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
45	0.002015	0.1494	bsu34040	yvfW	-14.27	0.041807	34 -- 68	10 -- 49	lactate utilization protein B	_____________33_______________________________________69\n_____________\|________________________________________\|\n5'-GCG...AAAAA___GA___G_________AAAC__________________GAUCG...GUC-3'\n______________GUC___AU_UG_UGGAGG_____GGGAGCAGAG_GU_GCU\n______________:\|\|___\|\|_\|\|_\|:\|\|\|\|_____\|\|\|\|:\|\|\|\|\|_\|\|_\|\|\|\n______________UAG___UA_AC_AUCUCC_____CCCUUGUCUC_CA_CGA\n3'-UUU...AAGCC___AAC__G__U______CCAAC__________U__U___AGAGA...AUA-5'\n_____________\|________________________________________\|\n_____________50_______________________________________9\n	55 -- 61	19 -- 25	-34.7578 kcal/mol	10.5343 kcal/mol	9.9558 kcal/mol	33 69@LB@ \| \|@LB@5'-GCG...AAAAA GA G AAAC GAUCG...GUC-3'@LB@ GUC AU UG UGGAGG GGGAGCAGAG GU GCU@LB@ :\|\| \|\| \|\| \|:\|\|\|\| \|\|\|\|:\|\|\|\|\| \|\| \|\|\|@LB@ UAG UA AC AUCUCC CCCUUGUCUC CA CGA@LB@3'-UUU...AAGCC AAC G U CCAAC U U AGAGA...AUA-5'@LB@ \| \|@LB@ 50 9@LB@@LB@@LB@Energy -14.27 kcal/mol@LB@Hybridization Energy -34.7578 kcal/mol@LB@Unfolding Energy - mRNA 10.5343 kcal/mol@LB@Unfolding Energy - sRNA 9.9558 kcal/mol@LB@@LB@Position - mRNA 34 -- 68@LB@Position - sRNA 10 -- 49@LB@Position Seed - mRNA 55 -- 61@LB@Position Seed - sRNA 19 -- 25@LB@
48	0.002156	0.1498	bsu34050	yvfV	-12.63	0.082536	177 -- 196	28 -- 46	lactate utilization protein A	_____________176__________________197\n_____________\|____________________\|\n5'-UCG...AUAUA____GGA___G_________CAUCA...UUG-3'\n______________UUGG___UGA_AGAGGGGUU\n______________\|\|\|:___\|\|\|_\|\|\|\|\|\|\|\|\|\n______________AACU___ACU_UCUCCCCAA\n3'-UUU...CCUAG____AG____A_________CCCCU...AUA-5'\n_____________\|____________________\|\n_____________47___________________27\n	190 -- 196	28 -- 34	-21.1804 kcal/mol	7.57881 kcal/mol	0.97023 kcal/mol	176 197@LB@ \| \|@LB@5'-UCG...AUAUA GGA G CAUCA...UUG-3'@LB@ UUGG UGA AGAGGGGUU@LB@ \|\|\|: \|\|\| \|\|\|\|\|\|\|\|\|@LB@ AACU ACU UCUCCCCAA@LB@3'-UUU...CCUAG AG A CCCCU...AUA-5'@LB@ \| \|@LB@ 47 27@LB@@LB@@LB@Energy -12.63 kcal/mol@LB@Hybridization Energy -21.1804 kcal/mol@LB@Unfolding Energy - mRNA 7.57881 kcal/mol@LB@Unfolding Energy - sRNA 0.97023 kcal/mol@LB@@LB@Position - mRNA 177 -- 196@LB@Position - sRNA 28 -- 46@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 28 -- 34@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@
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@
