Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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_000913 Escherichia coli str. K-12 substr. MG1655

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
6	0.0003621	0.1842	b3242	aaeX	-9.38	0.356280	9 -- 19	125 -- 135	DUF1656 family putative inner membrane efflux pump associated protein		_____________8_________20\n_____________\|_________\|\n5'-GCG...CAUAA_________UAAUA...GGG-3'\n______________CAGUUACGC\n______________\|\|\|\|:\|\|:\|\n______________GUCAGUGUG\n3'-UUU...UAUGA_________UACUA...UAG-5'\n_____________\|_________\|\n_____________136_______124\n	75 -- 81	168 -- 174	-12.5845 kcal/mol	1.53643 kcal/mol	0.276974 kcal/mol	8 20@LB@ \| \|@LB@5'-GCG...CAUAA UAAUA...GGG-3'@LB@ CAGUUACGC@LB@ \|\|\|\|:\|\|:\|@LB@ GUCAGUGUG@LB@3'-UUU...UAUGA UACUA...UAG-5'@LB@ \| \|@LB@ 136 124@LB@@LB@@LB@Energy -9.38 kcal/mol@LB@Hybridization Energy -12.5845 kcal/mol@LB@Unfolding Energy - mRNA 1.53643 kcal/mol@LB@Unfolding Energy - sRNA 0.276974 kcal/mol@LB@@LB@Position - mRNA 9 -- 19@LB@Position - sRNA 125 -- 135@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 168 -- 174@LB@
39	0.003509	0.2912	b1293	sapB	-10.75	0.197427	9 -- 16	196 -- 203	antimicrobial peptide transport ABC transporter permease		_____________8____________17\n_____________\|____________\|\n5'-UCG...UAUUU_______CA___GC-3'\n______________CACCCCU__UGC\n______________\|\|\|\|\|\|:__\|\|\|\n______________GUGGGGG__ACG\n3'-UUU...ACCCC_______A____AAGUAG-5'\n_____________\|____________\|\n_____________204__________195\n	287 -- 293	11 -- 17	-15.5024 kcal/mol	0.267702 kcal/mol	6.55606 kcal/mol	8 17@LB@ \| \|@LB@5'-UCG...UAUUU CA GC-3'@LB@ CACCCCU UGC@LB@ \|\|\|\|\|\|: \|\|\|@LB@ GUGGGGG ACG@LB@3'-UUU...ACCCC A AAGUAG-5'@LB@ \| \|@LB@ 204 195@LB@@LB@@LB@Energy -10.75 kcal/mol@LB@Hybridization Energy -15.5024 kcal/mol@LB@Unfolding Energy - mRNA 0.267702 kcal/mol@LB@Unfolding Energy - sRNA 6.55606 kcal/mol@LB@@LB@Position - mRNA 9 -- 16@LB@Position - sRNA 196 -- 203@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 11 -- 17@LB@
122	0.01342	0.3575	b4087	alsA	-13.14	0.065197	11 -- 23	124 -- 136	D-allose ABC transporter ATPase		_____________10___________24\n_____________\|____________\|\n5'-AAU...GGCAA____________GGAUA...UAC-3'\n______________GGUUAUCCCGCU\n______________\|\|\|:\|\|\|\|\|:\|\|\n______________CCAGUAGGGUGA\n3'-UUU...UAACG____________CGUAG...UAG-5'\n_____________\|____________\|\n_____________137__________123\n	16 -- 22	125 -- 131	-19.4238 kcal/mol	3.3353 kcal/mol	6.53419 kcal/mol	10 24@LB@ \| \|@LB@5'-AAU...GGCAA GGAUA...UAC-3'@LB@ GGUUAUCCCGCU@LB@ \|\|\|:\|\|\|\|\|:\|\|@LB@ CCAGUAGGGUGA@LB@3'-UUU...UAACG CGUAG...UAG-5'@LB@ \| \|@LB@ 137 123@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -19.4238 kcal/mol@LB@Unfolding Energy - mRNA 3.3353 kcal/mol@LB@Unfolding Energy - sRNA 6.53419 kcal/mol@LB@@LB@Position - mRNA 11 -- 23@LB@Position - sRNA 124 -- 136@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 125 -- 131@LB@
