Input and runtime details for job 4894743 (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 4894743 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:35:26 CET 2018
	CopraRNA Started		@ Fri Feb 16 21:36:09 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 05:38:38 CET 2018
	Post-Processing Finished		@ Sat Feb 17 05:38:45 CET 2018
	Job Completed		@ Sat Feb 17 05:39:16 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=4894743&toolName=CopraRNA ( 30 days expiry )

Description of the job

SR1

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
62	0.001958	0.1214	bsu25150	yqfQ	-10.78	0.228520	210 -- 221	125 -- 139	Evidence 4: Homologs of previously reported genes of unknown function	_____________209_____________222\n_____________\|_______________\|\n5'-AAU...UUUCA_______________AUGAG...UGC-3'\n______________CCGCAGCAG___CCA\n______________\|\|\|\|\|\|\|\|:___\|\|\|\n______________GGCGUCGUU___GGU\n3'-AUU...UAACA_________CAA___AUAUU...CAA-5'\n_____________\|_______________\|\n_____________140_____________124\n	212 -- 218	131 -- 137	-17.5181 kcal/mol	2.74724 kcal/mol	6.06036 kcal/mol	209 222@LB@ \| \|@LB@5'-AAU...UUUCA AUGAG...UGC-3'@LB@ CCGCAGCAG CCA@LB@ \|\|\|\|\|\|\|\|: \|\|\|@LB@ GGCGUCGUU GGU@LB@3'-AUU...UAACA CAA AUAUU...CAA-5'@LB@ \| \|@LB@ 140 124@LB@@LB@@LB@Energy -10.78 kcal/mol@LB@Hybridization Energy -17.5181 kcal/mol@LB@Unfolding Energy - mRNA 2.74724 kcal/mol@LB@Unfolding Energy - sRNA 6.06036 kcal/mol@LB@@LB@Position - mRNA 210 -- 221@LB@Position - sRNA 125 -- 139@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 131 -- 137@LB@
105	0.004352	0.1606	bsu05340	ydfA	-10.81	0.225539	212 -- 245	38 -- 75	arsenic pump protein	_____________211____________________________246\n_____________\|______________________________\|\n5'-AGC...UCAAU______________________________UAUUA...GAG-3'\n______________GAUUUUGGCA_______GUAUUCAUCUUUU\n______________:\|\|:\|\|\|\|\|\|_______\|\|\|::\|\|\|\|\|:\|\|\n______________UUAGAACCGU_______CAUGGGUAGAGAA\n3'-AUU...CAACG__________UUGUUAG_____________UAAGG...CAA-5'\n_____________\|______________________________\|\n_____________76_____________________________37\n	227 -- 233	47 -- 53	-24.4224 kcal/mol	4.10196 kcal/mol	8.49986 kcal/mol	211 246@LB@ \| \|@LB@5'-AGC...UCAAU UAUUA...GAG-3'@LB@ GAUUUUGGCA GUAUUCAUCUUUU@LB@ :\|\|:\|\|\|\|\|\| \|\|\|::\|\|\|\|\|:\|\|@LB@ UUAGAACCGU CAUGGGUAGAGAA@LB@3'-AUU...CAACG UUGUUAG UAAGG...CAA-5'@LB@ \| \|@LB@ 76 37@LB@@LB@@LB@Energy -10.81 kcal/mol@LB@Hybridization Energy -24.4224 kcal/mol@LB@Unfolding Energy - mRNA 4.10196 kcal/mol@LB@Unfolding Energy - sRNA 8.49986 kcal/mol@LB@@LB@Position - mRNA 212 -- 245@LB@Position - sRNA 38 -- 75@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 47 -- 53@LB@
86	0.003162	0.1423	bsu32080	yuiB	-17.14	0.011766	214 -- 271	6 -- 63	Evidence 4: Homologs of previously reported genes of unknown function	_____________213____________________________________________________________272\n_____________\|______________________________________________________________\|\n5'-UAG...UCUGC________A_______AA_______G_U____GUC___UUU_______U_____________AUUAA...GGA-3'\n______________CAGUCGUA_UCAUCUC__UUGUUUU_U_UUUU___UUG___UUUGGAA_CG____GUUUCUU\n______________\|\|:\|\|\|\|\|_:\|\|\|\|\|\|__\|\|:\|\|::_:_\|\|\|:___\|\|\|___\|\|\|\|:\|\|_\|\|____:\|\|\|\|\|\|\n______________GUUAGCAU_GGUAGAG__AAUAAGG_G_AAAG___AAC___AAACUUU_GC____UAAAGAA\n3'-AUU...CGUUU________G________________G_U____A_____UUU_______U__GAAU_______AACAA-5'\n_____________\|______________________________________________________________\|\n_____________64_____________________________________________________________5\n	