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
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@
35	0.003306	0.3101	b0551	quuD	-13.48	0.016718	188 -- 210	3 -- 24	DLP12 prophage; putative antitermination protein		_____________187_____________________211\n_____________\|_______________________\|\n5'-ACU...UUUUU_____GU_________C______UUCAG...GAU-3'\n______________GUGGA__AAGUUGAUG_GUGAUA\n______________:\|::\|__\|\|\|\|\|:\|\|\|_:\|\|\|\|\|\n______________UAUUU__UUCAAUUAC_UACUAU\n3'-UUU...GCCAU_____AU________________CG-5'\n_____________\|_______________________\|\n_____________25______________________2\n	197 -- 203	9 -- 15	-17.2545 kcal/mol	3.66311 kcal/mol	0.108279 kcal/mol	187 211@LB@ \| \|@LB@5'-ACU...UUUUU GU C UUCAG...GAU-3'@LB@ GUGGA AAGUUGAUG GUGAUA@LB@ :\|::\| \|\|\|\|\|:\|\|\| :\|\|\|\|\|@LB@ UAUUU UUCAAUUAC UACUAU@LB@3'-UUU...GCCAU AU CG-5'@LB@ \| \|@LB@ 25 2@LB@@LB@@LB@Energy -13.48 kcal/mol@LB@Hybridization Energy -17.2545 kcal/mol@LB@Unfolding Energy - mRNA 3.66311 kcal/mol@LB@Unfolding Energy - sRNA 0.108279 kcal/mol@LB@@LB@Position - mRNA 188 -- 210@LB@Position - sRNA 3 -- 24@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 9 -- 15@LB@
59	0.008416	0.4523	b0566	envY	-9.46	0.123665	249 -- 263	50 -- 64	porin thermoregulatory transcriptional activator	b1499 b0564 b3515 b4116 b3516	_____________248_____________264\n_____________\|_______________\|\n5'-GGC...AAAAA_______A_______GUCAA...ACU-3'\n______________GAGGUAG_GGUAAGC\n______________\|\|::\|\|\|_\|\|\|\|\|:\|\n______________CUUUAUC_CCAUUUG\n3'-UUU...GCCAA_______C_______UCUGU...UCG-5'\n_____________\|_______________\|\n_____________65______________49\n	257 -- 263	50 -- 56	-15.2892 kcal/mol	5.08919 kcal/mol	0.736811 kcal/mol	248 264@LB@ \| \|@LB@5'-GGC...AAAAA A GUCAA...ACU-3'@LB@ GAGGUAG GGUAAGC@LB@ \|\|::\|\|\| \|\|\|\|\|:\|@LB@ CUUUAUC CCAUUUG@LB@3'-UUU...GCCAA C UCUGU...UCG-5'@LB@ \| \|@LB@ 65 49@LB@@LB@@LB@Energy -9.46 kcal/mol@LB@Hybridization Energy -15.2892 kcal/mol@LB@Unfolding Energy - mRNA 5.08919 kcal/mol@LB@Unfolding Energy - sRNA 0.736811 kcal/mol@LB@@LB@Position - mRNA 249 -- 263@LB@Position - sRNA 50 -- 64@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 50 -- 56@LB@
57	0.007764	0.4472	b0585	fes	-12.40	0.029926	182 -- 237	1 -- 55	enterobactin/ferrienterobactin esterase		_____________181___________________________________________________________238\n_____________\|_____________________________________________________________\|\n5'-CAU...GCACA_______U__G____________U_______CGU____AGU__GA_____GAGC_______AGUCG...GGU-3'\n______________GUAAACA_GG_GUU_____AUGG_GUGACGG___UAAA___AG__AGUGA____UGGUGGC\n______________\|\|\|\|\|\|\|_\|:_:\|\|_____\|\|\|:_:\|\|\|\|\|\|___\|\|\|\|___\|\|__\|:\|\|\|____\|\|:\|:\|\|\n______________CAUUUGU_CU_UAA_____UACU_UACUGCC___AUUU___UC__UUACU____ACUAUCG\n3'-UUU...AUCCC__________G___GUCUU____________AUU____AUU__AA________________-5'\n_____________\|____________________________________________________________\|\n_____________56___________________________________________________________1\n	