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
93	0.009444	0.3104	b3822	recQ	-7.42	0.310549	176 -- 212	9 -- 45	ATP-dependent DNA helicase	_____________175____________________________________213\n_____________\|______________________________________\|\n5'-CGC...CUGUU________A__CAA__________AU______CAG___GAAGU...UUA-3'\n______________UUUAUUUC_GG___UC_GGGGUGA__GUGGCG___GCG\n______________\|\|:\|\|:\|\|_\|:___\|\|_\|\|\|:\|\|\|__:\|::\|:___\|\|\|\n______________AAGUAGAG_CU___AG_CCCUACU__UAUUGU___CGC\n3'-UUU...UUUUA________A__UA___U_______AC______UUA___GCAGAAAG-5'\n_____________\|______________________________________\|\n_____________46_____________________________________8\n	192 -- 198	23 -- 29	-25.6556 kcal/mol	8.78202 kcal/mol	9.45193 kcal/mol	175 213@LB@ \| \|@LB@5'-CGC...CUGUU A CAA AU CAG GAAGU...UUA-3'@LB@ UUUAUUUC GG UC GGGGUGA GUGGCG GCG@LB@ \|\|:\|\|:\|\| \|: \|\| \|\|\|:\|\|\| :\|::\|: \|\|\|@LB@ AAGUAGAG CU AG CCCUACU UAUUGU CGC@LB@3'-UUU...UUUUA A UA U AC UUA GCAGAAAG-5'@LB@ \| \|@LB@ 46 8@LB@@LB@@LB@Energy -7.42 kcal/mol@LB@Hybridization Energy -25.6556 kcal/mol@LB@Unfolding Energy - mRNA 8.78202 kcal/mol@LB@Unfolding Energy - sRNA 9.45193 kcal/mol@LB@@LB@Position - mRNA 176 -- 212@LB@Position - sRNA 9 -- 45@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 23 -- 29@LB@
90	0.009145	0.3104	b1079	flgH	-6.81	0.379144	179 -- 204	10 -- 38	flagellar protein of basal-body outer-membrane L ring	_____________178___________________________205\n_____________\|_____________________________\|\n5'-ACU...GUUUA____U___U____A_________C_____AAAAA...GGG-3'\n______________CUGA_UUU___GA_GAUGAUAGC__AUGC\n______________\|\|\|\|_\|\|:___\|\|_\|\|\|\|\|\|\|:\|__\|\|\|\|\n______________GACU_AAG___CU_CUACUAUUG__UACG\n3'-UUU...GUAGA____U___UCC__A_________UU____CGCAG...AAG-5'\n_____________\|_____________________________\|\n_____________39____________________________9\n	193 -- 199	16 -- 22	-21.1251 kcal/mol	4.97135 kcal/mol	9.34299 kcal/mol	178 205@LB@ \| \|@LB@5'-ACU...GUUUA U U A C AAAAA...GGG-3'@LB@ CUGA UUU GA GAUGAUAGC AUGC@LB@ \|\|\|\| \|\|: \|\| \|\|\|\|\|\|\|:\| \|\|\|\|@LB@ GACU AAG CU CUACUAUUG UACG@LB@3'-UUU...GUAGA U UCC A UU CGCAG...AAG-5'@LB@ \| \|@LB@ 39 9@LB@@LB@@LB@Energy -6.81 kcal/mol@LB@Hybridization Energy -21.1251 kcal/mol@LB@Unfolding Energy - mRNA 4.97135 kcal/mol@LB@Unfolding Energy - sRNA 9.34299 kcal/mol@LB@@LB@Position - mRNA 179 -- 204@LB@Position - sRNA 10 -- 38@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 16 -- 22@LB@
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@
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@
16	0.0004819	0.102	b0957	ompA	-13.00	0.036257	182 -- 195	8 -- 22	outer membrane protein A (3a;II*;G;d)	_____________181_____________196\n_____________\|_______________\|\n5'-CUU...UUGGA_______________AAAAA...AAC-3'\n______________UGAUAACGAG_GCGC\n______________\|\|\|\|\|\|\|:\|:_\|\|\|\|\n______________ACUAUUGUUU_CGCG\n3'-UUU...CUACU__________A____CAGAAAG-5'\n_____________\|_______________\|\n_____________23______________7\n	185 -- 191	13 -- 19	-17.7455 kcal/mol	3.5039 kcal/mol	1.23838 kcal/mol	181 196@LB@ \| \|@LB@5'-CUU...UUGGA AAAAA...AAC-3'@LB@ UGAUAACGAG GCGC@LB@ \|\|\|\|\|\|\|:\|: \|\|\|\|@LB@ ACUAUUGUUU CGCG@LB@3'-UUU...CUACU A CAGAAAG-5'@LB@ \| \|@LB@ 23 7@LB@@LB@@LB@Energy -13.00 kcal/mol@LB@Hybridization Energy -17.7455 kcal/mol@LB@Unfolding Energy - mRNA 3.5039 kcal/mol@LB@Unfolding Energy - sRNA 1.23838 kcal/mol@LB@@LB@Position - mRNA 182 -- 195@LB@Position - sRNA 8 -- 22@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 13 -- 19@LB@
