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
92	0.007313	0.2652	bsu34470	yveA	-16.72	0.013215	240 -- 265	25 -- 47	aspartate-proton symporter	_____________239________________________266\n_____________\|__________________________\|\n5'-CCU...CGCUG___________UUU__UU___A____AGCCA...UCA-3'\n______________UUUGAUCUGAU___GA__GGG_UGGG\n______________:\|\|\|\|\|\|\|\|\|\|___\|\|__\|\|\|_\|\|\|\|\n______________GAACUAGACUA___CU__CCC_ACCC\n3'-UUU...GCCUA___________U____C____A____CUUGU...AUA-5'\n_____________\|__________________________\|\n_____________48_________________________24\n	244 -- 250	37 -- 43	-24.6158 kcal/mol	6.92071 kcal/mol	0.975871 kcal/mol	239 266@LB@ \| \|@LB@5'-CCU...CGCUG UUU UU A AGCCA...UCA-3'@LB@ UUUGAUCUGAU GA GGG UGGG@LB@ :\|\|\|\|\|\|\|\|\|\| \|\| \|\|\| \|\|\|\|@LB@ GAACUAGACUA CU CCC ACCC@LB@3'-UUU...GCCUA U C A CUUGU...AUA-5'@LB@ \| \|@LB@ 48 24@LB@@LB@@LB@Energy -16.72 kcal/mol@LB@Hybridization Energy -24.6158 kcal/mol@LB@Unfolding Energy - mRNA 6.92071 kcal/mol@LB@Unfolding Energy - sRNA 0.975871 kcal/mol@LB@@LB@Position - mRNA 240 -- 265@LB@Position - sRNA 25 -- 47@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 37 -- 43@LB@
23	0.0004941	0.06638	bsu00930	cysE	-16.71	0.013304	161 -- 195	22 -- 53	serine acetyltransferase	_____________160_________________________________196\n_____________\|___________________________________\|\n5'-CCU...UUUUA______AGAG__AA__A_______AAACG______AGCAU...UAC-3'\n______________UUGGGU____GA__UC_GAUAGAG_____GGGGGA\n______________\|:\|\|:\|____\|\|__\|\|_\|\|\|\|\|\|\|_____\|\|\|\|:\|\n______________AGCCUA____CU__AG_CUAUCUC_____CCCCUU\n3'-UUU...AAAAA______GAA_______A_______CCCAA______GUCUC...AUA-5'\n_____________\|___________________________________\|\n_____________54__________________________________21\n	178 -- 184	33 -- 39	-24.9399 kcal/mol	6.34776 kcal/mol	1.88616 kcal/mol	160 196@LB@ \| \|@LB@5'-CCU...UUUUA AGAG AA A AAACG AGCAU...UAC-3'@LB@ UUGGGU GA UC GAUAGAG GGGGGA@LB@ \|:\|\|:\| \|\| \|\| \|\|\|\|\|\|\| \|\|\|\|:\|@LB@ AGCCUA CU AG CUAUCUC CCCCUU@LB@3'-UUU...AAAAA GAA A CCCAA GUCUC...AUA-5'@LB@ \| \|@LB@ 54 21@LB@@LB@@LB@Energy -16.71 kcal/mol@LB@Hybridization Energy -24.9399 kcal/mol@LB@Unfolding Energy - mRNA 6.34776 kcal/mol@LB@Unfolding Energy - sRNA 1.88616 kcal/mol@LB@@LB@Position - mRNA 161 -- 195@LB@Position - sRNA 22 -- 53@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 33 -- 39@LB@
10	0.0001049	0.035	bsu34190	yvfH	-16.62	0.013859	188 -- 201	23 -- 36	L-lactate permease	_____________187____________202\n_____________\|______________\|\n5'-UGG...UUCAA_________U____UGCAA...CGA-3'\n______________GGAGGGGUU_GGGA\n______________:\|\|\|\|\|\|\|\|_\|\|\|\|\n______________UCUCCCCAA_CCCU\n3'-UUU...GACUA_________C____UGUCU...AUA-5'\n_____________\|______________\|\n_____________37_____________22\n	190 -- 196	28 -- 34	-23.4111 kcal/mol	6.64684 kcal/mol	0.139628 kcal/mol	187 202@LB@ \| \|@LB@5'-UGG...UUCAA U UGCAA...CGA-3'@LB@ GGAGGGGUU GGGA@LB@ :\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UCUCCCCAA CCCU@LB@3'-UUU...GACUA C UGUCU...AUA-5'@LB@ \| \|@LB@ 37 22@LB@@LB@@LB@Energy -16.62 kcal/mol@LB@Hybridization Energy -23.4111 kcal/mol@LB@Unfolding Energy - mRNA 6.64684 kcal/mol@LB@Unfolding Energy - sRNA 0.139628 kcal/mol@LB@@LB@Position - mRNA 188 -- 201@LB@Position - sRNA 23 -- 36@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 28 -- 34@LB@
