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
138	0.01215	0.2883	bsu17940	yneI	-15.06	0.029368	176 -- 197	30 -- 52	plasmid maintenance protein CcdB	_____________175_____________________198\n_____________\|_______________________\|\n5'-GAA...AUCUG____AA_C____GU_________AAUAU...CGG-3'\n______________UGGA__U_GAUU___UGGAGGGG\n______________:\|\|\|__\|_\|\|\|:___\|:\|\|\|\|\|\|\n______________GCCU__A_CUAG___AUCUCCCC\n3'-UUU...AAAAA____AG_A____ACU________AACCC...AUA-5'\n_____________\|_______________________\|\n_____________53______________________29\n	191 -- 197	30 -- 36	-21.3361 kcal/mol	5.29839 kcal/mol	0.979974 kcal/mol	175 198@LB@ \| \|@LB@5'-GAA...AUCUG AA C GU AAUAU...CGG-3'@LB@ UGGA U GAUU UGGAGGGG@LB@ :\|\|\| \| \|\|\|: \|:\|\|\|\|\|\|@LB@ GCCU A CUAG AUCUCCCC@LB@3'-UUU...AAAAA AG A ACU AACCC...AUA-5'@LB@ \| \|@LB@ 53 29@LB@@LB@@LB@Energy -15.06 kcal/mol@LB@Hybridization Energy -21.3361 kcal/mol@LB@Unfolding Energy - mRNA 5.29839 kcal/mol@LB@Unfolding Energy - sRNA 0.979974 kcal/mol@LB@@LB@Position - mRNA 176 -- 197@LB@Position - sRNA 30 -- 52@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 30 -- 36@LB@
139	0.01217	0.2883	bsu30960	glgD	-11.28	0.137516	171 -- 191	30 -- 50	glycogen biosynthesis protein GlgD	_____________170____________________192\n_____________\|______________________\|\n5'-ACU...GAAUU_____AAUUA____________GCAGA...UUG-3'\n______________GAUUU_____CUGA_AGAGGGG\n______________\|\|\|:\|_____\|\|\|\|_\|\|\|\|\|\|\|\n______________CUAGA_____GACU_UCUCCCC\n3'-UUU...AAAGC_____ACUA_____A_______AACCC...AUA-5'\n_____________\|______________________\|\n_____________51_____________________29\n	185 -- 191	30 -- 36	-19.1028 kcal/mol	6.84884 kcal/mol	0.974272 kcal/mol	170 192@LB@ \| \|@LB@5'-ACU...GAAUU AAUUA GCAGA...UUG-3'@LB@ GAUUU CUGA AGAGGGG@LB@ \|\|\|:\| \|\|\|\| \|\|\|\|\|\|\|@LB@ CUAGA GACU UCUCCCC@LB@3'-UUU...AAAGC ACUA A AACCC...AUA-5'@LB@ \| \|@LB@ 51 29@LB@@LB@@LB@Energy -11.28 kcal/mol@LB@Hybridization Energy -19.1028 kcal/mol@LB@Unfolding Energy - mRNA 6.84884 kcal/mol@LB@Unfolding Energy - sRNA 0.974272 kcal/mol@LB@@LB@Position - mRNA 171 -- 191@LB@Position - sRNA 30 -- 50@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 30 -- 36@LB@
140	0.01224	0.2883	bsu36480	ywoD	-6.33	0.569704	31 -- 37	66 -- 72	MFS transporter	_____________30______38\n_____________\|_______\|\n5'-AUU...AUAUC_______AAAGC...AUA-3'\n______________GGGGUGG\n______________\|\|\|\|\|:\|\n______________CCCCAUC\n3'-UUU...ACCGC_______GCGGU...AUA-5'\n_____________\|_______\|\n_____________73______65\n	31 -- 37	66 -- 72	-11.1749 kcal/mol	4.83937 kcal/mol	0.00366414 kcal/mol	30 38@LB@ \| \|@LB@5'-AUU...AUAUC AAAGC...AUA-3'@LB@ GGGGUGG@LB@ \|\|\|\|\|:\|@LB@ CCCCAUC@LB@3'-UUU...ACCGC GCGGU...AUA-5'@LB@ \| \|@LB@ 73 65@LB@@LB@@LB@Energy -6.33 kcal/mol@LB@Hybridization Energy -11.1749 kcal/mol@LB@Unfolding Energy - mRNA 4.83937 kcal/mol@LB@Unfolding Energy - sRNA 0.00366414 kcal/mol@LB@@LB@Position - mRNA 31 -- 37@LB@Position - sRNA 66 -- 72@LB@Position Seed - mRNA 31 -- 37@LB@Position Seed - sRNA 66 -- 72@LB@
