Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
43	0.004693	0.3568	b1395	paaH	-8.91	0.157263	246 -- 258	49 -- 61	3-hydroxyadipyl-CoA dehydrogenase NAD+-dependent	_____________245___________259\n_____________\|_____________\|\n5'-GGC...GCACC_______C_____UUGCU...UGU-3'\n______________AUGGGGG_AGGCA\n______________\|\|:\|\|\|\|_\|::\|\|\n______________UAUCCCC_UUUGU\n3'-UUU...AACUU_______A_____CUGUA...UCG-5'\n_____________\|_____________\|\n_____________62____________48\n	246 -- 252	55 -- 61	-14.1165 kcal/mol	4.46726 kcal/mol	0.738192 kcal/mol	245 259@LB@ \| \|@LB@5'-GGC...GCACC C UUGCU...UGU-3'@LB@ AUGGGGG AGGCA@LB@ \|\|:\|\|\|\| \|::\|\|@LB@ UAUCCCC UUUGU@LB@3'-UUU...AACUU A CUGUA...UCG-5'@LB@ \| \|@LB@ 62 48@LB@@LB@@LB@Energy -8.91 kcal/mol@LB@Hybridization Energy -14.1165 kcal/mol@LB@Unfolding Energy - mRNA 4.46726 kcal/mol@LB@Unfolding Energy - sRNA 0.738192 kcal/mol@LB@@LB@Position - mRNA 246 -- 258@LB@Position - sRNA 49 -- 61@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 55 -- 61@LB@
72	0.01058	0.4523	b3458	livK	-8.91	0.157650	183 -- 215	28 -- 63	leucine transporter subunit	_____________182___________________________________216\n_____________\|_____________________________________\|\n5'-UGU...AUCAC________AUUUUU____UAU______CG________AAAAC...CGA-3'\n______________GAAUGGGG_______GAC_____GAAA__GAAUG_CG\n______________:\|\|\|:\|\|\|_______\|\|\|_____\|\|\|\|__\|\|\|\|\|_\|\|\n______________UUUAUCCC_______CUG_____CUUU__CUUAC_GC\n3'-UUU...CCAAC________CAUUUGU___UAAGU____A______U__CAUUA...UCG-5'\n_____________\|_____________________________________\|\n_____________64____________________________________27\n	184 -- 190	56 -- 62	-20.644 kcal/mol	5.44449 kcal/mol	6.29422 kcal/mol	182 216@LB@ \| \|@LB@5'-UGU...AUCAC AUUUUU UAU CG AAAAC...CGA-3'@LB@ GAAUGGGG GAC GAAA GAAUG CG@LB@ :\|\|\|:\|\|\| \|\|\| \|\|\|\| \|\|\|\|\| \|\|@LB@ UUUAUCCC CUG CUUU CUUAC GC@LB@3'-UUU...CCAAC CAUUUGU UAAGU A U CAUUA...UCG-5'@LB@ \| \|@LB@ 64 27@LB@@LB@@LB@Energy -8.91 kcal/mol@LB@Hybridization Energy -20.644 kcal/mol@LB@Unfolding Energy - mRNA 5.44449 kcal/mol@LB@Unfolding Energy - sRNA 6.29422 kcal/mol@LB@@LB@Position - mRNA 183 -- 215@LB@Position - sRNA 28 -- 63@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 56 -- 62@LB@
101	0.01605	0.5059	b3360	pabA	-8.89	0.158482	100 -- 107	55 -- 62	aminodeoxychorismate synthase subunit II	_____________99_______108\n_____________\|________\|\n5'-GCG...GGGGC________AUCUC...CGU-3'\n______________AAUGGGGG\n______________\|\|\|:\|\|\|\|\n______________UUAUCCCC\n3'-UUU...CAACU________AUUUG...UCG-5'\n_____________\|________\|\n_____________63_______54\n	101 -- 107	55 -- 61	-11.7531 kcal/mol	2.8331 kcal/mol	0.0270923 kcal/mol	99 108@LB@ \| \|@LB@5'-GCG...GGGGC AUCUC...CGU-3'@LB@ AAUGGGGG@LB@ \|\|\|:\|\|\|\|@LB@ UUAUCCCC@LB@3'-UUU...CAACU AUUUG...UCG-5'@LB@ \| \|@LB@ 63 54@LB@@LB@@LB@Energy -8.89 kcal/mol@LB@Hybridization Energy -11.7531 kcal/mol@LB@Unfolding Energy - mRNA 2.8331 kcal/mol@LB@Unfolding Energy - sRNA 0.0270923 kcal/mol@LB@@LB@Position - mRNA 100 -- 107@LB@Position - sRNA 55 -- 62@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 55 -- 61@LB@