265 -- 271	6 -- 12	-35.4392 kcal/mol	4.76592 kcal/mol	13.9327 kcal/mol	213 272@LB@ \| \|@LB@5'-UAG...UCUGC A AA G U GUC UUU U AUUAA...GGA-3'@LB@ CAGUCGUA UCAUCUC UUGUUUU U UUUU UUG UUUGGAA CG GUUUCUU@LB@ \|\|:\|\|\|\|\| :\|\|\|\|\|\| \|\|:\|\|:: : \|\|\|: \|\|\| \|\|\|\|:\|\| \|\| :\|\|\|\|\|\|@LB@ GUUAGCAU GGUAGAG AAUAAGG G AAAG AAC AAACUUU GC UAAAGAA@LB@3'-AUU...CGUUU G G U A UUU U GAAU AACAA-5'@LB@ \| \|@LB@ 64 5@LB@@LB@@LB@Energy -17.14 kcal/mol@LB@Hybridization Energy -35.4392 kcal/mol@LB@Unfolding Energy - mRNA 4.76592 kcal/mol@LB@Unfolding Energy - sRNA 13.9327 kcal/mol@LB@@LB@Position - mRNA 214 -- 271@LB@Position - sRNA 6 -- 63@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 6 -- 12@LB@
44	0.001404	0.1206	bsu30660	ytkA	-11.27	0.185588	215 -- 238	164 -- 186	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; Product type lp: lipoprotein'	_____________214_________239\n_____________\|___________\|\n5'-CAU...GCGCU___________GCGUU...UUU-3'\n______________AAACGUUUAAU\n______________\|\|\|\|\|:\|\|\|\|\|\n______________UUUGCGAAUUA\n3'-AUU...AAACU___________AAGAA...CAA-5'\n_____________\|___________\|\n_____________187_________163\n	23 -- 29	11 -- 17	-8.86173 kcal/mol	2.03186 kcal/mol	2.83264 kcal/mol	214 239@LB@ \| \|@LB@5'-CAU...GCGCU GCGUU...UUU-3'@LB@ AAACGUUUAAU@LB@ \|\|\|\|\|:\|\|\|\|\|@LB@ UUUGCGAAUUA@LB@3'-AUU...AAACU AAGAA...CAA-5'@LB@ \| \|@LB@ 187 163@LB@@LB@@LB@Energy -11.27 kcal/mol@LB@Hybridization Energy -8.86173 kcal/mol@LB@Unfolding Energy - mRNA 2.03186 kcal/mol@LB@Unfolding Energy - sRNA 2.83264 kcal/mol@LB@@LB@Position - mRNA 215 -- 238@LB@Position - sRNA 164 -- 186@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 11 -- 17@LB@
13	0.0004662	0.1011	bsu39950	yxaJ	-7.42	0.718209	218 -- 252	31 -- 81	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; PubMedId: 15743949 15849754 16850406; Product type pm: membrane component'	_____________217_________________________________________253\n_____________\|___________________________________________\|\n5'-CAU...AAUAG___G______A__A_____________________GC______UUUUU...CGG-3'\n______________CGU_GCGAUC_UG_CAA__________CCAUUUCU__GUUUCU\n______________\|\|\|_\|\|:\|\|\|_\|\|_\|\|\|__________\|\|\|\|:\|\|\|__:\|\|:\|:\n______________GCA_CGUUAG_AC_GUU__________GGUAGAGA__UAAGGG\n3'-AUU...CCGAA___A______A__C___UGUUAGCAUG________A_______GUAAA...CAA-5'\n_____________\|___________________________________________\|\n_____________82__________________________________________30\n	236 -- 242	47 -- 53	-25.2058 kcal/mol	7.74885 kcal/mol	10.909 kcal/mol	217 253@LB@ \| \|@LB@5'-CAU...AAUAG G A A GC UUUUU...CGG-3'@LB@ CGU GCGAUC UG CAA CCAUUUCU GUUUCU@LB@ \|\|\| \|\|:\|\|\| \|\| \|\|\| \|\|\|\|:\|\|\| :\|\|:\|:@LB@ GCA CGUUAG AC GUU GGUAGAGA UAAGGG@LB@3'-AUU...CCGAA A A C UGUUAGCAUG A GUAAA...CAA-5'@LB@ \| \|@LB@ 82 30@LB@@LB@@LB@Energy -7.42 kcal/mol@LB@Hybridization Energy -25.2058 kcal/mol@LB@Unfolding Energy - mRNA 7.74885 kcal/mol@LB@Unfolding Energy - sRNA 10.909 kcal/mol@LB@@LB@Position - mRNA 218 -- 252@LB@Position - sRNA 31 -- 81@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 47 -- 53@LB@
