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
181	0.0171	0.3152	bsu32040	yuiF	-15.17	0.027943	179 -- 194	29 -- 51	amino acid transporter YuiF	_____________178_____________________195\n_____________\|_______________________\|\n5'-ACA...CUAAA_______________________AUCAU...GGU-3'\n______________GGAUUUU_______UGGAGGGGU\n______________\|\|\|\|:\|\|_______\|:\|\|\|\|\|\|\|\n______________CCUAGAA_______AUCUCCCCA\n3'-UUU...AAAAG_______CUAGACU_________ACCCC...AUA-5'\n_____________\|_______________________\|\n_____________52______________________28\n	188 -- 194	29 -- 35	-21.3957 kcal/mol	5.25498 kcal/mol	0.974539 kcal/mol	178 195@LB@ \| \|@LB@5'-ACA...CUAAA AUCAU...GGU-3'@LB@ GGAUUUU UGGAGGGGU@LB@ \|\|\|\|:\|\| \|:\|\|\|\|\|\|\|@LB@ CCUAGAA AUCUCCCCA@LB@3'-UUU...AAAAG CUAGACU ACCCC...AUA-5'@LB@ \| \|@LB@ 52 28@LB@@LB@@LB@Energy -15.17 kcal/mol@LB@Hybridization Energy -21.3957 kcal/mol@LB@Unfolding Energy - mRNA 5.25498 kcal/mol@LB@Unfolding Energy - sRNA 0.974539 kcal/mol@LB@@LB@Position - mRNA 179 -- 194@LB@Position - sRNA 29 -- 51@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 29 -- 35@LB@
37	0.00164	0.1432	bsu32390	yunF	-13.99	0.047070	211 -- 231	31 -- 53	Evidence 4: Homologs of previously reported genes of unknown function	_____________210_____________________232\n_____________\|_______________________\|\n5'-UGU...UUAUA___________CGG_________AUCAU...UUC-3'\n______________UCGGA_C_UGA___GAUGGGGGG\n______________\|\|\|\|\|_\|_\|\|\|___\|\|\|:\|:\|\|\|\n______________AGCCU_G_ACU___CUAUCUCCC\n3'-UUU...AAAAA_____A_A___AGA_________CAACC...AUA-5'\n_____________\|_______________________\|\n_____________54______________________30\n	225 -- 231	31 -- 37	-23.274 kcal/mol	8.29838 kcal/mol	0.981784 kcal/mol	210 232@LB@ \| \|@LB@5'-UGU...UUAUA CGG AUCAU...UUC-3'@LB@ UCGGA C UGA GAUGGGGGG@LB@ \|\|\|\|\| \| \|\|\| \|\|\|:\|:\|\|\|@LB@ AGCCU G ACU CUAUCUCCC@LB@3'-UUU...AAAAA A A AGA CAACC...AUA-5'@LB@ \| \|@LB@ 54 30@LB@@LB@@LB@Energy -13.99 kcal/mol@LB@Hybridization Energy -23.274 kcal/mol@LB@Unfolding Energy - mRNA 8.29838 kcal/mol@LB@Unfolding Energy - sRNA 0.981784 kcal/mol@LB@@LB@Position - mRNA 211 -- 231@LB@Position - sRNA 31 -- 53@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 31 -- 37@LB@
27	0.0005687	0.07027	bsu32550	yurJ	-13.20	0.065709	183 -- 191	31 -- 39	ABC transporter ATP-binding protein	_____________182_______192\n_____________\|_________\|\n5'-AAC...CAAAA_________ACUUU...UGC-3'\n______________GAUAGGGGG\n______________\|\|\|\|\|:\|\|\|\n______________CUAUCUCCC\n3'-UUU...CUAGA_________CAACC...AUA-5'\n_____________\|_________\|\n_____________40________30\n	185 -- 191	31 -- 37	-15.8488 kcal/mol	1.87568 kcal/mol	0.774822 kcal/mol	182 192@LB@ \| \|@LB@5'-AAC...CAAAA ACUUU...UGC-3'@LB@ GAUAGGGGG@LB@ \|\|\|\|\|:\|\|\|@LB@ CUAUCUCCC@LB@3'-UUU...CUAGA CAACC...AUA-5'@LB@ \| \|@LB@ 40 30@LB@@LB@@LB@Energy -13.20 kcal/mol@LB@Hybridization Energy -15.8488 kcal/mol@LB@Unfolding Energy - mRNA 1.87568 kcal/mol@LB@Unfolding Energy - sRNA 0.774822 kcal/mol@LB@@LB@Position - mRNA 183 -- 191@LB@Position - sRNA 31 -- 39@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 31 -- 37@LB@
