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	Additional homologs
17	0.000872	0.1482	b3940	metL	-12.03	0.036099	191 -- 199	51 -- 59	Bifunctional aspartokinase/homoserine dehydrogenase 2		_____________190_______200\n_____________\|_________\|\n5'-ACG...AAACA_________AAUGA...GCA-3'\n______________AGGGGUAAA\n______________\|\|\|\|\|\|\|\|\|\n______________UCCCCAUUU\n3'-UUU...CUUUA_________GUCUG...UCG-5'\n_____________\|_________\|\n_____________60________50\n	193 -- 199	51 -- 57	-13.5839 kcal/mol	1.01846 kcal/mol	0.532875 kcal/mol	190 200@LB@ \| \|@LB@5'-ACG...AAACA AAUGA...GCA-3'@LB@ AGGGGUAAA@LB@ \|\|\|\|\|\|\|\|\|@LB@ UCCCCAUUU@LB@3'-UUU...CUUUA GUCUG...UCG-5'@LB@ \| \|@LB@ 60 50@LB@@LB@@LB@Energy -12.03 kcal/mol@LB@Hybridization Energy -13.5839 kcal/mol@LB@Unfolding Energy - mRNA 1.01846 kcal/mol@LB@Unfolding Energy - sRNA 0.532875 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 51 -- 59@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 51 -- 57@LB@
47	0.005156	0.3601	b2614	grpE	-12.03	0.036099	152 -- 179	1 -- 26	heat shock protein		_____________151__________________________180\n_____________\|____________________________\|\n5'-GAG...CCCCA_______C________CGA_____AU__GAAAA...CUG-3'\n______________UAAUAAG_GAAGUUAG___GAUGA__GC\n______________\|\|\|\|\|\|:_:\|\|\|\|\|\|:___\|\|\|\|\|__\|\|\n______________AUUAUUU_UUUCAAUU___CUACU__CG\n3'-UUU...CUGCC_______A________A_______AU__-5'\n_____________\|___________________________\|\n_____________27__________________________1\n	161 -- 167	11 -- 17	-17.6467 kcal/mol	5.03361 kcal/mol	0.580494 kcal/mol	151 180@LB@ \| \|@LB@5'-GAG...CCCCA C CGA AU GAAAA...CUG-3'@LB@ UAAUAAG GAAGUUAG GAUGA GC@LB@ \|\|\|\|\|\|: :\|\|\|\|\|\|: \|\|\|\|\| \|\|@LB@ AUUAUUU UUUCAAUU CUACU CG@LB@3'-UUU...CUGCC A A AU -5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -12.03 kcal/mol@LB@Hybridization Energy -17.6467 kcal/mol@LB@Unfolding Energy - mRNA 5.03361 kcal/mol@LB@Unfolding Energy - sRNA 0.580494 kcal/mol@LB@@LB@Position - mRNA 152 -- 179@LB@Position - sRNA 1 -- 26@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 11 -- 17@LB@
85	0.01268	0.4896	b1827	kdgR	-11.91	0.038409	291 -- 299	56 -- 64	KDG regulon transcriptional repressor		_____________290_______300\n_____________\|_________\|\n5'-GCC...AGCGC_________A-3'\n______________GAAAUAGGG\n______________\|\|\|\|\|\|\|\|\|\n______________CUUUAUCCC\n3'-UUU...GCCAA_________CAUUU...UCG-5'\n_____________\|_________\|\n_____________65________55\n	293 -- 299	56 -- 62	-12.6296 kcal/mol	0.690209 kcal/mol	0.02823 kcal/mol	290 300@LB@ \| \|@LB@5'-GCC...AGCGC A-3'@LB@ GAAAUAGGG@LB@ \|\|\|\|\|\|\|\|\|@LB@ CUUUAUCCC@LB@3'-UUU...GCCAA CAUUU...UCG-5'@LB@ \| \|@LB@ 65 55@LB@@LB@@LB@Energy -11.91 kcal/mol@LB@Hybridization Energy -12.6296 kcal/mol@LB@Unfolding Energy - mRNA 0.690209 kcal/mol@LB@Unfolding Energy - sRNA 0.02823 kcal/mol@LB@@LB@Position - mRNA 291 -- 299@LB@Position - sRNA 56 -- 64@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 56 -- 62@LB@
