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
23	0.0004941	0.06638	bsu00930	cysE	-16.71	0.013304	161 -- 195	22 -- 53	serine acetyltransferase	_____________160_________________________________196\n_____________\|___________________________________\|\n5'-CCU...UUUUA______AGAG__AA__A_______AAACG______AGCAU...UAC-3'\n______________UUGGGU____GA__UC_GAUAGAG_____GGGGGA\n______________\|:\|\|:\|____\|\|__\|\|_\|\|\|\|\|\|\|_____\|\|\|\|:\|\n______________AGCCUA____CU__AG_CUAUCUC_____CCCCUU\n3'-UUU...AAAAA______GAA_______A_______CCCAA______GUCUC...AUA-5'\n_____________\|___________________________________\|\n_____________54__________________________________21\n	178 -- 184	33 -- 39	-24.9399 kcal/mol	6.34776 kcal/mol	1.88616 kcal/mol	160 196@LB@ \| \|@LB@5'-CCU...UUUUA AGAG AA A AAACG AGCAU...UAC-3'@LB@ UUGGGU GA UC GAUAGAG GGGGGA@LB@ \|:\|\|:\| \|\| \|\| \|\|\|\|\|\|\| \|\|\|\|:\|@LB@ AGCCUA CU AG CUAUCUC CCCCUU@LB@3'-UUU...AAAAA GAA A CCCAA GUCUC...AUA-5'@LB@ \| \|@LB@ 54 21@LB@@LB@@LB@Energy -16.71 kcal/mol@LB@Hybridization Energy -24.9399 kcal/mol@LB@Unfolding Energy - mRNA 6.34776 kcal/mol@LB@Unfolding Energy - sRNA 1.88616 kcal/mol@LB@@LB@Position - mRNA 161 -- 195@LB@Position - sRNA 22 -- 53@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 33 -- 39@LB@
20	0.0003727	0.06216	bsu04690	rsbT	-12.89	0.074349	161 -- 193	22 -- 51	serine/threonine protein kinase	_____________160________________________________194\n_____________\|__________________________________\|\n5'-UUG...GAGCA__GG_____GACAU______C___AA________AUAGC...CGG-3'\n______________GG__CUUGA_____UGA_AG_GGG__UUGGGGGA\n______________\|\|__\|\|\|\|\|_____\|\|\|_\|\|_\|\|\|__\|\|\|\|\|\|:\|\n______________CC__GAACU_____ACU_UC_CCC__AACCCCUU\n3'-UUU...AAAAG__UA_____AG______A__U___C_________GUCUC...AUA-5'\n_____________\|__________________________________\|\n_____________52_________________________________21\n	187 -- 193	22 -- 28	-26.679 kcal/mol	11.9064 kcal/mol	1.87888 kcal/mol	160 194@LB@ \| \|@LB@5'-UUG...GAGCA GG GACAU C AA AUAGC...CGG-3'@LB@ GG CUUGA UGA AG GGG UUGGGGGA@LB@ \|\| \|\|\|\|\| \|\|\| \|\| \|\|\| \|\|\|\|\|\|:\|@LB@ CC GAACU ACU UC CCC AACCCCUU@LB@3'-UUU...AAAAG UA AG A U C GUCUC...AUA-5'@LB@ \| \|@LB@ 52 21@LB@@LB@@LB@Energy -12.89 kcal/mol@LB@Hybridization Energy -26.679 kcal/mol@LB@Unfolding Energy - mRNA 11.9064 kcal/mol@LB@Unfolding Energy - sRNA 1.87888 kcal/mol@LB@@LB@Position - mRNA 161 -- 193@LB@Position - sRNA 22 -- 51@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 22 -- 28@LB@
58	0.003185	0.1832	bsu24100	bkdR	-13.90	0.048953	199 -- 241	21 -- 51	sigma L-dependent transcriptional regulator YqiR	_____________198_________________________________________242\n_____________\|___________________________________________\|\n5'-AAU...UAUCG____GCAAAA___A_______U___UGCC__CAAAA_______GGCGU...ACA-3'\n______________GGAU______GGU_CUGAUAG_AGG____GG_____GGGGAAC\n______________\|\|\|\|______\|:\|_\|\|\|\|\|\|\|_\|\|\|____\|\|_____\|\|\|\|\|\|\|\n______________CCUA______CUA_GACUAUC_UCC____CC_____CCCCUUG\n3'-UUU...AAAAG____GAA________________________AA__________UCUCU...AUA-5'\n_____________\|___________________________________________\|\n_____________52__________________________________________20\n	235 -- 241	21 -- 27	-28.1295 kcal/mol	11.4588 kcal/mol	2.76846 kcal/mol	198 242@LB@ \| \|@LB@5'-AAU...UAUCG GCAAAA A U UGCC CAAAA GGCGU...ACA-3'@LB@ GGAU GGU CUGAUAG AGG GG GGGGAAC@LB@ \|\|\|\| \|:\| \|\|\|\|\|\|\| \|\|\| \|\| \|\|\|\|\|\|\|@LB@ CCUA CUA GACUAUC UCC CC CCCCUUG@LB@3'-UUU...AAAAG GAA AA UCUCU...AUA-5'@LB@ \| \|@LB@ 52 20@LB@@LB@@LB@Energy -13.90 kcal/mol@LB@Hybridization Energy -28.1295 kcal/mol@LB@Unfolding Energy - mRNA 11.4588 kcal/mol@LB@Unfolding Energy - sRNA 2.76846 kcal/mol@LB@@LB@Position - mRNA 199 -- 241@LB@Position - sRNA 21 -- 51@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 21 -- 27@LB@
