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
115	0.009897	0.2871	bsu22830	gpsA	-18.23	0.005947	227 -- 241	21 -- 34	glycerol-3-phosphate dehydrogenase		_____________226_____________242\n_____________\|_______________\|\n5'-GGU...GGAGC____A__________AGCAC...GUG-3'\n______________GGGG_GUUGGGGAAC\n______________:\|\|\|_\|\|\|\|\|\|\|\|\|\|\n______________UCCC_CAACCCCUUG\n3'-UUU...CUAUC_______________UCUCU...AUA-5'\n_____________\|_______________\|\n_____________35______________20\n	235 -- 241	21 -- 27	-24.3947 kcal/mol	4.254 kcal/mol	1.91139 kcal/mol	226 242@LB@ \| \|@LB@5'-GGU...GGAGC A AGCAC...GUG-3'@LB@ GGGG GUUGGGGAAC@LB@ :\|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ UCCC CAACCCCUUG@LB@3'-UUU...CUAUC UCUCU...AUA-5'@LB@ \| \|@LB@ 35 20@LB@@LB@@LB@Energy -18.23 kcal/mol@LB@Hybridization Energy -24.3947 kcal/mol@LB@Unfolding Energy - mRNA 4.254 kcal/mol@LB@Unfolding Energy - sRNA 1.91139 kcal/mol@LB@@LB@Position - mRNA 227 -- 241@LB@Position - sRNA 21 -- 34@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 21 -- 27@LB@
127	0.01117	0.2883	bsu05980	tatAY	-16.78	0.012784	171 -- 194	21 -- 43	Sec-independent protein translocase protein TatAy		_____________170______________________195\n_____________\|________________________\|\n5'-CCG...AGGAA___GA________AAA__A_____CCAAA...ACA-3'\n______________AUC__AUAGAGGG___GG_GGAGC\n______________\|\|\|__\|\|\|\|\|\|\|\|___\|\|_\|\|\|:\|\n______________UAG__UAUCUCCC___CC_CCUUG\n3'-UUU...AGAAC___AC________CAA________UCUCU...AUA-5'\n_____________\|________________________\|\n_____________44_______________________20\n	177 -- 183	31 -- 37	-24.2003 kcal/mol	4.65314 kcal/mol	2.76238 kcal/mol	170 195@LB@ \| \|@LB@5'-CCG...AGGAA GA AAA A CCAAA...ACA-3'@LB@ AUC AUAGAGGG GG GGAGC@LB@ \|\|\| \|\|\|\|\|\|\|\| \|\| \|\|\|:\|@LB@ UAG UAUCUCCC CC CCUUG@LB@3'-UUU...AGAAC AC CAA UCUCU...AUA-5'@LB@ \| \|@LB@ 44 20@LB@@LB@@LB@Energy -16.78 kcal/mol@LB@Hybridization Energy -24.2003 kcal/mol@LB@Unfolding Energy - mRNA 4.65314 kcal/mol@LB@Unfolding Energy - sRNA 2.76238 kcal/mol@LB@@LB@Position - mRNA 171 -- 194@LB@Position - sRNA 21 -- 43@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 31 -- 37@LB@
188	0.01873	0.3269	bsu10750	yisK	-12.58	0.084103	165 -- 222	21 -- 51	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; Product type pe: enzyme'		_____________164_________________________________________________________223\n_____________\|___________________________________________________________\|\n5'-UCC...AUGAA___GCAU________UAAAAGA_________AAUAACAUGAAAUUU_C_ACA_______UUUAC...UGU-3'\n______________GGA____UC_UGAUU_______UGAUGGAGG_______________G_G___GGGGAAC\n______________\|\|\|____\|\|_\|\|\|\|:_______\|\|\|\|:\|\|\|\|_______________\|_\|___\|\|\|\|\|\|\|\n______________CCU____AG_ACUAG_______ACUAUCUCC_______________C_C___CCCCUUG\n3'-UUU...AAAAG_________A_______________________________________AA________UCUCU...AUA-5'\n_____________\|___________________________________________________________\|\n_____________52__________________________________________________________20\n	