7	9.926e-05	0.04801	b1113	ldtC	-15.69	0.011765	184 -- 223	1 -- 45	L D-transpeptidase linking Lpp to murein	_____________183___________________________________________224\n_____________\|_____________________________________________\|\n5'-CGU...UUAUA______A________UU________________A___________UCGCU...UGC-3'\n______________UUUAUU__UGGAUUU___GGUGAUGAU__CAAA__CGCGUUUUUC\n______________\|\|:\|\|:__\|\|:\|\|\|:___\|:\|\|\|\|\|\|\|__\|\|\|\|__\|\|\|\|\|:\|\|\|\|\n______________AAGUAG__ACUUAAG___CUACUACUA__GUUU__GCGCAGAAAG\n3'-UUU...UUUUA______AG_______UCC_________UU____AC__________-5'\n_____________\|____________________________________________\|\n_____________46___________________________________________1\n	217 -- 223	1 -- 7	-33.7876 kcal/mol	8.63912 kcal/mol	9.46113 kcal/mol	183 224@LB@ \| \|@LB@5'-CGU...UUAUA A UU A UCGCU...UGC-3'@LB@ UUUAUU UGGAUUU GGUGAUGAU CAAA CGCGUUUUUC@LB@ \|\|:\|\|: \|\|:\|\|\|: \|:\|\|\|\|\|\|\| \|\|\|\| \|\|\|\|\|:\|\|\|\|@LB@ AAGUAG ACUUAAG CUACUACUA GUUU GCGCAGAAAG@LB@3'-UUU...UUUUA AG UCC UU AC -5'@LB@ \| \|@LB@ 46 1@LB@@LB@@LB@Energy -15.69 kcal/mol@LB@Hybridization Energy -33.7876 kcal/mol@LB@Unfolding Energy - mRNA 8.63912 kcal/mol@LB@Unfolding Energy - sRNA 9.46113 kcal/mol@LB@@LB@Position - mRNA 184 -- 223@LB@Position - sRNA 1 -- 45@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 1 -- 7@LB@
6	9.655e-05	0.04801	b4175	hflC	-9.47	0.148653	186 -- 211	5 -- 32	HflB protease modulator specific for phage lambda cII repressor	_____________185____________________________212\n_____________\|______________________________\|\n5'-UUA...CAGCG_________________________AA___AGUUA...GUU-3'\n______________UCAGGGG_GA__AUAAC_GAUGCGU__GUC\n______________\|\|\|\|\|\|:_\|\|__\|\|\|\|\|_:\|\|\|\|\|:__\|\|\|\n______________AGUCCCU_CU__UAUUG_UUACGCG__CAG\n3'-UUU...ACUUA_______A__AC_____U____________AAAG-5'\n_____________\|______________________________\|\n_____________33_____________________________4\n	200 -- 206	8 -- 14	-26.2754 kcal/mol	8.97237 kcal/mol	7.8362 kcal/mol	185 212@LB@ \| \|@LB@5'-UUA...CAGCG AA AGUUA...GUU-3'@LB@ UCAGGGG GA AUAAC GAUGCGU GUC@LB@ \|\|\|\|\|\|: \|\| \|\|\|\|\| :\|\|\|\|\|: \|\|\|@LB@ AGUCCCU CU UAUUG UUACGCG CAG@LB@3'-UUU...ACUUA A AC U AAAG-5'@LB@ \| \|@LB@ 33 4@LB@@LB@@LB@Energy -9.47 kcal/mol@LB@Hybridization Energy -26.2754 kcal/mol@LB@Unfolding Energy - mRNA 8.97237 kcal/mol@LB@Unfolding Energy - sRNA 7.8362 kcal/mol@LB@@LB@Position - mRNA 186 -- 211@LB@Position - sRNA 5 -- 32@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 8 -- 14@LB@
