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
138	0.00525	0.1336	b0031	dapB	-12.01	0.034078	16 -- 66	61 -- 114	dihydrodipicolinate reductase		_____________15____________________________________________________________67\n_____________\|_____________________________________________________________\|\n5'-GUG...GAGGU__________________________ACCU____CAUGUU_______________C_____UCGAC...UGG-3'\n______________GCUGGCUC________UGGCGUCGUA____GUCA______AUUG_GC_AUGCAGU_AUUCA\n______________\|\|:\|:\|\|\|________:\|\|\|\|\|\|\|\|\|____:\|\|\|______\|\|\|\|_\|\|_\|\|\|\|\|\|\|_\|\|\|\|\|\n______________CGGCUGAG________GCCGCAGCAU____UAGU______UAAC_CG_UACGUCA_UAAGU\n___3'-UUUUUUUU________UAGUUUCA__________GCU_______________A__A_______U_____UUUUU...ACG-5'\n_____________\|_____________________________________________________________\|\n_____________115___________________________________________________________60\n	54 -- 60	67 -- 73	-49.0979 kcal/mol	18.4253 kcal/mol	18.6631 kcal/mol	15 67@LB@ \| \|@LB@5'-GUG...GAGGU ACCU CAUGUU C UCGAC...UGG-3'@LB@ GCUGGCUC UGGCGUCGUA GUCA AUUG GC AUGCAGU AUUCA@LB@ \|\|:\|:\|\|\| :\|\|\|\|\|\|\|\|\| :\|\|\| \|\|\|\| \|\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ CGGCUGAG GCCGCAGCAU UAGU UAAC CG UACGUCA UAAGU@LB@ 3'-UUUUUUUU UAGUUUCA GCU A A U UUUUU...ACG-5'@LB@ \| \|@LB@ 115 60@LB@@LB@@LB@Energy -12.01 kcal/mol@LB@Hybridization Energy -49.0979 kcal/mol@LB@Unfolding Energy - mRNA 18.4253 kcal/mol@LB@Unfolding Energy - sRNA 18.6631 kcal/mol@LB@@LB@Position - mRNA 16 -- 66@LB@Position - sRNA 61 -- 114@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 67 -- 73@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@
106	0.003401	0.1114	b1848	yebG	-10.18	0.099613	222 -- 299	16 -- 71	DNA damage-inducible protein regulated by LexA		_____________221_______________________________________________________________________________300\n_____________\|_________________________________________________________________________________\|\n5'-GUU...AAUAC_____C_____U_____C_________A_____CGUUUACCAGCAAAAA__A______________GACAAAA________A-3'\n______________GUAGU_AUUCG_GAGGG_GAAG__AGA_AAUGU________________GG_AGC_CGAUGCUUAU_______UGCUUGAU\n______________\|:\|\|\|_\|\|\|\|:_:\|::\|_\|\|\|\|__\|\|\|_\|\|\|:\|________________\|\|_\|\|\|_\|:\|:\|\|::\|\|_______:\|\|\|\|\|\|:\n______________CGUCA_UAAGU_UUUUC_CUUC__UCU_UUAUA________________CC_UCG_GUUGCGGGUA_______GCGAACUG\n3'-UUU...CGAUA_____U_____U__________AU___G___________________________C_________________________CAACG...ACG-5'\n_____________\|_________________________________________________________________________________\|\n_____________72________________________________________________________________________________15\n	293 -- 299	16 -- 22	-43.4853 kcal/mol	15.7801 kcal/mol	17.5254 kcal/mol	221 300@LB@ \| \|@LB@5'-GUU...AAUAC C U C A CGUUUACCAGCAAAAA A GACAAAA A-3'@LB@ GUAGU AUUCG GAGGG GAAG AGA AAUGU GG AGC CGAUGCUUAU UGCUUGAU@LB@ \|:\|\|\| \|\|\|\|: :\|::\| \|\|\|\| \|\|\| \|\|\|:\| \|\| \|\|\| \|:\|:\|\|::\|\| :\|\|\|\|\|\|:@LB@ CGUCA UAAGU UUUUC CUUC UCU UUAUA CC UCG GUUGCGGGUA GCGAACUG@LB@3'-UUU...CGAUA U U AU G C CAACG...ACG-5'@LB@ \| \|@LB@ 72 15@LB@@LB@@LB@Energy -10.18 kcal/mol@LB@Hybridization Energy -43.4853 kcal/mol@LB@Unfolding Energy - mRNA 15.7801 kcal/mol@LB@Unfolding Energy - sRNA 17.5254 kcal/mol@LB@@LB@Position - mRNA 222 -- 299@LB@Position - sRNA 16 -- 71@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 16 -- 22@LB@
