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
50	0.002285	0.1525	bsu22460	ypjH	-13.49	0.058216	160 -- 194	23 -- 52	glycosyltransferase YpjH		_____________159____________________________________195\n_____________\|______________________________________\|\n5'-AAG...CCAAA_____GCUGAUG_______A_____U__C_________CGAAC...AUG-3'\n______________CGGAU_______CUUGAUC_UGAUG__G___UUGGGGG\n______________\|\|\|\|\|_______\|\|\|\|\|\|\|_\|\|\|\|:__\|___\|\|\|\|\|\|:\n______________GCCUA_______GAACUAG_ACUAU__C___AACCCCU\n3'-UUU...AAAAA_________________________CU_CCC_______UGUCU...AUA-5'\n_____________\|______________________________________\|\n_____________53_____________________________________22\n	188 -- 194	23 -- 29	-25.8094 kcal/mol	11.3359 kcal/mol	0.981961 kcal/mol	159 195@LB@ \| \|@LB@5'-AAG...CCAAA GCUGAUG A U C CGAAC...AUG-3'@LB@ CGGAU CUUGAUC UGAUG G UUGGGGG@LB@ \|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|: \| \|\|\|\|\|\|:@LB@ GCCUA GAACUAG ACUAU C AACCCCU@LB@3'-UUU...AAAAA CU CCC UGUCU...AUA-5'@LB@ \| \|@LB@ 53 22@LB@@LB@@LB@Energy -13.49 kcal/mol@LB@Hybridization Energy -25.8094 kcal/mol@LB@Unfolding Energy - mRNA 11.3359 kcal/mol@LB@Unfolding Energy - sRNA 0.981961 kcal/mol@LB@@LB@Position - mRNA 160 -- 194@LB@Position - sRNA 23 -- 52@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 23 -- 29@LB@
174	0.01668	0.3152	bsu22210	yprB	-13.05	0.069799	168 -- 191	31 -- 53	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; Product type pe: enzyme'		_____________167______________________192\n_____________\|________________________\|\n5'-AUU...AGCUG_______AAAU___GUAA______AGGCC...AUG-3'\n______________UUGGAUC____GUC____GGAGGG\n______________\|:\|\|\|\|\|____:\|\|____:\|\|\|\|\|\n______________AGCCUAG____UAG____UCUCCC\n3'-UUU...AAAAA_______AAC____ACUA______CAACC...AUA-5'\n_____________\|________________________\|\n_____________54_______________________30\n	168 -- 174	47 -- 53	-20.3327 kcal/mol	6.30079 kcal/mol	0.981784 kcal/mol	167 192@LB@ \| \|@LB@5'-AUU...AGCUG AAAU GUAA AGGCC...AUG-3'@LB@ UUGGAUC GUC GGAGGG@LB@ \|:\|\|\|\|\| :\|\| :\|\|\|\|\|@LB@ AGCCUAG UAG UCUCCC@LB@3'-UUU...AAAAA AAC ACUA CAACC...AUA-5'@LB@ \| \|@LB@ 54 30@LB@@LB@@LB@Energy -13.05 kcal/mol@LB@Hybridization Energy -20.3327 kcal/mol@LB@Unfolding Energy - mRNA 6.30079 kcal/mol@LB@Unfolding Energy - sRNA 0.981784 kcal/mol@LB@@LB@Position - mRNA 168 -- 191@LB@Position - sRNA 31 -- 53@LB@Position Seed - mRNA 168 -- 174@LB@Position Seed - sRNA 47 -- 53@LB@
