Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
83	0.004611	0.1855	b1593	ynfK	-13.15	0.034145	276 -- 295	66 -- 83	putative dethiobiotin synthetase		_____________275__________________296\n_____________\|____________________\|\n5'-CAC...UACAA________CUC_________AACGG-3'\n______________GCGUUAGC___CCAGGGAAA\n______________\|\|\|::\|:\|___\|\|\|\|\|\|\|\|\|\n______________CGCGGUUG___GGUCCCUUU\n3'-UUU...UAUGA________U___________AGAAC...GUG-5'\n_____________\|____________________\|\n_____________84___________________65\n	289 -- 295	66 -- 72	-26.3491 kcal/mol	5.84339 kcal/mol	7.35847 kcal/mol	275 296@LB@ \| \|@LB@5'-CAC...UACAA CUC AACGG-3'@LB@ GCGUUAGC CCAGGGAAA@LB@ \|\|\|::\|:\| \|\|\|\|\|\|\|\|\|@LB@ CGCGGUUG GGUCCCUUU@LB@3'-UUU...UAUGA U AGAAC...GUG-5'@LB@ \| \|@LB@ 84 65@LB@@LB@@LB@Energy -13.15 kcal/mol@LB@Hybridization Energy -26.3491 kcal/mol@LB@Unfolding Energy - mRNA 5.84339 kcal/mol@LB@Unfolding Energy - sRNA 7.35847 kcal/mol@LB@@LB@Position - mRNA 276 -- 295@LB@Position - sRNA 66 -- 83@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 66 -- 72@LB@
130	0.007275	0.1966	b1638	pdxH	-11.04	0.087983	237 -- 249	47 -- 59	pyridoxine 5'-phosphate oxidase		_____________236___________250\n_____________\|_____________\|\n5'-UCU...CGCAU_____________ACACC...CCC-3'\n______________CUGCGCCGUGAAU\n______________\|\|\|\|\|\|\|\|\|:\|\|\|\n______________GACGCGGCAUUUA\n3'-UUU...GAACC_____________AUAAU...GUG-5'\n_____________\|_____________\|\n_____________60____________46\n	243 -- 249	47 -- 53	-22.1181 kcal/mol	4.88729 kcal/mol	6.18672 kcal/mol	236 250@LB@ \| \|@LB@5'-UCU...CGCAU ACACC...CCC-3'@LB@ CUGCGCCGUGAAU@LB@ \|\|\|\|\|\|\|\|\|:\|\|\|@LB@ GACGCGGCAUUUA@LB@3'-UUU...GAACC AUAAU...GUG-5'@LB@ \| \|@LB@ 60 46@LB@@LB@@LB@Energy -11.04 kcal/mol@LB@Hybridization Energy -22.1181 kcal/mol@LB@Unfolding Energy - mRNA 4.88729 kcal/mol@LB@Unfolding Energy - sRNA 6.18672 kcal/mol@LB@@LB@Position - mRNA 237 -- 249@LB@Position - sRNA 47 -- 59@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 47 -- 53@LB@
27	0.001577	0.1727	b1679	sufE	-9.94	0.142549	247 -- 262	68 -- 86	sulfur acceptor protein		_____________246_________________263\n_____________\|___________________\|\n5'-AUG...UUUAC___________U_______AGAGA...GUC-3'\n______________GCUGCGCCAAC____GGGA\n______________:\|\|\|\|\|\|\|\|\|\|____\|\|\|\|\n______________UGACGCGGUUG____CCCU\n3'-UUU...GCUUA___________UGGU____UUAGA...GUG-5'\n_____________\|___________________\|\n_____________87__________________67\n	251 -- 257	76 -- 82	-25.4399 kcal/mol	8.12138 kcal/mol	7.37523 kcal/mol	246 263@LB@ \| \|@LB@5'-AUG...UUUAC U AGAGA...GUC-3'@LB@ GCUGCGCCAAC GGGA@LB@ :\|\|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UGACGCGGUUG CCCU@LB@3'-UUU...GCUUA UGGU UUAGA...GUG-5'@LB@ \| \|@LB@ 87 67@LB@@LB@@LB@Energy -9.94 kcal/mol@LB@Hybridization Energy -25.4399 kcal/mol@LB@Unfolding Energy - mRNA 8.12138 kcal/mol@LB@Unfolding Energy - sRNA 7.37523 kcal/mol@LB@@LB@Position - mRNA 247 -- 262@LB@Position - sRNA 68 -- 86@LB@Position Seed - mRNA 251 -- 257@LB@Position Seed - sRNA 76 -- 82@LB@
181	0.0108	0.2089	b1683	sufB	-11.33	0.077347	153 -- 175	52 -- 74	component of SufBCD Fe-S cluster assembly scaffold		_____________152_______________________176\n_____________\|_________________________\|\n5'-GUU...AAAGC____AAU___UG__________G__AAAGC...AGC-3'\n______________CCAG___GAA____UGGCUGUG_CG\n______________\|\|\|\|___\|\|\|____\|\|\|\|\|\|:\|_\|\|\n______________GGUC___CUU____ACCGACGC_GC\n3'-UUU...GUUGU____C_____UAGA________G__AUUUA...GUG-5'\n_____________\|_________________________\|\n_____________75________________________51\n	166 -- 172	55 -- 61	-23.8546 kcal/mol	3.76094 kcal/mol	8.7601 kcal/mol	152 176@LB@ \| \|@LB@5'-GUU...AAAGC AAU UG G AAAGC...AGC-3'@LB@ CCAG GAA UGGCUGUG CG@LB@ \|\|\|\| \|\|\| \|\|\|\|\|\|:\| \|\|@LB@ GGUC CUU ACCGACGC GC@LB@3'-UUU...GUUGU C UAGA G AUUUA...GUG-5'@LB@ \| \|@LB@ 75 51@LB@@LB@@LB@Energy -11.33 kcal/mol@LB@Hybridization Energy -23.8546 kcal/mol@LB@Unfolding Energy - mRNA 3.76094 kcal/mol@LB@Unfolding Energy - sRNA 8.7601 kcal/mol@LB@@LB@Position - mRNA 153 -- 175@LB@Position - sRNA 52 -- 74@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 55 -- 61@LB@
13	0.0004745	0.1198	b1688	ydiK	-12.82	0.039628	213 -- 226	68 -- 82	UPF0118 family inner membrane protein		_____________212_____________227\n_____________\|_______________\|\n5'-AUG...AUGUU_______________UGUCG...CCU-3'\n______________CGUCAGC_CCAGGGA\n______________\|\|:\|\|:\|_\|\|\|\|\|\|\|\n______________GCGGUUG_GGUCCCU\n3'-UUU...AUGAC_______U_______UUAGA...GUG-5'\n_____________\|_______________\|\n_____________83______________67\n	220 -- 226	68 -- 74	-23.7232 kcal/mol	3.92329 kcal/mol	6.98098 kcal/mol	212 227@LB@ \| \|@LB@5'-AUG...AUGUU UGUCG...CCU-3'@LB@ CGUCAGC CCAGGGA@LB@ \|\|:\|\|:\| \|\|\|\|\|\|\|@LB@ GCGGUUG GGUCCCU@LB@3'-UUU...AUGAC U UUAGA...GUG-5'@LB@ \| \|@LB@ 83 67@LB@@LB@@LB@Energy -12.82 kcal/mol@LB@Hybridization Energy -23.7232 kcal/mol@LB@Unfolding Energy - mRNA 3.92329 kcal/mol@LB@Unfolding Energy - sRNA 6.98098 kcal/mol@LB@@LB@Position - mRNA 213 -- 226@LB@Position - sRNA 68 -- 82@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 68 -- 74@LB@