62	0.003827	0.2059	bsu11360	appD	-16.60	0.014008	157 -- 196	21 -- 48	oligopeptide transport ATP-binding protein AppD	_____________156______________________________________197\n_____________\|________________________________________\|\n5'-AUG...CUUUC______AAACG_____CAACA_______GGAAA_______UAGCA...AAG-3'\n______________UCUUGA_____UUUGA_____AGAGGGG_____GGGGAGC\n______________\|\|\|\|\|\|_____\|:\|\|\|_____\|\|\|\|\|\|\|_____\|\|\|\|\|:\|\n______________AGAACU_____AGACU_____UCUCCCC_____CCCCUUG\n3'-UUU...AGCCU________________A___________AA__________UCUCU...AUA-5'\n_____________\|________________________________________\|\n_____________49_______________________________________20\n	190 -- 196	21 -- 27	-30.7931 kcal/mol	11.4214 kcal/mol	2.76831 kcal/mol	156 197@LB@ \| \|@LB@5'-AUG...CUUUC AAACG CAACA GGAAA UAGCA...AAG-3'@LB@ UCUUGA UUUGA AGAGGGG GGGGAGC@LB@ \|\|\|\|\|\| \|:\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|:\|@LB@ AGAACU AGACU UCUCCCC CCCCUUG@LB@3'-UUU...AGCCU A AA UCUCU...AUA-5'@LB@ \| \|@LB@ 49 20@LB@@LB@@LB@Energy -16.60 kcal/mol@LB@Hybridization Energy -30.7931 kcal/mol@LB@Unfolding Energy - mRNA 11.4214 kcal/mol@LB@Unfolding Energy - sRNA 2.76831 kcal/mol@LB@@LB@Position - mRNA 157 -- 196@LB@Position - sRNA 21 -- 48@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 21 -- 27@LB@
39	0.001675	0.1432	bsu23240	ypzK	-16.45	0.015090	173 -- 197	28 -- 52	riboflavin biosynthesis protein RibT	_____________172_________________________198\n_____________\|___________________________\|\n5'-GCG...CAGAC____CA______AU_____________UUUAU...UUA-3'\n______________UGGA__UUUUGG____AUAGAGGGGUU\n______________:\|\|\|__\|:\|\|\|:____\|\|\|\|\|\|\|\|\|\|\|\n______________GCCU__AGAACU____UAUCUCCCCAA\n3'-UUU...AAAAA____________AGAC___________CCCCU...AUA-5'\n_____________\|___________________________\|\n_____________53__________________________27\n	191 -- 197	28 -- 34	-23.4842 kcal/mol	6.04944 kcal/mol	0.980555 kcal/mol	172 198@LB@ \| \|@LB@5'-GCG...CAGAC CA AU UUUAU...UUA-3'@LB@ UGGA UUUUGG AUAGAGGGGUU@LB@ :\|\|\| \|:\|\|\|: \|\|\|\|\|\|\|\|\|\|\|@LB@ GCCU AGAACU UAUCUCCCCAA@LB@3'-UUU...AAAAA AGAC CCCCU...AUA-5'@LB@ \| \|@LB@ 53 27@LB@@LB@@LB@Energy -16.45 kcal/mol@LB@Hybridization Energy -23.4842 kcal/mol@LB@Unfolding Energy - mRNA 6.04944 kcal/mol@LB@Unfolding Energy - sRNA 0.980555 kcal/mol@LB@@LB@Position - mRNA 173 -- 197@LB@Position - sRNA 28 -- 52@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 28 -- 34@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@
