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
81	0.005945	0.2448	bsu06390	yebD	-16.11	0.017881	267 -- 291	30 -- 53	Evidence 5: No homology to any previously reported sequences		_____________266_______________________292\n_____________\|_________________________\|\n5'-UUU...UGCUC_____A___U___AA__A_______AACAG...UUG-3'\n______________UCGGA_UUU_AUC__GG_AGAGGGG\n______________\|\|\|\|\|_:\|\|_\|\|\|__\|:_\|\|\|\|\|\|\|\n______________AGCCU_GAA_UAG__CU_UCUCCCC\n3'-UUU...AAAAA_____A___C___A___A_______AACCC...AUA-5'\n_____________\|_________________________\|\n_____________54________________________29\n	285 -- 291	30 -- 36	-22.0812 kcal/mol	4.98677 kcal/mol	0.985344 kcal/mol	266 292@LB@ \| \|@LB@5'-UUU...UGCUC A U AA A AACAG...UUG-3'@LB@ UCGGA UUU AUC GG AGAGGGG@LB@ \|\|\|\|\| :\|\| \|\|\| \|: \|\|\|\|\|\|\|@LB@ AGCCU GAA UAG CU UCUCCCC@LB@3'-UUU...AAAAA A C A A AACCC...AUA-5'@LB@ \| \|@LB@ 54 29@LB@@LB@@LB@Energy -16.11 kcal/mol@LB@Hybridization Energy -22.0812 kcal/mol@LB@Unfolding Energy - mRNA 4.98677 kcal/mol@LB@Unfolding Energy - sRNA 0.985344 kcal/mol@LB@@LB@Position - mRNA 267 -- 291@LB@Position - sRNA 30 -- 53@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 30 -- 36@LB@
162	0.01461	0.3008	bsu28700	ysfE	-18.20	0.006050	31 -- 59	26 -- 51	Evidence 5: No homology to any previously reported sequences	bsu26940	_____________30____________________________60\n_____________\|_____________________________\|\n5'-AAG...UAGAA___CUA____AAA__CUG___________CAAUG...AAA-3'\n______________GGA___UUGA___UG___AGAGGGGUUGG\n______________\|\|\|___\|\|\|\|___\|\|___\|\|\|\|\|\|\|\|\|\|\|\n______________CCU___AACU___AC___UCUCCCCAACC\n3'-UUU...AAAAG___AG_____AG___UA____________CCUUG...AUA-5'\n_____________\|_____________________________\|\n_____________52____________________________25\n	53 -- 59	26 -- 32	-27.3955 kcal/mol	8.22133 kcal/mol	0.975822 kcal/mol	30 60@LB@ \| \|@LB@5'-AAG...UAGAA CUA AAA CUG CAAUG...AAA-3'@LB@ GGA UUGA UG AGAGGGGUUGG@LB@ \|\|\| \|\|\|\| \|\| \|\|\|\|\|\|\|\|\|\|\|@LB@ CCU AACU AC UCUCCCCAACC@LB@3'-UUU...AAAAG AG AG UA CCUUG...AUA-5'@LB@ \| \|@LB@ 52 25@LB@@LB@@LB@Energy -18.20 kcal/mol@LB@Hybridization Energy -27.3955 kcal/mol@LB@Unfolding Energy - mRNA 8.22133 kcal/mol@LB@Unfolding Energy - sRNA 0.975822 kcal/mol@LB@@LB@Position - mRNA 31 -- 59@LB@Position - sRNA 26 -- 51@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 26 -- 32@LB@
49	0.002227	0.1516	bsu11839	yjzE	-19.04	0.003744	170 -- 194	25 -- 51	Evidence 5: No homology to any previously reported sequences; PubMedId: 11976315		_____________169_________________________195\n_____________\|___________________________\|\n5'-UCC...UUAAG___AAA___GACAGC____________UAUUG...GCU-3'\n______________GGA____GA______AGAGGGGU_GGG\n______________\|\|\|____\|\|______\|\|\|\|\|\|\|\|_\|\|\|\n______________CCU____CU______UCUCCCCA_CCC\n3'-UUU...AAAAG___AGAA__AGACUA________A___CUUGU...AUA-5'\n_____________\|___________________________\|\n_____________52__________________________24\n	