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
148	0.01313	0.296	bsu02100	cypC	-16.43	0.015277	151 -- 198	11 -- 53	fatty-acid peroxygenase		_____________150______________________________________________199\n_____________\|________________________________________________\|\n5'-CAA...UAUAG_____AGAUAACG___AAA_______UAAAAA____G_C_____A___GGAUG...AUU-3'\n______________UCGGA________UGA___UAGAGGG______GGAA_G_AGGGU_AGC\n______________\|\|\|\|\|________\|\|\|___\|\|\|\|\|\|\|______\|\|\|\|_:_\|\|:\|\|_\|\|\|\n______________AGCCU________ACU___AUCUCCC______CCUU_U_UCUCA_UCG\n3'-UUU...AAAAA_____AGAACUAG_____________CAACC_____G_C_________AAGAG...AUA-5'\n_____________\|________________________________________________\|\n_____________54_______________________________________________10\n	170 -- 176	31 -- 37	-31.9294 kcal/mol	5.5363 kcal/mol	9.96369 kcal/mol	150 199@LB@ \| \|@LB@5'-CAA...UAUAG AGAUAACG AAA UAAAAA G C A GGAUG...AUU-3'@LB@ UCGGA UGA UAGAGGG GGAA G AGGGU AGC@LB@ \|\|\|\|\| \|\|\| \|\|\|\|\|\|\| \|\|\|\| : \|\|:\|\| \|\|\|@LB@ AGCCU ACU AUCUCCC CCUU U UCUCA UCG@LB@3'-UUU...AAAAA AGAACUAG CAACC G C AAGAG...AUA-5'@LB@ \| \|@LB@ 54 10@LB@@LB@@LB@Energy -16.43 kcal/mol@LB@Hybridization Energy -31.9294 kcal/mol@LB@Unfolding Energy - mRNA 5.5363 kcal/mol@LB@Unfolding Energy - sRNA 9.96369 kcal/mol@LB@@LB@Position - mRNA 151 -- 198@LB@Position - sRNA 11 -- 53@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 31 -- 37@LB@
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@
165	0.01546	0.3127	bsu02230	purT	-12.11	0.100898	185 -- 195	30 -- 39	phosphoribosylglycinamide formyltransferase		_____________184_________196\n_____________\|___________\|\n5'-GAU...GAACA___A_______CAAAG...UUG-3'\n______________GAU_GGAGGGG\n______________\|\|\|_:\|\|\|\|\|\|\n______________CUA_UCUCCCC\n3'-UUU...CUAGA___________AACCC...AUA-5'\n_____________\|___________\|\n_____________40__________29\n	189 -- 195	30 -- 36	-15.5568 kcal/mol	2.66346 kcal/mol	0.779184 kcal/mol	184 196@LB@ \| \|@LB@5'-GAU...GAACA A CAAAG...UUG-3'@LB@ GAU GGAGGGG@LB@ \|\|\| :\|\|\|\|\|\|@LB@ CUA UCUCCCC@LB@3'-UUU...CUAGA AACCC...AUA-5'@LB@ \| \|@LB@ 40 29@LB@@LB@@LB@Energy -12.11 kcal/mol@LB@Hybridization Energy -15.5568 kcal/mol@LB@Unfolding Energy - mRNA 2.66346 kcal/mol@LB@Unfolding Energy - sRNA 0.779184 kcal/mol@LB@@LB@Position - mRNA 185 -- 195@LB@Position - sRNA 30 -- 39@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 30 -- 36@LB@
130	0.01149	0.2883	bsu02620	phoD	-13.55	0.056825	174 -- 193	30 -- 50	alkaline phosphatase D		_____________173____________________194\n_____________\|______________________\|\n5'-GCC...GAGAC____AA___G____G_______AUCUU...CGG-3'\n______________GAUC__UGA___GA_AGAGGGG\n______________\|\|\|\|__\|\|\|___\|\|_\|\|\|\|\|\|\|\n______________CUAG__ACU___CU_UCUCCCC\n3'-UUU...AAAGC____A____AGA__A_______AACCC...AUA-5'\n_____________\|______________________\|\n_____________51_____________________29\n	187 -- 193	30 -- 36	-18.9864 kcal/mol	