216 -- 222	21 -- 27	-23.7404 kcal/mol	8.38838 kcal/mol	2.76846 kcal/mol	164 223@LB@ \| \|@LB@5'-UCC...AUGAA GCAU UAAAAGA AAUAACAUGAAAUUU C ACA UUUAC...UGU-3'@LB@ GGA UC UGAUU UGAUGGAGG G G GGGGAAC@LB@ \|\|\| \|\| \|\|\|\|: \|\|\|\|:\|\|\|\| \| \| \|\|\|\|\|\|\|@LB@ CCU AG ACUAG ACUAUCUCC C C CCCCUUG@LB@3'-UUU...AAAAG A AA UCUCU...AUA-5'@LB@ \| \|@LB@ 52 20@LB@@LB@@LB@Energy -12.58 kcal/mol@LB@Hybridization Energy -23.7404 kcal/mol@LB@Unfolding Energy - mRNA 8.38838 kcal/mol@LB@Unfolding Energy - sRNA 2.76846 kcal/mol@LB@@LB@Position - mRNA 165 -- 222@LB@Position - sRNA 21 -- 51@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 21 -- 27@LB@
195	0.01942	0.3269	bsu00690	ftsH	-11.53	0.125763	258 -- 269	21 -- 33	ATP-dependent zinc metalloprotease FtsH		_____________257___________270\n_____________\|_____________\|\n5'-AGU...UAAUC_______U_____UACUU...AAA-3'\n______________GGGGUUG__GAGC\n______________\|\|\|\|\|\|\|__\|\|:\|\n______________CCCCAAC__CUUG\n3'-UUU...UAUCU_______CC____UCUCU...AUA-5'\n_____________\|_____________\|\n_____________34____________20\n	258 -- 264	27 -- 33	-15.4755 kcal/mol	2.12746 kcal/mol	1.8225 kcal/mol	257 270@LB@ \| \|@LB@5'-AGU...UAAUC U UACUU...AAA-3'@LB@ GGGGUUG GAGC@LB@ \|\|\|\|\|\|\| \|\|:\|@LB@ CCCCAAC CUUG@LB@3'-UUU...UAUCU CC UCUCU...AUA-5'@LB@ \| \|@LB@ 34 20@LB@@LB@@LB@Energy -11.53 kcal/mol@LB@Hybridization Energy -15.4755 kcal/mol@LB@Unfolding Energy - mRNA 2.12746 kcal/mol@LB@Unfolding Energy - sRNA 1.8225 kcal/mol@LB@@LB@Position - mRNA 258 -- 269@LB@Position - sRNA 21 -- 33@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 27 -- 33@LB@
11	0.0001235	0.03747	bsu15610	sumT	-12.35	0.092299	189 -- 208	22 -- 34	uroporphyrinogen-iii C-methyltransferase		_____________188__________________209\n_____________\|____________________\|\n5'-GAA...AGAUC_____AAAUACGA_______AGUAU...AUG-3'\n______________GGGGG________UGGGGAA\n______________:\|\|\|\|________\|\|\|\|\|\|\|\n______________UCCCC________ACCCCUU\n3'-UUU...CUAUC_____A______________GUCUC...AUA-5'\n_____________\|____________________\|\n_____________35___________________21\n	202 -- 208	22 -- 28	-16.2617 kcal/mol	2.89451 kcal/mol	1.02154 kcal/mol	188 209@LB@ \| \|@LB@5'-GAA...AGAUC AAAUACGA AGUAU...AUG-3'@LB@ GGGGG UGGGGAA@LB@ :\|\|\|\| \|\|\|\|\|\|\|@LB@ UCCCC ACCCCUU@LB@3'-UUU...CUAUC A GUCUC...AUA-5'@LB@ \| \|@LB@ 35 21@LB@@LB@@LB@Energy -12.35 kcal/mol@LB@Hybridization Energy -16.2617 kcal/mol@LB@Unfolding Energy - mRNA 2.89451 kcal/mol@LB@Unfolding Energy - sRNA 1.02154 kcal/mol@LB@@LB@Position - mRNA 189 -- 208@LB@Position - sRNA 22 -- 34@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 22 -- 28@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@
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@
