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
78	0.005707	0.2441	bsu18040	yneP	-11.92	0.108570	96 -- 119	24 -- 45	acyl-CoA thioesterase	_____________95_______________________120\n_____________\|________________________\|\n5'-UUG...CUUUC_________UAU__UAAAA_____CUAAA...AAA-3'\n______________UGAUUUGAU___GG_____UGGGG\n______________\|\|\|\|:\|\|\|\|___\|\|_____\|\|\|\|\|\n______________ACUAGACUA___CC_____ACCCC\n3'-UUU...CUAGA_________UCU__CCA_______UUGUC...AUA-5'\n_____________\|________________________\|\n_____________46_______________________23\n	98 -- 104	37 -- 43	-18.893 kcal/mol	5.99443 kcal/mol	0.977634 kcal/mol	95 120@LB@ \| \|@LB@5'-UUG...CUUUC UAU UAAAA CUAAA...AAA-3'@LB@ UGAUUUGAU GG UGGGG@LB@ \|\|\|\|:\|\|\|\| \|\| \|\|\|\|\|@LB@ ACUAGACUA CC ACCCC@LB@3'-UUU...CUAGA UCU CCA UUGUC...AUA-5'@LB@ \| \|@LB@ 46 23@LB@@LB@@LB@Energy -11.92 kcal/mol@LB@Hybridization Energy -18.893 kcal/mol@LB@Unfolding Energy - mRNA 5.99443 kcal/mol@LB@Unfolding Energy - sRNA 0.977634 kcal/mol@LB@@LB@Position - mRNA 96 -- 119@LB@Position - sRNA 24 -- 45@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 37 -- 43@LB@
110	0.009311	0.2778	bsu18230	yngG	-6.09	0.597733	269 -- 285	32 -- 53	hydroxymethylglutaryl-CoA lyase YngG	_____________268____________________286\n_____________\|______________________\|\n5'-AAA...CCCGU_______GCAAC__________AUAAA...GGA-3'\n______________UUGGAUC__________AGAGG\n______________\|:\|\|\|\|\|__________\|\|\|\|\|\n______________AGCCUAG__________UCUCC\n3'-UUU...AAAAA_______AACUAGACUA_____CCAAC...AUA-5'\n_____________\|______________________\|\n_____________54_____________________31\n	269 -- 275	47 -- 53	-12.5955 kcal/mol	5.52332 kcal/mol	0.981755 kcal/mol	268 286@LB@ \| \|@LB@5'-AAA...CCCGU GCAAC AUAAA...GGA-3'@LB@ UUGGAUC AGAGG@LB@ \|:\|\|\|\|\| \|\|\|\|\|@LB@ AGCCUAG UCUCC@LB@3'-UUU...AAAAA AACUAGACUA CCAAC...AUA-5'@LB@ \| \|@LB@ 54 31@LB@@LB@@LB@Energy -6.09 kcal/mol@LB@Hybridization Energy -12.5955 kcal/mol@LB@Unfolding Energy - mRNA 5.52332 kcal/mol@LB@Unfolding Energy - sRNA 0.981755 kcal/mol@LB@@LB@Position - mRNA 269 -- 285@LB@Position - sRNA 32 -- 53@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 47 -- 53@LB@
38	0.001645	0.1432	bsu19540	yodB	-7.66	0.420262	259 -- 271	37 -- 51	ArsR family transcriptional regulator	_____________258_____________272\n_____________\|_______________\|\n5'-GAG...ACGAU___AC__________CAUCC...AAC-3'\n______________GGA____GGUCUGAU\n______________\|\|\|____\|:\|\|\|\|\|\|\n______________CCU____CUAGACUA\n3'-UUU...AAAAG___AGAA________UCUCC...AUA-5'\n_____________\|_______________\|\n_____________52______________36\n	265 -- 271	37 -- 43	-11.6813 kcal/mol	3.05786 kcal/mol	0.959935 kcal/mol	258 272@LB@ \| \|@LB@5'-GAG...ACGAU AC CAUCC...AAC-3'@LB@ GGA GGUCUGAU@LB@ \|\|\| \|:\|\|\|\|\|\|@LB@ CCU CUAGACUA@LB@3'-UUU...AAAAG AGAA UCUCC...AUA-5'@LB@ \| \|@LB@ 52 36@LB@@LB@@LB@Energy -7.66 kcal/mol@LB@Hybridization Energy -11.6813 kcal/mol@LB@Unfolding Energy - mRNA 3.05786 kcal/mol@LB@Unfolding Energy - sRNA 0.959935 kcal/mol@LB@@LB@Position - mRNA 259 -- 271@LB@Position - sRNA 37 -- 51@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 37 -- 43@LB@
57	0.003091	0.1809	bsu19720	yodR	-13.42	0.059995	155 -- 217	11 -- 51	coenzyme A transferase subunit beta	_____________154_________________________________________________________________218\n_____________\|___________________________________________________________________\|\n5'-GCU...ACCGG_______UG________________UACGAAGCGA____GUGAAGUGGAAAUGG__UU_________AGAAA...CCU-3'\n______________GGGUUUU___UUGA___GGGGGUUG__________GGGA_______________GC__GGGAGUAGC\n______________\|\|:\|:\|\|___:\|\|\|___:\|\|\|\|\|\|\|__________\|\|\|\|_______________:\|__\|:\|\|\|\|\|\|\|\n______________CCUAGAA___GACU___UCCCCAAC__________CCCU_______________UG__CUCUCAUCG\n3'-UUU...AAAAG_______CUA____AUC_______________________________________U__________AAGAG...AUA-5'\n_____________\|___________________________________________________________________\|\n_____________52__________________________________________________________________10\n	