185 -- 191	29 -- 35	-23.53 kcal/mol	3.51134 kcal/mol	0.976067 kcal/mol	169 195@LB@ \| \|@LB@5'-UCC...UUAAG AAA GACAGC UAUUG...GCU-3'@LB@ GGA GA AGAGGGGU GGG@LB@ \|\|\| \|\| \|\|\|\|\|\|\|\| \|\|\|@LB@ CCU CU UCUCCCCA CCC@LB@3'-UUU...AAAAG AGAA AGACUA A CUUGU...AUA-5'@LB@ \| \|@LB@ 52 24@LB@@LB@@LB@Energy -19.04 kcal/mol@LB@Hybridization Energy -23.53 kcal/mol@LB@Unfolding Energy - mRNA 3.51134 kcal/mol@LB@Unfolding Energy - sRNA 0.976067 kcal/mol@LB@@LB@Position - mRNA 170 -- 194@LB@Position - sRNA 25 -- 51@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 29 -- 35@LB@
189	0.01911	0.3269	bsu24290	xseB	-12.91	0.073825	187 -- 193	30 -- 36	exodeoxyribonuclease 7 small subunit		_____________186_____194\n_____________\|_______\|\n5'-CAU...AAAAG_______AAGAA...UAG-3'\n______________AGAGGGG\n______________\|\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	187 -- 193	30 -- 36	-14.0184 kcal/mol	0.973532 kcal/mol	0.133643 kcal/mol	186 194@LB@ \| \|@LB@5'-CAU...AAAAG AAGAA...UAG-3'@LB@ AGAGGGG@LB@ \|\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -12.91 kcal/mol@LB@Hybridization Energy -14.0184 kcal/mol@LB@Unfolding Energy - mRNA 0.973532 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 187 -- 193@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 30 -- 36@LB@
148	0.01313	0.296	bsu02100	cypC	-16.43	0.015277	151 -- 198	11 -- 53	fatty-acid peroxygenase		_____________150______________________________________________199\n_____________\|________________________________________________\|\n5'-CAA...UAUAG_____AGAUAACG___AAA_______UAAAAA____G_C_____A___GGAUG...AUU-3'\n______________UCGGA________UGA___UAGAGGG______GGAA_G_AGGGU_AGC\n______________\|\|\|\|\|________\|\|\|___\|\|\|\|\|\|\|______\|\|\|\|_:_\|\|:\|\|_\|\|\|\n______________AGCCU________ACU___AUCUCCC______CCUU_U_UCUCA_UCG\n3'-UUU...AAAAA_____AGAACUAG_____________CAACC_____G_C_________AAGAG...AUA-5'\n_____________\|________________________________________________\|\n_____________54_______________________________________________10\n	170 -- 176	31 -- 37	-31.9294 kcal/mol	5.5363 kcal/mol	9.96369 kcal/mol	150 199@LB@ \| \|@LB@5'-CAA...UAUAG AGAUAACG AAA UAAAAA G C A GGAUG...AUU-3'@LB@ UCGGA UGA UAGAGGG GGAA G AGGGU AGC@LB@ \|\|\|\|\| \|\|\| \|\|\|\|\|\|\| \|\|\|\| : \|\|:\|\| \|\|\|@LB@ AGCCU ACU AUCUCCC CCUU U UCUCA UCG@LB@3'-UUU...AAAAA AGAACUAG CAACC G C AAGAG...AUA-5'@LB@ \| \|@LB@ 54 10@LB@@LB@@LB@Energy -16.43 kcal/mol@LB@Hybridization Energy -31.9294 kcal/mol@LB@Unfolding Energy - mRNA 5.5363 kcal/mol@LB@Unfolding Energy - sRNA 9.96369 kcal/mol@LB@@LB@Position - mRNA 151 -- 198@LB@Position - sRNA 11 -- 53@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 31 -- 37@LB@