13	0.0002088	0.05257	bsu22150	ypvA	-19.04	0.003759	161 -- 194	26 -- 53	ATP-dependent helicase YpvA		_____________160____________________________________195\n_____________\|______________________________________\|\n5'-GUG...UAUUA________________AUGUCGAA___UU_________AACUA...CCG-3'\n______________UUGG____UGGUCUGA________UAG__GGGGGUUGG\n______________\|:\|\|____\|\|:\|\|\|\|\|________\|\|\|__:\|\|\|\|\|\|\|\|\n______________AGCC____ACUAGACU________AUC__UCCCCAACC\n3'-UUU...AAAAA____UAGA______________________________CCUUG...AUA-5'\n_____________\|______________________________________\|\n_____________54_____________________________________25\n	188 -- 194	26 -- 32	-27.605 kcal/mol	7.58324 kcal/mol	0.986187 kcal/mol	160 195@LB@ \| \|@LB@5'-GUG...UAUUA AUGUCGAA UU AACUA...CCG-3'@LB@ UUGG UGGUCUGA UAG GGGGGUUGG@LB@ \|:\|\| \|\|:\|\|\|\|\| \|\|\| :\|\|\|\|\|\|\|\|@LB@ AGCC ACUAGACU AUC UCCCCAACC@LB@3'-UUU...AAAAA UAGA CCUUG...AUA-5'@LB@ \| \|@LB@ 54 25@LB@@LB@@LB@Energy -19.04 kcal/mol@LB@Hybridization Energy -27.605 kcal/mol@LB@Unfolding Energy - mRNA 7.58324 kcal/mol@LB@Unfolding Energy - sRNA 0.986187 kcal/mol@LB@@LB@Position - mRNA 161 -- 194@LB@Position - sRNA 26 -- 53@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 26 -- 32@LB@
39	0.001675	0.1432	bsu23240	ypzK	-16.45	0.015090	173 -- 197	28 -- 52	riboflavin biosynthesis protein RibT		_____________172_________________________198\n_____________\|___________________________\|\n5'-GCG...CAGAC____CA______AU_____________UUUAU...UUA-3'\n______________UGGA__UUUUGG____AUAGAGGGGUU\n______________:\|\|\|__\|:\|\|\|:____\|\|\|\|\|\|\|\|\|\|\|\n______________GCCU__AGAACU____UAUCUCCCCAA\n3'-UUU...AAAAA____________AGAC___________CCCCU...AUA-5'\n_____________\|___________________________\|\n_____________53__________________________27\n	191 -- 197	28 -- 34	-23.4842 kcal/mol	6.04944 kcal/mol	0.980555 kcal/mol	172 198@LB@ \| \|@LB@5'-GCG...CAGAC CA AU UUUAU...UUA-3'@LB@ UGGA UUUUGG AUAGAGGGGUU@LB@ :\|\|\| \|:\|\|\|: \|\|\|\|\|\|\|\|\|\|\|@LB@ GCCU AGAACU UAUCUCCCCAA@LB@3'-UUU...AAAAA AGAC CCCCU...AUA-5'@LB@ \| \|@LB@ 53 27@LB@@LB@@LB@Energy -16.45 kcal/mol@LB@Hybridization Energy -23.4842 kcal/mol@LB@Unfolding Energy - mRNA 6.04944 kcal/mol@LB@Unfolding Energy - sRNA 0.980555 kcal/mol@LB@@LB@Position - mRNA 173 -- 197@LB@Position - sRNA 28 -- 52@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 28 -- 34@LB@
79	0.005838	0.2448	bsu25980	yqbT	-11.66	0.119794	52 -- 65	32 -- 53	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; Product type ps: structure'	bsu12730	_____________51_____________________66\n_____________\|______________________\|\n5'-CGU...AUCCC______________________AAGCA...CGU-3'\n______________UCGG________CUGAUAGAGG\n______________\|\|\|\|________\|\|\|\|\|\|\|\|\|\|\n______________AGCC________GACUAUCUCC\n3'-UUU...AAAAA____UAGAACUA__________CCAAC...AUA-5'\n_____________\|______________________\|\n_____________54_____________________31\n	59 -- 65	32 -- 38	-19.4839 kcal/mol	6.84464 kcal/mol	0.981755 kcal/mol	51 66@LB@ \| \|@LB@5'-CGU...AUCCC AAGCA...CGU-3'@LB@ UCGG CUGAUAGAGG@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ AGCC GACUAUCUCC@LB@3'-UUU...AAAAA UAGAACUA CCAAC...AUA-5'@LB@ \| \|@LB@ 54 31@LB@@LB@@LB@Energy -11.66 kcal/mol@LB@Hybridization Energy -19.4839 kcal/mol@LB@Unfolding Energy - mRNA 6.84464 kcal/mol@LB@Unfolding Energy - sRNA 0.981755 kcal/mol@LB@@LB@Position - mRNA 52 -- 65@LB@Position - sRNA 32 -- 53@LB@Position Seed - mRNA 59 -- 65@LB@Position Seed - sRNA 32 -- 38@LB@