168	0.02737	0.531	b1385	feaB	-11.89	0.038862	180 -- 210	1 -- 28	phenylacetaldehyde dehydrogenase		_____________179_____________________________211\n_____________\|_______________________________\|\n5'-UUG...CACUG_____AU_______AAA________CAG___CGCAU...GUG-3'\n______________GGUAA__AAUAAGG___AGUGAUGA___AGC\n______________\|\|\|\|\|__\|\|\|\|\|:\|___\|:\|\|\|\|\|\|___\|\|\|\n______________CCAUU__UUAUUUC___UUACUACU___UCG\n3'-UUU...UACUG_____AU_______AA_________A_____-5'\n_____________\|______________________________\|\n_____________29_____________________________1\n	198 -- 204	5 -- 11	-19.4278 kcal/mol	6.77275 kcal/mol	0.766821 kcal/mol	179 211@LB@ \| \|@LB@5'-UUG...CACUG AU AAA CAG CGCAU...GUG-3'@LB@ GGUAA AAUAAGG AGUGAUGA AGC@LB@ \|\|\|\|\| \|\|\|\|\|:\| \|:\|\|\|\|\|\| \|\|\|@LB@ CCAUU UUAUUUC UUACUACU UCG@LB@3'-UUU...UACUG AU AA A -5'@LB@ \| \|@LB@ 29 1@LB@@LB@@LB@Energy -11.89 kcal/mol@LB@Hybridization Energy -19.4278 kcal/mol@LB@Unfolding Energy - mRNA 6.77275 kcal/mol@LB@Unfolding Energy - sRNA 0.766821 kcal/mol@LB@@LB@Position - mRNA 180 -- 210@LB@Position - sRNA 1 -- 28@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 5 -- 11@LB@
200	0.03384	0.5555	b0316	yahB	-11.86	0.039401	41 -- 57	47 -- 61	putative DNA-bindng transcriptional regulator	b0504	_____________40________________58\n_____________\|_________________\|\n5'-CUG...ACUGC__________UUU____AUAUG...CUU-3'\n______________GUGGGGGUAA___CAGA\n______________:\|:\|\|\|\|\|\|\|___\|\|\|\|\n______________UAUCCCCAUU___GUCU\n3'-UUU...AACUU__________U______GUAAG...UCG-5'\n_____________\|_________________\|\n_____________62________________46\n	44 -- 50	52 -- 58	-17.391 kcal/mol	3.44789 kcal/mol	2.08204 kcal/mol	40 58@LB@ \| \|@LB@5'-CUG...ACUGC UUU AUAUG...CUU-3'@LB@ GUGGGGGUAA CAGA@LB@ :\|:\|\|\|\|\|\|\| \|\|\|\|@LB@ UAUCCCCAUU GUCU@LB@3'-UUU...AACUU U GUAAG...UCG-5'@LB@ \| \|@LB@ 62 46@LB@@LB@@LB@Energy -11.86 kcal/mol@LB@Hybridization Energy -17.391 kcal/mol@LB@Unfolding Energy - mRNA 3.44789 kcal/mol@LB@Unfolding Energy - sRNA 2.08204 kcal/mol@LB@@LB@Position - mRNA 41 -- 57@LB@Position - sRNA 47 -- 61@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 52 -- 58@LB@
