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
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@
174	0.01668	0.3152	bsu22210	yprB	-13.05	0.069799	168 -- 191	31 -- 53	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; Product type pe: enzyme'		_____________167______________________192\n_____________\|________________________\|\n5'-AUU...AGCUG_______AAAU___GUAA______AGGCC...AUG-3'\n______________UUGGAUC____GUC____GGAGGG\n______________\|:\|\|\|\|\|____:\|\|____:\|\|\|\|\|\n______________AGCCUAG____UAG____UCUCCC\n3'-UUU...AAAAA_______AAC____ACUA______CAACC...AUA-5'\n_____________\|________________________\|\n_____________54_______________________30\n	168 -- 174	47 -- 53	-20.3327 kcal/mol	6.30079 kcal/mol	0.981784 kcal/mol	167 192@LB@ \| \|@LB@5'-AUU...AGCUG AAAU GUAA AGGCC...AUG-3'@LB@ UUGGAUC GUC GGAGGG@LB@ \|:\|\|\|\|\| :\|\| :\|\|\|\|\|@LB@ AGCCUAG UAG UCUCCC@LB@3'-UUU...AAAAA AAC ACUA CAACC...AUA-5'@LB@ \| \|@LB@ 54 30@LB@@LB@@LB@Energy -13.05 kcal/mol@LB@Hybridization Energy -20.3327 kcal/mol@LB@Unfolding Energy - mRNA 6.30079 kcal/mol@LB@Unfolding Energy - sRNA 0.981784 kcal/mol@LB@@LB@Position - mRNA 168 -- 191@LB@Position - sRNA 31 -- 53@LB@Position Seed - mRNA 168 -- 174@LB@Position Seed - sRNA 47 -- 53@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@
12	0.0001633	0.0454	bsu11410	yjbA	-19.25	0.003321	222 -- 243	30 -- 52	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; Product type pf: factor'		_____________221_______________________244\n_____________\|_________________________\|\n5'-GAA...AUGUG______AA_________________AAGAA...UUG-3'\n______________UGGGUC__UUGGUUUGA___AGGGG\n______________:\|\|:\|\|__\|\|\|:\|:\|\|\|___\|\|\|\|\|\n______________GCCUAG__AACUAGACU___UCCCC\n3'-UUU...AAAAA_________________AUC_____AACCC...AUA-5'\n_____________\|_________________________\|\n_____________53________________________29\n	232 -- 238	38 -- 44	-23.9108 kcal/mol	3.6845 kcal/mol	0.979974 kcal/mol	221 244@LB@ \| \|@LB@5'-GAA...AUGUG AA AAGAA...UUG-3'@LB@ UGGGUC UUGGUUUGA AGGGG@LB@ :\|\|:\|\| \|\|\|:\|:\|\|\| \|\|\|\|\|@LB@ GCCUAG AACUAGACU UCCCC@LB@3'-UUU...AAAAA AUC AACCC...AUA-5'@LB@ \| \|@LB@ 53 29@LB@@LB@@LB@Energy -19.25 kcal/mol@LB@Hybridization Energy -23.9108 kcal/mol@LB@Unfolding Energy - mRNA 3.6845 kcal/mol@LB@Unfolding Energy - sRNA 0.979974 kcal/mol@LB@@LB@Position - mRNA 222 -- 243@LB@Position - sRNA 30 -- 52@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 38 -- 44@LB@
79	0.005838	0.2448	bsu25980	yqbT	-11.66	0.119794	52 -- 65	32 -- 53	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; Product type ps: structure'	bsu12730	_____________51_____________________66\n_____________\|______________________\|\n5'-CGU...AUCCC______________________AAGCA...CGU-3'\n______________UCGG________CUGAUAGAGG\n______________\|\|\|\|________\|\|\|\|\|\|\|\|\|\|\n______________AGCC________GACUAUCUCC\n3'-UUU...AAAAA____UAGAACUA__________CCAAC...AUA-5'\n_____________\|______________________\|\n_____________54_____________________31\n	59 -- 65	32 -- 38	-19.4839 kcal/mol	6.84464 kcal/mol	0.981755 kcal/mol	51 66@LB@ \| \|@LB@5'-CGU...AUCCC AAGCA...CGU-3'@LB@ UCGG CUGAUAGAGG@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ AGCC GACUAUCUCC@LB@3'-UUU...AAAAA UAGAACUA CCAAC...AUA-5'@LB@ \| \|@LB@ 54 31@LB@@LB@@LB@Energy -11.66 kcal/mol@LB@Hybridization Energy -19.4839 kcal/mol@LB@Unfolding Energy - mRNA 6.84464 kcal/mol@LB@Unfolding Energy - sRNA 0.981755 kcal/mol@LB@@LB@Position - mRNA 52 -- 65@LB@Position - sRNA 32 -- 53@LB@Position Seed - mRNA 59 -- 65@LB@Position Seed - sRNA 32 -- 38@LB@
