Input and runtime details for job 5774122 (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 5774122 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:30:38 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:16:08 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 23:32:42 CET 2018
	Post-Processing Finished		@ Fri Feb 16 23:32:50 CET 2018
	Job Completed		@ Fri Feb 16 23:33:10 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5774122&toolName=CopraRNA ( 30 days expiry )

Description of the job

FsrA

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_000964 Bacillus subtilis subsp. subtilis str. 168

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
200	0.01989	0.3269	bsu30150	ytdP	-13.03	0.070310	188 -- 210	28 -- 52	AraC family transcriptional regulator		_____________187________________________211\n_____________\|__________________________\|\n5'-UUU...UGAAG_____G_UA______AAU________UUAUG...UAU-3'\n______________UGGAU_U_____UGA___GGGGGGUU\n______________:\|\|\|\|_\|_____\|\|\|___\|:\|\|\|\|\|\|\n______________GCCUA_A_____ACU___CUCCCCAA\n3'-UUU...AAAAA_____G_ACUAG___AU_________CCCCU...AUA-5'\n_____________\|__________________________\|\n_____________53_________________________27\n	204 -- 210	28 -- 34	-18.7355 kcal/mol	4.72292 kcal/mol	0.980555 kcal/mol	187 211@LB@ \| \|@LB@5'-UUU...UGAAG G UA AAU UUAUG...UAU-3'@LB@ UGGAU U UGA GGGGGGUU@LB@ :\|\|\|\| \| \|\|\| \|:\|\|\|\|\|\|@LB@ GCCUA A ACU CUCCCCAA@LB@3'-UUU...AAAAA G ACUAG AU CCCCU...AUA-5'@LB@ \| \|@LB@ 53 27@LB@@LB@@LB@Energy -13.03 kcal/mol@LB@Hybridization Energy -18.7355 kcal/mol@LB@Unfolding Energy - mRNA 4.72292 kcal/mol@LB@Unfolding Energy - sRNA 0.980555 kcal/mol@LB@@LB@Position - mRNA 188 -- 210@LB@Position - sRNA 28 -- 52@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 28 -- 34@LB@
189	0.01911	0.3269	bsu24290	xseB	-12.91	0.073825	187 -- 193	30 -- 36	exodeoxyribonuclease 7 small subunit		_____________186_____194\n_____________\|_______\|\n5'-CAU...AAAAG_______AAGAA...UAG-3'\n______________AGAGGGG\n______________\|\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	187 -- 193	30 -- 36	-14.0184 kcal/mol	0.973532 kcal/mol	0.133643 kcal/mol	186 194@LB@ \| \|@LB@5'-CAU...AAAAG AAGAA...UAG-3'@LB@ AGAGGGG@LB@ \|\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -12.91 kcal/mol@LB@Hybridization Energy -14.0184 kcal/mol@LB@Unfolding Energy - mRNA 0.973532 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 187 -- 193@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 30 -- 36@LB@