19	0.0006629	0.1181	b2909	ygfB	-11.13	0.077732	186 -- 206	4 -- 22	UPF0149 family protein	_____________185___________________207\n_____________\|_____________________\|\n5'-AAA...CCCUU___C_________UUA_____AUACA...UCA-3'\n______________UGA_GACGAAUGC___UGUCU\n______________\|\|\|_:\|\|:\|\|\|\|\|___:\|\|\|\|\n______________ACU_UUGUUUACG___GCAGA\n3'-UUU...CUACU___A_________C_______AAG-5'\n_____________\|_____________________\|\n_____________23____________________3\n	192 -- 198	10 -- 16	-17.2827 kcal/mol	4.89762 kcal/mol	1.2572 kcal/mol	185 207@LB@ \| \|@LB@5'-AAA...CCCUU C UUA AUACA...UCA-3'@LB@ UGA GACGAAUGC UGUCU@LB@ \|\|\| :\|\|:\|\|\|\|\| :\|\|\|\|@LB@ ACU UUGUUUACG GCAGA@LB@3'-UUU...CUACU A C AAG-5'@LB@ \| \|@LB@ 23 3@LB@@LB@@LB@Energy -11.13 kcal/mol@LB@Hybridization Energy -17.2827 kcal/mol@LB@Unfolding Energy - mRNA 4.89762 kcal/mol@LB@Unfolding Energy - sRNA 1.2572 kcal/mol@LB@@LB@Position - mRNA 186 -- 206@LB@Position - sRNA 4 -- 22@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 10 -- 16@LB@
52	0.004683	0.3024	b1130	phoP	-12.79	0.039529	186 -- 208	6 -- 31	response regulator in two-component regulatory system with PhoQ	_____________185________________________209\n_____________\|__________________________\|\n5'-GAG...UAAGA_________A________________ACUGG...CCA-3'\n______________CAGGGA_GA__AUAA_AAAUGCGCGU\n______________\|\|\|\|\|\|_\|\|__\|\|\|\|_\|\|\|\|\|\|\|\|\|\|\n______________GUCCCU_CU__UAUU_UUUACGCGCA\n3'-UUU...CUUAA______A__AC____G__________GAAAG-5'\n_____________\|__________________________\|\n_____________32_________________________5\n	202 -- 208	6 -- 12	-26.853 kcal/mol	6.30535 kcal/mol	7.75407 kcal/mol	185 209@LB@ \| \|@LB@5'-GAG...UAAGA A ACUGG...CCA-3'@LB@ CAGGGA GA AUAA AAAUGCGCGU@LB@ \|\|\|\|\|\| \|\| \|\|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ GUCCCU CU UAUU UUUACGCGCA@LB@3'-UUU...CUUAA A AC G GAAAG-5'@LB@ \| \|@LB@ 32 5@LB@@LB@@LB@Energy -12.79 kcal/mol@LB@Hybridization Energy -26.853 kcal/mol@LB@Unfolding Energy - mRNA 6.30535 kcal/mol@LB@Unfolding Energy - sRNA 7.75407 kcal/mol@LB@@LB@Position - mRNA 186 -- 208@LB@Position - sRNA 6 -- 31@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 6 -- 12@LB@
35	0.002165	0.2094	b2714	ascG	-14.61	0.018547	188 -- 213	10 -- 30	asc operon transcriptional repressor; prpBC operon repressor	_____________187________________________214\n_____________\|__________________________\|\n5'-AAA...UGUAA________AAA_________CG____UGGAA...AAG-3'\n______________AGGGAUGA___UGAUGACGA__AUGC\n______________\|\|\|\|\|\|\|\|___\|\|\|\|:\|\|:\|__\|\|\|\|\n______________UCCCUACU___ACUAUUGUU__UACG\n3'-UUU...UUAAG__________________________CGCAG...AAG-5'\n_____________\|__________________________\|\n_____________31_________________________9\n	201 -- 207	14 -- 20	-25.4703 kcal/mol	3.44882 kcal/mol	7.41066 kcal/mol	187 214@LB@ \| \|@LB@5'-AAA...UGUAA AAA CG UGGAA...AAG-3'@LB@ AGGGAUGA UGAUGACGA AUGC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|:\|\|:\| \|\|\|\|@LB@ UCCCUACU ACUAUUGUU UACG@LB@3'-UUU...UUAAG CGCAG...AAG-5'@LB@ \| \|@LB@ 31 9@LB@@LB@@LB@Energy -14.61 kcal/mol@LB@Hybridization Energy -25.4703 kcal/mol@LB@Unfolding Energy - mRNA 3.44882 kcal/mol@LB@Unfolding Energy - sRNA 7.41066 kcal/mol@LB@@LB@Position - mRNA 188 -- 213@LB@Position - sRNA 10 -- 30@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 14 -- 20@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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