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
71	0.005061	0.2378	bsu02170	ybfB	-12.87	0.075045	244 -- 269	24 -- 48	MFS transporter	bsu03530	_____________243__________________________270\n_____________\|____________________________\|\n5'-CUU...CACCU_____________UU__C____CA____GUGCG...AGC-3'\n______________UUUUGAUCU__UA__GG_GGUU__GGGG\n______________\|:\|\|\|\|\|\|\|__\|\|__\|\|_\|\|\|\|__\|\|\|\|\n______________AGAACUAGA__AU__CC_CCAA__CCCC\n3'-UUU...AGCCU_________CU__CU_____________UUGUC...AUA-5'\n_____________\|____________________________\|\n_____________49___________________________23\n	246 -- 252	40 -- 46	-21.3597 kcal/mol	7.5105 kcal/mol	0.978761 kcal/mol	243 270@LB@ \| \|@LB@5'-CUU...CACCU UU C CA GUGCG...AGC-3'@LB@ UUUUGAUCU UA GG GGUU GGGG@LB@ \|:\|\|\|\|\|\|\| \|\| \|\| \|\|\|\| \|\|\|\|@LB@ AGAACUAGA AU CC CCAA CCCC@LB@3'-UUU...AGCCU CU CU UUGUC...AUA-5'@LB@ \| \|@LB@ 49 23@LB@@LB@@LB@Energy -12.87 kcal/mol@LB@Hybridization Energy -21.3597 kcal/mol@LB@Unfolding Energy - mRNA 7.5105 kcal/mol@LB@Unfolding Energy - sRNA 0.978761 kcal/mol@LB@@LB@Position - mRNA 244 -- 269@LB@Position - sRNA 24 -- 48@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 40 -- 46@LB@
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@
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@
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@
7	4.152e-05	0.01979	bsu05670	ydgJ	-17.13	0.010734	234 -- 258	25 -- 49	MarR family transcriptional regulator		_____________233_______________________259\n_____________\|_________________________\|\n5'-AAG...UAAUA_______CAG__A___A___A____UUUUG...AUC-3'\n______________GUUUUGA___GA_AGA_GGG_UGGG\n______________:\|:\|\|\|\|___\|\|_\|\|\|_\|\|\|_\|\|\|\|\n______________UAGAACU___CU_UCU_CCC_ACCC\n3'-UUU...AAGCC_______AGA__A___C___A____CUUGU...AUA-5'\n_____________\|_________________________\|\n_____________50________________________24\n	234 -- 240	43 -- 49	-20.9262 kcal/mol	2.82407 kcal/mol	0.976049 kcal/mol	233 259@LB@ \| \|@LB@5'-AAG...UAAUA CAG A A A UUUUG...AUC-3'@LB@ GUUUUGA GA AGA GGG UGGG@LB@ :\|:\|\|\|\| \|\| \|\|\| \|\|\| \|\|\|\|@LB@ UAGAACU CU UCU CCC ACCC@LB@3'-UUU...AAGCC AGA A C A CUUGU...AUA-5'@LB@ \| \|@LB@ 50 24@LB@@LB@@LB@Energy -17.13 kcal/mol@LB@Hybridization Energy -20.9262 kcal/mol@LB@Unfolding Energy - mRNA 2.82407 kcal/mol@LB@Unfolding Energy - sRNA 0.976049 kcal/mol@LB@@LB@Position - mRNA 234 -- 258@LB@Position - sRNA 25 -- 49@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 43 -- 49@LB@
19	0.0003652	0.06216	bsu29920	ytmP	-16.30	0.016289	3 -- 31	25 -- 51	phosphotransferase YtmP		_____________2_____________________________32\n_____________\|_____________________________\|\n_________5'-AU_____GAACA______U__ACU_______ACAAU...GUA-3'\n______________GGGUU_____UUGAUA_GA___GGUUGGG\n______________\|\|:\|:_____:\|\|\|\|\|_\|\|___\|\|\|\|\|\|\|\n______________CCUAG_____GACUAU_CU___CCAACCC\n3'-UUU...AAAAG_____AACUA_________CC________CUUGU...AUA-5'\n_____________\|_____________________________\|\n_____________52____________________________24\n	25 -- 31	25 -- 31	-23.4751 kcal/mol	6.19942 kcal/mol	0.976067 kcal/mol	2 32@LB@ \| \|@LB@ 5'-AU GAACA U ACU ACAAU...GUA-3'@LB@ GGGUU UUGAUA GA GGUUGGG@LB@ \|\|:\|: :\|\|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ CCUAG GACUAU CU CCAACCC@LB@3'-UUU...AAAAG AACUA CC CUUGU...AUA-5'@LB@ \| \|@LB@ 52 24@LB@@LB@@LB@Energy -16.30 kcal/mol@LB@Hybridization Energy -23.4751 kcal/mol@LB@Unfolding Energy - mRNA 6.19942 kcal/mol@LB@Unfolding Energy - sRNA 0.976067 kcal/mol@LB@@LB@Position - mRNA 3 -- 31@LB@Position - sRNA 25 -- 51@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 25 -- 31@LB@