20	0.0003727	0.06216	bsu04690	rsbT	-12.89	0.074349	161 -- 193	22 -- 51	serine/threonine protein kinase		_____________160________________________________194\n_____________\|__________________________________\|\n5'-UUG...GAGCA__GG_____GACAU______C___AA________AUAGC...CGG-3'\n______________GG__CUUGA_____UGA_AG_GGG__UUGGGGGA\n______________\|\|__\|\|\|\|\|_____\|\|\|_\|\|_\|\|\|__\|\|\|\|\|\|:\|\n______________CC__GAACU_____ACU_UC_CCC__AACCCCUU\n3'-UUU...AAAAG__UA_____AG______A__U___C_________GUCUC...AUA-5'\n_____________\|__________________________________\|\n_____________52_________________________________21\n	187 -- 193	22 -- 28	-26.679 kcal/mol	11.9064 kcal/mol	1.87888 kcal/mol	160 194@LB@ \| \|@LB@5'-UUG...GAGCA GG GACAU C AA AUAGC...CGG-3'@LB@ GG CUUGA UGA AG GGG UUGGGGGA@LB@ \|\| \|\|\|\|\| \|\|\| \|\| \|\|\| \|\|\|\|\|\|:\|@LB@ CC GAACU ACU UC CCC AACCCCUU@LB@3'-UUU...AAAAG UA AG A U C GUCUC...AUA-5'@LB@ \| \|@LB@ 52 21@LB@@LB@@LB@Energy -12.89 kcal/mol@LB@Hybridization Energy -26.679 kcal/mol@LB@Unfolding Energy - mRNA 11.9064 kcal/mol@LB@Unfolding Energy - sRNA 1.87888 kcal/mol@LB@@LB@Position - mRNA 161 -- 193@LB@Position - sRNA 22 -- 51@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 22 -- 28@LB@
71	0.005061	0.2378	bsu02170	ybfB	-12.87	0.075045	244 -- 269	24 -- 48	MFS transporter	bsu03530	_____________243__________________________270\n_____________\|____________________________\|\n5'-CUU...CACCU_____________UU__C____CA____GUGCG...AGC-3'\n______________UUUUGAUCU__UA__GG_GGUU__GGGG\n______________\|:\|\|\|\|\|\|\|__\|\|__\|\|_\|\|\|\|__\|\|\|\|\n______________AGAACUAGA__AU__CC_CCAA__CCCC\n3'-UUU...AGCCU_________CU__CU_____________UUGUC...AUA-5'\n_____________\|____________________________\|\n_____________49___________________________23\n	246 -- 252	40 -- 46	-21.3597 kcal/mol	7.5105 kcal/mol	0.978761 kcal/mol	243 270@LB@ \| \|@LB@5'-CUU...CACCU UU C CA GUGCG...AGC-3'@LB@ UUUUGAUCU UA GG GGUU GGGG@LB@ \|:\|\|\|\|\|\|\| \|\| \|\| \|\|\|\| \|\|\|\|@LB@ AGAACUAGA AU CC CCAA CCCC@LB@3'-UUU...AGCCU CU CU UUGUC...AUA-5'@LB@ \| \|@LB@ 49 23@LB@@LB@@LB@Energy -12.87 kcal/mol@LB@Hybridization Energy -21.3597 kcal/mol@LB@Unfolding Energy - mRNA 7.5105 kcal/mol@LB@Unfolding Energy - sRNA 0.978761 kcal/mol@LB@@LB@Position - mRNA 244 -- 269@LB@Position - sRNA 24 -- 48@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 40 -- 46@LB@
90	0.006982	0.2588	bsu40920	yyaF	-12.87	0.074972	6 -- 31	25 -- 50	GTP-dependent nucleic acid-binding protein EngD		_____________5___________________________32\n_____________\|___________________________\|\n______5'-CAAAU___ACAAAU_______AU__AA_____AAGUA...CGU-3'\n______________GAU______UCUGAUA__GG___UGGG\n______________\|\|\|______\|\|\|\|\|\|\|__\|\|___\|\|\|\|\n______________CUA______AGACUAU__CC___ACCC\n3'-UUU...AAAGC___GAACU________CU__CCA____CUUGU...AUA-5'\n_____________\|___________________________\|\n_____________51__________________________24\n	15 -- 21	36 -- 42	-17.5884 kcal/mol	3.73957 kcal/mol	0.976057 kcal/mol	5 32@LB@ \| \|@LB@ 5'-CAAAU ACAAAU AU AA AAGUA...CGU-3'@LB@ GAU UCUGAUA GG UGGG@LB@ \|\|\| \|\|\|\|\|\|\| \|\| \|\|\|\|@LB@ CUA AGACUAU CC ACCC@LB@3'-UUU...AAAGC GAACU CU CCA CUUGU...AUA-5'@LB@ \| \|@LB@ 51 24@LB@@LB@@LB@Energy -12.87 kcal/mol@LB@Hybridization Energy -17.5884 kcal/mol@LB@Unfolding Energy - mRNA 3.73957 kcal/mol@LB@Unfolding Energy - sRNA 0.976057 kcal/mol@LB@@LB@Position - mRNA 6 -- 31@LB@Position - sRNA 25 -- 50@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 36 -- 42@LB@
