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
148	0.01421	0.3104	b2379	alaC	-8.54	0.209762	290 -- 297	5 -- 12	glutamate-pyruvate aminotransferase; glutamic-pyruvic transaminase (GPT); alanine transaminase	_____________289______298\n_____________\|________\|\n5'-UGU...AUGGC________GGC-3'\n______________UGCGCGUC\n______________\|\|\|\|\|\|\|\|\n______________ACGCGCAG\n3'-UUU...UGUUU________AAAG-5'\n_____________\|________\|\n_____________13_______4\n	291 -- 297	5 -- 11	-14.909 kcal/mol	5.25295 kcal/mol	1.11508 kcal/mol	289 298@LB@ \| \|@LB@5'-UGU...AUGGC GGC-3'@LB@ UGCGCGUC@LB@ \|\|\|\|\|\|\|\|@LB@ ACGCGCAG@LB@3'-UUU...UGUUU AAAG-5'@LB@ \| \|@LB@ 13 4@LB@@LB@@LB@Energy -8.54 kcal/mol@LB@Hybridization Energy -14.909 kcal/mol@LB@Unfolding Energy - mRNA 5.25295 kcal/mol@LB@Unfolding Energy - sRNA 1.11508 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 5 -- 12@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 5 -- 11@LB@
103	0.01026	0.3104	b1083	flgL	-8.46	0.215699	195 -- 209	5 -- 21	flagellar hook-filament junction protein	_____________194_______________210\n_____________\|_________________\|\n5'-UUG...GGGGA______________U__AGUAC...GUA-3'\n______________GAUAA__GAUGCGU_UC\n______________\|\|\|\|\|__:\|\|\|\|\|:_\|\|\n______________CUAUU__UUACGCG_AG\n3'-UUU...UACUA_____GU_______C__AAAG-5'\n_____________\|_________________\|\n_____________22________________4\n	200 -- 206	8 -- 14	-13.0743 kcal/mol	3.36074 kcal/mol	1.24955 kcal/mol	194 210@LB@ \| \|@LB@5'-UUG...GGGGA U AGUAC...GUA-3'@LB@ GAUAA GAUGCGU UC@LB@ \|\|\|\|\| :\|\|\|\|\|: \|\|@LB@ CUAUU UUACGCG AG@LB@3'-UUU...UACUA GU C AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -8.46 kcal/mol@LB@Hybridization Energy -13.0743 kcal/mol@LB@Unfolding Energy - mRNA 3.36074 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 195 -- 209@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 8 -- 14@LB@
156	0.01464	0.3104	b4105	phnD	-8.45	0.216438	196 -- 209	4 -- 18	phosphonate ABC transporter periplasmic binding protein	_____________195_____________210\n_____________\|_______________\|\n5'-CCG...AGGAA________AA_____AAGAU...UGA-3'\n______________AACGAAUG__CG_CU\n______________\|\|\|:\|\|\|\|__\|\|_\|\|\n______________UUGUUUAC__GC_GA\n3'-UUU...UACUA________GC__A__AAG-5'\n_____________\|_______________\|\n_____________19______________3\n	197 -- 203	11 -- 17	-10.9184 kcal/mol	1.23392 kcal/mol	1.22995 kcal/mol	195 210@LB@ \| \|@LB@5'-CCG...AGGAA AA AAGAU...UGA-3'@LB@ AACGAAUG CG CU@LB@ \|\|\|:\|\|\|\| \|\| \|\|@LB@ UUGUUUAC GC GA@LB@3'-UUU...UACUA GC A AAG-5'@LB@ \| \|@LB@ 19 3@LB@@LB@@LB@Energy -8.45 kcal/mol@LB@Hybridization Energy -10.9184 kcal/mol@LB@Unfolding Energy - mRNA 1.23392 kcal/mol@LB@Unfolding Energy - sRNA 1.22995 kcal/mol@LB@@LB@Position - mRNA 196 -- 209@LB@Position - sRNA 4 -- 18@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 11 -- 17@LB@