4.46268 kcal/mol	0.974272 kcal/mol	173 194@LB@ \| \|@LB@5'-GCC...GAGAC AA G G AUCUU...CGG-3'@LB@ GAUC UGA GA AGAGGGG@LB@ \|\|\|\| \|\|\| \|\| \|\|\|\|\|\|\|@LB@ CUAG ACU CU UCUCCCC@LB@3'-UUU...AAAGC A AGA A AACCC...AUA-5'@LB@ \| \|@LB@ 51 29@LB@@LB@@LB@Energy -13.55 kcal/mol@LB@Hybridization Energy -18.9864 kcal/mol@LB@Unfolding Energy - mRNA 4.46268 kcal/mol@LB@Unfolding Energy - sRNA 0.974272 kcal/mol@LB@@LB@Position - mRNA 174 -- 193@LB@Position - sRNA 30 -- 50@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 30 -- 36@LB@
131	0.01151	0.2883	bsu03110	ycgH	-12.02	0.104581	161 -- 192	27 -- 50	transporter		_____________160______________________________193\n_____________\|________________________________\|\n5'-UUU...GGACA____ACA____AACCUUA____AA________AAUAA...UCG-3'\n______________GAUC___AUCU_______GAUA__AGGGGUUG\n______________\|\|\|\|___\|\|\|\|_______\|\|\|\|__\|\|\|\|\|\|\|\|\n______________CUAG___UAGA_______CUAU__UCCCCAAC\n3'-UUU...AAAGC____AAC_______________C_________CCCUU...AUA-5'\n_____________\|________________________________\|\n_____________51_______________________________26\n	186 -- 192	27 -- 33	-20.341 kcal/mol	7.34553 kcal/mol	0.975523 kcal/mol	160 193@LB@ \| \|@LB@5'-UUU...GGACA ACA AACCUUA AA AAUAA...UCG-3'@LB@ GAUC AUCU GAUA AGGGGUUG@LB@ \|\|\|\| \|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\|@LB@ CUAG UAGA CUAU UCCCCAAC@LB@3'-UUU...AAAGC AAC C CCCUU...AUA-5'@LB@ \| \|@LB@ 51 26@LB@@LB@@LB@Energy -12.02 kcal/mol@LB@Hybridization Energy -20.341 kcal/mol@LB@Unfolding Energy - mRNA 7.34553 kcal/mol@LB@Unfolding Energy - sRNA 0.975523 kcal/mol@LB@@LB@Position - mRNA 161 -- 192@LB@Position - sRNA 27 -- 50@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 27 -- 33@LB@
105	0.009074	0.2778	bsu03220	ycgO	-6.59	0.539508	105 -- 111	67 -- 73	symporter		_____________104_____112\n_____________\|_______\|\n5'-GAA...CCUGC_______UCCAU...GUG-3'\n______________GGGGGUG\n______________\|\|\|\|\|\|:\n______________CCCCCAU\n3'-UUU...AACCG_______CGCGG...AUA-5'\n_____________\|_______\|\n_____________74______66\n	105 -- 111	67 -- 73	-12.2711 kcal/mol	3.65196 kcal/mol	2.02624 kcal/mol	104 112@LB@ \| \|@LB@5'-GAA...CCUGC UCCAU...GUG-3'@LB@ GGGGGUG@LB@ \|\|\|\|\|\|:@LB@ CCCCCAU@LB@3'-UUU...AACCG CGCGG...AUA-5'@LB@ \| \|@LB@ 74 66@LB@@LB@@LB@Energy -6.59 kcal/mol@LB@Hybridization Energy -12.2711 kcal/mol@LB@Unfolding Energy - mRNA 3.65196 kcal/mol@LB@Unfolding Energy - sRNA 2.02624 kcal/mol@LB@@LB@Position - mRNA 105 -- 111@LB@Position - sRNA 67 -- 73@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 67 -- 73@LB@