2	2.736e-07	0.0004564	bsu10760	yisL	-18.52	0.005045	172 -- 193	31 -- 51	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; PubMedId: 15849754 16850406; Product type pm: membrane component'		_____________171____________________194\n_____________\|______________________\|\n5'-UAC...AAGUG____AAUUU_____________AACAU...UCA-3'\n______________GGGU_____AUCUGAUAGGGGG\n______________\|\|:\|_____\|\|\|\|\|\|\|\|\|:\|\|\|\n______________CCUA_____UAGACUAUCUCCC\n3'-UUU...AAAAG____GAAC______________CAACC...AUA-5'\n_____________\|______________________\|\n_____________52_____________________30\n	187 -- 193	31 -- 37	-25.2722 kcal/mol	5.77834 kcal/mol	0.970589 kcal/mol	171 194@LB@ \| \|@LB@5'-UAC...AAGUG AAUUU AACAU...UCA-3'@LB@ GGGU AUCUGAUAGGGGG@LB@ \|\|:\| \|\|\|\|\|\|\|\|\|:\|\|\|@LB@ CCUA UAGACUAUCUCCC@LB@3'-UUU...AAAAG GAAC CAACC...AUA-5'@LB@ \| \|@LB@ 52 30@LB@@LB@@LB@Energy -18.52 kcal/mol@LB@Hybridization Energy -25.2722 kcal/mol@LB@Unfolding Energy - mRNA 5.77834 kcal/mol@LB@Unfolding Energy - sRNA 0.970589 kcal/mol@LB@@LB@Position - mRNA 172 -- 193@LB@Position - sRNA 31 -- 51@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 31 -- 37@LB@
82	0.006245	0.254	bsu12400	yjnA	-14.90	0.031572	235 -- 273	19 -- 53	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; PubMedId: 15849754 16850406; Product type pm: membrane component'		_____________234_____________________________________274\n_____________\|_______________________________________\|\n5'-UUA...GUUUG_____GC___A___G___U__C___A__G__U_______CCUUA...UGC-3'\n______________UCGGA__CUU_GUC_GAU_GA_GGG_GU_GG_GGAGCGG\n______________\|\|\|\|\|__\|\|\|_:\|\|_\|\|\|_\|\|_\|\|\|_\|\|_\|\|_\|\|\|:\|:\|\n______________AGCCU__GAA_UAG_CUA_CU_CCC_CA_CC_CCUUGUC\n3'-UUU...AAAAA_____A____C___A___U_________A__________UCUCA...AUA-5'\n_____________\|_______________________________________\|\n_____________54______________________________________18\n	267 -- 273	19 -- 25	-33.8463 kcal/mol	12.0212 kcal/mol	6.92635 kcal/mol	234 274@LB@ \| \|@LB@5'-UUA...GUUUG GC A G U C A G U CCUUA...UGC-3'@LB@ UCGGA CUU GUC GAU GA GGG GU GG GGAGCGG@LB@ \|\|\|\|\| \|\|\| :\|\| \|\|\| \|\| \|\|\| \|\| \|\| \|\|\|:\|:\|@LB@ AGCCU GAA UAG CUA CU CCC CA CC CCUUGUC@LB@3'-UUU...AAAAA A C A U A UCUCA...AUA-5'@LB@ \| \|@LB@ 54 18@LB@@LB@@LB@Energy -14.90 kcal/mol@LB@Hybridization Energy -33.8463 kcal/mol@LB@Unfolding Energy - mRNA 12.0212 kcal/mol@LB@Unfolding Energy - sRNA 6.92635 kcal/mol@LB@@LB@Position - mRNA 235 -- 273@LB@Position - sRNA 19 -- 53@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 19 -- 25@LB@
135	0.01203	0.2883	bsu09920	yhaN	-10.31	0.192319	8 -- 29	28 -- 47	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; PubMedId: 16267290; Product type pe : enzyme'		_____________7______________________30\n_____________\|______________________\|\n____5'-AACAAAC_______CUUUUUUU__C____UAUUU...ACG-3'\n______________CUUGAUC________GG_GGUU\n______________\|\|\|\|\|\|\|________\|\|_\|\|\|\|\n______________GAACUAG________CC_CCAA\n3'-UUU...GCCUA_______ACUAUCU________CCCCU...AUA-5'\n_____________\|______________________\|\n_____________48_____________________27\n	