231 -- 237	1 -- 7	-34.1879 kcal/mol	15.4551 kcal/mol	6.33758 kcal/mol	181 238@LB@ \| \|@LB@5'-CAU...GCACA U G U CGU AGU GA GAGC AGUCG...GGU-3'@LB@ GUAAACA GG GUU AUGG GUGACGG UAAA AG AGUGA UGGUGGC@LB@ \|\|\|\|\|\|\| \|: :\|\| \|\|\|: :\|\|\|\|\|\| \|\|\|\| \|\| \|:\|\|\| \|\|:\|:\|\|@LB@ CAUUUGU CU UAA UACU UACUGCC AUUU UC UUACU ACUAUCG@LB@3'-UUU...AUCCC G GUCUU AUU AUU AA -5'@LB@ \| \|@LB@ 56 1@LB@@LB@@LB@Energy -12.40 kcal/mol@LB@Hybridization Energy -34.1879 kcal/mol@LB@Unfolding Energy - mRNA 15.4551 kcal/mol@LB@Unfolding Energy - sRNA 6.33758 kcal/mol@LB@@LB@Position - mRNA 182 -- 237@LB@Position - sRNA 1 -- 55@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 1 -- 7@LB@
181	0.02995	0.5424	b0601	ybdM	-11.52	0.046768	198 -- 207	55 -- 64	Spo0J family protein ParB-like nuclease domain		_____________197________208\n_____________\|__________\|\n5'-UUG...CGUCA__________AUACU...GCA-3'\n______________GGAAUGGGGG\n______________\|:\|\|\|:\|\|\|\|\n______________CUUUAUCCCC\n3'-UUU...GCCAA__________AUUUG...UCG-5'\n_____________\|__________\|\n_____________65_________54\n	201 -- 207	55 -- 61	-14.9628 kcal/mol	3.4127 kcal/mol	0.0291912 kcal/mol	197 208@LB@ \| \|@LB@5'-UUG...CGUCA AUACU...GCA-3'@LB@ GGAAUGGGGG@LB@ \|:\|\|\|:\|\|\|\|@LB@ CUUUAUCCCC@LB@3'-UUU...GCCAA AUUUG...UCG-5'@LB@ \| \|@LB@ 65 54@LB@@LB@@LB@Energy -11.52 kcal/mol@LB@Hybridization Energy -14.9628 kcal/mol@LB@Unfolding Energy - mRNA 3.4127 kcal/mol@LB@Unfolding Energy - sRNA 0.0291912 kcal/mol@LB@@LB@Position - mRNA 198 -- 207@LB@Position - sRNA 55 -- 64@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 55 -- 61@LB@
129	0.02061	0.5217	b0633	rlpA	-9.57	0.117965	261 -- 273	1 -- 12	septal ring protein suppressor of prc minor lipoprotein		_____________260___________274\n_____________\|_____________\|\n5'-CGG...CAAGC_________C___AACAG...CUG-3'\n______________GAUGAUGGU_AGC\n______________:\|\|\|\|\|\|:\|_\|\|\|\n______________UUACUACUA_UCG\n3'-UUU...UUCAA_____________-5'\n_____________\|____________\|\n_____________13___________1\n	263 -- 269	4 -- 10	-13.3317 kcal/mol	3.7231 kcal/mol	0.0394463 kcal/mol	260 274@LB@ \| \|@LB@5'-CGG...CAAGC C AACAG...CUG-3'@LB@ GAUGAUGGU AGC@LB@ :\|\|\|\|\|\|:\| \|\|\|@LB@ UUACUACUA UCG@LB@3'-UUU...UUCAA -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -9.57 kcal/mol@LB@Hybridization Energy -13.3317 kcal/mol@LB@Unfolding Energy - mRNA 3.7231 kcal/mol@LB@Unfolding Energy - sRNA 0.0394463 kcal/mol@LB@@LB@Position - mRNA 261 -- 273@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 4 -- 10@LB@