60	0.003464	0.1926	bsu03300	nasD	-15.33	0.025906	190 -- 205	34 -- 52	nitrite reductase		_____________189_________________206\n_____________\|___________________\|\n5'-UUU...AGGAG___________________AAAAA...CAA-3'\n______________CGGAUC___AUCUGAUGGG\n______________\|\|\|\|\|\|___\|\|\|\|\|\|\|:\|:\n______________GCCUAG___UAGACUAUCU\n3'-UUU...AAAAA______AAC__________CCCCA...AUA-5'\n_____________\|___________________\|\n_____________53__________________33\n	199 -- 205	34 -- 40	-21.0079 kcal/mol	4.70189 kcal/mol	0.976339 kcal/mol	189 206@LB@ \| \|@LB@5'-UUU...AGGAG AAAAA...CAA-3'@LB@ CGGAUC AUCUGAUGGG@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|:\|:@LB@ GCCUAG UAGACUAUCU@LB@3'-UUU...AAAAA AAC CCCCA...AUA-5'@LB@ \| \|@LB@ 53 33@LB@@LB@@LB@Energy -15.33 kcal/mol@LB@Hybridization Energy -21.0079 kcal/mol@LB@Unfolding Energy - mRNA 4.70189 kcal/mol@LB@Unfolding Energy - sRNA 0.976339 kcal/mol@LB@@LB@Position - mRNA 190 -- 205@LB@Position - sRNA 34 -- 52@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 34 -- 40@LB@
52	0.002415	0.1549	bsu03320	nasB	-8.41	0.344801	188 -- 199	36 -- 51	assimilatory nitrate reductase electron transfer subunit		_____________187______________200\n_____________\|________________\|\n5'-UUU...CCAAA________________CAUGA...UCA-3'\n______________GGA____GGUCUGAUA\n______________\|\|\|____\|:\|\|\|\|\|\|\|\n______________CCU____CUAGACUAU\n3'-UUU...AAAAG___AGAA_________CUCCC...AUA-5'\n_____________\|________________\|\n_____________52_______________35\n	193 -- 199	36 -- 42	-13.3061 kcal/mol	3.93547 kcal/mol	0.960469 kcal/mol	187 200@LB@ \| \|@LB@5'-UUU...CCAAA CAUGA...UCA-3'@LB@ GGA GGUCUGAUA@LB@ \|\|\| \|:\|\|\|\|\|\|\|@LB@ CCU CUAGACUAU@LB@3'-UUU...AAAAG AGAA CUCCC...AUA-5'@LB@ \| \|@LB@ 52 35@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -13.3061 kcal/mol@LB@Unfolding Energy - mRNA 3.93547 kcal/mol@LB@Unfolding Energy - sRNA 0.960469 kcal/mol@LB@@LB@Position - mRNA 188 -- 199@LB@Position - sRNA 36 -- 51@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 36 -- 42@LB@
36	0.001585	0.1432	bsu03680	yclG	-9.13	0.280303	226 -- 251	29 -- 52	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; Product type pe: enzyme'		_____________225________________________252\n_____________\|__________________________\|\n5'-UCA...UGCAG_______C___G_UCC_____AU___AAAAC...UUU-3'\n______________CGGAUUU_GGU_U___UAGAG__GGU\n______________\|\|\|\|\|:\|_\|:\|_\|___\|\|\|\|\|__\|\|\|\n______________GCCUAGA_CUA_A___AUCUC__CCA\n3'-UUU...AAAAA_______A___G_CU______C____ACCCC...AUA-5'\n_____________\|__________________________\|\n_____________53_________________________28\n	226 -- 232	46 -- 52	-18.2294 kcal/mol	8.1219 kcal/mol	0.980233 kcal/mol	225 252@LB@ \| \|@LB@5'-UCA...UGCAG C G UCC AU AAAAC...UUU-3'@LB@ CGGAUUU GGU U UAGAG GGU@LB@ \|\|\|\|\|:\| \|:\| \| \|\|\|\|\| \|\|\|@LB@ GCCUAGA CUA A AUCUC CCA@LB@3'-UUU...AAAAA A G CU C ACCCC...AUA-5'@LB@ \| \|@LB@ 53 28@LB@@LB@@LB@Energy -9.13 kcal/mol@LB@Hybridization Energy -18.2294 kcal/mol@LB@Unfolding Energy - mRNA 8.1219 kcal/mol@LB@Unfolding Energy - sRNA 0.980233 kcal/mol@LB@@LB@Position - mRNA 226 -- 251@LB@Position - sRNA 29 -- 52@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 46 -- 52@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@

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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