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
49	0.0005477	0.03933	b2715	ascF	-9.59	0.059292	173 -- 180	1 -- 8	cellobiose/arbutin/salicin-specific PTS enzymes IIB and IC components	_____________172______181\n_____________\|________\|\n5'-UGC...ACAUC________UGAUA...GCU-3'\n______________UACCCUAC\n______________\|\|\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	174 -- 180	1 -- 7	-12.1729 kcal/mol	0.486168 kcal/mol	2.11603 kcal/mol	172 181@LB@ \| \|@LB@5'-UGC...ACAUC UGAUA...GCU-3'@LB@ UACCCUAC@LB@ \|\|\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -12.1729 kcal/mol@LB@Unfolding Energy - mRNA 0.486168 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 173 -- 180@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 1 -- 7@LB@
75	0.001328	0.06227	b1748	astC	-8.39	0.124654	121 -- 127	1 -- 7	succinylornithine transaminase PLP-dependent	_____________120_____128\n_____________\|_______\|\n5'-UCA...CACGA_______AAUCU...UGU-3'\n______________ACCCUGC\n______________\|\|\|\|\|:\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	121 -- 127	1 -- 7	-11.9071 kcal/mol	1.50434 kcal/mol	2.03949 kcal/mol	120 128@LB@ \| \|@LB@5'-UCA...CACGA AAUCU...UGU-3'@LB@ ACCCUGC@LB@ \|\|\|\|\|:\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -8.39 kcal/mol@LB@Hybridization Energy -11.9071 kcal/mol@LB@Unfolding Energy - mRNA 1.50434 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@
157	0.006279	0.1407	b0312	betB	-8.02	0.153308	1 -- 12	52 -- 63	betaine aldehyde dehydrogenase NAD-dependent	______________1___________13\n______________\|___________\|\n___________5'-____________GAGCG...ACG-3'\n______________GUCGAAUCUGGU\n______________\|:\|:\|\|\|\|:\|:\|\n______________CGGUUUAGGCUA\n3'-AUU...UAAGU____________AUGCA...AUG-5'\n_____________\|____________\|\n_____________64___________51\n	6 -- 12	52 -- 58	-15.0997 kcal/mol	0.969406 kcal/mol	6.13017 kcal/mol	1 13@LB@ \| \|@LB@ 5'- GAGCG...ACG-3'@LB@ GUCGAAUCUGGU@LB@ \|:\|:\|\|\|\|:\|:\|@LB@ CGGUUUAGGCUA@LB@3'-AUU...UAAGU AUGCA...AUG-5'@LB@ \| \|@LB@ 64 51@LB@@LB@@LB@Energy -8.02 kcal/mol@LB@Hybridization Energy -15.0997 kcal/mol@LB@Unfolding Energy - mRNA 0.969406 kcal/mol@LB@Unfolding Energy - sRNA 6.13017 kcal/mol@LB@@LB@Position - mRNA 1 -- 12@LB@Position - sRNA 52 -- 63@LB@Position Seed - mRNA 6 -- 12@LB@Position Seed - sRNA 52 -- 58@LB@
54	0.0007615	0.04961	b0313	betI	-7.44	0.209816	47 -- 68	32 -- 57	choline-inducible betIBA-betT divergent operon transcriptional repressor	_____________46_________________________69\n_____________\|__________________________\|\n5'-CAG...CCUUU___C________U_____________UCAUC...CGC-3'\n______________UCC___UGC_UG__GUGAAAGGUCUG\n______________\|\|\|___\|:\|_\|\|__\|\|:\|\|\|\|\|\|\|\|\|\n______________AGG___AUG_AC__CAUUUUCCAGAC\n3'-AUU...GGUUU___CUA___C__UU____________UUUCU...AUG-5'\n_____________\|__________________________\|\n_____________58_________________________31\n	62 -- 68	32 -- 38	-22.1015 kcal/mol	6.64828 kcal/mol	7.92091 kcal/mol	46 69@LB@ \| \|@LB@5'-CAG...CCUUU C U UCAUC...CGC-3'@LB@ UCC UGC UG GUGAAAGGUCUG@LB@ \|\|\| \|:\| \|\| \|\|:\|\|\|\|\|\|\|\|\|@LB@ AGG AUG AC CAUUUUCCAGAC@LB@3'-AUU...GGUUU CUA C UU UUUCU...AUG-5'@LB@ \| \|@LB@ 58 31@LB@@LB@@LB@Energy -7.44 kcal/mol@LB@Hybridization Energy -22.1015 kcal/mol@LB@Unfolding Energy - mRNA 6.64828 kcal/mol@LB@Unfolding Energy - sRNA 7.92091 kcal/mol@LB@@LB@Position - mRNA 47 -- 68@LB@Position - sRNA 32 -- 57@LB@Position Seed - mRNA 62 -- 68@LB@Position Seed - sRNA 32 -- 38@LB@
