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
16	0.0002979	0.06212	bsu28440	sdhA	-14.86	0.032148	176 -- 195	24 -- 44	succinate dehydrogenase flavoprotein subunit	_____________175___________________196\n_____________\|_____________________\|\n5'-GUG...UACUA____AC________AGA____CUAUC...CCA-3'\n______________GAUU___UAGAGGG___GGGG\n______________\|\|\|:___\|\|\|\|\|\|\|___\|\|\|\|\n______________CUAG___AUCUCCC___CCCC\n3'-UUU...UAGAA____ACU_______CAA____UUGUC...AUA-5'\n_____________\|_____________________\|\n_____________45____________________23\n	182 -- 188	31 -- 37	-20.465 kcal/mol	4.62868 kcal/mol	0.977523 kcal/mol	175 196@LB@ \| \|@LB@5'-GUG...UACUA AC AGA CUAUC...CCA-3'@LB@ GAUU UAGAGGG GGGG@LB@ \|\|\|: \|\|\|\|\|\|\| \|\|\|\|@LB@ CUAG AUCUCCC CCCC@LB@3'-UUU...UAGAA ACU CAA UUGUC...AUA-5'@LB@ \| \|@LB@ 45 23@LB@@LB@@LB@Energy -14.86 kcal/mol@LB@Hybridization Energy -20.465 kcal/mol@LB@Unfolding Energy - mRNA 4.62868 kcal/mol@LB@Unfolding Energy - sRNA 0.977523 kcal/mol@LB@@LB@Position - mRNA 176 -- 195@LB@Position - sRNA 24 -- 44@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 31 -- 37@LB@
51	0.002362	0.1545	bsu28450	sdhC	-14.17	0.043697	178 -- 219	14 -- 47	succinate dehydrogenase cytochrome b558 subunit	_____________177_________________________________________220\n_____________\|___________________________________________\|\n5'-AAA...UCGCA_______AAAC______UAAAGUAAU__CU_____________UUUAU...AGU-3'\n______________CUU_AUC____AGGGGG_________GU__GGGAACAGAGAGU\n______________\|\|\|_\|\|\|____\|\|:\|\|\|_________\|\|__\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________GAA_UAG____UCUCCC_________CA__CCCUUGUCUCUCA\n3'-UUU...GCCUA___C___ACUA_________________AC_____________UCGAA...AUA-5'\n_____________\|___________________________________________\|\n_____________48__________________________________________13\n	213 -- 219	14 -- 20	-33.4599 kcal/mol	9.41028 kcal/mol	9.88362 kcal/mol	177 220@LB@ \| \|@LB@5'-AAA...UCGCA AAAC UAAAGUAAU CU UUUAU...AGU-3'@LB@ CUU AUC AGGGGG GU GGGAACAGAGAGU@LB@ \|\|\| \|\|\| \|\|:\|\|\| \|\| \|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ GAA UAG UCUCCC CA CCCUUGUCUCUCA@LB@3'-UUU...GCCUA C ACUA AC UCGAA...AUA-5'@LB@ \| \|@LB@ 48 13@LB@@LB@@LB@Energy -14.17 kcal/mol@LB@Hybridization Energy -33.4599 kcal/mol@LB@Unfolding Energy - mRNA 9.41028 kcal/mol@LB@Unfolding Energy - sRNA 9.88362 kcal/mol@LB@@LB@Position - mRNA 178 -- 219@LB@Position - sRNA 14 -- 47@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 14 -- 20@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@
196	0.01947	0.3269	bsu15810	spoVM	-12.63	0.082660	188 -- 194	30 -- 36	stage V sporulation protein M	_____________187_____195\n_____________\|_______\|\n5'-AAA...UUAUA_______ACAAA...GCC-3'\n______________GGAGGGG\n______________:\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	188 -- 194	30 -- 36	-13.8815 kcal/mol	1.12038 kcal/mol	0.133643 kcal/mol	187 195@LB@ \| \|@LB@5'-AAA...UUAUA ACAAA...GCC-3'@LB@ GGAGGGG@LB@ :\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -12.63 kcal/mol@LB@Hybridization Energy -13.8815 kcal/mol@LB@Unfolding Energy - mRNA 1.12038 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 188 -- 194@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 30 -- 36@LB@
159	0.01439	0.3008	bsu00560	spoVT	-10.85	0.160189	242 -- 254	41 -- 53	stage V sporulation protein T	_____________241___________255\n_____________\|_____________\|\n5'-ACA...UUAGG_______G_____CCUAA...CGC-3'\n______________UCGGGUC_UGAUU\n______________\|\|\|\|:\|\|_\|\|\|\|:\n______________AGCCUAG_ACUAG\n3'-UUU...AAAAA_______A_____ACUAU...AUA-5'\n_____________\|_____________\|\n_____________54____________40\n	242 -- 248	47 -- 53	-14.0147 kcal/mol	2.18551 kcal/mol	0.979862 kcal/mol	241 255@LB@ \| \|@LB@5'-ACA...UUAGG G CCUAA...CGC-3'@LB@ UCGGGUC UGAUU@LB@ \|\|\|\|:\|\| \|\|\|\|:@LB@ AGCCUAG ACUAG@LB@3'-UUU...AAAAA A ACUAU...AUA-5'@LB@ \| \|@LB@ 54 40@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -14.0147 kcal/mol@LB@Unfolding Energy - mRNA 2.18551 kcal/mol@LB@Unfolding Energy - sRNA 0.979862 kcal/mol@LB@@LB@Position - mRNA 242 -- 254@LB@Position - sRNA 41 -- 53@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 47 -- 53@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@
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@
118	0.01022	0.2883	bsu19370	sucA	-9.59	0.243554	183 -- 190	23 -- 30	2-oxoglutarate dehydrogenase subunit E1	_____________182______191\n_____________\|________\|\n5'-UUU...UUUAA________UAAUA...AUC-3'\n______________GUUGGGGG\n______________\|\|\|\|\|\|\|:\n______________CAACCCCU\n3'-UUU...CUCCC________UGUCU...AUA-5'\n_____________\|________\|\n_____________31_______22\n	184 -- 190	23 -- 29	-13.0923 kcal/mol	3.48895 kcal/mol	0.018115 kcal/mol	182 191@LB@ \| \|@LB@5'-UUU...UUUAA UAAUA...AUC-3'@LB@ GUUGGGGG@LB@ \|\|\|\|\|\|\|:@LB@ CAACCCCU@LB@3'-UUU...CUCCC UGUCU...AUA-5'@LB@ \| \|@LB@ 31 22@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -13.0923 kcal/mol@LB@Unfolding Energy - mRNA 3.48895 kcal/mol@LB@Unfolding Energy - sRNA 0.018115 kcal/mol@LB@@LB@Position - mRNA 183 -- 190@LB@Position - sRNA 23 -- 30@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 23 -- 29@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@
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@

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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