Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
1	0	0	b0757	galK	-15.06	0.000658	183 -- 231	8 -- 60	galactokinase	_____________182_____________________________________________________232\n_____________\|_______________________________________________________\|\n5'-CAU...UUCGC_______GA______U___AAAU_____________AAA____CA__________UUGCC...GUG-3'\n______________GAAUCCG_____GUG_AAG____GAG_UCUGAAAGA___AACA____AUCUCUGU\n______________:\|\|\|\|\|\|_____\|\|\|_\|\|\|____:\|\|_\|\|\|\|\|\|\|\|\|___\|\|\|\|____\|:\|\|\|\|\|\|\n______________UUUAGGC_____CAC_UUC____UUC_AGACUUUCU___UUGU____UGGAGACA\n3'-AUU...GUCGG_______UAAUG_______AUU____C_________AUC____AGAA________UGGGAUG-5'\n_____________\|_______________________________________________________\|\n_____________61______________________________________________________7\n	225 -- 231	8 -- 14	-35.0906 kcal/mol	7.3474 kcal/mol	12.6967 kcal/mol	182 232@LB@ \| \|@LB@5'-CAU...UUCGC GA U AAAU AAA CA UUGCC...GUG-3'@LB@ GAAUCCG GUG AAG GAG UCUGAAAGA AACA AUCUCUGU@LB@ :\|\|\|\|\|\| \|\|\| \|\|\| :\|\| \|\|\|\|\|\|\|\|\| \|\|\|\| \|:\|\|\|\|\|\|@LB@ UUUAGGC CAC UUC UUC AGACUUUCU UUGU UGGAGACA@LB@3'-AUU...GUCGG UAAUG AUU C AUC AGAA UGGGAUG-5'@LB@ \| \|@LB@ 61 7@LB@@LB@@LB@Energy -15.06 kcal/mol@LB@Hybridization Energy -35.0906 kcal/mol@LB@Unfolding Energy - mRNA 7.3474 kcal/mol@LB@Unfolding Energy - sRNA 12.6967 kcal/mol@LB@@LB@Position - mRNA 183 -- 231@LB@Position - sRNA 8 -- 60@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 8 -- 14@LB@
176	0.007357	0.147	b2905	gcvT	-7.40	0.214118	198 -- 224	6 -- 30	aminomethyltransferase tetrahydrofolate-dependent subunit (T protein) of glycine cleavage complex	_____________197__________________________225\n_____________\|____________________________\|\n5'-CUG...AGGAC_______CAC____GACU__________GAACA...AAA-3'\n______________AAGAUGG___AACA_____CCUUUGUAC\n______________\|\|\|\|\|:\|___\|\|\|\|_____\|\|\|:\|\|\|\|\|\n______________UUCUAUC___UUGU_____GGAGACAUG\n3'-AUU...AGACU______________AGAAU_________GGAUG-5'\n_____________\|____________________________\|\n_____________31___________________________5\n	218 -- 224	6 -- 12	-21.3805 kcal/mol	5.97871 kcal/mol	8.02863 kcal/mol	197 225@LB@ \| \|@LB@5'-CUG...AGGAC CAC GACU GAACA...AAA-3'@LB@ AAGAUGG AACA CCUUUGUAC@LB@ \|\|\|\|\|:\| \|\|\|\| \|\|\|:\|\|\|\|\|@LB@ UUCUAUC UUGU GGAGACAUG@LB@3'-AUU...AGACU AGAAU GGAUG-5'@LB@ \| \|@LB@ 31 5@LB@@LB@@LB@Energy -7.40 kcal/mol@LB@Hybridization Energy -21.3805 kcal/mol@LB@Unfolding Energy - mRNA 5.97871 kcal/mol@LB@Unfolding Energy - sRNA 8.02863 kcal/mol@LB@@LB@Position - mRNA 198 -- 224@LB@Position - sRNA 6 -- 30@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 6 -- 12@LB@
15	5.569e-05	0.01183	b1761	gdhA	-12.26	0.008568	280 -- 294	40 -- 56	glutamate dehydrogenase NADP-specific	_____________279_______________295\n_____________\|_________________\|\n5'-UAA...GCAAG___UU____________UGACCA-3'\n______________CCG____CGUGAAGUAA\n______________\|\|\|____\|\|\|\|\|\|\|\|\|\|\n______________GGC____GCACUUCAUU\n3'-AUU...GUUUA___UAAU__________UUCCA...AUG-5'\n_____________\|_________________\|\n_____________57________________39\n	288 -- 294	40 -- 46	-17.1153 kcal/mol	1.5283 kcal/mol	3.34823 kcal/mol	279 295@LB@ \| \|@LB@5'-UAA...GCAAG UU UGACCA-3'@LB@ CCG CGUGAAGUAA@LB@ \|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ GGC GCACUUCAUU@LB@3'-AUU...GUUUA UAAU UUCCA...AUG-5'@LB@ \| \|@LB@ 57 39@LB@@LB@@LB@Energy -12.26 kcal/mol@LB@Hybridization Energy -17.1153 kcal/mol@LB@Unfolding Energy - mRNA 1.5283 kcal/mol@LB@Unfolding Energy - sRNA 3.34823 kcal/mol@LB@@LB@Position - mRNA 280 -- 294@LB@Position - sRNA 40 -- 56@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 40 -- 46@LB@
