Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
141	0.00519	0.1284	b3550	yiaC	-7.29	0.227336	55 -- 76	1 -- 22	GNAT family putative N-acetyltransferase	_____________54______________________77\n_____________\|_______________________\|\n5'-AAU...CAUCU_____C______CGAC_______CUAAG...GGC-3'\n______________ACGUC__GCCUC____GCCCUAU\n______________\|\|:\|\|__:\|\|\|\|____:\|\|\|\|\|:\n______________UGUAG__UGGAG____UGGGAUG\n3'-AUU...UAUCU_____AA_____ACA________-5'\n_____________\|______________________\|\n_____________23_____________________1\n	70 -- 76	1 -- 7	-20.6815 kcal/mol	5.4259 kcal/mol	7.99236 kcal/mol	54 77@LB@ \| \|@LB@5'-AAU...CAUCU C CGAC CUAAG...GGC-3'@LB@ ACGUC GCCUC GCCCUAU@LB@ \|\|:\|\| :\|\|\|\| :\|\|\|\|\|:@LB@ UGUAG UGGAG UGGGAUG@LB@3'-AUU...UAUCU AA ACA -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -7.29 kcal/mol@LB@Hybridization Energy -20.6815 kcal/mol@LB@Unfolding Energy - mRNA 5.4259 kcal/mol@LB@Unfolding Energy - sRNA 7.99236 kcal/mol@LB@@LB@Position - mRNA 55 -- 76@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 1 -- 7@LB@
142	0.005204	0.1284	b3931	hslU	-6.88	0.277791	3 -- 17	52 -- 65	molecular chaperone and ATPase component of HslUV protease	_____________2_______________18\n_____________\|_______________\|\n_________5'-UG________AAA____CUUAU...ACC-3'\n______________CAGCCAGA___CGAU\n______________\|\|\|\|\|\|:\|___\|\|\|\|\n______________GUCGGUUU___GCUA\n3'-AUU...UAUAA________AG_____AUGCA...AUG-5'\n_____________\|_______________\|\n_____________66______________51\n	4 -- 10	58 -- 64	-14.8174 kcal/mol	1.78514 kcal/mol	6.17277 kcal/mol	2 18@LB@ \| \|@LB@ 5'-UG AAA CUUAU...ACC-3'@LB@ CAGCCAGA CGAU@LB@ \|\|\|\|\|\|:\| \|\|\|\|@LB@ GUCGGUUU GCUA@LB@3'-AUU...UAUAA AG AUGCA...AUG-5'@LB@ \| \|@LB@ 66 51@LB@@LB@@LB@Energy -6.88 kcal/mol@LB@Hybridization Energy -14.8174 kcal/mol@LB@Unfolding Energy - mRNA 1.78514 kcal/mol@LB@Unfolding Energy - sRNA 6.17277 kcal/mol@LB@@LB@Position - mRNA 3 -- 17@LB@Position - sRNA 52 -- 65@LB@Position Seed - mRNA 4 -- 10@LB@Position Seed - sRNA 58 -- 64@LB@
143	0.005218	0.1284	b1922	fliA	-8.86	0.094137	133 -- 141	50 -- 58	RNA polymerase sigma 28 (sigma F) factor	_____________132_______142\n_____________\|_________\|\n5'-AGG...UAAUC_________AAAAC...UUC-3'\n______________GUCCGAUUA\n______________:\|\|\|\|\|\|\|\|\n______________UAGGCUAAU\n3'-AUU...CGGUU_________GCACU...AUG-5'\n_____________\|_________\|\n_____________59________49\n	135 -- 141	50 -- 56	-11.3914 kcal/mol	2.23267 kcal/mol	0.317553 kcal/mol	132 142@LB@ \| \|@LB@5'-AGG...UAAUC AAAAC...UUC-3'@LB@ GUCCGAUUA@LB@ :\|\|\|\|\|\|\|\|@LB@ UAGGCUAAU@LB@3'-AUU...CGGUU GCACU...AUG-5'@LB@ \| \|@LB@ 59 49@LB@@LB@@LB@Energy -8.86 kcal/mol@LB@Hybridization Energy -11.3914 kcal/mol@LB@Unfolding Energy - mRNA 2.23267 kcal/mol@LB@Unfolding Energy - sRNA 0.317553 kcal/mol@LB@@LB@Position - mRNA 133 -- 141@LB@Position - sRNA 50 -- 58@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 50 -- 56@LB@