171	0.01954	0.3812	b3687	ibpA	-6.40	0.875621	11 -- 20	10 -- 18	heat shock chaperone		_____________10____________21\n_____________\|_____________\|\n5'-AAC...GCCCC_______U_____AUAGA...GCU-3'\n______________CUCAGUC_AUGCA\n______________\|\|\|\|\|\|\|_\|::\|\|\n______________GAGUCAG_UGUGU\n3'-UUU...GUUAU_____________ACUAC...UAG-5'\n_____________\|_____________\|\n_____________19____________9\n	19 -- 25	172 -- 178	-14.2159 kcal/mol	5.36362 kcal/mol	0.433674 kcal/mol	10 21@LB@ \| \|@LB@5'-AAC...GCCCC U AUAGA...GCU-3'@LB@ CUCAGUC AUGCA@LB@ \|\|\|\|\|\|\| \|::\|\|@LB@ GAGUCAG UGUGU@LB@3'-UUU...GUUAU ACUAC...UAG-5'@LB@ \| \|@LB@ 19 9@LB@@LB@@LB@Energy -6.40 kcal/mol@LB@Hybridization Energy -14.2159 kcal/mol@LB@Unfolding Energy - mRNA 5.36362 kcal/mol@LB@Unfolding Energy - sRNA 0.433674 kcal/mol@LB@@LB@Position - mRNA 11 -- 20@LB@Position - sRNA 10 -- 18@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 172 -- 178@LB@
112	0.01232	0.3575	b1540	rspR	-15.19	0.024761	13 -- 44	171 -- 202	transcriptional repressor for rspAB		_____________12_________________________________________________________45\n_____________\|__________________________________________________________\|\n5'-CAG...GCCGU__________UCA_______GCC______C___A____CAAUACCCUGGAA_______CGGUU...GCA-3'\n______________CUGGUGGGUG_____ACGCU___UGCUCA_GUC_AUAU_____________AUGAUGC\n______________\|\|\|\|:\|\|\|\|\|_____\|\|:\|:___\|:\|\|\|\|_\|\|\|_\|:\|:_____________\|\|\|\|\|\|\|\n______________GACCGCCCAC_____UGUGG___AUGAGU_CAG_UGUG_____________UACUACG\n3'-UUU...UAGAC__________UAAAA_____UU____________________________________UCCGU...UAG-5'\n_____________\|__________________________________________________________\|\n_____________203________________________________________________________170\n	62 -- 68	161 -- 167	-40.6001 kcal/mol	15.8189 kcal/mol	17.3482 kcal/mol	12 45@LB@ \| \|@LB@5'-CAG...GCCGU UCA GCC C A CAAUACCCUGGAA CGGUU...GCA-3'@LB@ CUGGUGGGUG ACGCU UGCUCA GUC AUAU AUGAUGC@LB@ \|\|\|\|:\|\|\|\|\| \|\|:\|: \|:\|\|\|\| \|\|\| \|:\|: \|\|\|\|\|\|\|@LB@ GACCGCCCAC UGUGG AUGAGU CAG UGUG UACUACG@LB@3'-UUU...UAGAC UAAAA UU UCCGU...UAG-5'@LB@ \| \|@LB@ 203 170@LB@@LB@@LB@Energy -15.19 kcal/mol@LB@Hybridization Energy -40.6001 kcal/mol@LB@Unfolding Energy - mRNA 15.8189 kcal/mol@LB@Unfolding Energy - sRNA 17.3482 kcal/mol@LB@@LB@Position - mRNA 13 -- 44@LB@Position - sRNA 171 -- 202@LB@Position Seed - mRNA 62 -- 68@LB@Position Seed - sRNA 161 -- 167@LB@