100	0.01591	0.5059	b0531	sfmC	-11.86	0.039421	211 -- 227	6 -- 22	putative periplasmic pilus chaperone	b4316	_____________210_______________228\n_____________\|_________________\|\n5'-AAU...GACUA___________U_____CUCAU...GUA-3'\n______________AAAUAAAGUUA_UGAUG\n______________\|\|\|\|\|\|\|\|\|\|\|_\|\|\|\|\|\n______________UUUAUUUCAAU_ACUAC\n3'-UUU...CAUUA___________U_____UAUCG-5'\n_____________\|_________________\|\n_____________23________________5\n	215 -- 221	12 -- 18	-15.888 kcal/mol	3.9302 kcal/mol	0.0976382 kcal/mol	210 228@LB@ \| \|@LB@5'-AAU...GACUA U CUCAU...GUA-3'@LB@ AAAUAAAGUUA UGAUG@LB@ \|\|\|\|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ UUUAUUUCAAU ACUAC@LB@3'-UUU...CAUUA U UAUCG-5'@LB@ \| \|@LB@ 23 5@LB@@LB@@LB@Energy -11.86 kcal/mol@LB@Hybridization Energy -15.888 kcal/mol@LB@Unfolding Energy - mRNA 3.9302 kcal/mol@LB@Unfolding Energy - sRNA 0.0976382 kcal/mol@LB@@LB@Position - mRNA 211 -- 227@LB@Position - sRNA 6 -- 22@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 12 -- 18@LB@
118	0.01863	0.5155	b0738	tolR	-11.80	0.040697	190 -- 199	50 -- 59	membrane spanning protein in TolA-TolQ-TolR complex		_____________189________200\n_____________\|__________\|\n5'-UGG...CAACA__________CAUGG...UGG-3'\n______________AGGGGUAAGC\n______________\|\|\|\|\|\|\|\|:\|\n______________UCCCCAUUUG\n3'-UUU...CUUUA__________UCUGU...UCG-5'\n_____________\|__________\|\n_____________60_________49\n	193 -- 199	50 -- 56	-16.6396 kcal/mol	4.1136 kcal/mol	0.728772 kcal/mol	189 200@LB@ \| \|@LB@5'-UGG...CAACA CAUGG...UGG-3'@LB@ AGGGGUAAGC@LB@ \|\|\|\|\|\|\|\|:\|@LB@ UCCCCAUUUG@LB@3'-UUU...CUUUA UCUGU...UCG-5'@LB@ \| \|@LB@ 60 49@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -16.6396 kcal/mol@LB@Unfolding Energy - mRNA 4.1136 kcal/mol@LB@Unfolding Energy - sRNA 0.728772 kcal/mol@LB@@LB@Position - mRNA 190 -- 199@LB@Position - sRNA 50 -- 59@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 50 -- 56@LB@
163	0.02649	0.526	b3156	yhbS	-11.68	0.043230	178 -- 217	16 -- 53	GNAT family putative N-acetyltransferase		_____________177_______________________________________218\n_____________\|_________________________________________\|\n5'-CCG...AAACC______________U_______CC___C____UC_______AAUUC...AUC-3'\n______________AAACAGACA_UCGG_AGGUGAA__AUG_UAAU__GAGUAGA\n______________\|\|\|\|\|\|\|\|\|_\|\|:\|_\|::\|\|\|\|__\|:\|_\|\|\|\|__:\|:\|\|:\|\n______________UUUGUCUGU_AGUC_UUUACUU__UGC_AUUA__UUUAUUU\n3'-UUU...CCCCA_________A____________AC___C_____________CAAUU...UCG-5'\n_____________\|_________________________________________\|\n_____________54________________________________________15\n	211 -- 217	16 -- 22	-26.1463 kcal/mol	8.14596 kcal/mol	6.32252 kcal/mol	177 218@LB@ \| \|@LB@5'-CCG...AAACC U CC C UC AAUUC...AUC-3'@LB@ AAACAGACA UCGG AGGUGAA AUG UAAU GAGUAGA@LB@ \|\|\|\|\|\|\|\|\| \|\|:\| \|::\|\|\|\| \|:\| \|\|\|\| :\|:\|\|:\|@LB@ UUUGUCUGU AGUC UUUACUU UGC AUUA UUUAUUU@LB@3'-UUU...CCCCA A AC C CAAUU...UCG-5'@LB@ \| \|@LB@ 54 15@LB@@LB@@LB@Energy -11.68 kcal/mol@LB@Hybridization Energy -26.1463 kcal/mol@LB@Unfolding Energy - mRNA 8.14596 kcal/mol@LB@Unfolding Energy - sRNA 6.32252 kcal/mol@LB@@LB@Position - mRNA 178 -- 217@LB@Position - sRNA 16 -- 53@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 16 -- 22@LB@