196	0.01202	0.2159	b1729	ydjN	-13.87	0.024594	143 -- 155	72 -- 84	putative transporter		_____________142___________156\n_____________\|_____________\|\n5'-CAU...AAUCU_____________UGACU...UGC-3'\n______________UGCGCCAACACUA\n______________\|\|\|\|\|\|\|\|\|\|\|:\|\n______________ACGCGGUUGUGGU\n3'-UUU...UUAUG_____________CCCUU...GUG-5'\n_____________\|_____________\|\n_____________85____________71\n	149 -- 155	72 -- 78	-23.7045 kcal/mol	2.6326 kcal/mol	7.20328 kcal/mol	142 156@LB@ \| \|@LB@5'-CAU...AAUCU UGACU...UGC-3'@LB@ UGCGCCAACACUA@LB@ \|\|\|\|\|\|\|\|\|\|\|:\|@LB@ ACGCGGUUGUGGU@LB@3'-UUU...UUAUG CCCUU...GUG-5'@LB@ \| \|@LB@ 85 71@LB@@LB@@LB@Energy -13.87 kcal/mol@LB@Hybridization Energy -23.7045 kcal/mol@LB@Unfolding Energy - mRNA 2.6326 kcal/mol@LB@Unfolding Energy - sRNA 7.20328 kcal/mol@LB@@LB@Position - mRNA 143 -- 155@LB@Position - sRNA 72 -- 84@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 72 -- 78@LB@
148	0.008708	0.2059	b1754	ynjB	-13.35	0.031185	160 -- 171	50 -- 61	putative ABC transporter periplasmic binding protein		_____________159__________172\n_____________\|____________\|\n5'-CCG...UCAGG____________UUCCU...AAA-3'\n______________GGCUGUGCCGUA\n______________\|\|\|\|\|:\|\|\|\|\|\|\n______________CCGACGCGGCAU\n3'-UUU...UAGAA____________UUAAU...GUG-5'\n_____________\|____________\|\n_____________62___________49\n	165 -- 171	50 -- 56	-23.078 kcal/mol	3.86799 kcal/mol	5.86332 kcal/mol	159 172@LB@ \| \|@LB@5'-CCG...UCAGG UUCCU...AAA-3'@LB@ GGCUGUGCCGUA@LB@ \|\|\|\|\|:\|\|\|\|\|\|@LB@ CCGACGCGGCAU@LB@3'-UUU...UAGAA UUAAU...GUG-5'@LB@ \| \|@LB@ 62 49@LB@@LB@@LB@Energy -13.35 kcal/mol@LB@Hybridization Energy -23.078 kcal/mol@LB@Unfolding Energy - mRNA 3.86799 kcal/mol@LB@Unfolding Energy - sRNA 5.86332 kcal/mol@LB@@LB@Position - mRNA 160 -- 171@LB@Position - sRNA 50 -- 61@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 50 -- 56@LB@
20	0.001165	0.1727	b1763	topB	-8.06	0.310309	3 -- 10	34 -- 41	DNA topoisomerase III		_____________2________11\n_____________\|________\|\n_________5'-UC________GAAAU...GUA-3'\n______________UGAUGGGU\n______________\|\|\|\|\|:\|\|\n______________ACUACUCA\n3'-UUU...AUAAU________AUGUU...GUG-5'\n_____________\|________\|\n_____________42_______33\n	4 -- 10	34 -- 40	-9.5271 kcal/mol	0.324007 kcal/mol	1.14413 kcal/mol	2 11@LB@ \| \|@LB@ 5'-UC GAAAU...GUA-3'@LB@ UGAUGGGU@LB@ \|\|\|\|\|:\|\|@LB@ ACUACUCA@LB@3'-UUU...AUAAU AUGUU...GUG-5'@LB@ \| \|@LB@ 42 33@LB@@LB@@LB@Energy -8.06 kcal/mol@LB@Hybridization Energy -9.5271 kcal/mol@LB@Unfolding Energy - mRNA 0.324007 kcal/mol@LB@Unfolding Energy - sRNA 1.14413 kcal/mol@LB@@LB@Position - mRNA 3 -- 10@LB@Position - sRNA 34 -- 41@LB@Position Seed - mRNA 4 -- 10@LB@Position Seed - sRNA 34 -- 40@LB@