30	0.002398	0.2633	b0494	tesA	-12.69	0.080698	14 -- 26	126 -- 138	acyl-CoA thioesterase 1 and protease I and lysophospholipase L1		_____________13____________27\n_____________\|_____________\|\n5'-UCC...AUGUA_____________CAGAC...UGG-3'\n______________GCGGUUGUCCCAC\n______________\|\|\|\|\|::\|\|\|\|\|\|\n______________CGCCAGUAGGGUG\n3'-UUU...CUUAA_____________ACGUA...UAG-5'\n_____________\|_____________\|\n_____________139___________125\n	20 -- 26	126 -- 132	-24.3083 kcal/mol	5.59054 kcal/mol	8.249 kcal/mol	13 27@LB@ \| \|@LB@5'-UCC...AUGUA CAGAC...UGG-3'@LB@ GCGGUUGUCCCAC@LB@ \|\|\|\|\|::\|\|\|\|\|\|@LB@ CGCCAGUAGGGUG@LB@3'-UUU...CUUAA ACGUA...UAG-5'@LB@ \| \|@LB@ 139 125@LB@@LB@@LB@Energy -12.69 kcal/mol@LB@Hybridization Energy -24.3083 kcal/mol@LB@Unfolding Energy - mRNA 5.59054 kcal/mol@LB@Unfolding Energy - sRNA 8.249 kcal/mol@LB@@LB@Position - mRNA 14 -- 26@LB@Position - sRNA 126 -- 138@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 126 -- 132@LB@
41	0.003653	0.2912	b2842	kduD	-13.01	0.069205	14 -- 50	128 -- 174	2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase; KDG oxidoreductase; 20-ketosteroid reductase	b4266 b2774	_____________13_______________________________________________51\n_____________\|________________________________________________\|\n5'-CCG...AACGC______U____________________GAG____________G_____CCCGA...CGG-3'\n______________GUCAUA_UGUGAUGCA_______UAAC___CAG____GCGGU_AUCUC\n______________\|\|\|\|:\|_::\|\|\|\|\|\|\|_______:\|\|\|___\|\|\|____\|\|\|\|\|_\|\|\|:\|\n______________CAGUGU_GUACUACGU_______GUUG___GUC____CGCCA_UAGGG\n3'-UUU...UGAGU________________CCGUUCA____AAA___UUAA_____G_____UGACG...UAG-5'\n_____________\|________________________________________________\|\n_____________175______________________________________________127\n	23 -- 29	160 -- 166	-35.8105 kcal/mol	9.71011 kcal/mol	15.5834 kcal/mol	13 51@LB@ \| \|@LB@5'-CCG...AACGC U GAG G CCCGA...CGG-3'@LB@ GUCAUA UGUGAUGCA UAAC CAG GCGGU AUCUC@LB@ \|\|\|\|:\| ::\|\|\|\|\|\|\| :\|\|\| \|\|\| \|\|\|\|\| \|\|\|:\|@LB@ CAGUGU GUACUACGU GUUG GUC CGCCA UAGGG@LB@3'-UUU...UGAGU CCGUUCA AAA UUAA G UGACG...UAG-5'@LB@ \| \|@LB@ 175 127@LB@@LB@@LB@Energy -13.01 kcal/mol@LB@Hybridization Energy -35.8105 kcal/mol@LB@Unfolding Energy - mRNA 9.71011 kcal/mol@LB@Unfolding Energy - sRNA 15.5834 kcal/mol@LB@@LB@Position - mRNA 14 -- 50@LB@Position - sRNA 128 -- 174@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 160 -- 166@LB@
48	0.004626	0.3205	b3462	ftsX	-13.20	0.063258	14 -- 27	192 -- 205	putative ABC transporter permease		_____________13_____________28\n_____________\|______________\|\n5'-CAA...CGGUA__________AC__ACCGA...ACG-3'\n______________CUGCUGGCGG__GA\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\n______________GACGACCGCC__CU\n3'-UUU...UAUUA__________CA__AAAAU...UAG-5'\n_____________\|______________\|\n_____________206____________191\n	17 -- 23	196 -- 202	-23.0043 kcal/mol	4.65554 kcal/mol	9.06563 kcal/mol	13 28@LB@ \| \|@LB@5'-CAA...CGGUA AC ACCGA...ACG-3'@LB@ CUGCUGGCGG GA@LB@ \|\|\|\|\|\|\|\|\|\| \|\|@LB@ GACGACCGCC CU@LB@3'-UUU...UAUUA CA AAAAU...UAG-5'@LB@ \| \|@LB@ 206 191@LB@@LB@@LB@Energy -13.20 kcal/mol@LB@Hybridization Energy -23.0043 kcal/mol@LB@Unfolding Energy - mRNA 4.65554 kcal/mol@LB@Unfolding Energy - sRNA 9.06563 kcal/mol@LB@@LB@Position - mRNA 14 -- 27@LB@Position - sRNA 192 -- 205@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 196 -- 202@LB@