158	0.01436	0.3008	bsu10130	hemH	-12.69	0.080628	178 -- 227	6 -- 44	ferrochelatase		_____________177____________________________________________________228\n_____________\|______________________________________________________\|\n5'-GAG...UAUCA____AUUAA______U__A_________U____AGAAAGAAAAUGG________GUGAU...GAA-3'\n______________GAUC_____AGAGGG_GU_____AACAG_GAGU_____________GGCUUCUC\n______________\|\|\|\|_____\|\|\|\|\|\|_\|\|_____\|\|\|\|\|_\|\|\|\|_____________:\|\|\|\|\|\|\|\n______________CUAG_____UCUCCC_CA_____UUGUC_CUCA_____________UCGAAGAG\n3'-UUU...UAGAA____ACUA__________ACCCC_____U_________________________AGAUA-5'\n_____________\|______________________________________________________\|\n_____________45_____________________________________________________5\n	220 -- 226	7 -- 13	-32.766 kcal/mol	10.122 kcal/mol	9.95356 kcal/mol	177 228@LB@ \| \|@LB@5'-GAG...UAUCA AUUAA U A U AGAAAGAAAAUGG GUGAU...GAA-3'@LB@ GAUC AGAGGG GU AACAG GAGU GGCUUCUC@LB@ \|\|\|\| \|\|\|\|\|\| \|\| \|\|\|\|\| \|\|\|\| :\|\|\|\|\|\|\|@LB@ CUAG UCUCCC CA UUGUC CUCA UCGAAGAG@LB@3'-UUU...UAGAA ACUA ACCCC U AGAUA-5'@LB@ \| \|@LB@ 45 5@LB@@LB@@LB@Energy -12.69 kcal/mol@LB@Hybridization Energy -32.766 kcal/mol@LB@Unfolding Energy - mRNA 10.122 kcal/mol@LB@Unfolding Energy - sRNA 9.95356 kcal/mol@LB@@LB@Position - mRNA 178 -- 227@LB@Position - sRNA 6 -- 44@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 7 -- 13@LB@
126	0.0111	0.2883	bsu16220	fliG	-14.68	0.034861	264 -- 293	1 -- 29	flagellar motor switch protein FliG		_____________263_____________________________294\n_____________\|_______________________________\|\n5'-GGG...UUUCC______U_____U_U__C_______G_____AAGCACU-3'\n______________UUGGGG__UAGA_G_GU_AGCUUCU_UCUAU\n______________\|\|\|\|\|\|__:\|\|\|_\|_\|\|_\|\|\|\|\|\|\|_\|\|\|\|\|\n______________AACCCC__GUCU_C_CA_UCGAAGA_AGAUA\n3'-UUU...UCCCC______UU______U__________G_____-5'\n_____________\|______________________________\|\n_____________30_____________________________1\n	281 -- 287	7 -- 13	-31.0613 kcal/mol	7.38869 kcal/mol	8.9939 kcal/mol	263 294@LB@ \| \|@LB@5'-GGG...UUUCC U U U C G AAGCACU-3'@LB@ UUGGGG UAGA G GU AGCUUCU UCUAU@LB@ \|\|\|\|\|\| :\|\|\| \| \|\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ AACCCC GUCU C CA UCGAAGA AGAUA@LB@3'-UUU...UCCCC UU U G -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -14.68 kcal/mol@LB@Hybridization Energy -31.0613 kcal/mol@LB@Unfolding Energy - mRNA 7.38869 kcal/mol@LB@Unfolding Energy - sRNA 8.9939 kcal/mol@LB@@LB@Position - mRNA 264 -- 293@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 7 -- 13@LB@