211 -- 217	11 -- 17	-37.5623 kcal/mol	14.1868 kcal/mol	9.95641 kcal/mol	154 218@LB@ \| \|@LB@5'-GCU...ACCGG UG UACGAAGCGA GUGAAGUGGAAAUGG UU AGAAA...CCU-3'@LB@ GGGUUUU UUGA GGGGGUUG GGGA GC GGGAGUAGC@LB@ \|\|:\|:\|\| :\|\|\| :\|\|\|\|\|\|\| \|\|\|\| :\| \|:\|\|\|\|\|\|\|@LB@ CCUAGAA GACU UCCCCAAC CCCU UG CUCUCAUCG@LB@3'-UUU...AAAAG CUA AUC U AAGAG...AUA-5'@LB@ \| \|@LB@ 52 10@LB@@LB@@LB@Energy -13.42 kcal/mol@LB@Hybridization Energy -37.5623 kcal/mol@LB@Unfolding Energy - mRNA 14.1868 kcal/mol@LB@Unfolding Energy - sRNA 9.95641 kcal/mol@LB@@LB@Position - mRNA 155 -- 217@LB@Position - sRNA 11 -- 51@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 11 -- 17@LB@
99	0.00842	0.2778	bsu19470	yojF	-13.80	0.051174	184 -- 193	30 -- 39	Evidence 4: Homologs of previously reported genes of unknown function	_____________183________194\n_____________\|__________\|\n5'-GAA...AAGAA__A_______AGCAA...CAG-3'\n______________GA_AGAGGGG\n______________\|\|_\|\|\|\|\|\|\|\n______________CU_UCUCCCC\n3'-UUU...CUAGA__A_______AACCC...AUA-5'\n_____________\|__________\|\n_____________40_________29\n	187 -- 193	30 -- 36	-15.454 kcal/mol	0.87683 kcal/mol	0.779184 kcal/mol	183 194@LB@ \| \|@LB@5'-GAA...AAGAA A AGCAA...CAG-3'@LB@ GA AGAGGGG@LB@ \|\| \|\|\|\|\|\|\|@LB@ CU UCUCCCC@LB@3'-UUU...CUAGA A AACCC...AUA-5'@LB@ \| \|@LB@ 40 29@LB@@LB@@LB@Energy -13.80 kcal/mol@LB@Hybridization Energy -15.454 kcal/mol@LB@Unfolding Energy - mRNA 0.87683 kcal/mol@LB@Unfolding Energy - sRNA 0.779184 kcal/mol@LB@@LB@Position - mRNA 184 -- 193@LB@Position - sRNA 30 -- 39@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 30 -- 36@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@
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@
15	0.0002364	0.05257	bsu19290	yozO	-13.57	0.056229	184 -- 195	28 -- 39	Evidence 4: Homologs of previously reported genes of unknown function	_____________183__________196\n_____________\|____________\|\n5'-AAA...AUGCA__A_________CUUCA...UGG-3'\n______________GA_AGAGGGGUU\n______________\|\|_\|\|\|\|\|\|\|\|\|\n______________CU_UCUCCCCAA\n3'-UUU...CUAGA__A_________CCCCU...AUA-5'\n_____________\|____________\|\n_____________40___________27\n	189 -- 195	28 -- 34	-16.9963 kcal/mol	2.64187 kcal/mol	0.77983 kcal/mol	183 196@LB@ \| \|@LB@5'-AAA...AUGCA A CUUCA...UGG-3'@LB@ GA AGAGGGGUU@LB@ \|\| \|\|\|\|\|\|\|\|\|@LB@ CU UCUCCCCAA@LB@3'-UUU...CUAGA A CCCCU...AUA-5'@LB@ \| \|@LB@ 40 27@LB@@LB@@LB@Energy -13.57 kcal/mol@LB@Hybridization Energy -16.9963 kcal/mol@LB@Unfolding Energy - mRNA 2.64187 kcal/mol@LB@Unfolding Energy - sRNA 0.77983 kcal/mol@LB@@LB@Position - mRNA 184 -- 195@LB@Position - sRNA 28 -- 39@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 28 -- 34@LB@
123	0.01093	0.2883	bsu22970	ypbH	-15.60	0.022809	254 -- 275	27 -- 45	adapter protein MecA	_____________253____________________276\n_____________\|______________________\|\n5'-GAG...CUCGA________C___CC____A___ACAAA...ACU-3'\n______________UGAUUUGA_AGA__GGGG_UUG\n______________\|\|\|\|:\|\|\|_\|\|\|__\|\|\|\|_\|\|\|\n______________ACUAGACU_UCU__CCCC_AAC\n3'-UUU...CUAGA________A_____________CCCUU...AUA-5'\n_____________\|______________________\|\n_____________46_____________________26\n	255 -- 261	38 -- 44	-20.0369 kcal/mol	3.46393 kcal/mol	0.971562 kcal/mol	253 276@LB@ \| \|@LB@5'-GAG...CUCGA C CC A ACAAA...ACU-3'@LB@ UGAUUUGA AGA GGGG UUG@LB@ \|\|\|\|:\|\|\| \|\|\| \|\|\|\| \|\|\|@LB@ ACUAGACU UCU CCCC AAC@LB@3'-UUU...CUAGA A CCCUU...AUA-5'@LB@ \| \|@LB@ 46 26@LB@@LB@@LB@Energy -15.60 kcal/mol@LB@Hybridization Energy -20.0369 kcal/mol@LB@Unfolding Energy - mRNA 3.46393 kcal/mol@LB@Unfolding Energy - sRNA 0.971562 kcal/mol@LB@@LB@Position - mRNA 254 -- 275@LB@Position - sRNA 27 -- 45@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 38 -- 44@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@

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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