116	0.01008	0.2881	bsu32800	yusH	-9.74	0.231897	187 -- 194	31 -- 38	glycine cleavage system H protein	_____________186______195\n_____________\|________\|\n5'-AUC...AAAAA________AUUCA...CCG-3'\n______________AUGGAGGG\n______________\|\|:\|\|\|\|\|\n______________UAUCUCCC\n3'-UUU...UAGAC________CAACC...AUA-5'\n_____________\|________\|\n_____________39_______30\n	188 -- 194	31 -- 37	-12.574 kcal/mol	2.17853 kcal/mol	0.65488 kcal/mol	186 195@LB@ \| \|@LB@5'-AUC...AAAAA AUUCA...CCG-3'@LB@ AUGGAGGG@LB@ \|\|:\|\|\|\|\|@LB@ UAUCUCCC@LB@3'-UUU...UAGAC CAACC...AUA-5'@LB@ \| \|@LB@ 39 30@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -12.574 kcal/mol@LB@Unfolding Energy - mRNA 2.17853 kcal/mol@LB@Unfolding Energy - sRNA 0.65488 kcal/mol@LB@@LB@Position - mRNA 187 -- 194@LB@Position - sRNA 31 -- 38@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 31 -- 37@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@
4	1.471e-05	0.01227	bsu32200	yutJ	-17.92	0.007061	210 -- 239	21 -- 53	NADH dehydrogenase-like protein YutJ	_____________209_______________________________240\n_____________\|_________________________________\|\n5'-UGA...AAAAA________________C_____UUAC_______AUGCG...UAA-3'\n______________UUGG_UCUUGAUC_GG_GGAGG_____GGGAAC\n______________\|:\|\|_\|\|\|\|\|\|\|\|_\|:_:\|\|\|\|_____\|\|\|\|\|\|\n______________AGCC_AGAACUAG_CU_UCUCC_____CCCUUG\n3'-UUU...AAAAA____U________A__A_____CCAAC______UCUCU...AUA-5'\n_____________\|_________________________________\|\n_____________54________________________________20\n	215 -- 221	41 -- 47	-30.8017 kcal/mol	10.1098 kcal/mol	2.77573 kcal/mol	209 240@LB@ \| \|@LB@5'-UGA...AAAAA C UUAC AUGCG...UAA-3'@LB@ UUGG UCUUGAUC GG GGAGG GGGAAC@LB@ \|:\|\| \|\|\|\|\|\|\|\| \|: :\|\|\|\| \|\|\|\|\|\|@LB@ AGCC AGAACUAG CU UCUCC CCCUUG@LB@3'-UUU...AAAAA U A A CCAAC UCUCU...AUA-5'@LB@ \| \|@LB@ 54 20@LB@@LB@@LB@Energy -17.92 kcal/mol@LB@Hybridization Energy -30.8017 kcal/mol@LB@Unfolding Energy - mRNA 10.1098 kcal/mol@LB@Unfolding Energy - sRNA 2.77573 kcal/mol@LB@@LB@Position - mRNA 210 -- 239@LB@Position - sRNA 21 -- 53@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 41 -- 47@LB@
167	0.01619	0.3152	bsu31500	yuxK	-13.98	0.047449	182 -- 199	26 -- 51	Evidence 4: Homologs of previously reported genes of unknown function	_____________181__________________________200\n_____________\|____________________________\|\n5'-UAC...UUAAA______________________AUA___AGUGA...ACG-3'\n______________GGAUC__________GGAGGGG___UGG\n______________\|\|\|\|\|__________:\|\|\|\|\|\|___\|\|\|\n______________CCUAG__________UCUCCCC___ACC\n3'-UUU...AAAAG_____AACUAGACUA_______A_____CCUUG...AUA-5'\n_____________\|____________________________\|\n_____________52___________________________25\n	