40	0.001724	0.1438	bsu18440	gltD	-13.77	0.051762	193 -- 208	22 -- 36	glutamate synthase [NADPH] small chain		_____________192______________209\n_____________\|________________\|\n5'-AGA...AGGGG_____AACA_______ACCAA...CUU-3'\n______________AGAGG____UGGGGAA\n______________\|\|\|\|\|____\|\|\|\|\|\|\|\n______________UCUCC____ACCCCUU\n3'-UUU...GACUA_____CCA________GUCUC...AUA-5'\n_____________\|________________\|\n_____________37_______________21\n	202 -- 208	22 -- 28	-17.8722 kcal/mol	3.06294 kcal/mol	1.03819 kcal/mol	192 209@LB@ \| \|@LB@5'-AGA...AGGGG AACA ACCAA...CUU-3'@LB@ AGAGG UGGGGAA@LB@ \|\|\|\|\| \|\|\|\|\|\|\|@LB@ UCUCC ACCCCUU@LB@3'-UUU...GACUA CCA GUCUC...AUA-5'@LB@ \| \|@LB@ 37 21@LB@@LB@@LB@Energy -13.77 kcal/mol@LB@Hybridization Energy -17.8722 kcal/mol@LB@Unfolding Energy - mRNA 3.06294 kcal/mol@LB@Unfolding Energy - sRNA 1.03819 kcal/mol@LB@@LB@Position - mRNA 193 -- 208@LB@Position - sRNA 22 -- 36@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 22 -- 28@LB@
63	0.003897	0.2064	bsu14900	ctaD	-14.39	0.039562	155 -- 192	22 -- 52	cytochrome c oxidase subunit 1		_____________154____________________________________193\n_____________\|______________________________________\|\n5'-GUG...AAAAG____AAGCAA__AG__A___AA___AGAUA________GGUCA...UGG-3'\n______________CGGA______GU__GG_AGA__GGG_____UUGGGGGA\n______________\|\|\|\|______:\|__\|:_\|\|\|__\|\|\|_____\|\|\|\|\|\|:\|\n______________GCCU______UA__CU_UCU__CCC_____AACCCCUU\n3'-UUU...AAAAA____AGAAC___GA__A___C_________________GUCUC...AUA-5'\n_____________\|______________________________________\|\n_____________53_____________________________________21\n	186 -- 192	22 -- 28	-20.3858 kcal/mol	4.11152 kcal/mol	1.8808 kcal/mol	154 193@LB@ \| \|@LB@5'-GUG...AAAAG AAGCAA AG A AA AGAUA GGUCA...UGG-3'@LB@ CGGA GU GG AGA GGG UUGGGGGA@LB@ \|\|\|\| :\| \|: \|\|\| \|\|\| \|\|\|\|\|\|:\|@LB@ GCCU UA CU UCU CCC AACCCCUU@LB@3'-UUU...AAAAA AGAAC GA A C GUCUC...AUA-5'@LB@ \| \|@LB@ 53 21@LB@@LB@@LB@Energy -14.39 kcal/mol@LB@Hybridization Energy -20.3858 kcal/mol@LB@Unfolding Energy - mRNA 4.11152 kcal/mol@LB@Unfolding Energy - sRNA 1.8808 kcal/mol@LB@@LB@Position - mRNA 155 -- 192@LB@Position - sRNA 22 -- 52@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 22 -- 28@LB@
119	0.01041	0.2883	bsu11480	yjbB	-12.30	0.094041	10 -- 19	22 -- 31	MFS transporter	bsu07460	_____________9__________20\n_____________\|__________\|\n5'-UCA...UUAAA__A_______ACGAU...GGA-3'\n______________GG_UGGGGAA\n______________\|\|_\|\|\|\|\|\|\|\n______________CC_ACCCCUU\n3'-UUU...UCUCC__A_______GUCUC...AUA-5'\n_____________\|__________\|\n_____________32_________21\n	13 -- 19	22 -- 28	-13.9571 kcal/mol	0.741777 kcal/mol	0.918006 kcal/mol	9 20@LB@ \| \|@LB@5'-UCA...UUAAA A ACGAU...GGA-3'@LB@ GG UGGGGAA@LB@ \|\| \|\|\|\|\|\|\|@LB@ CC ACCCCUU@LB@3'-UUU...UCUCC A GUCUC...AUA-5'@LB@ \| \|@LB@ 32 21@LB@@LB@@LB@Energy -12.30 kcal/mol@LB@Hybridization Energy -13.9571 kcal/mol@LB@Unfolding Energy - mRNA 0.741777 kcal/mol@LB@Unfolding Energy - sRNA 0.918006 kcal/mol@LB@@LB@Position - mRNA 10 -- 19@LB@Position - sRNA 22 -- 31@LB@Position Seed - mRNA 13 -- 19@LB@Position Seed - sRNA 22 -- 28@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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