141	0.01225	0.2883	bsu32310	yutD	-11.41	0.131333	145 -- 158	24 -- 40	Evidence 4: Homologs of previously reported genes of unknown function; PubMedId: 12770717	_____________144_______________159\n_____________\|_________________\|\n5'-ACA...GCAAU________AC_______CAAUG...AUA-3'\n______________UGAUGGGG_____GGGG\n______________\|\|\|\|:\|:\|_____\|\|\|\|\n______________ACUAUCUC_____CCCC\n3'-UUU...ACUAG________CCCAA____UUGUC...AUA-5'\n_____________\|_________________\|\n_____________41________________23\n	146 -- 152	33 -- 39	-14.827 kcal/mol	2.62921 kcal/mol	0.790979 kcal/mol	144 159@LB@ \| \|@LB@5'-ACA...GCAAU AC CAAUG...AUA-3'@LB@ UGAUGGGG GGGG@LB@ \|\|\|\|:\|:\| \|\|\|\|@LB@ ACUAUCUC CCCC@LB@3'-UUU...ACUAG CCCAA UUGUC...AUA-5'@LB@ \| \|@LB@ 41 23@LB@@LB@@LB@Energy -11.41 kcal/mol@LB@Hybridization Energy -14.827 kcal/mol@LB@Unfolding Energy - mRNA 2.62921 kcal/mol@LB@Unfolding Energy - sRNA 0.790979 kcal/mol@LB@@LB@Position - mRNA 145 -- 158@LB@Position - sRNA 24 -- 40@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 33 -- 39@LB@
142	0.01236	0.2883	bsu37940	ywdJ	-14.78	0.033255	157 -- 193	27 -- 52	purine permease YwdJ	_____________156___________________________________194\n_____________\|_____________________________________\|\n5'-GGA...GGAAA____GAG____U_______UUUUAAAG____A_____AGCUU...ACU-3'\n______________CGGA___UCUU_AUUUGAU________AGAG_GGUUG\n______________\|\|\|\|___\|\|\|\|_\|\|:\|\|\|\|________\|\|\|\|_\|\|\|\|\|\n______________GCCU___AGAA_UAGACUA________UCUC_CCAAC\n3'-UUU...AAAAA___________C___________________C_____CCCUU...AUA-5'\n_____________\|_____________________________________\|\n_____________53____________________________________26\n	169 -- 175	37 -- 43	-23.5373 kcal/mol	7.77274 kcal/mol	0.980744 kcal/mol	156 194@LB@ \| \|@LB@5'-GGA...GGAAA GAG U UUUUAAAG A AGCUU...ACU-3'@LB@ CGGA UCUU AUUUGAU AGAG GGUUG@LB@ \|\|\|\| \|\|\|\| \|\|:\|\|\|\| \|\|\|\| \|\|\|\|\|@LB@ GCCU AGAA UAGACUA UCUC CCAAC@LB@3'-UUU...AAAAA C C CCCUU...AUA-5'@LB@ \| \|@LB@ 53 26@LB@@LB@@LB@Energy -14.78 kcal/mol@LB@Hybridization Energy -23.5373 kcal/mol@LB@Unfolding Energy - mRNA 7.77274 kcal/mol@LB@Unfolding Energy - sRNA 0.980744 kcal/mol@LB@@LB@Position - mRNA 157 -- 193@LB@Position - sRNA 27 -- 52@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 37 -- 43@LB@
143	0.01244	0.2883	bsu13980	pbpH	-18.09	0.006437	121 -- 135	29 -- 45	penicillin-binding enzyme for formation of rod-shaped peptidoglycan cell wall	_____________120_______________136\n_____________\|_________________\|\n5'-UUU...UUGAA_________________AACCA...ACG-3'\n______________UGAUUUGA__GAGGGGU\n______________\|\|\|\|:\|\|\|__\|\|\|\|\|\|\|\n______________ACUAGACU__CUCCCCA\n3'-UUU...CUAGA________AU_______ACCCC...AUA-5'\n_____________\|_________________\|\n_____________46________________28\n	129 -- 135	29 -- 35	-21.9726 kcal/mol	2.91712 kcal/mol	0.969832 kcal/mol	120 136@LB@ \| \|@LB@5'-UUU...UUGAA AACCA...ACG-3'@LB@ UGAUUUGA GAGGGGU@LB@ \|\|\|\|:\|\|\| \|\|\|\|\|\|\|@LB@ ACUAGACU CUCCCCA@LB@3'-UUU...CUAGA AU ACCCC...AUA-5'@LB@ \| \|@LB@ 46 28@LB@@LB@@LB@Energy -18.09 kcal/mol@LB@Hybridization Energy -21.9726 kcal/mol@LB@Unfolding Energy - mRNA 2.91712 kcal/mol@LB@Unfolding Energy - sRNA 0.969832 kcal/mol@LB@@LB@Position - mRNA 121 -- 135@LB@Position - sRNA 29 -- 45@LB@Position Seed - mRNA 129 -- 135@LB@Position Seed - sRNA 29 -- 35@LB@
144	0.01244	0.2883	bsu15720	def	-10.99	0.152648	175 -- 193	31 -- 50	peptide deformylase	_____________174___________________194\n_____________\|_____________________\|\n5'-GCG...UGUAA_____CAC_____________UAACA...AUG-3'\n______________GAUCU___GUCU__UGGAGGG\n______________\|\|\|\|\|___:\|\|\|__\|:\|\|\|\|\|\n______________CUAGA___UAGA__AUCUCCC\n3'-UUU...AAAGC_____AC_____CU_______CAACC...AUA-5'\n_____________\|_____________________\|\n_____________51____________________30\n	187 -- 193	31 -- 37	-18.0798 kcal/mol	6.12249 kcal/mol	0.970579 kcal/mol	174 194@LB@ \| \|@LB@5'-GCG...UGUAA CAC UAACA...AUG-3'@LB@ GAUCU GUCU UGGAGGG@LB@ \|\|\|\|\| :\|\|\| \|:\|\|\|\|\|@LB@ CUAGA UAGA AUCUCCC@LB@3'-UUU...AAAGC AC CU CAACC...AUA-5'@LB@ \| \|@LB@ 51 30@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -18.0798 kcal/mol@LB@Unfolding Energy - mRNA 6.12249 kcal/mol@LB@Unfolding Energy - sRNA 0.970579 kcal/mol@LB@@LB@Position - mRNA 175 -- 193@LB@Position - sRNA 31 -- 50@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 31 -- 37@LB@
