Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
182	0.01795	0.3104	b0403	malZ	-8.22	0.235274	180 -- 211	10 -- 46	maltodextrin glucosidase	_____________179_____________________________________212\n_____________\|_______________________________________\|\n5'-UUU...CAGAU_______A_____________AAUU______U_______AUGGC...AGC-3'\n______________UUUCAUC________CAGGGG____AUGAUG_UAAAUGC\n______________\|\|\|\|\|\|\|________\|\|\|\|\|:____\|\|\|\|\|:_:\|\|\|\|\|\|\n______________AAAGUAG________GUCCCU____UACUAU_GUUUACG\n3'-UUU...GUUUU_______AGACUUAA______AC________U_______CGCAG...AAG-5'\n_____________\|_______________________________________\|\n_____________47______________________________________9\n	205 -- 211	10 -- 16	-25.6812 kcal/mol	8.00905 kcal/mol	9.44998 kcal/mol	179 212@LB@ \| \|@LB@5'-UUU...CAGAU A AAUU U AUGGC...AGC-3'@LB@ UUUCAUC CAGGGG AUGAUG UAAAUGC@LB@ \|\|\|\|\|\|\| \|\|\|\|\|: \|\|\|\|\|: :\|\|\|\|\|\|@LB@ AAAGUAG GUCCCU UACUAU GUUUACG@LB@3'-UUU...GUUUU AGACUUAA AC U CGCAG...AAG-5'@LB@ \| \|@LB@ 47 9@LB@@LB@@LB@Energy -8.22 kcal/mol@LB@Hybridization Energy -25.6812 kcal/mol@LB@Unfolding Energy - mRNA 8.00905 kcal/mol@LB@Unfolding Energy - sRNA 9.44998 kcal/mol@LB@@LB@Position - mRNA 180 -- 211@LB@Position - sRNA 10 -- 46@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 10 -- 16@LB@
3	3.559e-05	0.03436	b0168	map	-14.62	0.018437	228 -- 248	5 -- 21	methionine aminopeptidase	_____________227___________________249\n_____________\|_____________________\|\n5'-CUU...CAGAA____UCGAAA___________GCUGG...AAC-3'\n______________GAUA______AAAUGCGCGUC\n______________\|\|\|\|______\|\|\|\|\|\|\|\|\|\|\|\n______________CUAU______UUUACGCGCAG\n3'-UUU...UACUA____UG_______________AAAG-5'\n_____________\|_____________________\|\n_____________22____________________4\n	242 -- 248	5 -- 11	-19.3611 kcal/mol	3.48659 kcal/mol	1.24955 kcal/mol	227 249@LB@ \| \|@LB@5'-CUU...CAGAA UCGAAA GCUGG...AAC-3'@LB@ GAUA AAAUGCGCGUC@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|\|\|@LB@ CUAU UUUACGCGCAG@LB@3'-UUU...UACUA UG AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -14.62 kcal/mol@LB@Hybridization Energy -19.3611 kcal/mol@LB@Unfolding Energy - mRNA 3.48659 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 228 -- 248@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 5 -- 11@LB@
109	0.01118	0.3104	b3195	mlaF	-11.81	0.058997	89 -- 105	1 -- 18	ABC transporter maintaining OM lipid asymmetry ATP-binding protein	_____________88_________________106\n_____________\|__________________\|\n5'-UUU...AGUAA___________AG_____GCUAA...GAG-3'\n______________AACAAAUGC_C__CUUUC\n______________\|\|\|\|\|\|\|\|\|_\|__\|\|\|\|\|\n______________UUGUUUACG_G__GAAAG\n3'-UUU...UACUA_________C_CA_____-5'\n_____________\|_________________\|\n_____________19________________1\n	91 -- 97	10 -- 16	-16.9522 kcal/mol	3.89814 kcal/mol	1.24077 kcal/mol	88 106@LB@ \| \|@LB@5'-UUU...AGUAA AG GCUAA...GAG-3'@LB@ AACAAAUGC C CUUUC@LB@ \|\|\|\|\|\|\|\|\| \| \|\|\|\|\|@LB@ UUGUUUACG G GAAAG@LB@3'-UUU...UACUA C CA -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -11.81 kcal/mol@LB@Hybridization Energy -16.9522 kcal/mol@LB@Unfolding Energy - mRNA 3.89814 kcal/mol@LB@Unfolding Energy - sRNA 1.24077 kcal/mol@LB@@LB@Position - mRNA 89 -- 105@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 91 -- 97@LB@Position Seed - sRNA 10 -- 16@LB@