8 -- 14	41 -- 47	-14.5368 kcal/mol	3.24797 kcal/mol	0.974663 kcal/mol	7 30@LB@ \| \|@LB@ 5'-AACAAAC CUUUUUUU C UAUUU...ACG-3'@LB@ CUUGAUC GG GGUU@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\|@LB@ GAACUAG CC CCAA@LB@3'-UUU...GCCUA ACUAUCU CCCCU...AUA-5'@LB@ \| \|@LB@ 48 27@LB@@LB@@LB@Energy -10.31 kcal/mol@LB@Hybridization Energy -14.5368 kcal/mol@LB@Unfolding Energy - mRNA 3.24797 kcal/mol@LB@Unfolding Energy - sRNA 0.974663 kcal/mol@LB@@LB@Position - mRNA 8 -- 29@LB@Position - sRNA 28 -- 47@LB@Position Seed - mRNA 8 -- 14@LB@Position Seed - sRNA 41 -- 47@LB@
8	5.206e-05	0.02171	bsu37180	fadF	-12.43	0.089383	154 -- 199	26 -- 74	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; PubMedId: 17189250; Product type pe : enzyme'		_____________153____________________________________________________200\n_____________\|______________________________________________________\|\n5'-CAA...AGAUU_________G_GA___________C______U___A_UAAAA______AA____AAUGA...ACA-3'\n______________CGGGGGUAG_G__________UCG_GGUCUU_AUC_G_____AGGGGG__UUGG\n______________\|\|\|\|\|\|\|\|\|_\|__________\|\|\|_\|:\|\|\|\|_\|\|\|_\|_____\|\|:\|\|\|__\|\|\|\|\n______________GCCCCCAUC_C__________AGC_CUAGAA_UAG_C_____UCUCCC__AACC\n3'-UUU...GAACC_________G_GGUUCAAAAA__________C___A_UA_________C_____CCUUG...AUA-5'\n_____________\|______________________________________________________\|\n_____________75_____________________________________________________25\n	156 -- 162	66 -- 72	-40.4869 kcal/mol	12.2576 kcal/mol	15.8011 kcal/mol	153 200@LB@ \| \|@LB@5'-CAA...AGAUU G GA C U A UAAAA AA AAUGA...ACA-3'@LB@ CGGGGGUAG G UCG GGUCUU AUC G AGGGGG UUGG@LB@ \|\|\|\|\|\|\|\|\| \| \|\|\| \|:\|\|\|\| \|\|\| \| \|\|:\|\|\| \|\|\|\|@LB@ GCCCCCAUC C AGC CUAGAA UAG C UCUCCC AACC@LB@3'-UUU...GAACC G GGUUCAAAAA C A UA C CCUUG...AUA-5'@LB@ \| \|@LB@ 75 25@LB@@LB@@LB@Energy -12.43 kcal/mol@LB@Hybridization Energy -40.4869 kcal/mol@LB@Unfolding Energy - mRNA 12.2576 kcal/mol@LB@Unfolding Energy - sRNA 15.8011 kcal/mol@LB@@LB@Position - mRNA 154 -- 199@LB@Position - sRNA 26 -- 74@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 66 -- 72@LB@
86	0.006791	0.2588	bsu17010	ymcB	-10.99	0.152529	169 -- 190	33 -- 52	(dimethylallyl)adenosine tRNA methylthiotransferase MiaB		_____________168____________________191\n_____________\|______________________\|\n5'-AUC...AAGGG____AG__________AA____AAAAU...CGC-3'\n______________UGGA__UUUGGUUUGA__GGAG\n______________:\|\|\|__:\|\|\|:\|:\|\|\|__:\|\|\|\n______________GCCU__GAACUAGACU__UCUC\n3'-UUU...AAAAA____A___________A_____CCCAA...AUA-5'\n_____________\|______________________\|\n_____________53_____________________32\n	178 -- 184	38 -- 44	-16.81 kcal/mol	4.84464 kcal/mol	0.976367 kcal/mol	168 191@LB@ \| \|@LB@5'-AUC...AAGGG AG AA AAAAU...CGC-3'@LB@ UGGA UUUGGUUUGA GGAG@LB@ :\|\|\| :\|\|\|:\|:\|\|\| :\|\|\|@LB@ GCCU GAACUAGACU UCUC@LB@3'-UUU...AAAAA A A CCCAA...AUA-5'@LB@ \| \|@LB@ 53 32@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -16.81 kcal/mol@LB@Unfolding Energy - mRNA 4.84464 kcal/mol@LB@Unfolding Energy - sRNA 0.976367 kcal/mol@LB@@LB@Position - mRNA 169 -- 190@LB@Position - sRNA 33 -- 52@LB@Position Seed - mRNA 178 -- 184@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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