19	0.0003652	0.06216	bsu29920	ytmP	-16.30	0.016289	3 -- 31	25 -- 51	phosphotransferase YtmP	_____________2_____________________________32\n_____________\|_____________________________\|\n_________5'-AU_____GAACA______U__ACU_______ACAAU...GUA-3'\n______________GGGUU_____UUGAUA_GA___GGUUGGG\n______________\|\|:\|:_____:\|\|\|\|\|_\|\|___\|\|\|\|\|\|\|\n______________CCUAG_____GACUAU_CU___CCAACCC\n3'-UUU...AAAAG_____AACUA_________CC________CUUGU...AUA-5'\n_____________\|_____________________________\|\n_____________52____________________________24\n	25 -- 31	25 -- 31	-23.4751 kcal/mol	6.19942 kcal/mol	0.976067 kcal/mol	2 32@LB@ \| \|@LB@ 5'-AU GAACA U ACU ACAAU...GUA-3'@LB@ GGGUU UUGAUA GA GGUUGGG@LB@ \|\|:\|: :\|\|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ CCUAG GACUAU CU CCAACCC@LB@3'-UUU...AAAAG AACUA CC CUUGU...AUA-5'@LB@ \| \|@LB@ 52 24@LB@@LB@@LB@Energy -16.30 kcal/mol@LB@Hybridization Energy -23.4751 kcal/mol@LB@Unfolding Energy - mRNA 6.19942 kcal/mol@LB@Unfolding Energy - sRNA 0.976067 kcal/mol@LB@@LB@Position - mRNA 3 -- 31@LB@Position - sRNA 25 -- 51@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 25 -- 31@LB@
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@
21	0.0003947	0.0627	bsu28260	leuC	-16.01	0.018761	166 -- 191	26 -- 52	3-isopropylmalate dehydratase large subunit	_____________165___________________________192\n_____________\|_____________________________\|\n5'-GAA...UUAAG________A_C___A_________A____AAAUA...UUC-3'\n______________CGG_UCUU_G_UCU_GGUAGAGGG___GG\n______________\|\|\|_\|\|\|\|_\|_\|\|\|_\|:\|\|\|\|\|\|\|___\|\|\n______________GCC_AGAA_C_AGA_CUAUCUCCC___CC\n3'-UUU...AAAAA___U______U_____________CAA__CCUUG...AUA-5'\n_____________\|_____________________________\|\n_____________53____________________________25\n	182 -- 188	31 -- 37	-26.3594 kcal/mol	9.36849 kcal/mol	0.980817 kcal/mol	165 192@LB@ \| \|@LB@5'-GAA...UUAAG A C A A AAAUA...UUC-3'@LB@ CGG UCUU G UCU GGUAGAGGG GG@LB@ \|\|\| \|\|\|\| \| \|\|\| \|:\|\|\|\|\|\|\| \|\|@LB@ GCC AGAA C AGA CUAUCUCCC CC@LB@3'-UUU...AAAAA U U CAA CCUUG...AUA-5'@LB@ \| \|@LB@ 53 25@LB@@LB@@LB@Energy -16.01 kcal/mol@LB@Hybridization Energy -26.3594 kcal/mol@LB@Unfolding Energy - mRNA 9.36849 kcal/mol@LB@Unfolding Energy - sRNA 0.980817 kcal/mol@LB@@LB@Position - mRNA 166 -- 191@LB@Position - sRNA 26 -- 52@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 31 -- 37@LB@
163	0.01533	0.3122	bsu19639	yoyE	-15.95	0.019304	185 -- 198	25 -- 39	Evidence 4: Homologs of previously reported genes of unknown function	_____________184_____________199\n_____________\|_______________\|\n5'-UCA...CGCAG__A____________ACAUG...AAU-3'\n______________GA_GGAGGGGU_GGG\n______________\|\|_:\|\|\|\|\|\|\|_\|\|\|\n______________CU_UCUCCCCA_CCC\n3'-UUU...CUAGA__A________A___CUUGU...AUA-5'\n_____________\|_______________\|\n_____________40______________24\n	189 -- 195	29 -- 35	-22.4813 kcal/mol	5.74668 kcal/mol	0.783603 kcal/mol	184 199@LB@ \| \|@LB@5'-UCA...CGCAG A ACAUG...AAU-3'@LB@ GA GGAGGGGU GGG@LB@ \|\| :\|\|\|\|\|\|\| \|\|\|@LB@ CU UCUCCCCA CCC@LB@3'-UUU...CUAGA A A CUUGU...AUA-5'@LB@ \| \|@LB@ 40 24@LB@@LB@@LB@Energy -15.95 kcal/mol@LB@Hybridization Energy -22.4813 kcal/mol@LB@Unfolding Energy - mRNA 5.74668 kcal/mol@LB@Unfolding Energy - sRNA 0.783603 kcal/mol@LB@@LB@Position - mRNA 185 -- 198@LB@Position - sRNA 25 -- 39@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 29 -- 35@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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