145	0.01267	0.2913	bsu36760	murAA	-10.92	0.156018	188 -- 194	30 -- 36	UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1	_____________187_____195\n_____________\|_______\|\n5'-UAG...GACGC_______AAUAC...UAU-3'\n______________GGAGGGG\n______________:\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	188 -- 194	30 -- 36	-13.3986 kcal/mol	2.34028 kcal/mol	0.133643 kcal/mol	187 195@LB@ \| \|@LB@5'-UAG...GACGC AAUAC...UAU-3'@LB@ GGAGGGG@LB@ :\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -10.92 kcal/mol@LB@Hybridization Energy -13.3986 kcal/mol@LB@Unfolding Energy - mRNA 2.34028 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 188 -- 194@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 30 -- 36@LB@
146	0.01275	0.2913	bsu00450	sspF	-8.40	0.345478	283 -- 295	24 -- 38	small acid-soluble spore protein SspF	_____________282_____________296\n_____________\|_______________\|\n5'-UGA...AAAAA_______C_______UGAAA-3'\n______________AUGGAGG___UGGGG\n______________\|\|:\|\|\|\|___\|\|\|\|\|\n______________UAUCUCC___ACCCC\n3'-UUU...UAGAC_______CCA_____UUGUC...AUA-5'\n_____________\|_______________\|\n_____________39______________23\n	283 -- 289	32 -- 38	-17.1295 kcal/mol	8.05792 kcal/mol	0.668509 kcal/mol	282 296@LB@ \| \|@LB@5'-UGA...AAAAA C UGAAA-3'@LB@ AUGGAGG UGGGG@LB@ \|\|:\|\|\|\| \|\|\|\|\|@LB@ UAUCUCC ACCCC@LB@3'-UUU...UAGAC CCA UUGUC...AUA-5'@LB@ \| \|@LB@ 39 23@LB@@LB@@LB@Energy -8.40 kcal/mol@LB@Hybridization Energy -17.1295 kcal/mol@LB@Unfolding Energy - mRNA 8.05792 kcal/mol@LB@Unfolding Energy - sRNA 0.668509 kcal/mol@LB@@LB@Position - mRNA 283 -- 295@LB@Position - sRNA 24 -- 38@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 32 -- 38@LB@
147	0.013	0.2949	bsu12910	proG	-10.46	0.183122	211 -- 241	23 -- 53	pyrroline-5-carboxylate reductase 3	_____________210________________________________242\n_____________\|__________________________________\|\n5'-UUC...ACAGA_____________G____U___CAGCA___C___UAUGA...UUG-3'\n______________UUGGAUU__GAUU_GAUA__GG_____UGG_GGA\n______________\|:\|\|\|\|:__\|\|\|:_\|\|\|\|__\|\|_____\|\|\|_\|\|\|\n______________AGCCUAG__CUAG_CUAU__CC_____ACC_CCU\n3'-UUU...AAAAA_______AA____A____CU__CCA_________UGUCU...AUA-5'\n_____________\|__________________________________\|\n_____________54_________________________________22\n	211 -- 217	47 -- 53	-18.7228 kcal/mol	7.27559 kcal/mol	0.987321 kcal/mol	210 242@LB@ \| \|@LB@5'-UUC...ACAGA G U CAGCA C UAUGA...UUG-3'@LB@ UUGGAUU GAUU GAUA GG UGG GGA@LB@ \|:\|\|\|\|: \|\|\|: \|\|\|\| \|\| \|\|\| \|\|\|@LB@ AGCCUAG CUAG CUAU CC ACC CCU@LB@3'-UUU...AAAAA AA A CU CCA UGUCU...AUA-5'@LB@ \| \|@LB@ 54 22@LB@@LB@@LB@Energy -10.46 kcal/mol@LB@Hybridization Energy -18.7228 kcal/mol@LB@Unfolding Energy - mRNA 7.27559 kcal/mol@LB@Unfolding Energy - sRNA 0.987321 kcal/mol@LB@@LB@Position - mRNA 211 -- 241@LB@Position - sRNA 23 -- 53@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 47 -- 53@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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