144	0.005273	0.1288	b1652	rnt	-8.26	0.134019	203 -- 213	48 -- 58	RNase T; exoribonuclease T; structured DNA 3' exonuclease; RNA processing; DNA repair	_____________202_________214\n_____________\|___________\|\n5'-AAG...CAGAU_______A___CUCAA...CCG-3'\n______________GUCCGAU_ACG\n______________:\|\|\|\|\|\|_\|\|\|\n______________UAGGCUA_UGC\n3'-AUU...CGGUU_______A___ACUUC...AUG-5'\n_____________\|___________\|\n_____________59__________47\n	203 -- 209	52 -- 58	-12.2442 kcal/mol	2.4043 kcal/mol	1.55987 kcal/mol	202 214@LB@ \| \|@LB@5'-AAG...CAGAU A CUCAA...CCG-3'@LB@ GUCCGAU ACG@LB@ :\|\|\|\|\|\| \|\|\|@LB@ UAGGCUA UGC@LB@3'-AUU...CGGUU A ACUUC...AUG-5'@LB@ \| \|@LB@ 59 47@LB@@LB@@LB@Energy -8.26 kcal/mol@LB@Hybridization Energy -12.2442 kcal/mol@LB@Unfolding Energy - mRNA 2.4043 kcal/mol@LB@Unfolding Energy - sRNA 1.55987 kcal/mol@LB@@LB@Position - mRNA 203 -- 213@LB@Position - sRNA 48 -- 58@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 52 -- 58@LB@
145	0.005462	0.1325	b3239	yhcO	-10.93	0.023720	179 -- 225	2 -- 55	putative barnase inhibitor	_____________178______________________________________________________226\n_____________\|________________________________________________________\|\n5'-CUA...CGCCG___A_______C___________AAC______________A_______________AUGAG...GCG-3'\n______________CGA__ACGUGA_GGU____GG_C____AGAU_GAAUAUUU_UACCUUUG_AUUUUG\n______________\|\|\|__\|\|\|\|\|\|_:\|\|____\|\|_\|____\|\|\|\|_\|\|\|:\|\|:\|_\|\|\|\|\|:\|\|_\|:::\|:\n______________GCU__UGCACU_UCA____CC_G____UCUA_CUUGUAGA_AUGGAGAC_UGGGAU\n3'-AUU...UUUAG___AA__________UUUU__A_ACUU____U_________________A______G-5'\n_____________\|________________________________________________________\|\n_____________56_______________________________________________________1\n	213 -- 219	9 -- 15	-30.2735 kcal/mol	6.67064 kcal/mol	12.6986 kcal/mol	178 226@LB@ \| \|@LB@5'-CUA...CGCCG A C AAC A AUGAG...GCG-3'@LB@ CGA ACGUGA GGU GG C AGAU GAAUAUUU UACCUUUG AUUUUG@LB@ \|\|\| \|\|\|\|\|\| :\|\| \|\| \| \|\|\|\| \|\|\|:\|\|:\| \|\|\|\|\|:\|\| \|:::\|:@LB@ GCU UGCACU UCA CC G UCUA CUUGUAGA AUGGAGAC UGGGAU@LB@3'-AUU...UUUAG AA UUUU A ACUU U A G-5'@LB@ \| \|@LB@ 56 1@LB@@LB@@LB@Energy -10.93 kcal/mol@LB@Hybridization Energy -30.2735 kcal/mol@LB@Unfolding Energy - mRNA 6.67064 kcal/mol@LB@Unfolding Energy - sRNA 12.6986 kcal/mol@LB@@LB@Position - mRNA 179 -- 225@LB@Position - sRNA 2 -- 55@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 9 -- 15@LB@
