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
155	0.01391	0.2994	bsu24780	yqgY	-10.29	0.193646	188 -- 194	30 -- 36	Evidence 4: Homologs of previously reported genes of unknown function		_____________187_____195\n_____________\|_______\|\n5'-UGU...UCUCG_______AUAAA...GAC-3'\n______________GGAGGGG\n______________:\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	188 -- 194	30 -- 36	-13.7207 kcal/mol	3.29345 kcal/mol	0.133643 kcal/mol	187 195@LB@ \| \|@LB@5'-UGU...UCUCG AUAAA...GAC-3'@LB@ GGAGGGG@LB@ :\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -10.29 kcal/mol@LB@Hybridization Energy -13.7207 kcal/mol@LB@Unfolding Energy - mRNA 3.29345 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@
156	0.0141	0.3008	bsu23600	yqxK	-15.33	0.025853	66 -- 91	32 -- 51	Evidence 4: Homologs of previously reported genes of unknown function		_____________65_________________________92\n_____________\|__________________________\|\n5'-GAA...GAUGA___CGAGUU_G____AG_________UGACG...GAA-3'\n______________GGA______U_UUGA__UGAUGGAGG\n______________\|\|\|______\|_\|\|\|\|__\|\|\|\|:\|\|\|\|\n______________CCU______A_AACU__ACUAUCUCC\n3'-UUU...AAAAG__________G____AG_________CCAAC...AUA-5'\n_____________\|__________________________\|\n_____________52_________________________31\n	85 -- 91	32 -- 38	-19.9693 kcal/mol	3.66503 kcal/mol	0.97021 kcal/mol	65 92@LB@ \| \|@LB@5'-GAA...GAUGA CGAGUU G AG UGACG...GAA-3'@LB@ GGA U UUGA UGAUGGAGG@LB@ \|\|\| \| \|\|\|\| \|\|\|\|:\|\|\|\|@LB@ CCU A AACU ACUAUCUCC@LB@3'-UUU...AAAAG G AG CCAAC...AUA-5'@LB@ \| \|@LB@ 52 31@LB@@LB@@LB@Energy -15.33 kcal/mol@LB@Hybridization Energy -19.9693 kcal/mol@LB@Unfolding Energy - mRNA 3.66503 kcal/mol@LB@Unfolding Energy - sRNA 0.97021 kcal/mol@LB@@LB@Position - mRNA 66 -- 91@LB@Position - sRNA 32 -- 51@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 32 -- 38@LB@
163	0.01533	0.3122	bsu19639	yoyE	-15.95	0.019304	185 -- 198	25 -- 39	Evidence 4: Homologs of previously reported genes of unknown function		_____________184_____________199\n_____________\|_______________\|\n5'-UCA...CGCAG__A____________ACAUG...AAU-3'\n______________GA_GGAGGGGU_GGG\n______________\|\|_:\|\|\|\|\|\|\|_\|\|\|\n______________CU_UCUCCCCA_CCC\n3'-UUU...CUAGA__A________A___CUUGU...AUA-5'\n_____________\|_______________\|\n_____________40______________24\n	189 -- 195	29 -- 35	-22.4813 kcal/mol	5.74668 kcal/mol	0.783603 kcal/mol	184 199@LB@ \| \|@LB@5'-UCA...CGCAG A ACAUG...AAU-3'@LB@ GA GGAGGGGU GGG@LB@ \|\| :\|\|\|\|\|\|\| \|\|\|@LB@ CU UCUCCCCA CCC@LB@3'-UUU...CUAGA A A CUUGU...AUA-5'@LB@ \| \|@LB@ 40 24@LB@@LB@@LB@Energy -15.95 kcal/mol@LB@Hybridization Energy -22.4813 kcal/mol@LB@Unfolding Energy - mRNA 5.74668 kcal/mol@LB@Unfolding Energy - sRNA 0.783603 kcal/mol@LB@@LB@Position - mRNA 185 -- 198@LB@Position - sRNA 25 -- 39@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 29 -- 35@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@