106	0.009109	0.2778	bsu01390	infA	-12.86	0.075307	175 -- 189	30 -- 45	translation initiation factor IF-1		_____________174______________190\n_____________\|________________\|\n5'-CCA...GUUAC____________A___AGAAC...UGG-3'\n______________UGAUUUGA_AGA_GGG\n______________\|\|\|\|:\|\|\|_\|\|\|_\|\|\|\n______________ACUAGACU_UCU_CCC\n3'-UUU...CUAGA________A___C___AACCC...AUA-5'\n_____________\|________________\|\n_____________46_______________29\n	176 -- 182	38 -- 44	-16.3452 kcal/mol	2.51395 kcal/mol	0.969561 kcal/mol	174 190@LB@ \| \|@LB@5'-CCA...GUUAC A AGAAC...UGG-3'@LB@ UGAUUUGA AGA GGG@LB@ \|\|\|\|:\|\|\| \|\|\| \|\|\|@LB@ ACUAGACU UCU CCC@LB@3'-UUU...CUAGA A C AACCC...AUA-5'@LB@ \| \|@LB@ 46 29@LB@@LB@@LB@Energy -12.86 kcal/mol@LB@Hybridization Energy -16.3452 kcal/mol@LB@Unfolding Energy - mRNA 2.51395 kcal/mol@LB@Unfolding Energy - sRNA 0.969561 kcal/mol@LB@@LB@Position - mRNA 175 -- 189@LB@Position - sRNA 30 -- 45@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 38 -- 44@LB@
100	0.008436	0.2778	bsu35250	ftsX	-12.75	0.078592	182 -- 188	30 -- 36	cell division protein FtsX		_____________181_____189\n_____________\|_______\|\n5'-UGC...AGUCA_______AGUAU...CGC-3'\n______________AGAGGGG\n______________\|\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	182 -- 188	30 -- 36	-13.7147 kcal/mol	0.82624 kcal/mol	0.133643 kcal/mol	181 189@LB@ \| \|@LB@5'-UGC...AGUCA AGUAU...CGC-3'@LB@ AGAGGGG@LB@ \|\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -12.75 kcal/mol@LB@Hybridization Energy -13.7147 kcal/mol@LB@Unfolding Energy - mRNA 0.82624 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 182 -- 188@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 30 -- 36@LB@
43	0.00194	0.1492	bsu01370	adk	-12.74	0.079154	128 -- 149	32 -- 52	adenylate kinase		_____________127____________________150\n_____________\|______________________\|\n5'-UUU...UACCG_______A___AAAAC______AAAUG...AUA-3'\n______________UGGAUUU_UGA_____UAGAGG\n______________:\|\|\|\|:\|_\|\|\|_____\|\|\|\|\|\|\n______________GCCUAGA_ACU_____AUCUCC\n3'-UUU...AAAAA___________AGACU______CCAAC...AUA-5'\n_____________\|______________________\|\n_____________53_____________________31\n	128 -- 134	46 -- 52	-16.4639 kcal/mol	2.75066 kcal/mol	0.976384 kcal/mol	127 150@LB@ \| \|@LB@5'-UUU...UACCG A AAAAC AAAUG...AUA-3'@LB@ UGGAUUU UGA UAGAGG@LB@ :\|\|\|\|:\| \|\|\| \|\|\|\|\|\|@LB@ GCCUAGA ACU AUCUCC@LB@3'-UUU...AAAAA AGACU CCAAC...AUA-5'@LB@ \| \|@LB@ 53 31@LB@@LB@@LB@Energy -12.74 kcal/mol@LB@Hybridization Energy -16.4639 kcal/mol@LB@Unfolding Energy - mRNA 2.75066 kcal/mol@LB@Unfolding Energy - sRNA 0.976384 kcal/mol@LB@@LB@Position - mRNA 128 -- 149@LB@Position - sRNA 32 -- 52@LB@Position Seed - mRNA 128 -- 134@LB@Position Seed - sRNA 46 -- 52@LB@