3	7.57e-07	0.0008889	b1763	topB	-11.97	0.035059	233 -- 258	1 -- 37	DNA topoisomerase III		_____________232___________________________________259\n_____________\|_____________________________________\|\n5'-UCU...AGUCU_____________________________________CCAAA...GUA-3'\n______________GGCGC_GCG_CCAUUGCU_GAUGU________CCUGC\n______________:\|\|\|\|_:\|\|_\|\|\|\|:\|\|\|_\|\|:\|\|________\|\|\|\|\|\n______________UCGCG_UGC_GGUAGCGA_CUGCA________GGACG\n3'-UUU...AUACC_____U___G________A_____ACGUAAGU_____-5'\n_____________\|____________________________________\|\n_____________38___________________________________1\n	242 -- 248	20 -- 26	-35.9728 kcal/mol	8.72127 kcal/mol	15.288 kcal/mol	232 259@LB@ \| \|@LB@5'-UCU...AGUCU CCAAA...GUA-3'@LB@ GGCGC GCG CCAUUGCU GAUGU CCUGC@LB@ :\|\|\|\| :\|\| \|\|\|\|:\|\|\| \|\|:\|\| \|\|\|\|\|@LB@ UCGCG UGC GGUAGCGA CUGCA GGACG@LB@3'-UUU...AUACC U G A ACGUAAGU -5'@LB@ \| \|@LB@ 38 1@LB@@LB@@LB@Energy -11.97 kcal/mol@LB@Hybridization Energy -35.9728 kcal/mol@LB@Unfolding Energy - mRNA 8.72127 kcal/mol@LB@Unfolding Energy - sRNA 15.288 kcal/mol@LB@@LB@Position - mRNA 233 -- 258@LB@Position - sRNA 1 -- 37@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 20 -- 26@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@
102	0.003332	0.1114	b1279	yciS	-9.50	0.143375	3 -- 9	1 -- 7	DUF1049 family inner membrane protein function unknown		_____________2_______10\n_____________\|_______\|\n_________5'-AC_______GGAAG...UGU-3'\n______________CACCUGC\n______________\|\|\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	3 -- 9	1 -- 7	-13.2462 kcal/mol	1.40693 kcal/mol	2.34039 kcal/mol	2 10@LB@ \| \|@LB@ 5'-AC GGAAG...UGU-3'@LB@ CACCUGC@LB@ \|\|\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.50 kcal/mol@LB@Hybridization Energy -13.2462 kcal/mol@LB@Unfolding Energy - mRNA 1.40693 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 3 -- 9@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 1 -- 7@LB@
128	0.004569	0.1258	b3033	yqiB	-9.35	0.155553	90 -- 130	43 -- 87	DUF1249 protein YqiB		_____________89_____________________________________________131\n_____________\|______________________________________________\|\n5'-UGG...GCCGG_____________AUAC______GUA__________AAAUC_____CGCAG...GCG-3'\n______________GAA_CAG____GC____CAGUGG___GAAGAGGGGA_____GACAA\n______________\|\|\|_\|\|:____\|\|____\|\|\|\|::___:\|\|:\|:\|\|:\|_____\|\|\|\|\|\n______________CUU_GUU____CG____GUCAUU___UUUUUUCCUU_____CUGUU\n3'-UUU...GCAUG___A___AACA__AUAC______AAG__________CAUU______AUACC...ACG-5'\n_____________\|______________________________________________\|\n_____________88_____________________________________________42\n	114 -- 120	52 -- 