132	0.01286	0.3104	b3176	glmM	-8.35	0.224806	246 -- 258	8 -- 20	phosphoglucosamine mutase	_____________245___________259\n_____________\|_____________\|\n5'-GUU...GUCGU____G________CGAUC...CGG-3'\n______________GUAG_GGAUGCGC\n______________:\|\|:_::\|\|\|\|\|\|\n______________UAUU_UUUACGCG\n3'-UUU...ACUAC____G________CAGAAAG-5'\n_____________\|_____________\|\n_____________21____________7\n	252 -- 258	8 -- 14	-14.3134 kcal/mol	4.73041 kcal/mol	1.23367 kcal/mol	245 259@LB@ \| \|@LB@5'-GUU...GUCGU G CGAUC...CGG-3'@LB@ GUAG GGAUGCGC@LB@ :\|\|: ::\|\|\|\|\|\|@LB@ UAUU UUUACGCG@LB@3'-UUU...ACUAC G CAGAAAG-5'@LB@ \| \|@LB@ 21 7@LB@@LB@@LB@Energy -8.35 kcal/mol@LB@Hybridization Energy -14.3134 kcal/mol@LB@Unfolding Energy - mRNA 4.73041 kcal/mol@LB@Unfolding Energy - sRNA 1.23367 kcal/mol@LB@@LB@Position - mRNA 246 -- 258@LB@Position - sRNA 8 -- 20@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 8 -- 14@LB@
161	0.01501	0.3104	b1709	btuD	-8.32	0.227073	129 -- 137	1 -- 9	vitamin B12 ABC transporter ATPase	_____________128_______138\n_____________\|_________\|\n5'-GCA...AUCCA_________CCCGG...GGC-3'\n______________GCGUUUUUC\n______________\|\|\|\|:\|\|\|\|\n______________CGCAGAAAG\n3'-UUU...UUACG_________-5'\n_____________\|________\|\n_____________10_______1\n	131 -- 137	1 -- 7	-11.771 kcal/mol	2.3321 kcal/mol	1.11751 kcal/mol	128 138@LB@ \| \|@LB@5'-GCA...AUCCA CCCGG...GGC-3'@LB@ GCGUUUUUC@LB@ \|\|\|\|:\|\|\|\|@LB@ CGCAGAAAG@LB@3'-UUU...UUACG -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -8.32 kcal/mol@LB@Hybridization Energy -11.771 kcal/mol@LB@Unfolding Energy - mRNA 2.3321 kcal/mol@LB@Unfolding Energy - sRNA 1.11751 kcal/mol@LB@@LB@Position - mRNA 129 -- 137@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 131 -- 137@LB@Position Seed - sRNA 1 -- 7@LB@
87	0.008927	0.3104	b0195	tsaA	-8.24	0.234029	220 -- 237	1 -- 18	tRNA-Thr(GGU) m(6)t(6)A37 methyltransferase SAM-dependent	_____________219________________238\n_____________\|__________________\|\n5'-GAA...GUUCG_______AG_____A___GCUCG...ACG-3'\n______________AGCAAAU__GCGUU_UUC\n______________\|:\|\|\|\|\|__\|\|\|\|:_\|\|\|\n______________UUGUUUA__CGCAG_AAG\n3'-UUU...UACUA_______CG_____A___-5'\n_____________\|_________________\|\n_____________19________________1\n	220 -- 226	12 -- 18	-15.6275 kcal/mol	6.14962 kcal/mol	1.24077 kcal/mol	219 238@LB@ \| \|@LB@5'-GAA...GUUCG AG A GCUCG...ACG-3'@LB@ AGCAAAU GCGUU UUC@LB@ \|:\|\|\|\|\| \|\|\|\|: \|\|\|@LB@ UUGUUUA CGCAG AAG@LB@3'-UUU...UACUA CG A -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -8.24 kcal/mol@LB@Hybridization Energy -15.6275 kcal/mol@LB@Unfolding Energy - mRNA 6.14962 kcal/mol@LB@Unfolding Energy - sRNA 1.24077 kcal/mol@LB@@LB@Position - mRNA 220 -- 237@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 12 -- 18@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@
