRNA 73 -- 79@LB@
101	0.003313	0.1114	b1193	emtA	-10.98	0.063602	227 -- 257	55 -- 82	lytic murein endotransglycosylase E		_____________226_____________________________258\n_____________\|_______________________________\|\n5'-UUG...UUUUU___________UA____GUU_____UC____CAUGA...UGC-3'\n______________GAUUGUGUUAU__GCGG___GUUCA__AAAG\n______________:\|\|\|\|\|\|:\|\|\|__\|\|:\|___:\|\|\|\|__\|\|\|\|\n______________UUAACACGAUA__CGUC___UAAGU__UUUC\n3'-UUU...CUUAG_________________AU______UU____CUUCA...ACG-5'\n_____________\|_______________________________\|\n_____________83______________________________54\n	231 -- 237	72 -- 78	-21.9468 kcal/mol	7.33111 kcal/mol	3.63929 kcal/mol	226 258@LB@ \| \|@LB@5'-UUG...UUUUU UA GUU UC CAUGA...UGC-3'@LB@ GAUUGUGUUAU GCGG GUUCA AAAG@LB@ :\|\|\|\|\|\|:\|\|\| \|\|:\| :\|\|\|\| \|\|\|\|@LB@ UUAACACGAUA CGUC UAAGU UUUC@LB@3'-UUU...CUUAG AU UU CUUCA...ACG-5'@LB@ \| \|@LB@ 83 54@LB@@LB@@LB@Energy -10.98 kcal/mol@LB@Hybridization Energy -21.9468 kcal/mol@LB@Unfolding Energy - mRNA 7.33111 kcal/mol@LB@Unfolding Energy - sRNA 3.63929 kcal/mol@LB@@LB@Position - mRNA 227 -- 257@LB@Position - sRNA 55 -- 82@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 72 -- 78@LB@
16	3.593e-05	0.007912	b2294	yfbU	-10.97	0.063921	276 -- 297	1 -- 22	UPF0304 family protein		_____________275____________________298\n_____________\|______________________\|\n5'-GCA...CAAAU___GA_____ACCG________AAA-3'\n______________GCU__ACGUU____UCGCCUGC\n______________\|\|\|__\|\|\|\|\|____\|\|:\|\|\|\|\|\n______________CGA__UGCAA____AGUGGACG\n3'-UUU...GGUAG___AC_____CGUA________-5'\n_____________\|_____________________\|\n_____________23____________________1\n	291 -- 297	1 -- 7	-25.1893 kcal/mol	6.12655 kcal/mol	8.09964 kcal/mol	275 298@LB@ \| \|@LB@5'-GCA...CAAAU GA ACCG AAA-3'@LB@ GCU ACGUU UCGCCUGC@LB@ \|\|\| \|\|\|\|\| \|\|:\|\|\|\|\|@LB@ CGA UGCAA AGUGGACG@LB@3'-UUU...GGUAG AC CGUA -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -10.97 kcal/mol@LB@Hybridization Energy -25.1893 kcal/mol@LB@Unfolding Energy - mRNA 6.12655 kcal/mol@LB@Unfolding Energy - sRNA 8.09964 kcal/mol@LB@@LB@Position - mRNA 276 -- 297@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 1 -- 7@LB@
107	0.003422	0.1114	b0415	ribE	-10.96	0.064092	190 -- 254	4 -- 58	riboflavin synthase beta chain		_____________189_________________________________________________________________255\n_____________\|___________________________________________________________________\|\n5'-CGG...AACCC________AAAAU_A___U___U_A_________UUGCUAC____GA____C_____C__CA_____AUCGC...GUG-3'\n______________GAAGGAAG_____G_ACA_UAU_G_AGC_UAACG_______CCCG__CGCU__GCGU_GC__UCACC\n______________:\|\|\|\|\|\|\|_____\|_\|\|\|_\|\|\|_\|_\|\|\|_:\|\|\|\|_______\|\|\|:__\|\|\|\|__:\|\|\|_\|\|__\|\|\|\|\|\n______________UUUCCUUC_____C_UGU_AUA_C_UCG_GUUGC_______GGGU__GCGA__UGCA_CG__AGUGG\n3'-UUU...AGUUU________AUU_______U___C_____C________________A_____AC____A__UA_____ACG-5'\n_____________\|___________________________________________________________________\|\n_____________59__________________________________________________________________3\n	