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	Additional homologs
63	0.001974	0.1214	bsu34640	yvdD	-9.92	0.323853	41 -- 65	33 -- 60	LOG family protein YvdD		_____________40___________________________66\n_____________\|____________________________\|\n5'-GAC...GUAAA______UCAUCCAUUUUUCUG_______CAGCU...GAA-3'\n______________ACUCUU_______________CAUCAGC\n______________\|\|\|\|\|\|_______________\|\|\|\|\|:\|\n______________UGAGAA_______________GUAGUUG\n3'-AUU...AAAAA____________________________UCCUG...CAA-5'\n_____________\|____________________________\|\n_____________61___________________________32\n	69 -- 75	156 -- 162	-11.7297 kcal/mol	2.56294 kcal/mol	1.40592 kcal/mol	40 66@LB@ \| \|@LB@5'-GAC...GUAAA UCAUCCAUUUUUCUG CAGCU...GAA-3'@LB@ ACUCUU CAUCAGC@LB@ \|\|\|\|\|\| \|\|\|\|\|:\|@LB@ UGAGAA GUAGUUG@LB@3'-AUU...AAAAA UCCUG...CAA-5'@LB@ \| \|@LB@ 61 32@LB@@LB@@LB@Energy -9.92 kcal/mol@LB@Hybridization Energy -11.7297 kcal/mol@LB@Unfolding Energy - mRNA 2.56294 kcal/mol@LB@Unfolding Energy - sRNA 1.40592 kcal/mol@LB@@LB@Position - mRNA 41 -- 65@LB@Position - sRNA 33 -- 60@LB@Position Seed - mRNA 69 -- 75@LB@Position Seed - sRNA 156 -- 162@LB@
99	0.004027	0.1561	bsu13870	ykvZ	-9.91	0.324242	1 -- 15	1 -- 17	LacI family transcriptional regulator		______________1________________16\n______________\|________________\|\n___________5'-__________A______UUUGG...GAA-3'\n______________GUUUAAUUUC___UGUU\n______________\|:\|\|\|\|\|\|\|\|___\|\|\|\|\n______________CGAAUUAAAG___ACAA\n3'-AUU...UUUUG__________AAA____-5'\n_____________\|________________\|\n_____________18_______________1\n	4 -- 10	8 -- 14	-10.8546 kcal/mol	0.387335 kcal/mol	1.29438 kcal/mol	1 16@LB@ \| \|@LB@ 5'- A UUUGG...GAA-3'@LB@ GUUUAAUUUC UGUU@LB@ \|:\|\|\|\|\|\|\|\| \|\|\|\|@LB@ CGAAUUAAAG ACAA@LB@3'-AUU...UUUUG AAA -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -9.91 kcal/mol@LB@Hybridization Energy -10.8546 kcal/mol@LB@Unfolding Energy - mRNA 0.387335 kcal/mol@LB@Unfolding Energy - sRNA 1.29438 kcal/mol@LB@@LB@Position - mRNA 1 -- 15@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 4 -- 10@LB@Position Seed - sRNA 8 -- 14@LB@
50	0.001627	0.1212	bsu38130	ywcE	-9.91	0.324646	1 -- 15	39 -- 56	spore morphogenesis and germination protein YwcE		_____________0_______________________________________________________________16\n_____________\|_______________________________________________________________\|\n5'-GCC...AAAAA_____ACA______________A__A___A______U____________UU____U_______AUCAC...CAA-3'\n______________CAAUC_____AAACAG____AC_CA_CUC__GUUCC_CUAUUUC____A__UUUG_AAACGUU\n______________\|\|\|\|\|_____\|\|\|\|\|:____\|\|_\|\|_\|\|\|__:\|\|\|\|_\|:\|\|\|\|\|____\|__\|\|\|\|_\|\|\|\|\|:\|\n______________GUUAG_____UUUGUU____UG_GU_GAG__UAAGG_GGUAAAG____U__AAAC_UUUGCGA\n3'-AUU...GCAAC_____AACCG______AGCA__G__A___AA_____________AAAC_UU____U_______AUUAA...CAA-5'\n_____________\|_______________________________________________________________\|\n_____________57______________________________________________________________38\n	170 -- 176	15 -- 21	-29.8413 kcal/mol	5.55001 kcal/mol	15.9749 kcal/mol	0 16@LB@ \| \|@LB@5'-GCC...AAAAA ACA A A A U UU U AUCAC...CAA-3'@LB@ CAAUC AAACAG AC CA CUC GUUCC CUAUUUC A UUUG AAACGUU@LB@ \|\|\|\|\| \|\|\|\|\|: \|\| \|\| \|\|\| :\|\|\|\| \|:\|\|\|\|\| \| \|\|\|\| \|\|\|\|\|:\|@LB@ GUUAG UUUGUU UG GU GAG UAAGG GGUAAAG U AAAC UUUGCGA@LB@3'-AUU...GCAAC AACCG AGCA G A AA AAAC UU U AUUAA...CAA-5'@LB@ \| \|@LB@ 57 38@LB@@LB@@LB@Energy -9.91 kcal/mol@LB@Hybridization Energy -29.8413 kcal/mol@LB@Unfolding Energy - mRNA 5.55001 kcal/mol@LB@Unfolding Energy - sRNA 15.9749 kcal/mol@LB@@LB@Position - mRNA 1 -- 15@LB@Position - sRNA 39 -- 56@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 15 -- 21@LB@