48	0.0005438	0.03933	b0811	glnH	-6.95	0.268265	70 -- 77	1 -- 8	glutamine transporter subunit	_____________69_______78\n_____________\|________\|\n5'-AUC...GGUAU________AAAUC...CCG-3'\n______________UGCCCUAU\n______________\|:\|\|\|\|\|:\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	71 -- 77	1 -- 7	-10.5963 kcal/mol	1.549 kcal/mol	2.11603 kcal/mol	69 78@LB@ \| \|@LB@5'-AUC...GGUAU AAAUC...CCG-3'@LB@ UGCCCUAU@LB@ \|:\|\|\|\|\|:@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -6.95 kcal/mol@LB@Hybridization Energy -10.5963 kcal/mol@LB@Unfolding Energy - mRNA 1.549 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 70 -- 77@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 71 -- 77@LB@Position Seed - sRNA 1 -- 7@LB@
165	0.006672	0.1423	b1651	gloA	-7.94	0.160716	101 -- 108	49 -- 56	glyoxalase I Ni-dependent	_____________100______109\n_____________\|________\|\n5'-UGG...CUAUA________CCGAC...AAA-3'\n______________CCGAUUAC\n______________\|\|\|\|\|\|\|\|\n______________GGCUAAUG\n3'-AUU...GUUUA________CACUU...AUG-5'\n_____________\|________\|\n_____________57_______48\n	102 -- 108	49 -- 55	-10.6899 kcal/mol	2.44421 kcal/mol	0.317884 kcal/mol	100 109@LB@ \| \|@LB@5'-UGG...CUAUA CCGAC...AAA-3'@LB@ CCGAUUAC@LB@ \|\|\|\|\|\|\|\|@LB@ GGCUAAUG@LB@3'-AUU...GUUUA CACUU...AUG-5'@LB@ \| \|@LB@ 57 48@LB@@LB@@LB@Energy -7.94 kcal/mol@LB@Hybridization Energy -10.6899 kcal/mol@LB@Unfolding Energy - mRNA 2.44421 kcal/mol@LB@Unfolding Energy - sRNA 0.317884 kcal/mol@LB@@LB@Position - mRNA 101 -- 108@LB@Position - sRNA 49 -- 56@LB@Position Seed - mRNA 102 -- 108@LB@Position Seed - sRNA 49 -- 55@LB@
148	0.00596	0.1406	b3426	glpD	-7.81	0.172743	213 -- 222	50 -- 59	sn-glycerol-3-phosphate dehydrogenase aerobic FAD/NAD(P)-binding	_____________212________223\n_____________\|__________\|\n5'-AAC...CCAAA__________UGAUA...AGG-3'\n______________GAUCUGAUUG\n______________:\|\|\|:\|\|\|\|:\n______________UUAGGCUAAU\n3'-AUU...UCGGU__________GCACU...AUG-5'\n_____________\|__________\|\n_____________60_________49\n	216 -- 222	50 -- 56	-9.79708 kcal/mol	1.6903 kcal/mol	0.31771 kcal/mol	212 223@LB@ \| \|@LB@5'-AAC...CCAAA UGAUA...AGG-3'@LB@ GAUCUGAUUG@LB@ :\|\|\|:\|\|\|\|:@LB@ UUAGGCUAAU@LB@3'-AUU...UCGGU GCACU...AUG-5'@LB@ \| \|@LB@ 60 49@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -9.79708 kcal/mol@LB@Unfolding Energy - mRNA 1.6903 kcal/mol@LB@Unfolding Energy - sRNA 0.31771 kcal/mol@LB@@LB@Position - mRNA 213 -- 222@LB@Position - sRNA 50 -- 59@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 50 -- 56@LB@