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@
18	0.00036	0.06216	bsu24510	yqhO	-21.34	0.000873	175 -- 205	13 -- 44	Evidence 4: Homologs of previously reported genes of unknown function		_____________174_______________________________206\n_____________\|_________________________________\|\n5'-UAU...UAAAC____G__________GA____________U___UAUUG...GAG-3'\n______________GAUC_GAUGGAGGGG___GGGAAU_GAGA_GUA\n______________\|\|\|\|_\|\|\|:\|\|\|\|\|\|___\|\|\|\|\|:_\|\|\|\|_\|\|\|\n______________CUAG_CUAUCUCCCC___CCCUUG_CUCU_CAU\n3'-UUU...UAGAA____A__________AAC______U________CGAAG...AUA-5'\n_____________\|_________________________________\|\n_____________45________________________________12\n	183 -- 189	30 -- 36	-39.4543 kcal/mol	8.17177 kcal/mol	9.94171 kcal/mol	174 206@LB@ \| \|@LB@5'-UAU...UAAAC G GA U UAUUG...GAG-3'@LB@ GAUC GAUGGAGGGG GGGAAU GAGA GUA@LB@ \|\|\|\| \|\|\|:\|\|\|\|\|\| \|\|\|\|\|: \|\|\|\| \|\|\|@LB@ CUAG CUAUCUCCCC CCCUUG CUCU CAU@LB@3'-UUU...UAGAA A AAC U CGAAG...AUA-5'@LB@ \| \|@LB@ 45 12@LB@@LB@@LB@Energy -21.34 kcal/mol@LB@Hybridization Energy -39.4543 kcal/mol@LB@Unfolding Energy - mRNA 8.17177 kcal/mol@LB@Unfolding Energy - sRNA 9.94171 kcal/mol@LB@@LB@Position - mRNA 175 -- 205@LB@Position - sRNA 13 -- 44@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 30 -- 36@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@
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@
94	0.007849	0.2778	bsu27000	yraB	-9.14	0.279232	183 -- 193	29 -- 39	MerR family transcriptional regulator		_____________182_________194\n_____________\|___________\|\n5'-AGU...UACAG_______A___GAAGA...ACA-3'\n______________GAUAGAG_GGU\n______________\|\|\|\|\|\|\|_\|\|\|\n______________CUAUCUC_CCA\n3'-UUU...CUAGA_______C___ACCCC...AUA-5'\n_____________\|___________\|\n_____________40__________28\n	183 -- 189	33 -- 39	-13.977 kcal/mol	4.05751 kcal/mol	0.779471 kcal/mol	182 194@LB@ \| \|@LB@5'-AGU...UACAG A GAAGA...ACA-3'@LB@ GAUAGAG GGU@LB@ \|\|\|\|\|\|\| \|\|\|@LB@ CUAUCUC CCA@LB@3'-UUU...CUAGA C ACCCC...AUA-5'@LB@ \| \|@LB@ 40 28@LB@@LB@@LB@Energy -9.14 kcal/mol@LB@Hybridization Energy -13.977 kcal/mol@LB@Unfolding Energy - mRNA 4.05751 kcal/mol@LB@Unfolding Energy - sRNA 0.779471 kcal/mol@LB@@LB@Position - mRNA 183 -- 193@LB@Position - sRNA 29 -- 39@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 33 -- 39@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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