187 -- 193	30 -- 36	-20.9361 kcal/mol	5.98517 kcal/mol	0.975822 kcal/mol	181 200@LB@ \| \|@LB@5'-UAC...UUAAA AUA AGUGA...ACG-3'@LB@ GGAUC GGAGGGG UGG@LB@ \|\|\|\|\| :\|\|\|\|\|\| \|\|\|@LB@ CCUAG UCUCCCC ACC@LB@3'-UUU...AAAAG AACUAGACUA A CCUUG...AUA-5'@LB@ \| \|@LB@ 52 25@LB@@LB@@LB@Energy -13.98 kcal/mol@LB@Hybridization Energy -20.9361 kcal/mol@LB@Unfolding Energy - mRNA 5.98517 kcal/mol@LB@Unfolding Energy - sRNA 0.975822 kcal/mol@LB@@LB@Position - mRNA 182 -- 199@LB@Position - sRNA 26 -- 51@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 30 -- 36@LB@
92	0.007313	0.2652	bsu34470	yveA	-16.72	0.013215	240 -- 265	25 -- 47	aspartate-proton symporter	_____________239________________________266\n_____________\|__________________________\|\n5'-CCU...CGCUG___________UUU__UU___A____AGCCA...UCA-3'\n______________UUUGAUCUGAU___GA__GGG_UGGG\n______________:\|\|\|\|\|\|\|\|\|\|___\|\|__\|\|\|_\|\|\|\|\n______________GAACUAGACUA___CU__CCC_ACCC\n3'-UUU...GCCUA___________U____C____A____CUUGU...AUA-5'\n_____________\|__________________________\|\n_____________48_________________________24\n	244 -- 250	37 -- 43	-24.6158 kcal/mol	6.92071 kcal/mol	0.975871 kcal/mol	239 266@LB@ \| \|@LB@5'-CCU...CGCUG UUU UU A AGCCA...UCA-3'@LB@ UUUGAUCUGAU GA GGG UGGG@LB@ :\|\|\|\|\|\|\|\|\|\| \|\| \|\|\| \|\|\|\|@LB@ GAACUAGACUA CU CCC ACCC@LB@3'-UUU...GCCUA U C A CUUGU...AUA-5'@LB@ \| \|@LB@ 48 24@LB@@LB@@LB@Energy -16.72 kcal/mol@LB@Hybridization Energy -24.6158 kcal/mol@LB@Unfolding Energy - mRNA 6.92071 kcal/mol@LB@Unfolding Energy - sRNA 0.975871 kcal/mol@LB@@LB@Position - mRNA 240 -- 265@LB@Position - sRNA 25 -- 47@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 37 -- 43@LB@
10	0.0001049	0.035	bsu34190	yvfH	-16.62	0.013859	188 -- 201	23 -- 36	L-lactate permease	_____________187____________202\n_____________\|______________\|\n5'-UGG...UUCAA_________U____UGCAA...CGA-3'\n______________GGAGGGGUU_GGGA\n______________:\|\|\|\|\|\|\|\|_\|\|\|\|\n______________UCUCCCCAA_CCCU\n3'-UUU...GACUA_________C____UGUCU...AUA-5'\n_____________\|______________\|\n_____________37_____________22\n	190 -- 196	28 -- 34	-23.4111 kcal/mol	6.64684 kcal/mol	0.139628 kcal/mol	187 202@LB@ \| \|@LB@5'-UGG...UUCAA U UGCAA...CGA-3'@LB@ GGAGGGGUU GGGA@LB@ :\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UCUCCCCAA CCCU@LB@3'-UUU...GACUA C UGUCU...AUA-5'@LB@ \| \|@LB@ 37 22@LB@@LB@@LB@Energy -16.62 kcal/mol@LB@Hybridization Energy -23.4111 kcal/mol@LB@Unfolding Energy - mRNA 6.64684 kcal/mol@LB@Unfolding Energy - sRNA 0.139628 kcal/mol@LB@@LB@Position - mRNA 188 -- 201@LB@Position - sRNA 23 -- 36@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 28 -- 34@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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