183	0.01776	0.3237	bsu08550	sspK	-13.38	0.060997	172 -- 193	31 -- 48	small acid-soluble spore protein K	_____________171____________________194\n_____________\|______________________\|\n5'-UUU...CAACU_________C__ACC_______AUAUG...ACG-3'\n______________UUUUGAUCU_GA___UAGGGGG\n______________\|:\|\|\|\|\|\|\|_\|\|___\|\|\|:\|\|\|\n______________AGAACUAGA_CU___AUCUCCC\n3'-UUU...AGCCU______________________CAACC...AUA-5'\n_____________\|______________________\|\n_____________49_____________________30\n	187 -- 193	31 -- 37	-20.1262 kcal/mol	5.7766 kcal/mol	0.970395 kcal/mol	171 194@LB@ \| \|@LB@5'-UUU...CAACU C ACC AUAUG...ACG-3'@LB@ UUUUGAUCU GA UAGGGGG@LB@ \|:\|\|\|\|\|\|\| \|\| \|\|\|:\|\|\|@LB@ AGAACUAGA CU AUCUCCC@LB@3'-UUU...AGCCU CAACC...AUA-5'@LB@ \| \|@LB@ 49 30@LB@@LB@@LB@Energy -13.38 kcal/mol@LB@Hybridization Energy -20.1262 kcal/mol@LB@Unfolding Energy - mRNA 5.7766 kcal/mol@LB@Unfolding Energy - sRNA 0.970395 kcal/mol@LB@@LB@Position - mRNA 172 -- 193@LB@Position - sRNA 31 -- 48@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 31 -- 37@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@
180	0.01704	0.3152	bsu28380	gerM	-9.54	0.246988	269 -- 291	32 -- 52	spore germination protein GerM	_____________268______________________292\n_____________\|________________________\|\n5'-AGU...GGAUG___UUU____CA____________CAGCC...AGG-3'\n______________CGG___GUUU__AUCUGAUA_AGG\n______________\|\|\|___:\|:\|__\|\|\|\|\|\|\|\|_\|\|\|\n______________GCC___UAGA__UAGACUAU_UCC\n3'-UUU...AAAAA__________AC________C___CCAAC...AUA-5'\n_____________\|________________________\|\n_____________53_______________________31\n	282 -- 288	36 -- 42	-15.6565 kcal/mol	5.13957 kcal/mol	0.976384 kcal/mol	268 292@LB@ \| \|@LB@5'-AGU...GGAUG UUU CA CAGCC...AGG-3'@LB@ CGG GUUU AUCUGAUA AGG@LB@ \|\|\| :\|:\| \|\|\|\|\|\|\|\| \|\|\|@LB@ GCC UAGA UAGACUAU UCC@LB@3'-UUU...AAAAA AC C CCAAC...AUA-5'@LB@ \| \|@LB@ 53 31@LB@@LB@@LB@Energy -9.54 kcal/mol@LB@Hybridization Energy -15.6565 kcal/mol@LB@Unfolding Energy - mRNA 5.13957 kcal/mol@LB@Unfolding Energy - sRNA 0.976384 kcal/mol@LB@@LB@Position - mRNA 269 -- 291@LB@Position - sRNA 32 -- 52@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 36 -- 42@LB@
70	0.004864	0.2318	bsu03720	gerKB	-15.05	0.029438	176 -- 191	30 -- 44	spore germination protein KB	_____________175_______________192\n_____________\|_________________\|\n5'-UUA...GAUUA___________AA____AAGUG...GCA-3'\n______________GGUCUGA_AGA__GGGG\n______________\|:\|\|\|\|\|_\|\|\|__\|\|\|\|\n______________CUAGACU_UCU__CCCC\n3'-UUU...UAGAA_______A_________AACCC...AUA-5'\n_____________\|_________________\|\n_____________45________________29\n	176 -- 182	38 -- 44	-18.3492 kcal/mol	2.32731 kcal/mol	0.969452 kcal/mol	175 192@LB@ \| \|@LB@5'-UUA...GAUUA AA AAGUG...GCA-3'@LB@ GGUCUGA AGA GGGG@LB@ \|:\|\|\|\|\| \|\|\| \|\|\|\|@LB@ CUAGACU UCU CCCC@LB@3'-UUU...UAGAA A AACCC...AUA-5'@LB@ \| \|@LB@ 45 29@LB@@LB@@LB@Energy -15.05 kcal/mol@LB@Hybridization Energy -18.3492 kcal/mol@LB@Unfolding Energy - mRNA 2.32731 kcal/mol@LB@Unfolding Energy - sRNA 0.969452 kcal/mol@LB@@LB@Position - mRNA 176 -- 191@LB@Position - sRNA 30 -- 44@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 38 -- 44@LB@