35	0.001389	0.1324	bsu24570	gcvT	-12.27	0.095214	256 -- 273	25 -- 46	aminomethyltransferase		_____________255____________________274\n_____________\|______________________\|\n5'-CUC...AACGA_______C_______C______AGCUU...UAA-3'\n______________UUGAUUU___GGAGG___UGGG\n______________\|\|\|\|\|:\|___:\|\|\|\|___\|\|\|\|\n______________AACUAGA___UCUCC___ACCC\n3'-UUU...CCUAG_______CUA_____CCA____CUUGU...AUA-5'\n_____________\|______________________\|\n_____________47_____________________24\n	256 -- 262	40 -- 46	-17.62 kcal/mol	4.38211 kcal/mol	0.972727 kcal/mol	255 274@LB@ \| \|@LB@5'-CUC...AACGA C C AGCUU...UAA-3'@LB@ UUGAUUU GGAGG UGGG@LB@ \|\|\|\|\|:\| :\|\|\|\| \|\|\|\|@LB@ AACUAGA UCUCC ACCC@LB@3'-UUU...CCUAG CUA CCA CUUGU...AUA-5'@LB@ \| \|@LB@ 47 24@LB@@LB@@LB@Energy -12.27 kcal/mol@LB@Hybridization Energy -17.62 kcal/mol@LB@Unfolding Energy - mRNA 4.38211 kcal/mol@LB@Unfolding Energy - sRNA 0.972727 kcal/mol@LB@@LB@Position - mRNA 256 -- 273@LB@Position - sRNA 25 -- 46@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 40 -- 46@LB@
49	0.002227	0.1516	bsu11839	yjzE	-19.04	0.003744	170 -- 194	25 -- 51	Evidence 5: No homology to any previously reported sequences; PubMedId: 11976315		_____________169_________________________195\n_____________\|___________________________\|\n5'-UCC...UUAAG___AAA___GACAGC____________UAUUG...GCU-3'\n______________GGA____GA______AGAGGGGU_GGG\n______________\|\|\|____\|\|______\|\|\|\|\|\|\|\|_\|\|\|\n______________CCU____CU______UCUCCCCA_CCC\n3'-UUU...AAAAG___AGAA__AGACUA________A___CUUGU...AUA-5'\n_____________\|___________________________\|\n_____________52__________________________24\n	185 -- 191	29 -- 35	-23.53 kcal/mol	3.51134 kcal/mol	0.976067 kcal/mol	169 195@LB@ \| \|@LB@5'-UCC...UUAAG AAA GACAGC UAUUG...GCU-3'@LB@ GGA GA AGAGGGGU GGG@LB@ \|\|\| \|\| \|\|\|\|\|\|\|\| \|\|\|@LB@ CCU CU UCUCCCCA CCC@LB@3'-UUU...AAAAG AGAA AGACUA A CUUGU...AUA-5'@LB@ \| \|@LB@ 52 24@LB@@LB@@LB@Energy -19.04 kcal/mol@LB@Hybridization Energy -23.53 kcal/mol@LB@Unfolding Energy - mRNA 3.51134 kcal/mol@LB@Unfolding Energy - sRNA 0.976067 kcal/mol@LB@@LB@Position - mRNA 170 -- 194@LB@Position - sRNA 25 -- 51@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 29 -- 35@LB@
54	0.002747	0.1697	bsu35790	yvyI	-14.15	0.043919	186 -- 197	25 -- 36	mannose-6-phosphate isomerase YvyI		_____________185__________198\n_____________\|____________\|\n5'-UCU...ACAGG________AC__AUCAU...AAU-3'\n______________GGAGGGGU__GG\n______________:\|\|\|\|\|\|\|__\|\|\n______________UCUCCCCA__CC\n3'-UUU...GACUA________AC__CUUGU...AUA-5'\n_____________\|____________\|\n_____________37___________24\n	187 -- 193	29 -- 35	-17.2174 kcal/mol	2.92719 kcal/mol	0.135926 kcal/mol	185 198@LB@ \| \|@LB@5'-UCU...ACAGG AC AUCAU...AAU-3'@LB@ GGAGGGGU GG@LB@ :\|\|\|\|\|\|\| \|\|@LB@ UCUCCCCA CC@LB@3'-UUU...GACUA AC CUUGU...AUA-5'@LB@ \| \|@LB@ 37 24@LB@@LB@@LB@Energy -14.15 kcal/mol@LB@Hybridization Energy -17.2174 kcal/mol@LB@Unfolding Energy - mRNA 2.92719 kcal/mol@LB@Unfolding Energy - sRNA 0.135926 kcal/mol@LB@@LB@Position - mRNA 186 -- 197@LB@Position - sRNA 25 -- 36@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 29 -- 35@LB@
56	0.002918	0.1738	bsu04390	ydbA	-13.95	0.047884	245 -- 258	25 -- 39	Evidence 4: Homologs of previously reported genes of unknown function		_____________244_____________259\n_____________\|_______________\|\n5'-UUC...AAAGA_______AAA_____AAAAA...GCC-3'\n______________GAUAGAG____UGGG\n______________\|\|\|\|\|\|\|____\|\|\|\|\n______________CUAUCUC____ACCC\n3'-UUU...CUAGA_______CCCA____CUUGU...AUA-5'\n_____________\|_______________\|\n_____________40______________24\n	245 -- 251	33 -- 39	-15.533 kcal/mol	0.795684 kcal/mol	0.783603 kcal/mol	244 259@LB@ \| \|@LB@5'-UUC...AAAGA AAA AAAAA...GCC-3'@LB@ GAUAGAG UGGG@LB@ \|\|\|\|\|\|\| \|\|\|\|@LB@ CUAUCUC ACCC@LB@3'-UUU...CUAGA CCCA CUUGU...AUA-5'@LB@ \| \|@LB@ 40 24@LB@@LB@@LB@Energy -13.95 kcal/mol@LB@Hybridization Energy -15.533 kcal/mol@LB@Unfolding Energy - mRNA 0.795684 kcal/mol@LB@Unfolding Energy - sRNA 0.783603 kcal/mol@LB@@LB@Position - mRNA 245 -- 258@LB@Position - sRNA 25 -- 39@LB@Position Seed - mRNA 245 -- 251@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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