158	0.01436	0.3008	bsu10130	hemH	-12.69	0.080628	178 -- 227	6 -- 44	ferrochelatase		_____________177____________________________________________________228\n_____________\|______________________________________________________\|\n5'-GAG...UAUCA____AUUAA______U__A_________U____AGAAAGAAAAUGG________GUGAU...GAA-3'\n______________GAUC_____AGAGGG_GU_____AACAG_GAGU_____________GGCUUCUC\n______________\|\|\|\|_____\|\|\|\|\|\|_\|\|_____\|\|\|\|\|_\|\|\|\|_____________:\|\|\|\|\|\|\|\n______________CUAG_____UCUCCC_CA_____UUGUC_CUCA_____________UCGAAGAG\n3'-UUU...UAGAA____ACUA__________ACCCC_____U_________________________AGAUA-5'\n_____________\|______________________________________________________\|\n_____________45_____________________________________________________5\n	220 -- 226	7 -- 13	-32.766 kcal/mol	10.122 kcal/mol	9.95356 kcal/mol	177 228@LB@ \| \|@LB@5'-GAG...UAUCA AUUAA U A U AGAAAGAAAAUGG GUGAU...GAA-3'@LB@ GAUC AGAGGG GU AACAG GAGU GGCUUCUC@LB@ \|\|\|\| \|\|\|\|\|\| \|\| \|\|\|\|\| \|\|\|\| :\|\|\|\|\|\|\|@LB@ CUAG UCUCCC CA UUGUC CUCA UCGAAGAG@LB@3'-UUU...UAGAA ACUA ACCCC U AGAUA-5'@LB@ \| \|@LB@ 45 5@LB@@LB@@LB@Energy -12.69 kcal/mol@LB@Hybridization Energy -32.766 kcal/mol@LB@Unfolding Energy - mRNA 10.122 kcal/mol@LB@Unfolding Energy - sRNA 9.95356 kcal/mol@LB@@LB@Position - mRNA 178 -- 227@LB@Position - sRNA 6 -- 44@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 7 -- 13@LB@
48	0.002156	0.1498	bsu34050	yvfV	-12.63	0.082536	177 -- 196	28 -- 46	lactate utilization protein A		_____________176__________________197\n_____________\|____________________\|\n5'-UCG...AUAUA____GGA___G_________CAUCA...UUG-3'\n______________UUGG___UGA_AGAGGGGUU\n______________\|\|\|:___\|\|\|_\|\|\|\|\|\|\|\|\|\n______________AACU___ACU_UCUCCCCAA\n3'-UUU...CCUAG____AG____A_________CCCCU...AUA-5'\n_____________\|____________________\|\n_____________47___________________27\n	190 -- 196	28 -- 34	-21.1804 kcal/mol	7.57881 kcal/mol	0.97023 kcal/mol	176 197@LB@ \| \|@LB@5'-UCG...AUAUA GGA G CAUCA...UUG-3'@LB@ UUGG UGA AGAGGGGUU@LB@ \|\|\|: \|\|\| \|\|\|\|\|\|\|\|\|@LB@ AACU ACU UCUCCCCAA@LB@3'-UUU...CCUAG AG A CCCCU...AUA-5'@LB@ \| \|@LB@ 47 27@LB@@LB@@LB@Energy -12.63 kcal/mol@LB@Hybridization Energy -21.1804 kcal/mol@LB@Unfolding Energy - mRNA 7.57881 kcal/mol@LB@Unfolding Energy - sRNA 0.97023 kcal/mol@LB@@LB@Position - mRNA 177 -- 196@LB@Position - sRNA 28 -- 46@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 28 -- 34@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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