98	0.003906	0.1544	bsu29990	pbuO	-11.33	0.180719	218 -- 233	123 -- 137	guanine/hypoxanthine permease PbuO	_____________217______________234\n_____________\|________________\|\n5'-GGU...AAAGA_______ACA______AAGCA...CGG-3'\n______________GCAGCAA___UCCAUA\n______________\|\|\|\|\|\|\|___\|\|\|\|\|\|\n______________CGUCGUU___AGGUAU\n3'-AUU...ACAGG_______CA_______AUUAC...CAA-5'\n_____________\|________________\|\n_____________138______________122\n	218 -- 224	131 -- 137	-16.3971 kcal/mol	2.46726 kcal/mol	3.21202 kcal/mol	217 234@LB@ \| \|@LB@5'-GGU...AAAGA ACA AAGCA...CGG-3'@LB@ GCAGCAA UCCAUA@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ CGUCGUU AGGUAU@LB@3'-AUU...ACAGG CA AUUAC...CAA-5'@LB@ \| \|@LB@ 138 122@LB@@LB@@LB@Energy -11.33 kcal/mol@LB@Hybridization Energy -16.3971 kcal/mol@LB@Unfolding Energy - mRNA 2.46726 kcal/mol@LB@Unfolding Energy - sRNA 3.21202 kcal/mol@LB@@LB@Position - mRNA 218 -- 233@LB@Position - sRNA 123 -- 137@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 131 -- 137@LB@
84	0.003073	0.1418	bsu31450	kinB	-10.05	0.307083	220 -- 261	31 -- 74	sporulation kinase B	_____________219___________________262\n_____________\|_____________________\|\n5'-AUG...CUUUA______________CU_____ACCAA...UGC-3'\n______________UUUUGUUUCCUAUU__UCUUU\n______________\|:\|\|:\|\|:\|\|:\|\|\|__\|\|\|\|\|\n______________AGAAUAAGGGGUAA__AGAAA\n3'-AUU...GGUAG_____________________CUUUA...CAA-5'\n_____________\|_____________________\|\n_____________75____________________30\n	248 -- 254	36 -- 42	-15.4229 kcal/mol	1.85906 kcal/mol	5.65941 kcal/mol	219 262@LB@ \| \|@LB@5'-AUG...CUUUA CU ACCAA...UGC-3'@LB@ UUUUGUUUCCUAUU UCUUU@LB@ \|:\|\|:\|\|:\|\|:\|\|\| \|\|\|\|\|@LB@ AGAAUAAGGGGUAA AGAAA@LB@3'-AUU...GGUAG CUUUA...CAA-5'@LB@ \| \|@LB@ 75 30@LB@@LB@@LB@Energy -10.05 kcal/mol@LB@Hybridization Energy -15.4229 kcal/mol@LB@Unfolding Energy - mRNA 1.85906 kcal/mol@LB@Unfolding Energy - sRNA 5.65941 kcal/mol@LB@@LB@Position - mRNA 220 -- 261@LB@Position - sRNA 31 -- 74@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 36 -- 42@LB@
168	0.007777	0.1751	bsu32270	yutH	-11.70	0.153975	226 -- 259	121 -- 158	endospore coat-associated protein YutH	_____________225____________________________________260\n_____________\|______________________________________\|\n5'-UGC...AGAAA____C______C____CAG_______U___________CCAGC...ACU-3'\n______________AAUA_GGCAUU_ACAU_____GCAGC___UUCCAUGUA\n______________\|\|:\|_\|:\|\|\|\|_\|\|\|\|_____\|\|\|\|\|___\|\|\|\|\|\|:\|\|\n______________UUGU_CUGUAA_UGUA_____CGUCG___AAGGUAUAU\n3'-AUU...AGUAG____C______C____ACAGG_____UUC_________UACAA...CAA-5'\n_____________\|______________________________________\|\n_____________159____________________________________120\n	253 -- 259	121 -- 127	-28.4364 kcal/mol	6.47482 kcal/mol	10.499 kcal/mol	225 260@LB@ \| \|@LB@5'-UGC...AGAAA C C CAG U CCAGC...ACU-3'@LB@ AAUA GGCAUU ACAU GCAGC UUCCAUGUA@LB@ \|\|:\| \|:\|\|\|\| \|\|\|\| \|\|\|\|\| \|\|\|\|\|\|:\|\|@LB@ UUGU CUGUAA UGUA CGUCG AAGGUAUAU@LB@3'-AUU...AGUAG C C ACAGG UUC UACAA...CAA-5'@LB@ \| \|@LB@ 159 120@LB@@LB@@LB@Energy -11.70 kcal/mol@LB@Hybridization Energy -28.4364 kcal/mol@LB@Unfolding Energy - mRNA 6.47482 kcal/mol@LB@Unfolding Energy - sRNA 10.499 kcal/mol@LB@@LB@Position - mRNA 226 -- 259@LB@Position - sRNA 121 -- 158@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 121 -- 127@LB@
