Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
149	0.006962	0.1638	b0935	ssuD	-8.45	0.421381	102 -- 123	48 -- 71	alkanesulfonate monooxygenase FMNH(2)-dependent	_____________101______________________124\n_____________\|________________________\|\n5'-AAA...CAGCA___A_______A____________GAAAA...AAC-3'\n______________GCA_ACGGCAG_UC__UGUUUUAU\n______________:\|\|_\|\|:\|\|\|:_\|\|__\|\|\|\|\|:\|:\n______________UGU_UGUCGUU_AG__ACAAAGUG\n3'-UUU...UCUGA___G_______A__CA________AGUCC...GCA-5'\n_____________\|________________________\|\n_____________72_______________________47\n	117 -- 123	48 -- 54	-17.2917 kcal/mol	5.19453 kcal/mol	3.65243 kcal/mol	101 124@LB@ \| \|@LB@5'-AAA...CAGCA A A GAAAA...AAC-3'@LB@ GCA ACGGCAG UC UGUUUUAU@LB@ :\|\| \|\|:\|\|\|: \|\| \|\|\|\|\|:\|:@LB@ UGU UGUCGUU AG ACAAAGUG@LB@3'-UUU...UCUGA G A CA AGUCC...GCA-5'@LB@ \| \|@LB@ 72 47@LB@@LB@@LB@Energy -8.45 kcal/mol@LB@Hybridization Energy -17.2917 kcal/mol@LB@Unfolding Energy - mRNA 5.19453 kcal/mol@LB@Unfolding Energy - sRNA 3.65243 kcal/mol@LB@@LB@Position - mRNA 102 -- 123@LB@Position - sRNA 48 -- 71@LB@Position Seed - mRNA 117 -- 123@LB@Position Seed - sRNA 48 -- 54@LB@
164	0.007775	0.1668	b2097	fbaB	-9.67	0.277966	247 -- 265	48 -- 68	fructose-bisphosphate aldolase class I	_____________246___________________266\n_____________\|_____________________\|\n5'-AAU...CCUUU_______C________A_G__AAUUC...AUG-3'\n______________UACAGCA___CGUUGU_U_AC\n______________:\|\|\|\|\|\|___\|\|\|\|\|\|_\|_\|\|\n______________GUGUCGU___GCAACA_A_UG\n3'-UUU...GAUGU_______UAA______A_G__AGUCC...GCA-5'\n_____________\|_____________________\|\n_____________69____________________47\n	247 -- 253	62 -- 68	-18.0796 kcal/mol	4.78239 kcal/mol	3.63277 kcal/mol	246 266@LB@ \| \|@LB@5'-AAU...CCUUU C A G AAUUC...AUG-3'@LB@ UACAGCA CGUUGU U AC@LB@ :\|\|\|\|\|\| \|\|\|\|\|\| \| \|\|@LB@ GUGUCGU GCAACA A UG@LB@3'-UUU...GAUGU UAA A G AGUCC...GCA-5'@LB@ \| \|@LB@ 69 47@LB@@LB@@LB@Energy -9.67 kcal/mol@LB@Hybridization Energy -18.0796 kcal/mol@LB@Unfolding Energy - mRNA 4.78239 kcal/mol@LB@Unfolding Energy - sRNA 3.63277 kcal/mol@LB@@LB@Position - mRNA 247 -- 265@LB@Position - sRNA 48 -- 68@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 62 -- 68@LB@
196	0.01003	0.1776	b0344	lacZ	-8.86	0.369200	215 -- 237	48 -- 76	beta-D-galactosidase	_____________214___________________________238\n_____________\|_____________________________\|\n5'-ACC...AUUAC_____________________C_______AACGU...CUU-3'\n______________GGAUU_CAC_UGGC____CGU_GUUUUAC\n______________:\|\|:\|_\|\|\|_::\|\|____\|\|\|_\|\|\|\|:\|\|\n______________UCUGA_GUG_GUCG____GCA_CAAAGUG\n3'-UUU...CCGUU_____U___U____UUAA___A_______AGUCC...GCA-5'\n_____________\|_____________________________\|\n_____________77____________________________47\n	231 -- 237	48 -- 54	-17.9156 kcal/mol	5.37156 kcal/mol	3.68714 kcal/mol	214 238@LB@ \| \|@LB@5'-ACC...AUUAC C AACGU...CUU-3'@LB@ GGAUU CAC UGGC CGU GUUUUAC@LB@ :\|\|:\| \|\|\| ::\|\| \|\|\| \|\|\|\|:\|\|@LB@ UCUGA GUG GUCG GCA CAAAGUG@LB@3'-UUU...CCGUU U U UUAA A AGUCC...GCA-5'@LB@ \| \|@LB@ 77 47@LB@@LB@@LB@Energy -8.86 kcal/mol@LB@Hybridization Energy -17.9156 kcal/mol@LB@Unfolding Energy - mRNA 5.37156 kcal/mol@LB@Unfolding Energy - sRNA 3.68714 kcal/mol@LB@@LB@Position - mRNA 215 -- 237@LB@Position - sRNA 48 -- 76@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 48 -- 54@LB@
42	0.0009586	0.08031	b3747	kup	-11.44	0.134185	159 -- 185	49 -- 77	potassium transporter	_____________158___________________________186\n_____________\|_____________________________\|\n5'-AAA...GCCAA_______A________U___AUA______ACGAA...GUG-3'\n______________GGGACUA_GCACA_CA_UUC____UUUCA\n______________::\|\|\|\|\|_:\|\|\|\|_\|\|_\|\|\|____\|\|\|\|\|\n______________UUCUGAU_UGUGU_GU_AAG____AAAGU\n3'-UUU...CCCGU_______G_____C__U___CAAC_____GAGUC...GCA-5'\n_____________\|_____________________________\|\n_____________78____________________________48\n	159 -- 165	71 -- 77	-19.3471 kcal/mol	4.22429 kcal/mol	3.68465 kcal/mol	158 186@LB@ \| \|@LB@5'-AAA...GCCAA A U AUA ACGAA...GUG-3'@LB@ GGGACUA GCACA CA UUC UUUCA@LB@ ::\|\|\|\|\| :\|\|\|\| \|\| \|\|\| \|\|\|\|\|@LB@ UUCUGAU UGUGU GU AAG AAAGU@LB@3'-UUU...CCCGU G C U CAAC GAGUC...GCA-5'@LB@ \| \|@LB@ 78 48@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -19.3471 kcal/mol@LB@Unfolding Energy - mRNA 4.22429 kcal/mol@LB@Unfolding Energy - sRNA 3.68465 kcal/mol@LB@@LB@Position - mRNA 159 -- 185@LB@Position - sRNA 49 -- 77@LB@Position Seed - mRNA 159 -- 165@LB@Position Seed - sRNA 71 -- 77@LB@
97	0.004509	0.1538	b0465	mscK	-15.00	0.020897	217 -- 248	49 -- 74	mechanosensitive channel protein intermediate conductance K+ regulated	_____________216______________________________249\n_____________\|________________________________\|\n5'-CGA...CCAGU______AACGAU_______U______U_____GCAUU...CGC-3'\n______________AUUACA______CACGGCA_UUUGUU_UUUCA\n______________\|:\|\|\|\|______\|\|\|:\|\|\|_\|\|:\|\|\|_\|\|\|\|\|\n______________UGAUGU______GUGUCGU_AAGCAA_AAAGU\n3'-UUU...GUUUC___________________U______C_____GAGUC...GCA-5'\n_____________\|________________________________\|\n_____________75_______________________________48\n	229 -- 235	62 -- 68	-21.8954 kcal/mol	3.22234 kcal/mol	3.67122 kcal/mol	216 249@LB@ \| \|@LB@5'-CGA...CCAGU AACGAU U U GCAUU...CGC-3'@LB@ AUUACA CACGGCA UUUGUU UUUCA@LB@ \|:\|\|\|\| \|\|\|:\|\|\| \|\|:\|\|\| \|\|\|\|\|@LB@ UGAUGU GUGUCGU AAGCAA AAAGU@LB@3'-UUU...GUUUC U C GAGUC...GCA-5'@LB@ \| \|@LB@ 75 48@LB@@LB@@LB@Energy -15.00 kcal/mol@LB@Hybridization Energy -21.8954 kcal/mol@LB@Unfolding Energy - mRNA 3.22234 kcal/mol@LB@Unfolding Energy - sRNA 3.67122 kcal/mol@LB@@LB@Position - mRNA 217 -- 248@LB@Position - sRNA 49 -- 74@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 62 -- 68@LB@