146	0.005604	0.1342	b1637	tyrS	-10.18	0.040102	30 -- 71	2 -- 50	tyrosyl-tRNA synthetase	_____________29________________________________________________72\n_____________\|_________________________________________________\|\n5'-CAU...UACCA_______AAU___U_CG________U__U____________________AAAAG...CGA-3'\n______________GCGUGAA____GA_G__UGGAAGAU_GA_CGUCUUGC______ACCCUG\n______________:\|\|\|\|\|\|____:\|_\|__\|\|:\|\|\|\|\|_\|\|_\|:\|\|\|\|:\|______\|\|\|\|\|:\n______________UGCACUU____UU_C__ACUUUCUA_CU_GUAGAAUG______UGGGAU\n3'-AUU...GCUAA_______CAUU__C_AG________U__U________GAGACA______G-5'\n_____________\|_________________________________________________\|\n_____________51________________________________________________1\n	30 -- 36	44 -- 50	-35.883 kcal/mol	13.0482 kcal/mol	12.6769 kcal/mol	29 72@LB@ \| \|@LB@5'-CAU...UACCA AAU U CG U U AAAAG...CGA-3'@LB@ GCGUGAA GA G UGGAAGAU GA CGUCUUGC ACCCUG@LB@ :\|\|\|\|\|\| :\| \| \|\|:\|\|\|\|\| \|\| \|:\|\|\|\|:\| \|\|\|\|\|:@LB@ UGCACUU UU C ACUUUCUA CU GUAGAAUG UGGGAU@LB@3'-AUU...GCUAA CAUU C AG U U GAGACA G-5'@LB@ \| \|@LB@ 51 1@LB@@LB@@LB@Energy -10.18 kcal/mol@LB@Hybridization Energy -35.883 kcal/mol@LB@Unfolding Energy - mRNA 13.0482 kcal/mol@LB@Unfolding Energy - sRNA 12.6769 kcal/mol@LB@@LB@Position - mRNA 30 -- 71@LB@Position - sRNA 2 -- 50@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 44 -- 50@LB@
147	0.005606	0.1342	b3085	ygjP	-7.80	0.173342	13 -- 33	55 -- 72	putative metal dependent hydrolase	_____________12____________________34\n_____________\|_____________________\|\n5'-AAC...GCAGC_________UCC____CU___CACGC...AAC-3'\n______________AAAUAUUCA___GCCG__UCC\n______________\|\|\|\|\|\|\|\|\|___\|\|\|:__\|\|\|\n______________UUUAUAAGU___CGGU__AGG\n3'-AUU...CCGAU________________UU___CUAAU...AUG-5'\n_____________\|_____________________\|\n_____________73____________________54\n	14 -- 20	65 -- 71	-15.2572 kcal/mol	1.39359 kcal/mol	6.08601 kcal/mol	12 34@LB@ \| \|@LB@5'-AAC...GCAGC UCC CU CACGC...AAC-3'@LB@ AAAUAUUCA GCCG UCC@LB@ \|\|\|\|\|\|\|\|\| \|\|\|: \|\|\|@LB@ UUUAUAAGU CGGU AGG@LB@3'-AUU...CCGAU UU CUAAU...AUG-5'@LB@ \| \|@LB@ 73 54@LB@@LB@@LB@Energy -7.80 kcal/mol@LB@Hybridization Energy -15.2572 kcal/mol@LB@Unfolding Energy - mRNA 1.39359 kcal/mol@LB@Unfolding Energy - sRNA 6.08601 kcal/mol@LB@@LB@Position - mRNA 13 -- 33@LB@Position - sRNA 55 -- 72@LB@Position Seed - mRNA 14 -- 20@LB@Position Seed - sRNA 65 -- 71@LB@
148	0.00596	0.1406	b3426	glpD	-7.81	0.172743	213 -- 222	50 -- 59	sn-glycerol-3-phosphate dehydrogenase aerobic FAD/NAD(P)-binding	_____________212________223\n_____________\|__________\|\n5'-AAC...CCAAA__________UGAUA...AGG-3'\n______________GAUCUGAUUG\n______________:\|\|\|:\|\|\|\|:\n______________UUAGGCUAAU\n3'-AUU...UCGGU__________GCACU...AUG-5'\n_____________\|__________\|\n_____________60_________49\n	216 -- 222	50 -- 56	-9.79708 kcal/mol	1.6903 kcal/mol	0.31771 kcal/mol	212 223@LB@ \| \|@LB@5'-AAC...CCAAA UGAUA...AGG-3'@LB@ GAUCUGAUUG@LB@ :\|\|\|:\|\|\|\|:@LB@ UUAGGCUAAU@LB@3'-AUU...UCGGU GCACU...AUG-5'@LB@ \| \|@LB@ 60 49@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -9.79708 kcal/mol@LB@Unfolding Energy - mRNA 1.6903 kcal/mol@LB@Unfolding Energy - sRNA 0.31771 kcal/mol@LB@@LB@Position - mRNA 213 -- 222@LB@Position - sRNA 50 -- 59@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 50 -- 56@LB@