52	0.0063	0.3902	b1473	yddG	-8.84	0.162012	257 -- 264	2 -- 9	aromatic amino acid exporter	_____________256______265\n_____________\|________\|\n5'-GCG...AGCAC________GAUUG...CGG-3'\n______________GAUGGUAG\n______________\|\|\|\|:\|\|\|\n______________CUACUAUC\n3'-UUU...AAUUA________G-5'\n_____________\|________\|\n_____________10_______1\n	258 -- 264	2 -- 8	-10.1209 kcal/mol	1.26064 kcal/mol	0.0191352 kcal/mol	256 265@LB@ \| \|@LB@5'-GCG...AGCAC GAUUG...CGG-3'@LB@ GAUGGUAG@LB@ \|\|\|\|:\|\|\|@LB@ CUACUAUC@LB@3'-UUU...AAUUA G-5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -10.1209 kcal/mol@LB@Unfolding Energy - mRNA 1.26064 kcal/mol@LB@Unfolding Energy - sRNA 0.0191352 kcal/mol@LB@@LB@Position - mRNA 257 -- 264@LB@Position - sRNA 2 -- 9@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 2 -- 8@LB@
137	0.02279	0.526	b1739	osmE	-8.84	0.162198	202 -- 246	21 -- 65	osmotically-inducible lipoprotein	_____________201____________________________________________247\n_____________\|______________________________________________\|\n5'-GAA...GAAUA____CA__AAUAU______A____U______C__C_______U___CCAUG...AGC-3'\n______________UGAA__AG_____GGCAGG_AUUC__GAGUG_AG_GGCGGUA_UAA\n______________\|\|\|\|__\|\|_____::\|\|\|:_\|\|\|\|__:\|:\|\|_\|:_\|:\|\|\|\|\|_\|\|\|\n______________ACUU__UC_____UUGUCU_UAAG__UUUAC_UU_CUGCCAU_AUU\n3'-UUU...GGCCA____UA__CCCAU______G____UC________A_______U___UAUUU...UCG-5'\n_____________\|______________________________________________\|\n_____________66_____________________________________________20\n	236 -- 242	25 -- 31	-25.0909 kcal/mol	9.03477 kcal/mol	7.21767 kcal/mol	201 247@LB@ \| \|@LB@5'-GAA...GAAUA CA AAUAU A U C C U CCAUG...AGC-3'@LB@ UGAA AG GGCAGG AUUC GAGUG AG GGCGGUA UAA@LB@ \|\|\|\| \|\| ::\|\|\|: \|\|\|\| :\|:\|\| \|: \|:\|\|\|\|\| \|\|\|@LB@ ACUU UC UUGUCU UAAG UUUAC UU CUGCCAU AUU@LB@3'-UUU...GGCCA UA CCCAU G UC A U UAUUU...UCG-5'@LB@ \| \|@LB@ 66 20@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -25.0909 kcal/mol@LB@Unfolding Energy - mRNA 9.03477 kcal/mol@LB@Unfolding Energy - sRNA 7.21767 kcal/mol@LB@@LB@Position - mRNA 202 -- 246@LB@Position - sRNA 21 -- 65@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 25 -- 31@LB@