66	0.002697	0.1417	b1306	pspC	-11.06	0.158336	44 -- 64	55 -- 75	psp operon transcription co-activator	_____________43_____________________65\n_____________\|______________________\|\n5'-CCG...GUUAU_______U______________CUGGU...CGG-3'\n______________GGCUGCA_UACAGCAAU_CGUU\n______________\|:\|\|:\|\|_:\|\|\|\|\|\|\|\|_\|\|\|\|\n______________CUGAUGU_GUGUCGUUA_GCAA\n3'-UUU...CGUUU_________________A____CAAAG...GCA-5'\n_____________\|______________________\|\n_____________76_____________________54\n	54 -- 60	60 -- 66	-24.9269 kcal/mol	10.2549 kcal/mol	3.6092 kcal/mol	43 65@LB@ \| \|@LB@5'-CCG...GUUAU U CUGGU...CGG-3'@LB@ GGCUGCA UACAGCAAU CGUU@LB@ \|:\|\|:\|\| :\|\|\|\|\|\|\|\| \|\|\|\|@LB@ CUGAUGU GUGUCGUUA GCAA@LB@3'-UUU...CGUUU A CAAAG...GCA-5'@LB@ \| \|@LB@ 76 54@LB@@LB@@LB@Energy -11.06 kcal/mol@LB@Hybridization Energy -24.9269 kcal/mol@LB@Unfolding Energy - mRNA 10.2549 kcal/mol@LB@Unfolding Energy - sRNA 3.6092 kcal/mol@LB@@LB@Position - mRNA 44 -- 64@LB@Position - sRNA 55 -- 75@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 60 -- 66@LB@
69	0.002809	0.1417	b1925	fliS	-16.42	0.008504	133 -- 153	57 -- 74	flagellar protein potentiates polymerization	_____________132___________________154\n_____________\|_____________________\|\n5'-UUA...CAGCA_____UUA_____________AAAAC...AUG-3'\n______________GCUAC___ACGCAGCAGUUCG\n______________:\|\|\|\|___\|\|:\|\|\|\|\|:\|\|\|\|\n______________UGAUG___UGUGUCGUUAAGC\n3'-UUU...GUUUC_____________________AACAA...GCA-5'\n_____________\|_____________________\|\n_____________75____________________56\n	147 -- 153	57 -- 63	-25.0139 kcal/mol	5.019 kcal/mol	3.57148 kcal/mol	132 154@LB@ \| \|@LB@5'-UUA...CAGCA UUA AAAAC...AUG-3'@LB@ GCUAC ACGCAGCAGUUCG@LB@ :\|\|\|\| \|\|:\|\|\|\|\|:\|\|\|\|@LB@ UGAUG UGUGUCGUUAAGC@LB@3'-UUU...GUUUC AACAA...GCA-5'@LB@ \| \|@LB@ 75 56@LB@@LB@@LB@Energy -16.42 kcal/mol@LB@Hybridization Energy -25.0139 kcal/mol@LB@Unfolding Energy - mRNA 5.019 kcal/mol@LB@Unfolding Energy - sRNA 3.57148 kcal/mol@LB@@LB@Position - mRNA 133 -- 153@LB@Position - sRNA 57 -- 74@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 57 -- 63@LB@
41	0.0008963	0.07693	b1378	pfo	-13.27	0.055135	136 -- 164	58 -- 78	pyruvate-flavodoxin oxidoreductase	_____________135___________________________165\n_____________\|_____________________________\|\n5'-GCU...AAUUG_________UACUGGGC____________CGUGC...CAG-3'\n______________AAAGAUUAC________GCGCAGCAAUUU\n______________\|\|\|\|\|:\|\|\|________:\|:\|\|\|\|\|\|\|\|:\n______________UUUCUGAUG________UGUGUCGUUAAG\n3'-UUU...ACCCG_____________________________CAACA...GCA-5'\n_____________\|_____________________________\|\n_____________79____________________________57\n	158 -- 164	58 -- 64	-22.0871 kcal/mol	5.50788 kcal/mol	3.31018 kcal/mol	135 165@LB@ \| \|@LB@5'-GCU...AAUUG UACUGGGC CGUGC...CAG-3'@LB@ AAAGAUUAC