152	0.006831	0.1741	bsu09480	yhdI	-9.89	0.327778	76 -- 101	102 -- 130	GntR family transcriptional regulator	bsu05240	_____________75__________________________102\n_____________\|___________________________\|\n5'-UCU...UAAUU___________A________C______AUCCC...CAA-3'\n______________GUUUCAUAUGG_____UCAU_UUCUCA\n______________\|\|\|:\|\|\|\|\|::_____\|\|\|:_\|\|\|\|\|\|\n______________CAAGGUAUAUU_____AGUG_AAGAGU\n3'-AUU...UCGUU___________ACAAC____A______AGAAG...CAA-5'\n_____________\|___________________________\|\n_____________131_________________________101\n	79 -- 85	121 -- 127	-18.1477 kcal/mol	2.87073 kcal/mol	6.25825 kcal/mol	75 102@LB@ \| \|@LB@5'-UCU...UAAUU A C AUCCC...CAA-3'@LB@ GUUUCAUAUGG UCAU UUCUCA@LB@ \|\|\|:\|\|\|\|\|:: \|\|\|: \|\|\|\|\|\|@LB@ CAAGGUAUAUU AGUG AAGAGU@LB@3'-AUU...UCGUU ACAAC A AGAAG...CAA-5'@LB@ \| \|@LB@ 131 101@LB@@LB@@LB@Energy -9.89 kcal/mol@LB@Hybridization Energy -18.1477 kcal/mol@LB@Unfolding Energy - mRNA 2.87073 kcal/mol@LB@Unfolding Energy - sRNA 6.25825 kcal/mol@LB@@LB@Position - mRNA 76 -- 101@LB@Position - sRNA 102 -- 130@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 121 -- 127@LB@
146	0.00677	0.1741	bsu29690	acuA	-9.85	0.331997	126 -- 137	14 -- 25	acetoin utilization protein AcuA		_____________125____________138\n_____________\|______________\|\n5'-UAU...AUUCA______________UUUUA...AUG-3'\n______________UAUUCUUC_UCAAU\n______________\|\|:\|\|\|\|\|_\|\|\|\|:\n______________AUGAGAAG_AGUUG\n3'-AUU...AAAAA________U_____UCCUG...CAA-5'\n_____________\|______________\|\n_____________26_____________13\n	95 -- 101	162 -- 168	-12.3213 kcal/mol	1.49895 kcal/mol	1.40683 kcal/mol	125 138@LB@ \| \|@LB@5'-UAU...AUUCA UUUUA...AUG-3'@LB@ UAUUCUUC UCAAU@LB@ \|\|:\|\|\|\|\| \|\|\|\|:@LB@ AUGAGAAG AGUUG@LB@3'-AUU...AAAAA U UCCUG...CAA-5'@LB@ \| \|@LB@ 26 13@LB@@LB@@LB@Energy -9.85 kcal/mol@LB@Hybridization Energy -12.3213 kcal/mol@LB@Unfolding Energy - mRNA 1.49895 kcal/mol@LB@Unfolding Energy - sRNA 1.40683 kcal/mol@LB@@LB@Position - mRNA 126 -- 137@LB@Position - sRNA 14 -- 25@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 162 -- 168@LB@
193	0.008782	0.1751	bsu13160	ohrB	-9.78	0.341127	32 -- 61	100 -- 129	organic hydroperoxide resistance protein OhrB		_____________31_________62\n_____________\|__________\|\n5'-CAU...GGACG__________AUUAC...AUG-3'\n______________AGCAGGACAU\n______________\|:\|\|\|\|\|\|\|\|\n______________UUGUCCUGUA\n3'-AUU...AGUAG__________ACUGU...CAA-5'\n_____________\|__________\|\n_____________130________99\n	245 -- 251	149 -- 155	-15.2334 kcal/mol	1.87143 kcal/mol	5.55277 kcal/mol	31 62@LB@ \| \|@LB@5'-CAU...GGACG AUUAC...AUG-3'@LB@ AGCAGGACAU@LB@ \|:\|\|\|\|\|\|\|\|@LB@ UUGUCCUGUA@LB@3'-AUU...AGUAG ACUGU...CAA-5'@LB@ \| \|@LB@ 130 99@LB@@LB@@LB@Energy -9.78 kcal/mol@LB@Hybridization Energy -15.2334 kcal/mol@LB@Unfolding Energy - mRNA 1.87143 kcal/mol@LB@Unfolding Energy - sRNA 5.55277 kcal/mol@LB@@LB@Position - mRNA 32 -- 61@LB@Position - sRNA 100 -- 129@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 149 -- 155@LB@