181	0.01793	0.3104	b1594	mlc	-11.10	0.078496	11 -- 37	1 -- 18	glucosamine anaerobic growth regulon transcriptional repressor; autorepressor	_____________10__________________________38\n_____________\|___________________________\|\n5'-AAA...UCAUG______GUCCGGC_______AA_____GUAUU...GUA-3'\n______________AACAAA_______UGCGCGU__CUUUC\n______________\|\|\|\|\|\|_______\|\|\|\|\|\|\|__\|\|\|\|\|\n______________UUGUUU_______ACGCGCA__GAAAG\n3'-UUU...UACUA___________________________-5'\n_____________\|__________________________\|\n_____________19_________________________1\n	24 -- 30	6 -- 12	-16.8416 kcal/mol	4.49753 kcal/mol	1.24077 kcal/mol	10 38@LB@ \| \|@LB@5'-AAA...UCAUG GUCCGGC AA GUAUU...GUA-3'@LB@ AACAAA UGCGCGU CUUUC@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ UUGUUU ACGCGCA GAAAG@LB@3'-UUU...UACUA -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -11.10 kcal/mol@LB@Hybridization Energy -16.8416 kcal/mol@LB@Unfolding Energy - mRNA 4.49753 kcal/mol@LB@Unfolding Energy - sRNA 1.24077 kcal/mol@LB@@LB@Position - mRNA 11 -- 37@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 6 -- 12@LB@
80	0.007305	0.3087	b2392	mntH	-9.52	0.145914	200 -- 218	5 -- 21	manganese/divalent cation transporter	_____________199_________________219\n_____________\|___________________\|\n5'-GCU...CACAA_________CUAU______GAGAG...UCG-3'\n______________GAUGACGAA____CGCGUU\n______________\|\|\|:\|\|:\|\|____\|\|\|\|\|:\n______________CUAUUGUUU____GCGCAG\n3'-UUU...UACUA_________AC________AAAG-5'\n_____________\|___________________\|\n_____________22__________________4\n	202 -- 208	13 -- 19	-16.4824 kcal/mol	5.71706 kcal/mol	1.24955 kcal/mol	199 219@LB@ \| \|@LB@5'-GCU...CACAA CUAU GAGAG...UCG-3'@LB@ GAUGACGAA CGCGUU@LB@ \|\|\|:\|\|:\|\| \|\|\|\|\|:@LB@ CUAUUGUUU GCGCAG@LB@3'-UUU...UACUA AC AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -9.52 kcal/mol@LB@Hybridization Energy -16.4824 kcal/mol@LB@Unfolding Energy - mRNA 5.71706 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 200 -- 218@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 13 -- 19@LB@
95	0.009629	0.3104	b0781	moaA	-11.57	0.065137	257 -- 279	1 -- 21	molybdopterin biosynthesis protein A	_____________256_____________________280\n_____________\|_______________________\|\n5'-ACG...CUGUC___U__C_________AA_____GUUGC...CGG-3'\n______________GAU_AC_GAUGUGUGU__CUUUC\n______________\|\|\|_\|\|_:\|\|\|:\|:\|\|__\|\|\|\|\|\n______________CUA_UG_UUACGCGCA__GAAAG\n3'-UUU...UACUA___U__U________________-5'\n_____________\|______________________\|\n_____________22_____________________1\n	266 -- 272	6 -- 12	-18.6522 kcal/mol	5.82624 kcal/mol	1.25763 kcal/mol	256 280@LB@ \| \|@LB@5'-ACG...CUGUC U C AA GUUGC...CGG-3'@LB@ GAU AC GAUGUGUGU CUUUC@LB@ \|\|\| \|\| :\|\|\|:\|:\|\| \|\|\|\|\|@LB@ CUA UG UUACGCGCA GAAAG@LB@3'-UUU...UACUA U U -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -11.57 kcal/mol@LB@Hybridization Energy -18.6522 kcal/mol@LB@Unfolding Energy - mRNA 5.82624 kcal/mol@LB@Unfolding Energy - sRNA 1.25763 kcal/mol@LB@@LB@Position - mRNA 257 -- 279@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 6 -- 12@LB@
71	0.006638	0.3087	b3857	mobA	-12.61	0.042607	253 -- 264	7 -- 18	molybdopterin-guanine dinucleotide synthase	_____________252__________265\n_____________\|____________\|\n5'-UCC...AGCCA________G___GCGUA...AAC-3'\n______________GACGAAUG_GCG\n______________:\|\|:\|\|\|\|_\|\|\|\n______________UUGUUUAC_CGC\n3'-UUU...UACUA________G___AGAAAG-5'\n_____________\|____________\|\n_____________19___________6\n	254 -- 260	11 -- 17	-15.9619 kcal/mol	2.14186 kcal/mol	1.20891 kcal/mol	252 265@LB@ \| \|@LB@5'-UCC...AGCCA G GCGUA...AAC-3'@LB@ GACGAAUG GCG@LB@ :\|\|:\|\|\|\| \|\|\|@LB@ UUGUUUAC CGC@LB@3'-UUU...UACUA G AGAAAG-5'@LB@ \| \|@LB@ 19 6@LB@@LB@@LB@Energy -12.61 kcal/mol@LB@Hybridization Energy -15.9619 kcal/mol@LB@Unfolding Energy - mRNA 2.14186 kcal/mol@LB@Unfolding Energy - sRNA 1.20891 kcal/mol@LB@@LB@Position - mRNA 253 -- 264@LB@Position - sRNA 7 -- 18@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 11 -- 17@LB@