62	0.001059	0.05856	b3927	glpF	-11.40	0.016677	192 -- 203	48 -- 59	glycerol facilitator	_____________191__________204\n_____________\|____________\|\n5'-GAU...UUCAG____________AGUCA...AAG-3'\n______________GAUCCGAUUAUG\n______________:\|\|\|\|\|\|\|\|\|:\|\n______________UUAGGCUAAUGC\n3'-AUU...UCGGU____________ACUUC...AUG-5'\n_____________\|____________\|\n_____________60___________47\n	197 -- 203	48 -- 54	-15.6898 kcal/mol	2.7066 kcal/mol	1.55995 kcal/mol	191 204@LB@ \| \|@LB@5'-GAU...UUCAG AGUCA...AAG-3'@LB@ GAUCCGAUUAUG@LB@ :\|\|\|\|\|\|\|\|\|:\|@LB@ UUAGGCUAAUGC@LB@3'-AUU...UCGGU ACUUC...AUG-5'@LB@ \| \|@LB@ 60 47@LB@@LB@@LB@Energy -11.40 kcal/mol@LB@Hybridization Energy -15.6898 kcal/mol@LB@Unfolding Energy - mRNA 2.7066 kcal/mol@LB@Unfolding Energy - sRNA 1.55995 kcal/mol@LB@@LB@Position - mRNA 192 -- 203@LB@Position - sRNA 48 -- 59@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 48 -- 54@LB@
7	1.5e-05	0.00754	b0720	gltA	-8.97	0.087950	70 -- 79	4 -- 13	citrate synthase	_____________69_________80\n_____________\|__________\|\n5'-CGG...CAGAG__________AGGUU...GUA-3'\n______________CUCUGUACCC\n______________\|\|\|\|\|\|\|\|\|\|\n______________GAGACAUGGG\n3'-AUU...GAAUG__________AUG-5'\n_____________\|__________\|\n_____________14_________3\n	73 -- 79	4 -- 10	-18.8657 kcal/mol	4.79377 kcal/mol	5.12835 kcal/mol	69 80@LB@ \| \|@LB@5'-CGG...CAGAG AGGUU...GUA-3'@LB@ CUCUGUACCC@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ GAGACAUGGG@LB@3'-AUU...GAAUG AUG-5'@LB@ \| \|@LB@ 14 3@LB@@LB@@LB@Energy -8.97 kcal/mol@LB@Hybridization Energy -18.8657 kcal/mol@LB@Unfolding Energy - mRNA 4.79377 kcal/mol@LB@Unfolding Energy - sRNA 5.12835 kcal/mol@LB@@LB@Position - mRNA 70 -- 79@LB@Position - sRNA 4 -- 13@LB@Position Seed - mRNA 73 -- 79@LB@Position Seed - sRNA 4 -- 10@LB@
188	0.008316	0.1556	b3406	greB	-8.11	0.146040	42 -- 55	52 -- 65	transcript cleavage factor	_____________41_____________56\n_____________\|______________\|\n5'-AUU...GUCAC______________AUGAA...UGA-3'\n______________CAGCUAAAUCUGGU\n______________\|\|\|\|:\|\|\|\|\|:\|:\|\n______________GUCGGUUUAGGCUA\n3'-AUU...UAUAA______________AUGCA...AUG-5'\n_____________\|______________\|\n_____________66_____________51\n	49 -- 55	52 -- 58	-18.5321 kcal/mol	4.27254 kcal/mol	6.17277 kcal/mol	41 56@LB@ \| \|@LB@5'-AUU...GUCAC AUGAA...UGA-3'@LB@ CAGCUAAAUCUGGU@LB@ \|\|\|\|:\|\|\|\|\|:\|:\|@LB@ GUCGGUUUAGGCUA@LB@3'-AUU...UAUAA AUGCA...AUG-5'@LB@ \| \|@LB@ 66 51@LB@@LB@@LB@Energy -8.11 kcal/mol@LB@Hybridization Energy -18.5321 kcal/mol@LB@Unfolding Energy - mRNA 4.27254 kcal/mol@LB@Unfolding Energy - sRNA 6.17277 kcal/mol@LB@@LB@Position - mRNA 42 -- 55@LB@Position - sRNA 52 -- 65@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 52 -- 58@LB@
32	0.0003261	0.03519	b2789	gudP	-8.38	0.124980	121 -- 127	1 -- 7	putative D-glucarate transporter	_____________120_____128\n_____________\|_______\|\n5'-UGA...AAAAC_______GUCAC...ACG-3'\n______________ACCCUAC\n______________\|\|\|\|\|\|\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	121 -- 127	1 -- 7	-11.2076 kcal/mol	0.809325 kcal/mol	2.03949 kcal/mol	120 128@LB@ \| \|@LB@5'-UGA...AAAAC GUCAC...ACG-3'@LB@ ACCCUAC@LB@ \|\|\|\|\|\|\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -8.38 kcal/mol@LB@Hybridization Energy -11.2076 kcal/mol@LB@Unfolding Energy - mRNA 0.809325 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 121 -- 127@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 1 -- 7@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)

Job resubmission

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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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