184	0.01795	0.3254	bsu30470	ytzC	-13.40	0.060457	189 -- 197	28 -- 36	Evidence 4: Homologs of previously reported genes of unknown function		_____________188_______198\n_____________\|_________\|\n5'-UUC...CAAGA_________ACUGU...AUU-3'\n______________GGAGGGGUU\n______________:\|\|\|\|\|\|\|\|\n______________UCUCCCCAA\n3'-UUU...GACUA_________CCCCU...AUA-5'\n_____________\|_________\|\n_____________37________27\n	191 -- 197	28 -- 34	-16.1349 kcal/mol	2.59994 kcal/mol	0.134381 kcal/mol	188 198@LB@ \| \|@LB@5'-UUC...CAAGA ACUGU...AUU-3'@LB@ GGAGGGGUU@LB@ :\|\|\|\|\|\|\|\|@LB@ UCUCCCCAA@LB@3'-UUU...GACUA CCCCU...AUA-5'@LB@ \| \|@LB@ 37 27@LB@@LB@@LB@Energy -13.40 kcal/mol@LB@Hybridization Energy -16.1349 kcal/mol@LB@Unfolding Energy - mRNA 2.59994 kcal/mol@LB@Unfolding Energy - sRNA 0.134381 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 28 -- 36@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 28 -- 34@LB@
192	0.01921	0.3269	bsu12649	ykzM	-11.69	0.118448	82 -- 103	11 -- 32	Evidence 4: Homologs of previously reported genes of unknown function	bsu26089	_____________81______________________104\n_____________\|_______________________\|\n5'-AAG...GACAA____A____________C_A___GGCCA...UCG-3'\n______________GGGU__GGGGACAGGGG_G_GGC\n______________\|\|\|\|__\|\|\|:\|\|\|\|:\|:_\|_:\|\|\n______________CCCA__CCCUUGUCUCU_C_UCG\n3'-UUU...AUCUC____AC_____________A___AAGAG...AUA-5'\n_____________\|_______________________\|\n_____________33______________________10\n	88 -- 94	19 -- 25	-26.088 kcal/mol	7.89329 kcal/mol	6.50677 kcal/mol	81 104@LB@ \| \|@LB@5'-AAG...GACAA A C A GGCCA...UCG-3'@LB@ GGGU GGGGACAGGGG G GGC@LB@ \|\|\|\| \|\|\|:\|\|\|\|:\|: \| :\|\|@LB@ CCCA CCCUUGUCUCU C UCG@LB@3'-UUU...AUCUC AC A AAGAG...AUA-5'@LB@ \| \|@LB@ 33 10@LB@@LB@@LB@Energy -11.69 kcal/mol@LB@Hybridization Energy -26.088 kcal/mol@LB@Unfolding Energy - mRNA 7.89329 kcal/mol@LB@Unfolding Energy - sRNA 6.50677 kcal/mol@LB@@LB@Position - mRNA 82 -- 103@LB@Position - sRNA 11 -- 32@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 19 -- 25@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@
68	0.004453	0.2184	bsu22580	ypiB	-13.80	0.051176	183 -- 197	21 -- 39	Evidence 4: Homologs of previously reported genes of unknown function; PubMedId: 16847875		_____________182_________________198\n_____________\|___________________\|\n5'-AGC...CGAAC________A__________UACAU...ACU-3'\n______________GAUAGAGG_____GGGAAU\n______________\|\|\|\|\|\|\|\|_____\|\|\|\|\|:\n______________CUAUCUCC_____CCCUUG\n3'-UUU...CUAGA________CCAAC______UCUCU...AUA-5'\n_____________\|___________________\|\n_____________40__________________20\n	184 -- 190	32 -- 38	-18.5124 kcal/mol	2.13446 kcal/mol	2.58006 kcal/mol	182 198@LB@ \| \|@LB@5'-AGC...CGAAC A UACAU...ACU-3'@LB@ GAUAGAGG GGGAAU@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|:@LB@ CUAUCUCC CCCUUG@LB@3'-UUU...CUAGA CCAAC UCUCU...AUA-5'@LB@ \| \|@LB@ 40 20@LB@@LB@@LB@Energy -13.80 kcal/mol@LB@Hybridization Energy -18.5124 kcal/mol@LB@Unfolding Energy - mRNA 2.13446 kcal/mol@LB@Unfolding Energy - sRNA 2.58006 kcal/mol@LB@@LB@Position - mRNA 183 -- 197@LB@Position - sRNA 21 -- 39@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 32 -- 38@LB@
65	0.004149	0.2071	bsu25230	yqxD	-11.91	0.108824	196 -- 217	21 -- 43	Evidence 4: Homologs of previously reported genes of unknown function; PubMedId: 9387153		_____________195_____________________218\n_____________\|_______________________\|\n5'-ACA...CAGGA____A________A____A____UACUC...CAU-3'\n______________GUUU_AUGGAGGG__UGG_GAAU\n______________:\|:\|_\|\|:\|\|\|\|\|__\|\|\|_\|\|\|:\n______________UAGA_UAUCUCCC__ACC_CUUG\n3'-UUU...AGAAC____C________CA___C____UCUCU...AUA-5'\n_____________\|_______________________\|\n_____________44______________________20\n	202 -- 208	31 -- 37	-19.0868 kcal/mol	4.40975 kcal/mol	2.76238 kcal/mol	195 218@LB@ \| \|@LB@5'-ACA...CAGGA A A A UACUC...CAU-3'@LB@ GUUU AUGGAGGG UGG GAAU@LB@ :\|:\| \|\|:\|\|\|\|\| \|\|\| \|\|\|:@LB@ UAGA UAUCUCCC ACC CUUG@LB@3'-UUU...AGAAC C CA C UCUCU...AUA-5'@LB@ \| \|@LB@ 44 20@LB@@LB@@LB@Energy -11.91 kcal/mol@LB@Hybridization Energy -19.0868 kcal/mol@LB@Unfolding Energy - mRNA 4.40975 kcal/mol@LB@Unfolding Energy - sRNA 2.76238 kcal/mol@LB@@LB@Position - mRNA 196 -- 217@LB@Position - sRNA 21 -- 43@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 31 -- 37@LB@
75	0.005596	0.2441	bsu19669	yoyF	-14.84	0.032440	230 -- 255	26 -- 52	Evidence 5: No homology to any previously reported sequences		_____________229_________________________256\n_____________\|___________________________\|\n5'-GUA...CUGGA____GAAA_________UCAUAA____AAAAA...GUC-3'\n______________CGGA____GAUUUGAUA_______UGG\n______________\|\|\|\|____\|\|\|:\|\|\|\|\|_______\|\|\|\n______________GCCU____CUAGACUAU_______ACC\n3'-UUU...AAAAA____AGAA_________CUCCCCA___CCUUG...AUA-5'\n_____________\|___________________________\|\n_____________53__________________________25\n	240 -- 246	36 -- 42	-17.4265 kcal/mol	1.6069 kcal/mol	0.980817 kcal/mol	229 256@LB@ \| \|@LB@5'-GUA...CUGGA GAAA UCAUAA AAAAA...GUC-3'@LB@ CGGA GAUUUGAUA UGG@LB@ \|\|\|\| \|\|\|:\|\|\|\|\| \|\|\|@LB@ GCCU CUAGACUAU ACC@LB@3'-UUU...AAAAA AGAA CUCCCCA CCUUG...AUA-5'@LB@ \| \|@LB@ 53 25@LB@@LB@@LB@Energy -14.84 kcal/mol@LB@Hybridization Energy -17.4265 kcal/mol@LB@Unfolding Energy - mRNA 1.6069 kcal/mol@LB@Unfolding Energy - sRNA 0.980817 kcal/mol@LB@@LB@Position - mRNA 230 -- 255@LB@Position - sRNA 26 -- 52@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 36 -- 42@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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