93	0.0151	0.5059	b1675	ydhZ	-8.81	0.164498	185 -- 226	5 -- 54	uncharacterized protein	_____________184________________________________________________227\n_____________\|__________________________________________________\|\n5'-CUU...CAUGA___________AA____UG___AAU___AC____________________ACUGU...AGC-3'\n______________UAAAUAGGUAU__AGAA__GGA___CGG____AAA_AGAG_____GAUGA\n______________\|\|\|\|:\|\|::\|\|__\|\|\|\|__\|:\|___\|\|\|____\|\|\|_\|:\|\|_____\|\|\|\|\|\n______________AUUUGUCUGUA__UCUU__CUU___GCC____UUU_UUUC_____CUACU\n3'-UUU...UCCCC___________AG____UA___ACU___AUUA___A____AAUUA_____AUCG-5'\n_____________\|__________________________________________________\|\n_____________55_________________________________________________4\n	186 -- 192	47 -- 53	-19.2855 kcal/mol	4.14282 kcal/mol	6.33746 kcal/mol	184 227@LB@ \| \|@LB@5'-CUU...CAUGA AA UG AAU AC ACUGU...AGC-3'@LB@ UAAAUAGGUAU AGAA GGA CGG AAA AGAG GAUGA@LB@ \|\|\|\|:\|\|::\|\| \|\|\|\| \|:\| \|\|\| \|\|\| \|:\|\| \|\|\|\|\|@LB@ AUUUGUCUGUA UCUU CUU GCC UUU UUUC CUACU@LB@3'-UUU...UCCCC AG UA ACU AUUA A AAUUA AUCG-5'@LB@ \| \|@LB@ 55 4@LB@@LB@@LB@Energy -8.81 kcal/mol@LB@Hybridization Energy -19.2855 kcal/mol@LB@Unfolding Energy - mRNA 4.14282 kcal/mol@LB@Unfolding Energy - sRNA 6.33746 kcal/mol@LB@@LB@Position - mRNA 185 -- 226@LB@Position - sRNA 5 -- 54@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 47 -- 53@LB@
193	0.03268	0.5507	b2513	yfgM	-8.78	0.166450	282 -- 288	52 -- 58	ancillary SecYEG translocon subunit; putative anti-RcsB factor	_____________281_____289\n_____________\|_______\|\n5'-GGC...CUGUU_______UUUUG...UUG-3'\n______________GGGGUGA\n______________\|\|\|\|\|:\|\n______________CCCCAUU\n3'-UUU...UUUAU_______UGUCU...UCG-5'\n_____________\|_______\|\n_____________59______51\n	282 -- 288	52 -- 58	-10.2706 kcal/mol	1.44003 kcal/mol	0.0533 kcal/mol	281 289@LB@ \| \|@LB@5'-GGC...CUGUU UUUUG...UUG-3'@LB@ GGGGUGA@LB@ \|\|\|\|\|:\|@LB@ CCCCAUU@LB@3'-UUU...UUUAU UGUCU...UCG-5'@LB@ \| \|@LB@ 59 51@LB@@LB@@LB@Energy -8.78 kcal/mol@LB@Hybridization Energy -10.2706 kcal/mol@LB@Unfolding Energy - mRNA 1.44003 kcal/mol@LB@Unfolding Energy - sRNA 0.0533 kcal/mol@LB@@LB@Position - mRNA 282 -- 288@LB@Position - sRNA 52 -- 58@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 52 -- 58@LB@
157	0.02559	0.526	b2057	wcaC	-8.75	0.168472	165 -- 205	16 -- 58	putative glycosyl transferase	_____________164___________________________________________206\n_____________\|_____________________________________________\|\n5'-GUC...GCGCU__U__________AAA____CGC_______A_____U________UAUUU...CAC-3'\n______________GG_GGUGGG_AGA_____AG____GAGUGA_GGUAA_UAAAUGAA\n______________\|\|_\|\|\|:::_\|\|\|_____\|\|____\|\|:\|\|\|_\|\|\|\|\|_\|\|\|\|\|:\|\|\n______________CC_CCAUUU_UCU_____UC____CUUACU_CCAUU_AUUUAUUU\n3'-UUU...UUUAU_________G___GUAAG__UUUA______G______________CAAUU...UCG-5'\n_____________\|_____________________________________________\|\n_____________59____________________________________________15\n	199 -- 205	16 -- 22	-25.2337 kcal/mol	10.162 kcal/mol	6.32308 kcal/mol	164 206@LB@ \| \|@LB@5'-GUC...GCGCU U AAA CGC A U