168	0.01631	0.3152	bsu14170	ykuP	-12.43	0.089417	80 -- 100	11 -- 27	flavodoxin-2		_____________79____________________101\n_____________\|_____________________\|\n5'-CAC...AUUAA___ACAU______________CAAUC...UAG-3'\n______________GGG____GGAUGGAGAGUGGC\n______________\|\|\|____\|:\|::\|\|\|\|\|\|:\|\|\n______________CCC____CUUGUCUCUCAUCG\n3'-UUU...CCCAA_____________________AAGAG...AUA-5'\n_____________\|_____________________\|\n_____________28____________________10\n	94 -- 100	11 -- 17	-24.7716 kcal/mol	6.31596 kcal/mol	6.0284 kcal/mol	79 101@LB@ \| \|@LB@5'-CAC...AUUAA ACAU CAAUC...UAG-3'@LB@ GGG GGAUGGAGAGUGGC@LB@ \|\|\| \|:\|::\|\|\|\|\|\|:\|\|@LB@ CCC CUUGUCUCUCAUCG@LB@3'-UUU...CCCAA AAGAG...AUA-5'@LB@ \| \|@LB@ 28 10@LB@@LB@@LB@Energy -12.43 kcal/mol@LB@Hybridization Energy -24.7716 kcal/mol@LB@Unfolding Energy - mRNA 6.31596 kcal/mol@LB@Unfolding Energy - sRNA 6.0284 kcal/mol@LB@@LB@Position - mRNA 80 -- 100@LB@Position - sRNA 11 -- 27@LB@Position Seed - mRNA 94 -- 100@LB@Position Seed - sRNA 11 -- 17@LB@
166	0.01583	0.3152	bsu38190	galT	-8.42	0.343831	170 -- 181	16 -- 26	galactose-1-phosphate uridylyltransferase		_____________169__________182\n_____________\|____________\|\n5'-GGG...GGAGA_______A____ACUAA...AUG-3'\n______________GGGAGCG_GAGA\n______________\|\|\|\|:\|:_\|\|\|\|\n______________CCCUUGU_CUCU\n3'-UUU...CCAAC____________CAUCG...AUA-5'\n_____________\|____________\|\n_____________27___________15\n	170 -- 176	20 -- 26	-15.5563 kcal/mol	1.12924 kcal/mol	6.00672 kcal/mol	169 182@LB@ \| \|@LB@5'-GGG...GGAGA A ACUAA...AUG-3'@LB@ GGGAGCG GAGA@LB@ \|\|\|\|:\|: \|\|\|\|@LB@ CCCUUGU CUCU@LB@3'-UUU...CCAAC CAUCG...AUA-5'@LB@ \| \|@LB@ 27 15@LB@@LB@@LB@Energy -8.42 kcal/mol@LB@Hybridization Energy -15.5563 kcal/mol@LB@Unfolding Energy - mRNA 1.12924 kcal/mol@LB@Unfolding Energy - sRNA 6.00672 kcal/mol@LB@@LB@Position - mRNA 170 -- 181@LB@Position - sRNA 16 -- 26@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 20 -- 26@LB@
169	0.01639	0.3152	bsu07850	yfkM	-11.33	0.135062	186 -- 208	22 -- 34	general stress protein 18		_____________185_____________________209\n_____________\|_______________________\|\n5'-UGU...AAAGC___A___UAUGAAUCA_______AAAAA...CUG-3'\n______________GGG_GGU_________UGGGGAA\n______________:\|\|_\|\|\|_________\|\|\|\|\|\|\|\n______________UCC_CCA_________ACCCCUU\n3'-UUU...CUAUC_______________________GUCUC...AUA-5'\n_____________\|_______________________\|\n_____________35______________________21\n	202 -- 208	22 -- 28	-15.0114 kcal/mol	2.66027 kcal/mol	1.02154 kcal/mol	185 209@LB@ \| \|@LB@5'-UGU...AAAGC A UAUGAAUCA AAAAA...CUG-3'@LB@ GGG GGU UGGGGAA@LB@ :\|\| \|\|\| \|\|\|\|\|\|\|@LB@ UCC CCA ACCCCUU@LB@3'-UUU...CUAUC GUCUC...AUA-5'@LB@ \| \|@LB@ 35 21@LB@@LB@@LB@Energy -11.33 kcal/mol@LB@Hybridization Energy -15.0114 kcal/mol@LB@Unfolding Energy - mRNA 2.66027 kcal/mol@LB@Unfolding Energy - sRNA 1.02154 kcal/mol@LB@@LB@Position - mRNA 186 -- 208@LB@Position - sRNA 22 -- 34@LB@Position Seed - mRNA 202 -- 208@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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