104	0.004338	0.1606	bsu08000	yfjQ	-9.77	0.342120	136 -- 162	103 -- 137	metal ion transporter YfjQ	bsu24740	_____________135_______________163\n_____________\|_________________\|\n5'-CAU...AUUAG____A____A_______CUUUU...AUU-3'\n______________GCAG_GAGU_CCGUAUA\n______________\|\|\|\|_:\|\|\|_\|\|:\|\|\|\|\n______________CGUC_UUCA_GGUAUAU\n3'-AUU...ACAGG____G____A_______UACAA...CAA-5'\n_____________\|_________________\|\n_____________138_______________102\n	146 -- 152	121 -- 127	-16.4629 kcal/mol	4.99509 kcal/mol	3.33887 kcal/mol	135 163@LB@ \| \|@LB@5'-CAU...AUUAG A A CUUUU...AUU-3'@LB@ GCAG GAGU CCGUAUA@LB@ \|\|\|\| :\|\|\| \|\|:\|\|\|\|@LB@ CGUC UUCA GGUAUAU@LB@3'-AUU...ACAGG G A UACAA...CAA-5'@LB@ \| \|@LB@ 138 102@LB@@LB@@LB@Energy -9.77 kcal/mol@LB@Hybridization Energy -16.4629 kcal/mol@LB@Unfolding Energy - mRNA 4.99509 kcal/mol@LB@Unfolding Energy - sRNA 3.33887 kcal/mol@LB@@LB@Position - mRNA 136 -- 162@LB@Position - sRNA 103 -- 137@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 121 -- 127@LB@
88	0.003231	0.1423	bsu34620	mdxD	-9.76	0.344052	128 -- 173	81 -- 130	glucan 1 4-alpha-maltohexaosidase		_____________127____________174\n_____________\|______________\|\n5'-GUU...AUGCA__GA_______C__GCCAU...GUG-3'\n______________GC__UUCAUCA_CA\n______________:\|__\|\|\|\|\|\|\|_\|\|\n______________UG__AAGUAGU_GU\n3'-AUU...AAAAA__AG_______U__CCUGU...CAA-5'\n_____________\|______________\|\n_____________131____________80\n	220 -- 226	158 -- 164	-10.4913 kcal/mol	1.73429 kcal/mol	1.41528 kcal/mol	127 174@LB@ \| \|@LB@5'-GUU...AUGCA GA C GCCAU...GUG-3'@LB@ GC UUCAUCA CA@LB@ :\| \|\|\|\|\|\|\| \|\|@LB@ UG AAGUAGU GU@LB@3'-AUU...AAAAA AG U CCUGU...CAA-5'@LB@ \| \|@LB@ 131 80@LB@@LB@@LB@Energy -9.76 kcal/mol@LB@Hybridization Energy -10.4913 kcal/mol@LB@Unfolding Energy - mRNA 1.73429 kcal/mol@LB@Unfolding Energy - sRNA 1.41528 kcal/mol@LB@@LB@Position - mRNA 128 -- 173@LB@Position - sRNA 81 -- 130@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 158 -- 164@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@
178	0.008149	0.1751	bsu39610	yxeB	-9.68	0.354141	1 -- 23	37 -- 58	iron(3+)-hydroxamate-binding protein YxeB	bsu33320	_____________0_______24\n_____________\|_______\|\n5'-GCA...UGUAA_______AUUUU...CUG-3'\n______________UUCCCAU\n______________\|:\|\|\|\|\|\n______________AGGGGUA\n3'-AUU...GAAUA_______AAGAA...CAA-5'\n_____________\|_______\|\n_____________59______36\n	17 -- 23	37 -- 43	-9.25042 kcal/mol	0.0358808 kcal/mol	2.53706 kcal/mol	0 24@LB@ \| \|@LB@5'-GCA...UGUAA AUUUU...CUG-3'@LB@ UUCCCAU@LB@ \|:\|\|\|\|\|@LB@ AGGGGUA@LB@3'-AUU...GAAUA AAGAA...CAA-5'@LB@ \| \|@LB@ 59 36@LB@@LB@@LB@Energy -9.68 kcal/mol@LB@Hybridization Energy -9.25042 kcal/mol@LB@Unfolding Energy - mRNA 0.0358808 kcal/mol@LB@Unfolding Energy - sRNA 2.53706 kcal/mol@LB@@LB@Position - mRNA 1 -- 23@LB@Position - sRNA 37 -- 58@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 37 -- 43@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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