46	0.002102	0.1496	bsu35160	uvrA	-18.29	0.005742	210 -- 232	21 -- 44	UvrABC system protein A	_____________209______________________233\n_____________\|________________________\|\n5'-CAC...CUAUG____G________UGAA_______CAGGG...GUU-3'\n______________GAUC_GAUAGAGG_____GGGAGC\n______________\|\|\|\|_\|\|\|\|\|\|\|\|_____\|\|\|\|:\|\n______________CUAG_CUAUCUCC_____CCCUUG\n3'-UUU...UAGAA____A________CCAAC______UCUCU...AUA-5'\n_____________\|________________________\|\n_____________45_______________________20\n	216 -- 222	32 -- 38	-26.4443 kcal/mol	5.3846 kcal/mol	2.7671 kcal/mol	209 233@LB@ \| \|@LB@5'-CAC...CUAUG G UGAA CAGGG...GUU-3'@LB@ GAUC GAUAGAGG GGGAGC@LB@ \|\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|:\|@LB@ CUAG CUAUCUCC CCCUUG@LB@3'-UUU...UAGAA A CCAAC UCUCU...AUA-5'@LB@ \| \|@LB@ 45 20@LB@@LB@@LB@Energy -18.29 kcal/mol@LB@Hybridization Energy -26.4443 kcal/mol@LB@Unfolding Energy - mRNA 5.3846 kcal/mol@LB@Unfolding Energy - sRNA 2.7671 kcal/mol@LB@@LB@Position - mRNA 210 -- 232@LB@Position - sRNA 21 -- 44@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 32 -- 38@LB@
77	0.005688	0.2441	bsu35180	csbA	-19.97	0.002143	87 -- 126	11 -- 50	general stress protein CsbA	_____________86__________________________________________127\n_____________\|___________________________________________\|\n5'-UGA...UGAUU_____________AA_______A___U_U__G___________GAAUG...CAG-3'\n______________GAUUUUGG_CUGA___AGGGGU_UGG_G_AA_UAGAGGG_AGC\n______________\|\|\|:\|\|\|:_\|\|\|\|___\|\|\|\|\|\|_\|\|\|_\|_\|\|_:\|\|\|\|:\|_\|\|\|\n______________CUAGAACU_GACU___UCCCCA_ACC_C_UU_GUCUCUC_UCG\n3'-UUU...AAAGC________A____AUC____________C__________A___AAGAG...AUA-5'\n_____________\|___________________________________________\|\n_____________51__________________________________________10\n	117 -- 123	15 -- 21	-37.9995 kcal/mol	8.07502 kcal/mol	9.95602 kcal/mol	86 127@LB@ \| \|@LB@5'-UGA...UGAUU AA A U U G GAAUG...CAG-3'@LB@ GAUUUUGG CUGA AGGGGU UGG G AA UAGAGGG AGC@LB@ \|\|\|:\|\|\|: \|\|\|\| \|\|\|\|\|\| \|\|\| \| \|\| :\|\|\|\|:\| \|\|\|@LB@ CUAGAACU GACU UCCCCA ACC C UU GUCUCUC UCG@LB@3'-UUU...AAAGC A AUC C A AAGAG...AUA-5'@LB@ \| \|@LB@ 51 10@LB@@LB@@LB@Energy -19.97 kcal/mol@LB@Hybridization Energy -37.9995 kcal/mol@LB@Unfolding Energy - mRNA 8.07502 kcal/mol@LB@Unfolding Energy - sRNA 9.95602 kcal/mol@LB@@LB@Position - mRNA 87 -- 126@LB@Position - sRNA 11 -- 50@LB@Position Seed - mRNA 117 -- 123@LB@Position Seed - sRNA 15 -- 21@LB@
100	0.008436	0.2778	bsu35250	ftsX	-12.75	0.078592	182 -- 188	30 -- 36	cell division protein FtsX	_____________181_____189\n_____________\|_______\|\n5'-UGC...AGUCA_______AGUAU...CGC-3'\n______________AGAGGGG\n______________\|\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	182 -- 188	30 -- 36	-13.7147 kcal/mol	0.82624 kcal/mol	0.133643 kcal/mol	181 189@LB@ \| \|@LB@5'-UGC...AGUCA AGUAU...CGC-3'@LB@ AGAGGGG@LB@ \|\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -12.75 kcal/mol@LB@Hybridization Energy -13.7147 kcal/mol@LB@Unfolding Energy - mRNA 0.82624 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 182 -- 188@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 30 -- 36@LB@