194	0.008808	0.1751	bsu16370	fliR	-9.70	0.351361	227 -- 250	157 -- 179	flagellar biosynthetic protein FliR	_____________226____________________________________251\n_____________\|______________________________________\|\n5'-UAU...CGACA____AA____CAGG________U________UAU____AAAAU...UGC-3'\n______________ACUC___AUC____AACA_GAC_UUGGCGUU___UCCG\n______________\|\|\|\|___\|\|\|____\|\|\|\|_\|\|\|_\|\|\|:\|:\|\|___\|\|\|\|\n______________UGAG___UAG____UUGU_CUG_AACUGUAA___AGGC\n3'-AUU...AAAAA____AAG___________C___U________C______GUCGU...CAA-5'\n_____________\|______________________________________\|\n_____________180____________________________________156\n	69 -- 75	142 -- 148	-23.642 kcal/mol	8.17018 kcal/mol	7.49537 kcal/mol	226 251@LB@ \| \|@LB@5'-UAU...CGACA AA CAGG U UAU AAAAU...UGC-3'@LB@ ACUC AUC AACA GAC UUGGCGUU UCCG@LB@ \|\|\|\| \|\|\| \|\|\|\| \|\|\| \|\|\|:\|:\|\| \|\|\|\|@LB@ UGAG UAG UUGU CUG AACUGUAA AGGC@LB@3'-AUU...AAAAA AAG C U C GUCGU...CAA-5'@LB@ \| \|@LB@ 180 156@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -23.642 kcal/mol@LB@Unfolding Energy - mRNA 8.17018 kcal/mol@LB@Unfolding Energy - sRNA 7.49537 kcal/mol@LB@@LB@Position - mRNA 227 -- 250@LB@Position - sRNA 157 -- 179@LB@Position Seed - mRNA 69 -- 75@LB@Position Seed - sRNA 142 -- 148@LB@
114	0.005219	0.1741	bsu18630	exlX	-14.36	0.045196	231 -- 263	38 -- 88	expansin-YoaJ	_____________230________________________________________________________264\n_____________\|__________________________________________________________\|\n5'-GGG...AGAUC_______CA_______GUA________UU________U____________________CAAGC...GUU-3'\n______________AUGAGUG__UUUGUUG___UGGUUUUG___GACGAUC___UCUGUUUU____UCCCCG\n______________\|\|\|\|:\|\|__\|\|:\|\|\|\|___:::\|:\|\|\|___:\|\|:\|\|\|___:\|::\|:\|:____\|\|\|\|\|:\n______________UACUUAC__AAGCAAC___GUUAGAAC___UUGUUAG___GGGUAGAG____AGGGGU\n3'-AUU...UUCAU_______CG__________________CGU_______CAU________AAUA______AAAGA...CAA-5'\n_____________\|__________________________________________________________\|\n_____________89_________________________________________________________37\n	242 -- 248	59 -- 65	-36.6264 kcal/mol	9.40493 kcal/mol	14.3562 kcal/mol	230 264@LB@ \| \|@LB@5'-GGG...AGAUC CA GUA UU U CAAGC...GUU-3'@LB@ AUGAGUG UUUGUUG UGGUUUUG GACGAUC UCUGUUUU UCCCCG@LB@ \|\|\|\|:\|\| \|\|:\|\|\|\| :::\|:\|\|\| :\|\|:\|\|\| :\|::\|:\|: \|\|\|\|\|:@LB@ UACUUAC AAGCAAC GUUAGAAC UUGUUAG GGGUAGAG AGGGGU@LB@3'-AUU...UUCAU CG CGU CAU AAUA AAAGA...CAA-5'@LB@ \| \|@LB@ 89 37@LB@@LB@@LB@Energy -14.36 kcal/mol@LB@Hybridization Energy -36.6264 kcal/mol@LB@Unfolding Energy - mRNA 9.40493 kcal/mol@LB@Unfolding Energy - sRNA 14.3562 kcal/mol@LB@@LB@Position - mRNA 231 -- 263@LB@Position - sRNA 38 -- 88@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 59 -- 65@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)

Job resubmission

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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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