125	0.01241	0.3104	b0002	thrA	-8.21	0.235915	191 -- 205	9 -- 21	Bifunctional aspartokinase/homoserine dehydrogenase 1	_____________190_____________206\n_____________\|_______________\|\n5'-CCA...AACGA________CC_____AGUGU...UGG-3'\n______________GGUAACAA__AUGCG\n______________\|:\|\|\|\|\|\|__\|\|\|\|\|\n______________CUAUUGUU__UACGC\n3'-UUU...UACUA_______________GCAGAAAG-5'\n_____________\|_______________\|\n_____________22______________8\n	192 -- 198	14 -- 20	-12.9357 kcal/mol	3.48482 kcal/mol	1.23627 kcal/mol	190 206@LB@ \| \|@LB@5'-CCA...AACGA CC AGUGU...UGG-3'@LB@ GGUAACAA AUGCG@LB@ \|:\|\|\|\|\|\| \|\|\|\|\|@LB@ CUAUUGUU UACGC@LB@3'-UUU...UACUA GCAGAAAG-5'@LB@ \| \|@LB@ 22 8@LB@@LB@@LB@Energy -8.21 kcal/mol@LB@Hybridization Energy -12.9357 kcal/mol@LB@Unfolding Energy - mRNA 3.48482 kcal/mol@LB@Unfolding Energy - sRNA 1.23627 kcal/mol@LB@@LB@Position - mRNA 191 -- 205@LB@Position - sRNA 9 -- 21@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 14 -- 20@LB@
124	0.0124	0.3104	b1860	ruvB	-8.20	0.236824	252 -- 265	8 -- 20	ATP-dependent DNA helicase component of RuvABC resolvasome	_____________251____________266\n_____________\|______________\|\n5'-ACG...AAGAU_________C____CAUUC...GUC-3'\n______________GUAGCAGAU_GCGC\n______________:\|\|:\|\|:\|\|_\|\|\|\|\n______________UAUUGUUUA_CGCG\n3'-UUU...ACUAC______________CAGAAAG-5'\n_____________\|______________\|\n_____________21_____________7\n	252 -- 258	14 -- 20	-14.7986 kcal/mol	5.36112 kcal/mol	1.23367 kcal/mol	251 266@LB@ \| \|@LB@5'-ACG...AAGAU C CAUUC...GUC-3'@LB@ GUAGCAGAU GCGC@LB@ :\|\|:\|\|:\|\| \|\|\|\|@LB@ UAUUGUUUA CGCG@LB@3'-UUU...ACUAC CAGAAAG-5'@LB@ \| \|@LB@ 21 7@LB@@LB@@LB@Energy -8.20 kcal/mol@LB@Hybridization Energy -14.7986 kcal/mol@LB@Unfolding Energy - mRNA 5.36112 kcal/mol@LB@Unfolding Energy - sRNA 1.23367 kcal/mol@LB@@LB@Position - mRNA 252 -- 265@LB@Position - sRNA 8 -- 20@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 14 -- 20@LB@
72	0.006739	0.3087	b2520	yfhM	-8.19	0.237735	190 -- 217	6 -- 30	bacterial alpha2-macroglobulin colonization factor ECAM; anti-host protease defense factor; periplasmic inner membrane-anchored lipoprotein	_____________189__________________________218\n_____________\|____________________________\|\n5'-CUC...GUGGC________AAA____AA____UA_____AGCCG...CUU-3'\n______________AGGGAUGA___AUGA__AAGU__CGCGU\n______________\|\|\|\|\|\|\|\|___\|\|:\|__\|\|:\|__\|\|\|\|\|\n______________UCCCUACU___UAUU__UUUA__GCGCA\n3'-UUU...UUAAG________AC_____G_____C______GAAAG-5'\n_____________\|____________________________\|\n_____________31___________________________5\n	191 -- 197	23 -- 29	-19.496 kcal/mol	3.87755 kcal/mol	7.4255 kcal/mol	189 218@LB@ \| \|@LB@5'-CUC...GUGGC AAA AA UA AGCCG...CUU-3'@LB@ AGGGAUGA AUGA AAGU CGCGU@LB@ \|\|\|\|\|\|\|\| \|\|:\| \|\|:\| \|\|\|\|\|@LB@ UCCCUACU UAUU UUUA GCGCA@LB@3'-UUU...UUAAG AC G C GAAAG-5'@LB@ \| \|@LB@ 31 5@LB@@LB@@LB@Energy -8.19 kcal/mol@LB@Hybridization Energy -19.496 kcal/mol@LB@Unfolding Energy - mRNA 3.87755 kcal/mol@LB@Unfolding Energy - sRNA 7.4255 kcal/mol@LB@@LB@Position - mRNA 190 -- 217@LB@Position - sRNA 6 -- 30@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 23 -- 29@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)

Job resubmission

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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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