136	0.01205	0.2883	bsu35319	yvzG	-14.21	0.042782	258 -- 272	27 -- 43	Evidence 4: Homologs of previously reported genes of unknown function	_____________257_______________273\n_____________\|_________________\|\n5'-AAG...UUACC_________________UGUUA...AUU-3'\n______________AUC_GA_AGAGGGGUUG\n______________\|\|\|_\|\|_\|\|\|\|\|\|\|\|\|\|\n______________UAG_CU_UCUCCCCAAC\n3'-UUU...AGAAC___A__A__________CCCUU...AUA-5'\n_____________\|_________________\|\n_____________44________________26\n	266 -- 272	27 -- 33	-20.1473 kcal/mol	4.96591 kcal/mol	0.966729 kcal/mol	257 273@LB@ \| \|@LB@5'-AAG...UUACC UGUUA...AUU-3'@LB@ AUC GA AGAGGGGUUG@LB@ \|\|\| \|\| \|\|\|\|\|\|\|\|\|\|@LB@ UAG CU UCUCCCCAAC@LB@3'-UUU...AGAAC A A CCCUU...AUA-5'@LB@ \| \|@LB@ 44 26@LB@@LB@@LB@Energy -14.21 kcal/mol@LB@Hybridization Energy -20.1473 kcal/mol@LB@Unfolding Energy - mRNA 4.96591 kcal/mol@LB@Unfolding Energy - sRNA 0.966729 kcal/mol@LB@@LB@Position - mRNA 258 -- 272@LB@Position - sRNA 27 -- 43@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 27 -- 33@LB@
54	0.002747	0.1697	bsu35790	yvyI	-14.15	0.043919	186 -- 197	25 -- 36	mannose-6-phosphate isomerase YvyI	_____________185__________198\n_____________\|____________\|\n5'-UCU...ACAGG________AC__AUCAU...AAU-3'\n______________GGAGGGGU__GG\n______________:\|\|\|\|\|\|\|__\|\|\n______________UCUCCCCA__CC\n3'-UUU...GACUA________AC__CUUGU...AUA-5'\n_____________\|____________\|\n_____________37___________24\n	187 -- 193	29 -- 35	-17.2174 kcal/mol	2.92719 kcal/mol	0.135926 kcal/mol	185 198@LB@ \| \|@LB@5'-UCU...ACAGG AC AUCAU...AAU-3'@LB@ GGAGGGGU GG@LB@ :\|\|\|\|\|\|\| \|\|@LB@ UCUCCCCA CC@LB@3'-UUU...GACUA AC CUUGU...AUA-5'@LB@ \| \|@LB@ 37 24@LB@@LB@@LB@Energy -14.15 kcal/mol@LB@Hybridization Energy -17.2174 kcal/mol@LB@Unfolding Energy - mRNA 2.92719 kcal/mol@LB@Unfolding Energy - sRNA 0.135926 kcal/mol@LB@@LB@Position - mRNA 186 -- 197@LB@Position - sRNA 25 -- 36@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 29 -- 35@LB@
129	0.01144	0.2883	bsu36230	ywqF	-11.45	0.129133	185 -- 195	31 -- 41	UDP-glucose 6-dehydrogenase YwqF	_____________184_________196\n_____________\|___________\|\n5'-UUU...UUUAA___U_______AAACA...CUC-3'\n______________CUG_UGGAGGG\n______________\|\|\|_\|:\|\|\|\|\|\n______________GAC_AUCUCCC\n3'-UUU...AACUA___U_______CAACC...AUA-5'\n_____________\|___________\|\n_____________42__________30\n	189 -- 195	31 -- 37	-16.042 kcal/mol	3.66073 kcal/mol	0.928126 kcal/mol	184 196@LB@ \| \|@LB@5'-UUU...UUUAA U AAACA...CUC-3'@LB@ CUG UGGAGGG@LB@ \|\|\| \|:\|\|\|\|\|@LB@ GAC AUCUCCC@LB@3'-UUU...AACUA U CAACC...AUA-5'@LB@ \| \|@LB@ 42 30@LB@@LB@@LB@Energy -11.45 kcal/mol@LB@Hybridization Energy -16.042 kcal/mol@LB@Unfolding Energy - mRNA 3.66073 kcal/mol@LB@Unfolding Energy - sRNA 0.928126 kcal/mol@LB@@LB@Position - mRNA 185 -- 195@LB@Position - sRNA 31 -- 41@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 31 -- 37@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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