191 -- 197	51 -- 57	-41.366 kcal/mol	13.5359 kcal/mol	16.8715 kcal/mol	189 255@LB@ \| \|@LB@5'-CGG...AACCC AAAAU A U U A UUGCUAC GA C C CA AUCGC...GUG-3'@LB@ GAAGGAAG G ACA UAU G AGC UAACG CCCG CGCU GCGU GC UCACC@LB@ :\|\|\|\|\|\|\| \| \|\|\| \|\|\| \| \|\|\| :\|\|\|\| \|\|\|: \|\|\|\| :\|\|\| \|\| \|\|\|\|\|@LB@ UUUCCUUC C UGU AUA C UCG GUUGC GGGU GCGA UGCA CG AGUGG@LB@3'-UUU...AGUUU AUU U C C A AC A UA ACG-5'@LB@ \| \|@LB@ 59 3@LB@@LB@@LB@Energy -10.96 kcal/mol@LB@Hybridization Energy -41.366 kcal/mol@LB@Unfolding Energy - mRNA 13.5359 kcal/mol@LB@Unfolding Energy - sRNA 16.8715 kcal/mol@LB@@LB@Position - mRNA 190 -- 254@LB@Position - sRNA 4 -- 58@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 51 -- 57@LB@
113	0.00365	0.1131	b3154	yhbP	-10.91	0.065979	249 -- 297	26 -- 85	UPF0306 family protein		_____________248___________________________________________________________298\n_____________\|_____________________________________________________________\|\n5'-AAA...AUGUU____C___GUG_______C_____________________ACUC____U____U_______UUU-3'\n______________GUCA_UUG___UGUGCAG___________AGGAAG_GGGA_____UGG_GCGC_AAUGCCU\n______________:\|\|\|_\|\|\|___\|:\|\|\|\|\|___________\|\|\|\|\|\|_::\|\|_____\|\|\|_\|\|\|\|_\|\|:\|\|\|:\n______________UAGU_AAC___AUACGUC___________UCCUUC_UUCU_____ACC_CGCG_UUGCGGG\n3'-UUU...AUGCU____U___ACG_______AUUAAGUUUUU______A____GUUAU___U____________UAGCG...ACG-5'\n_____________\|_____________________________________________________________\|\n_____________86____________________________________________________________25\n	260 -- 266	68 -- 74	-42.816 kcal/mol	18.2405 kcal/mol	13.6657 kcal/mol	248 298@LB@ \| \|@LB@5'-AAA...AUGUU C GUG C ACUC U U UUU-3'@LB@ GUCA UUG UGUGCAG AGGAAG GGGA UGG GCGC AAUGCCU@LB@ :\|\|\| \|\|\| \|:\|\|\|\|\| \|\|\|\|\|\| ::\|\| \|\|\| \|\|\|\| \|\|:\|\|\|:@LB@ UAGU AAC AUACGUC UCCUUC UUCU ACC CGCG UUGCGGG@LB@3'-UUU...AUGCU U ACG AUUAAGUUUUU A GUUAU U UAGCG...ACG-5'@LB@ \| \|@LB@ 86 25@LB@@LB@@LB@Energy -10.91 kcal/mol@LB@Hybridization Energy -42.816 kcal/mol@LB@Unfolding Energy - mRNA 18.2405 kcal/mol@LB@Unfolding Energy - sRNA 13.6657 kcal/mol@LB@@LB@Position - mRNA 249 -- 297@LB@Position - sRNA 26 -- 85@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 68 -- 74@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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