113	0.005997	0.1855	b1765	ydjA	-10.36	0.119141	118 -- 144	49 -- 76	putative oxidoreductase		_____________117___________________________145\n_____________\|_____________________________\|\n5'-AUU...CUUGU__G__________GC__A___________CAAAA...GUA-3'\n______________CA_CAGG__AAUU__GG_CUGUGCUGUAA\n______________\|\|_\|\|\|\|__\|\|\|:__\|\|_\|\|\|:\|\|:\|\|\|\|\n______________GU_GUCC__UUAG__CC_GACGCGGCAUU\n3'-UUU...CGGUU__G____CU____AA______________UAAUA...GUG-5'\n_____________\|_____________________________\|\n_____________77____________________________48\n	138 -- 144	49 -- 55	-28.7704 kcal/mol	9.07167 kcal/mol	9.34253 kcal/mol	117 145@LB@ \| \|@LB@5'-AUU...CUUGU G GC A CAAAA...GUA-3'@LB@ CA CAGG AAUU GG CUGUGCUGUAA@LB@ \|\| \|\|\|\| \|\|\|: \|\| \|\|\|:\|\|:\|\|\|\|@LB@ GU GUCC UUAG CC GACGCGGCAUU@LB@3'-UUU...CGGUU G CU AA UAAUA...GUG-5'@LB@ \| \|@LB@ 77 48@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -28.7704 kcal/mol@LB@Unfolding Energy - mRNA 9.07167 kcal/mol@LB@Unfolding Energy - sRNA 9.34253 kcal/mol@LB@@LB@Position - mRNA 118 -- 144@LB@Position - sRNA 49 -- 76@LB@Position Seed - mRNA 138 -- 144@LB@Position Seed - sRNA 49 -- 55@LB@
117	0.006292	0.1893	b1769	ydjE	-12.05	0.056060	116 -- 139	36 -- 59	putative MFS sugar transporter membrane protein	b1775	_____________115______________________140\n_____________\|________________________\|\n5'-AUU...UGUUC_______U____A__AA_______UAAAG...UAA-3'\n______________CUGCGCC_UGAA_UA__AUGAUGA\n______________\|\|\|\|\|\|\|_\|:\|\|_\|\|__\|\|\|\|\|\|\|\n______________GACGCGG_AUUU_AU__UACUACU\n3'-UUU...GAACC_______C____A__AA_______CAAUG...GUG-5'\n_____________\|________________________\|\n_____________60_______________________35\n	133 -- 139	36 -- 42	-22.8542 kcal/mol	3.06151 kcal/mol	7.74108 kcal/mol	115 140@LB@ \| \|@LB@5'-AUU...UGUUC U A AA UAAAG...UAA-3'@LB@ CUGCGCC UGAA UA AUGAUGA@LB@ \|\|\|\|\|\|\| \|:\|\| \|\| \|\|\|\|\|\|\|@LB@ GACGCGG AUUU AU UACUACU@LB@3'-UUU...GAACC C A AA CAAUG...GUG-5'@LB@ \| \|@LB@ 60 35@LB@@LB@@LB@Energy -12.05 kcal/mol@LB@Hybridization Energy -22.8542 kcal/mol@LB@Unfolding Energy - mRNA 3.06151 kcal/mol@LB@Unfolding Energy - sRNA 7.74108 kcal/mol@LB@@LB@Position - mRNA 116 -- 139@LB@Position - sRNA 36 -- 59@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 36 -- 42@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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