85	0.008151	0.3104	b0914	msbA	-12.09	0.052799	181 -- 198	1 -- 18	lipid ABC transporter permease/ATPase	_____________180________________199\n_____________\|__________________\|\n5'-AGC...AUUUC_________UG_______GAAUG...CGU-3'\n______________AACAAAUGC__GUUUUUU\n______________\|\|\|\|\|\|\|\|\|__\|\|:\|\|\|:\n______________UUGUUUACG__CAGAAAG\n3'-UUU...UACUA_________CG_______-5'\n_____________\|_________________\|\n_____________19________________1\n	192 -- 198	1 -- 7	-16.7201 kcal/mol	3.39277 kcal/mol	1.24077 kcal/mol	180 199@LB@ \| \|@LB@5'-AGC...AUUUC UG GAAUG...CGU-3'@LB@ AACAAAUGC GUUUUUU@LB@ \|\|\|\|\|\|\|\|\| \|\|:\|\|\|:@LB@ UUGUUUACG CAGAAAG@LB@3'-UUU...UACUA CG -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -12.09 kcal/mol@LB@Hybridization Energy -16.7201 kcal/mol@LB@Unfolding Energy - mRNA 3.39277 kcal/mol@LB@Unfolding Energy - sRNA 1.24077 kcal/mol@LB@@LB@Position - mRNA 181 -- 198@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 1 -- 7@LB@
122	0.01233	0.3104	b3599	mtlA	-8.56	0.208645	247 -- 281	4 -- 32	mannitol-specific PTS enzyme: IIA IIB and IIC components	_____________246_________________________________282\n_____________\|___________________________________\|\n5'-GAU...UUUCC____CAAC_________C_____AUCG________AUCGC...UCA-3'\n______________UCAG____AUGGUGAUG_CAAAU____GCGCGUUU\n______________\|\|\|\|____\|\|\|:\|\|\|\|:_\|\|\|\|\|____\|\|\|\|\|\|:\|\n______________AGUC____UACUACUAU_GUUUA____CGCGCAGA\n3'-UUU...ACUUA____CC___________U_________________AAG-5'\n_____________\|___________________________________\|\n_____________33__________________________________3\n	275 -- 281	4 -- 10	-27.4972 kcal/mol	11.1013 kcal/mol	7.84022 kcal/mol	246 282@LB@ \| \|@LB@5'-GAU...UUUCC CAAC C AUCG AUCGC...UCA-3'@LB@ UCAG AUGGUGAUG CAAAU GCGCGUUU@LB@ \|\|\|\| \|\|\|:\|\|\|\|: \|\|\|\|\| \|\|\|\|\|\|:\|@LB@ AGUC UACUACUAU GUUUA CGCGCAGA@LB@3'-UUU...ACUUA CC U AAG-5'@LB@ \| \|@LB@ 33 3@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -27.4972 kcal/mol@LB@Unfolding Energy - mRNA 11.1013 kcal/mol@LB@Unfolding Energy - sRNA 7.84022 kcal/mol@LB@@LB@Position - mRNA 247 -- 281@LB@Position - sRNA 4 -- 32@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 4 -- 10@LB@
198	0.0193	0.3104	b2961	mutY	-10.33	0.106403	22 -- 38	1 -- 15	adenine DNA glycosylase	_____________21________________39\n_____________\|_________________\|\n5'-CGU...CGGUG_____A__U________AUAAA...UAU-3'\n______________AAAUG_CG_CGUUUUUC\n______________\|\|\|\|\|_\|\|_\|\|\|:\|\|\|\|\n______________UUUAC_GC_GCAGAAAG\n3'-UUU...UAUUG_________________-5'\n_____________\|________________\|\n_____________16_______________1\n	32 -- 38	1 -- 7	-14.8981 kcal/mol	3.3462 kcal/mol	1.21803 kcal/mol	21 39@LB@ \| \|@LB@5'-CGU...CGGUG A U AUAAA...UAU-3'@LB@ AAAUG CG CGUUUUUC@LB@ \|\|\|\|\| \|\| \|\|\|:\|\|\|\|@LB@ UUUAC GC GCAGAAAG@LB@3'-UUU...UAUUG -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -10.33 kcal/mol@LB@Hybridization Energy -14.8981 kcal/mol@LB@Unfolding Energy - mRNA 3.3462 kcal/mol@LB@Unfolding Energy - sRNA 1.21803 kcal/mol@LB@@LB@Position - mRNA 22 -- 38@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 32 -- 38@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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