98	0.01073	0.3575	b0424	yajL	-11.45	0.143367	14 -- 29	155 -- 170	oxidative-stress-resistance chaperone		_____________13_______________30\n_____________\|________________\|\n5'-AGA...GUGAU________________UUGAU...CCA-3'\n______________UACGUGAUGCAGGUGA\n______________:\|\|:\|\|\|\|\|\|\|\|\|::\|\n______________GUGUACUACGUCCGUU\n3'-UUU...UCAGU________________CAGUU...UAG-5'\n_____________\|________________\|\n_____________171______________154\n	22 -- 28	156 -- 162	-24.1359 kcal/mol	6.48358 kcal/mol	7.06607 kcal/mol	13 30@LB@ \| \|@LB@5'-AGA...GUGAU UUGAU...CCA-3'@LB@ UACGUGAUGCAGGUGA@LB@ :\|\|:\|\|\|\|\|\|\|\|\|::\|@LB@ GUGUACUACGUCCGUU@LB@3'-UUU...UCAGU CAGUU...UAG-5'@LB@ \| \|@LB@ 171 154@LB@@LB@@LB@Energy -11.45 kcal/mol@LB@Hybridization Energy -24.1359 kcal/mol@LB@Unfolding Energy - mRNA 6.48358 kcal/mol@LB@Unfolding Energy - sRNA 7.06607 kcal/mol@LB@@LB@Position - mRNA 14 -- 29@LB@Position - sRNA 155 -- 170@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 156 -- 162@LB@
117	0.01283	0.3575	b3096	mzrA	-10.41	0.230387	15 -- 55	168 -- 208	modulator of EnvZ/OmpR regulon		_____________14________________________________________________________56\n_____________\|_________________________________________________________\|\n_____5'-UCAACU____G____________________________GAUCCUGA___CU__G________GCUCG...AGC-3'\n______________GGAU_AGCGG______UCUGCU_GUGGGU_AUU________CAA__CU_GGUUACAU\n______________::\|:_\|\|\|:\|______\|\|\|\|\|\|_\|:\|\|\|\|_\|\|\|________\|\|\|__\|\|_:\|\|:\|\|\|:\n______________UUUG_UCGUC______AGACGA_CGCCCA_UAA________GUU__GA_UCAGUGUG\n______3'-UUUUU____G_____CAUAUU______C______C___AAUGUG_____AU__G________UACUA...UAG-5'\n_____________\|_________________________________________________________\|\n_____________209_______________________________________________________167\n	49 -- 55	168 -- 174	-40.4023 kcal/mol	11.8856 kcal/mol	18.3074 kcal/mol	14 56@LB@ \| \|@LB@ 5'-UCAACU G GAUCCUGA CU G GCUCG...AGC-3'@LB@ GGAU AGCGG UCUGCU GUGGGU AUU CAA CU GGUUACAU@LB@ ::\|: \|\|\|:\| \|\|\|\|\|\| \|:\|\|\|\| \|\|\| \|\|\| \|\| :\|\|:\|\|\|:@LB@ UUUG UCGUC AGACGA CGCCCA UAA GUU GA UCAGUGUG@LB@ 3'-UUUUU G CAUAUU C C AAUGUG AU G UACUA...UAG-5'@LB@ \| \|@LB@ 209 167@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -40.4023 kcal/mol@LB@Unfolding Energy - mRNA 11.8856 kcal/mol@LB@Unfolding Energy - sRNA 18.3074 kcal/mol@LB@@LB@Position - mRNA 15 -- 55@LB@Position - sRNA 168 -- 208@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 168 -- 174@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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