89	0.01433	0.5059	b0636	rlmH	-12.18	0.033475	189 -- 207	1 -- 19	23S rRNA m(3)Psi1915 pseudouridine methyltransferase SAM-dependent		_____________188__________________208\n_____________\|____________________\|\n5'-CGG...AACUC___________C________UGCAA...UCG-3'\n______________UGGAGUUAAUG_GUGA_AGC\n______________\|::\|\|\|\|\|\|\|\|_:\|\|\|_\|\|\|\n______________AUUUCAAUUAC_UACU_UCG\n3'-UUU...UAUUU________________A___-5'\n_____________\|___________________\|\n_____________20__________________1\n	193 -- 199	9 -- 15	-16.4949 kcal/mol	4.25175 kcal/mol	0.0638423 kcal/mol	188 208@LB@ \| \|@LB@5'-CGG...AACUC C UGCAA...UCG-3'@LB@ UGGAGUUAAUG GUGA AGC@LB@ \|::\|\|\|\|\|\|\|\| :\|\|\| \|\|\|@LB@ AUUUCAAUUAC UACU UCG@LB@3'-UUU...UAUUU A -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -12.18 kcal/mol@LB@Hybridization Energy -16.4949 kcal/mol@LB@Unfolding Energy - mRNA 4.25175 kcal/mol@LB@Unfolding Energy - sRNA 0.0638423 kcal/mol@LB@@LB@Position - mRNA 189 -- 207@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 9 -- 15@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@
7	0.0001529	0.07172	b0687	seqA	-15.48	0.005290	212 -- 226	5 -- 19	negative modulator of initiation of replication		_____________211_____________227\n_____________\|_______________\|\n5'-GGA...ACGAU_______________ACUCU...UGA-3'\n______________UGAAGUUGAUGAUGA\n______________\|:\|\|\|\|\|:\|\|\|\|\|\|\|\n______________AUUUCAAUUACUACU\n3'-UUU...UAUUU_______________AUCG-5'\n_____________\|_______________\|\n_____________20______________4\n	220 -- 226	5 -- 11	-18.3215 kcal/mol	2.77487 kcal/mol	0.0620344 kcal/mol	211 227@LB@ \| \|@LB@5'-GGA...ACGAU ACUCU...UGA-3'@LB@ UGAAGUUGAUGAUGA@LB@ \|:\|\|\|\|\|:\|\|\|\|\|\|\|@LB@ AUUUCAAUUACUACU@LB@3'-UUU...UAUUU AUCG-5'@LB@ \| \|@LB@ 20 4@LB@@LB@@LB@Energy -15.48 kcal/mol@LB@Hybridization Energy -18.3215 kcal/mol@LB@Unfolding Energy - mRNA 2.77487 kcal/mol@LB@Unfolding Energy - sRNA 0.0620344 kcal/mol@LB@@LB@Position - mRNA 212 -- 226@LB@Position - sRNA 5 -- 19@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 5 -- 11@LB@
22	0.001016	0.1516	b0734	cydB	-13.57	0.015928	285 -- 300	49 -- 64	cytochrome d terminal oxidase subunit II		_____________284_____________300\n_____________\|_______________\|\n5'-CGA...GUUUC__C_____________-3'\n______________GA_AUGGGGGUGGGCA\n______________\|\|_\|\|:\|\|\|\|\|:::\|\|\n______________CU_UAUCCCCAUUUGU\n3'-UUU...GCCAA__U_____________CUGUA...UCG-5'\n_____________\|________________\|\n_____________65_______________48\n	294 -- 300	49 -- 55	-19.142 kcal/mol	4.83222 kcal/mol	0.738518 kcal/mol	284 300@LB@ \| \|@LB@5'-CGA...GUUUC C -3'@LB@ GA AUGGGGGUGGGCA@LB@ \|\| \|\|:\|\|\|\|\|:::\|\|@LB@ CU UAUCCCCAUUUGU@LB@3'-UUU...GCCAA U CUGUA...UCG-5'@LB@ \| \|@LB@ 65 48@LB@@LB@@LB@Energy -13.57 kcal/mol@LB@Hybridization Energy -19.142 kcal/mol@LB@Unfolding Energy - mRNA 4.83222 kcal/mol@LB@Unfolding Energy - sRNA 0.738518 kcal/mol@LB@@LB@Position - mRNA 285 -- 300@LB@Position - sRNA 49 -- 64@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 49 -- 55@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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