149	0.005967	0.1406	b0472	recR	-13.66	0.002580	134 -- 160	3 -- 29	gap repair protein	_____________133_________________________161\n_____________\|___________________________\|\n5'-GUG...AACGC___A____AAAAUG_____________CCGGA...UUC-3'\n______________AGA_AGAA______GCCUCUGUAUCCU\n______________\|\|\|_\|\|\|\|______:\|\|\|\|\|\|\|\|:\|\|\|\n______________UCU_UCUU______UGGAGACAUGGGA\n3'-AUU...GACUU___A____GUAGAA_____________UG-5'\n_____________\|___________________________\|\n_____________30__________________________2\n	154 -- 160	3 -- 9	-27.6106 kcal/mol	5.92472 kcal/mol	8.05021 kcal/mol	133 161@LB@ \| \|@LB@5'-GUG...AACGC A AAAAUG CCGGA...UUC-3'@LB@ AGA AGAA GCCUCUGUAUCCU@LB@ \|\|\| \|\|\|\| :\|\|\|\|\|\|\|\|:\|\|\|@LB@ UCU UCUU UGGAGACAUGGGA@LB@3'-AUU...GACUU A GUAGAA UG-5'@LB@ \| \|@LB@ 30 2@LB@@LB@@LB@Energy -13.66 kcal/mol@LB@Hybridization Energy -27.6106 kcal/mol@LB@Unfolding Energy - mRNA 5.92472 kcal/mol@LB@Unfolding Energy - sRNA 8.05021 kcal/mol@LB@@LB@Position - mRNA 134 -- 160@LB@Position - sRNA 3 -- 29@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 3 -- 9@LB@
150	0.00611	0.1406	b0735	ybgE	-10.35	0.035619	38 -- 71	5 -- 31	putative inner membrane protein in cydABX-ybgE operon	_____________37_________________________________72\n_____________\|__________________________________\|\n5'-CUG...CCAAA_______UU______AAC___CACUC________AAGUA...UUU-3'\n______________GAAGAUA__GAACGU___ACC_____UCUGUACU\n______________:\|\|\|\|\|\|__\|\|\|\|:\|___\|\|\|_____\|\|\|\|\|\|\|:\n______________UUUCUAU__CUUGUA___UGG_____AGACAUGG\n3'-AUU...CAGAC_______________GAA________________GAUG-5'\n_____________\|__________________________________\|\n_____________32_________________________________4\n	65 -- 71	5 -- 11	-23.0678 kcal/mol	4.68737 kcal/mol	8.05162 kcal/mol	37 72@LB@ \| \|@LB@5'-CUG...CCAAA UU AAC CACUC AAGUA...UUU-3'@LB@ GAAGAUA GAACGU ACC UCUGUACU@LB@ :\|\|\|\|\|\| \|\|\|\|:\| \|\|\| \|\|\|\|\|\|\|:@LB@ UUUCUAU CUUGUA UGG AGACAUGG@LB@3'-AUU...CAGAC GAA GAUG-5'@LB@ \| \|@LB@ 32 4@LB@@LB@@LB@Energy -10.35 kcal/mol@LB@Hybridization Energy -23.0678 kcal/mol@LB@Unfolding Energy - mRNA 4.68737 kcal/mol@LB@Unfolding Energy - sRNA 8.05162 kcal/mol@LB@@LB@Position - mRNA 38 -- 71@LB@Position - sRNA 5 -- 31@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 5 -- 11@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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