160	0.01451	0.3008	bsu30080	yteV	-11.71	0.117611	279 -- 298	34 -- 53	sporulation protein cse60	_____________278__________________299\n_____________\|____________________\|\n5'-UUU...GGAUA_____GGAGCAG________UA-3'\n______________UCGGA_______CUGAUAGA\n______________\|\|\|\|\|_______\|\|\|\|\|\|\|\|\n______________AGCCU_______GACUAUCU\n3'-UUU...AAAAA_____AGAACUA________CCCCA...AUA-5'\n_____________\|____________________\|\n_____________54___________________33\n	292 -- 298	34 -- 40	-18.1644 kcal/mol	5.47565 kcal/mol	0.98171 kcal/mol	278 299@LB@ \| \|@LB@5'-UUU...GGAUA GGAGCAG UA-3'@LB@ UCGGA CUGAUAGA@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ AGCCU GACUAUCU@LB@3'-UUU...AAAAA AGAACUA CCCCA...AUA-5'@LB@ \| \|@LB@ 54 33@LB@@LB@@LB@Energy -11.71 kcal/mol@LB@Hybridization Energy -18.1644 kcal/mol@LB@Unfolding Energy - mRNA 5.47565 kcal/mol@LB@Unfolding Energy - sRNA 0.98171 kcal/mol@LB@@LB@Position - mRNA 279 -- 298@LB@Position - sRNA 34 -- 53@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 34 -- 40@LB@
175	0.01672	0.3152	bsu04630	ydcC	-11.64	0.120416	196 -- 203	27 -- 34	sporulation protein YdcC	_____________195______204\n_____________\|________\|\n5'-CCG...GAAAA________AAAAA...UGG-3'\n______________AGGGGUUG\n______________\|\|\|\|\|\|\|\|\n______________UCCCCAAC\n3'-UUU...CUAUC________CCCUU...AUA-5'\n_____________\|________\|\n_____________35_______26\n	197 -- 203	27 -- 33	-14.5305 kcal/mol	2.76844 kcal/mol	0.118612 kcal/mol	195 204@LB@ \| \|@LB@5'-CCG...GAAAA AAAAA...UGG-3'@LB@ AGGGGUUG@LB@ \|\|\|\|\|\|\|\|@LB@ UCCCCAAC@LB@3'-UUU...CUAUC CCCUU...AUA-5'@LB@ \| \|@LB@ 35 26@LB@@LB@@LB@Energy -11.64 kcal/mol@LB@Hybridization Energy -14.5305 kcal/mol@LB@Unfolding Energy - mRNA 2.76844 kcal/mol@LB@Unfolding Energy - sRNA 0.118612 kcal/mol@LB@@LB@Position - mRNA 196 -- 203@LB@Position - sRNA 27 -- 34@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 27 -- 33@LB@
80	0.005932	0.2448	bsu24430	spoIIIAA	-11.72	0.117179	88 -- 116	28 -- 52	stage III sporulation protein AA	_____________87______________________________117\n_____________\|_______________________________\|\n5'-GUC...UUUUA___GUGUU_______________C___U___CAUAA...GGA-3'\n______________CGG_____GUCUUGAUUU__UGG_GGG_GUU\n______________\|\|\|_____:\|\|\|\|\|\|\|:\|__\|:\|_\|\|\|_\|\|\|\n______________GCC_____UAGAACUAGA__AUC_CCC_CAA\n3'-UUU...AAAAA__________________CU___U_______CCCCU...AUA-5'\n_____________\|_______________________________\|\n_____________53______________________________27\n	99 -- 105	40 -- 46	-20.9874 kcal/mol	8.2899 kcal/mol	0.980555 kcal/mol	87 117@LB@ \| \|@LB@5'-GUC...UUUUA GUGUU C U CAUAA...GGA-3'@LB@ CGG GUCUUGAUUU UGG GGG GUU@LB@ \|\|\| :\|\|\|\|\|\|\|:\| \|:\| \|\|\| \|\|\|@LB@ GCC UAGAACUAGA AUC CCC CAA@LB@3'-UUU...AAAAA CU U CCCCU...AUA-5'@LB@ \| \|@LB@ 53 27@LB@@LB@@LB@Energy -11.72 kcal/mol@LB@Hybridization Energy -20.9874 kcal/mol@LB@Unfolding Energy - mRNA 8.2899 kcal/mol@LB@Unfolding Energy - sRNA 0.980555 kcal/mol@LB@@LB@Position - mRNA 88 -- 116@LB@Position - sRNA 28 -- 52@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 40 -- 46@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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