30	0.002455	0.2686	b4551	yheV	-11.67	0.043500	186 -- 213	38 -- 63	DUF2387 family putative metal-binding protein		_____________185__________________________214\n_____________\|____________________________\|\n5'-AUC...AAUUU______A_______G_U____A__C___AACGU...UUG-3'\n______________GAGUAG_GGGUAAA_A_GGCA_UC_GAA\n______________:\|:\|\|\|_\|\|\|\|\|\|\|_\|_\|:\|\|_\|\|_\|\|\|\n______________UUUAUC_CCCAUUU_U_CUGU_AG_CUU\n3'-UUU...CCAAC______________G______A__U___UACUU...UCG-5'\n_____________\|____________________________\|\n_____________64___________________________37\n	193 -- 199	51 -- 57	-22.6178 kcal/mol	4.69416 kcal/mol	6.25833 kcal/mol	185 214@LB@ \| \|@LB@5'-AUC...AAUUU A G U A C AACGU...UUG-3'@LB@ GAGUAG GGGUAAA A GGCA UC GAA@LB@ :\|:\|\|\| \|\|\|\|\|\|\| \| \|:\|\| \|\| \|\|\|@LB@ UUUAUC CCCAUUU U CUGU AG CUU@LB@3'-UUU...CCAAC G A U UACUU...UCG-5'@LB@ \| \|@LB@ 64 37@LB@@LB@@LB@Energy -11.67 kcal/mol@LB@Hybridization Energy -22.6178 kcal/mol@LB@Unfolding Energy - mRNA 4.69416 kcal/mol@LB@Unfolding Energy - sRNA 6.25833 kcal/mol@LB@@LB@Position - mRNA 186 -- 213@LB@Position - sRNA 38 -- 63@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 51 -- 57@LB@
15	0.0006204	0.1358	b0652	gltL	-11.66	0.043639	269 -- 295	1 -- 25	glutamate/aspartate ABC transporter ATPase		_____________268_________________________296\n_____________\|___________________________\|\n5'-CUC...ACCGA______A____GCGA____________UUGCG-3'\n______________AGUGAA_AAAG____AGUGGUGGUGGU\n______________\|:\|:\|\|_\|\|\|\|____\|:\|\|:\|\|:\|:\|:\n______________UUAUUU_UUUC____UUACUACUAUCG\n3'-UUU...UGCCA______A____AA______________-5'\n_____________\|__________________________\|\n_____________26_________________________1\n	289 -- 295	1 -- 7	-17.2962 kcal/mol	5.52495 kcal/mol	0.112205 kcal/mol	268 296@LB@ \| \|@LB@5'-CUC...ACCGA A GCGA UUGCG-3'@LB@ AGUGAA AAAG AGUGGUGGUGGU@LB@ \|:\|:\|\| \|\|\|\| \|:\|\|:\|\|:\|:\|:@LB@ UUAUUU UUUC UUACUACUAUCG@LB@3'-UUU...UGCCA A AA -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -11.66 kcal/mol@LB@Hybridization Energy -17.2962 kcal/mol@LB@Unfolding Energy - mRNA 5.52495 kcal/mol@LB@Unfolding Energy - sRNA 0.112205 kcal/mol@LB@@LB@Position - mRNA 269 -- 295@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 1 -- 7@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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