GCGCAGCAAUUU@LB@ \|\|\|\|\|:\|\|\| :\|:\|\|\|\|\|\|\|\|:@LB@ UUUCUGAUG UGUGUCGUUAAG@LB@3'-UUU...ACCCG CAACA...GCA-5'@LB@ \| \|@LB@ 79 57@LB@@LB@@LB@Energy -13.27 kcal/mol@LB@Hybridization Energy -22.0871 kcal/mol@LB@Unfolding Energy - mRNA 5.50788 kcal/mol@LB@Unfolding Energy - sRNA 3.31018 kcal/mol@LB@@LB@Position - mRNA 136 -- 164@LB@Position - sRNA 58 -- 78@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 58 -- 64@LB@
87	0.003844	0.1538	b3124	garK	-12.12	0.097757	2 -- 34	58 -- 88	glycerate kinase I	_____________1_________________________________35\n_____________\|_________________________________\|\n__________5'-U_______AU_____C______A____A______AGGAA...AUG-3'\n______________GGAGAUG__GCAGG_ACUGCG_GCAG_UGGUUU\n______________\|\|\|\|\|\|\|__\|\|\|::_\|\|\|:\|:_:\|\|\|_:::\|\|:\n______________CCUCUAC__CGUUU_UGAUGU_UGUC_GUUAAG\n3'-UUU...AGCAC_______C______C______G___________CAACA...GCA-5'\n_____________\|_________________________________\|\n_____________89________________________________57\n	2 -- 8	82 -- 88	-28.4892 kcal/mol	6.08629 kcal/mol	10.2803 kcal/mol	1 35@LB@ \| \|@LB@ 5'-U AU C A A AGGAA...AUG-3'@LB@ GGAGAUG GCAGG ACUGCG GCAG UGGUUU@LB@ \|\|\|\|\|\|\| \|\|\|:: \|\|\|:\|: :\|\|\| :::\|\|:@LB@ CCUCUAC CGUUU UGAUGU UGUC GUUAAG@LB@3'-UUU...AGCAC C C G CAACA...GCA-5'@LB@ \| \|@LB@ 89 57@LB@@LB@@LB@Energy -12.12 kcal/mol@LB@Hybridization Energy -28.4892 kcal/mol@LB@Unfolding Energy - mRNA 6.08629 kcal/mol@LB@Unfolding Energy - sRNA 10.2803 kcal/mol@LB@@LB@Position - mRNA 2 -- 34@LB@Position - sRNA 58 -- 88@LB@Position Seed - mRNA 2 -- 8@LB@Position Seed - sRNA 82 -- 88@LB@
107	0.004745	0.1538	b2413	cysZ	-9.47	0.298503	222 -- 238	58 -- 74	sulfate transporter sulfite inhibited	_____________221_______________239\n_____________\|_________________\|\n5'-ACC...CAUCU__CC_____________UUACU...UUU-3'\n______________GC__CACGCAGCGGUUU\n______________:\|__\|\|\|:\|\|\|\|::\|\|:\n______________UG__GUGUGUCGUUAAG\n3'-UUU...GUUUC__AU_____________CAACA...GCA-5'\n_____________\|_________________\|\n_____________75________________57\n	232 -- 238	58 -- 64	-18.5455 kcal/mol	5.77464 kcal/mol	3.3008 kcal/mol	221 239@LB@ \| \|@LB@5'-ACC...CAUCU CC UUACU...UUU-3'@LB@ GC CACGCAGCGGUUU@LB@ :\| \|\|\|:\|\|\|\|::\|\|:@LB@ UG GUGUGUCGUUAAG@LB@3'-UUU...GUUUC AU CAACA...GCA-5'@LB@ \| \|@LB@ 75 57@LB@@LB@@LB@Energy -9.47 kcal/mol@LB@Hybridization Energy -18.5455 kcal/mol@LB@Unfolding Energy - mRNA 5.77464 kcal/mol@LB@Unfolding Energy - sRNA 3.3008 kcal/mol@LB@@LB@Position - mRNA 222 -- 238@LB@Position - sRNA 58 -- 74@LB@Position Seed - mRNA 232 -- 238@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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usability assessment

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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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