58	-22.1335 kcal/mol	7.07839 kcal/mol	5.71172 kcal/mol	89 131@LB@ \| \|@LB@5'-UGG...GCCGG AUAC GUA AAAUC CGCAG...GCG-3'@LB@ GAA CAG GC CAGUGG GAAGAGGGGA GACAA@LB@ \|\|\| \|\|: \|\| \|\|\|\|:: :\|\|:\|:\|\|:\| \|\|\|\|\|@LB@ CUU GUU CG GUCAUU UUUUUUCCUU CUGUU@LB@3'-UUU...GCAUG A AACA AUAC AAG CAUU AUACC...ACG-5'@LB@ \| \|@LB@ 88 42@LB@@LB@@LB@Energy -9.35 kcal/mol@LB@Hybridization Energy -22.1335 kcal/mol@LB@Unfolding Energy - mRNA 7.07839 kcal/mol@LB@Unfolding Energy - sRNA 5.71172 kcal/mol@LB@@LB@Position - mRNA 90 -- 130@LB@Position - sRNA 43 -- 87@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 52 -- 58@LB@
26	0.000123	0.01616	b3280	yrdB	-11.55	0.045184	198 -- 244	43 -- 92	DUF1488 family protein		_____________197__________________________________________________245\n_____________\|____________________________________________________\|\n5'-CCA...UUGUC__CG______________C__C____UUC_____C_____AG__________GAAUA...GCG-3'\n______________CG__UGAAUCAG____GC_AU_CAGU____CGGA_AGGGA__AGUGGGACGA\n______________\|\|__:\|\|\|\|\|\|:____\|\|_\|\|_\|\|\|\|____\|::\|_\|:\|\|\|__\|\|\|::\|\|\|:\|\n______________GC__GCUUAGUU____CG_UA_GUCA____GUUU_UUCCU__UCAUUCUGUU\n3'-UUU...CCGCA__AU________AACA__A__C____UUAA____U_________________AUACC...ACG-5'\n_____________\|____________________________________________________\|\n_____________93___________________________________________________42\n	238 -- 244	43 -- 49	-31.3697 kcal/mol	13.9577 kcal/mol	5.86211 kcal/mol	197 245@LB@ \| \|@LB@5'-CCA...UUGUC CG C C UUC C AG GAAUA...GCG-3'@LB@ CG UGAAUCAG GC AU CAGU CGGA AGGGA AGUGGGACGA@LB@ \|\| :\|\|\|\|\|\|: \|\| \|\| \|\|\|\| \|::\| \|:\|\|\| \|\|\|::\|\|\|:\|@LB@ GC GCUUAGUU CG UA GUCA GUUU UUCCU UCAUUCUGUU@LB@3'-UUU...CCGCA AU AACA A C UUAA U AUACC...ACG-5'@LB@ \| \|@LB@ 93 42@LB@@LB@@LB@Energy -11.55 kcal/mol@LB@Hybridization Energy -31.3697 kcal/mol@LB@Unfolding Energy - mRNA 13.9577 kcal/mol@LB@Unfolding Energy - sRNA 5.86211 kcal/mol@LB@@LB@Position - mRNA 198 -- 244@LB@Position - sRNA 43 -- 92@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 43 -- 49@LB@
131	0.004841	0.1302	b3242	aaeX	-9.57	0.138370	170 -- 176	1 -- 7	DUF1656 family putative inner membrane efflux pump associated protein		_____________169_____177\n_____________\|_______\|\n5'-GCG...AAUAA_______UCUCU...GGG-3'\n______________CGCCUGC\n______________\|:\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	170 -- 176	1 -- 7	-12.9142 kcal/mol	1.00865 kcal/mol	2.34039 kcal/mol	169 177@LB@ \| \|@LB@5'-GCG...AAUAA UCUCU...GGG-3'@LB@ CGCCUGC@LB@ \|:\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.57 kcal/mol@LB@Hybridization Energy -12.9142 kcal/mol@LB@Unfolding Energy - mRNA 1.00865 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 170 -- 176@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 1 -- 7@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@

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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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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