UAUUU...CAC-3'@LB@ GG GGUGGG AGA AG GAGUGA GGUAA UAAAUGAA@LB@ \|\| \|\|\|::: \|\|\| \|\| \|\|:\|\|\| \|\|\|\|\| \|\|\|\|\|:\|\|@LB@ CC CCAUUU UCU UC CUUACU CCAUU AUUUAUUU@LB@3'-UUU...UUUAU G GUAAG UUUA G CAAUU...UCG-5'@LB@ \| \|@LB@ 59 15@LB@@LB@@LB@Energy -8.75 kcal/mol@LB@Hybridization Energy -25.2337 kcal/mol@LB@Unfolding Energy - mRNA 10.162 kcal/mol@LB@Unfolding Energy - sRNA 6.32308 kcal/mol@LB@@LB@Position - mRNA 165 -- 205@LB@Position - sRNA 16 -- 58@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 16 -- 22@LB@
147	0.02463	0.526	b2830	rppH	-8.72	0.170707	205 -- 218	1 -- 14	RNA pyrophosphohydrolase	_____________204____________219\n_____________\|______________\|\n5'-UUC...GGUGA_______C______UACCG...GGC-3'\n______________UUGAUGA_GAUGGC\n______________\|\|:\|\|\|\|_\|\|\|:\|\|\n______________AAUUACU_CUAUCG\n3'-UUU...AUUUC_______A______-5'\n_____________\|_____________\|\n_____________15____________1\n	205 -- 211	8 -- 14	-13.7427 kcal/mol	4.97796 kcal/mol	0.0473494 kcal/mol	204 219@LB@ \| \|@LB@5'-UUC...GGUGA C UACCG...GGC-3'@LB@ UUGAUGA GAUGGC@LB@ \|\|:\|\|\|\| \|\|\|:\|\|@LB@ AAUUACU CUAUCG@LB@3'-UUU...AUUUC A -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -13.7427 kcal/mol@LB@Unfolding Energy - mRNA 4.97796 kcal/mol@LB@Unfolding Energy - sRNA 0.0473494 kcal/mol@LB@@LB@Position - mRNA 205 -- 218@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 8 -- 14@LB@
155	0.02521	0.526	b4208	cycA	-8.71	0.171102	175 -- 207	24 -- 51	D-alanine/D-serine/glycine transporter	_____________174________________________________208\n_____________\|__________________________________\|\n5'-AUU...ACAAC_______GGUA__________AAAAAC_______AUCAG...UUG-3'\n______________ACAGACA____CAGGAA_GAA______AUGGUAG\n______________\|\|\|\|\|\|\|____\|\|\|:\|\|_\|\|\|______\|:\|\|\|\|:\n______________UGUCUGU____GUCUUU_CUU______UGCCAUU\n3'-UUU...CCAUU_______AA________A___AC___________AUUUA...UCG-5'\n_____________\|__________________________________\|\n_____________52_________________________________23\n	201 -- 207	24 -- 30	-19.5671 kcal/mol	4.55835 kcal/mol	6.29692 kcal/mol	174 208@LB@ \| \|@LB@5'-AUU...ACAAC GGUA AAAAAC AUCAG...UUG-3'@LB@ ACAGACA CAGGAA GAA AUGGUAG@LB@ \|\|\|\|\|\|\| \|\|\|:\|\| \|\|\| \|:\|\|\|\|:@LB@ UGUCUGU GUCUUU CUU UGCCAUU@LB@3'-UUU...CCAUU AA A AC AUUUA...UCG-5'@LB@ \| \|@LB@ 52 23@LB@@LB@@LB@Energy -8.71 kcal/mol@LB@Hybridization Energy -19.5671 kcal/mol@LB@Unfolding Energy - mRNA 4.55835 kcal/mol@LB@Unfolding Energy - sRNA 6.29692 kcal/mol@LB@@LB@Position - mRNA 175 -- 207@LB@Position - sRNA 24 -- 51@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 24 -- 30@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)

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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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