23	0.0001777	0.02687	b0774	bioA	-12.72	0.005870	209 -- 228	5 -- 24	7 8-diaminopelargonic acid synthase PLP-dependent	_____________208___________________229\n_____________\|_____________________\|\n5'-ACG...ACAAC____G________________AACGC...AAG-3'\n______________GGAC_AUCUUGCCUUUG_ACC\n______________\|:\|\|_\|\|\|\|\|:\|\|\|:\|\|_\|\|\|\n______________CUUG_UAGAAUGGAGAC_UGG\n3'-AUU...UCUAU_________________A___GAUG-5'\n_____________\|_____________________\|\n_____________25____________________4\n	219 -- 225	9 -- 15	-24.4474 kcal/mol	3.74608 kcal/mol	8.01095 kcal/mol	208 229@LB@ \| \|@LB@5'-ACG...ACAAC G AACGC...AAG-3'@LB@ GGAC AUCUUGCCUUUG ACC@LB@ \|:\|\| \|\|\|\|\|:\|\|\|:\|\| \|\|\|@LB@ CUUG UAGAAUGGAGAC UGG@LB@3'-AUU...UCUAU A GAUG-5'@LB@ \| \|@LB@ 25 4@LB@@LB@@LB@Energy -12.72 kcal/mol@LB@Hybridization Energy -24.4474 kcal/mol@LB@Unfolding Energy - mRNA 3.74608 kcal/mol@LB@Unfolding Energy - sRNA 8.01095 kcal/mol@LB@@LB@Position - mRNA 209 -- 228@LB@Position - sRNA 5 -- 24@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 9 -- 15@LB@
45	0.0004826	0.03773	b4133	cadC	-9.27	0.072737	38 -- 110	5 -- 66	cadBA operon transcriptional activator	_____________37______________________________________________________________________________111\n_____________\|_______________________________________________________________________________\|\n5'-GAU...GGUUC_____A______U_______AAUACUAUGUAAUCAA_____UUAU_______UAAAAAU__________A_________AAUAA...UAA-3'\n______________UCAGU_AAAUCC__UU_CGU________________GAAGU____GG_CUGG_______AACGUCUUGC_UUC___ACC\n______________\|\|\|\|:_\|\|\|\|\|\|__\|\|_\|\|\|________________\|\|\|\|\|____\|\|_\|\|\|:_______\|\|\|:\|\|\|\|:\|_:\|\|___\|\|\|\n______________AGUCG_UUUAGG__AA_GCA________________CUUCA____CC_GACU_______UUGUAGAAUG_GAG___UGG\n3'-AUU...UUAUA_____G______CU__U________________________UUUU__A____UUCUAUC______________ACA___GAUG-5'\n_____________\|_______________________________________________________________________________\|\n_____________67______________________________________________________________________________4\n	97 -- 103	14 -- 20	-38.0459 kcal/mol	10.2122 kcal/mol	18.5819 kcal/mol	37 111@LB@ \| \|@LB@5'-GAU...GGUUC A U AAUACUAUGUAAUCAA UUAU UAAAAAU A AAUAA...UAA-3'@LB@ UCAGU AAAUCC UU CGU GAAGU GG CUGG AACGUCUUGC UUC ACC@LB@ \|\|\|\|: \|\|\|\|\|\| \|\| \|\|\| \|\|\|\|\| \|\| \|\|\|: \|\|\|:\|\|\|\|:\| :\|\| \|\|\|@LB@ AGUCG UUUAGG AA GCA CUUCA CC GACU UUGUAGAAUG GAG UGG@LB@3'-AUU...UUAUA G CU U UUUU A UUCUAUC ACA GAUG-5'@LB@ \| \|@LB@ 67 4@LB@@LB@@LB@Energy -9.27 kcal/mol@LB@Hybridization Energy -38.0459 kcal/mol@LB@Unfolding Energy - mRNA 10.2122 kcal/mol@LB@Unfolding Energy - sRNA 18.5819 kcal/mol@LB@@LB@Position - mRNA 38 -- 110@LB@Position - sRNA 5 -- 66@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 14 -- 20@LB@
190	0.008456	0.1558	b0036	caiD	-8.40	0.123663	110 -- 117	1 -- 8	carnitinyl-CoA dehydratase	_____________109______118\n_____________\|________\|\n5'-UGG...GGAAC________CAGCU...AAA-3'\n______________UACCCUGC\n______________\|\|\|\|\|\|:\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	111 -- 117	1 -- 7	-12.4513 kcal/mol	1.95818 kcal/mol	2.11603 kcal/mol	109 118@LB@ \| \|@LB@5'-UGG...GGAAC CAGCU...AAA-3'@LB@ UACCCUGC@LB@ \|\|\|\|\|\|:\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -8.40 kcal/mol@LB@Hybridization Energy -12.4513 kcal/mol@LB@Unfolding Energy - mRNA 1.95818 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 110 -- 117@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 1 -- 7@LB@
128	0.004347	0.1195	b3690	cbrA	-9.56	0.060736	197 -- 211	17 -- 31	colicin M resistance protein; FAD-binding protein putative oxidoreductase	_____________196_____________212\n_____________\|_______________\|\n5'-CAG...AGUGA_______________CGACG...AAA-3'\n______________AAAGAUGGAACAUUU\n______________\|\|\|\|\|\|:\|\|\|\|\|\|:\|\n______________UUUCUAUCUUGUAGA\n3'-AUU...CAGAC_______________AUGGA...AUG-5'\n_____________\|_______________\|\n_____________32______________16\n	204 -- 210	18 -- 24	-17.0326 kcal/mol	3.22818 kcal/mol	4.26586 kcal/mol	196 212@LB@ \| \|@LB@5'-CAG...AGUGA CGACG...AAA-3'@LB@ AAAGAUGGAACAUUU@LB@ \|\|\|\|\|\|:\|\|\|\|\|\|:\|@LB@ UUUCUAUCUUGUAGA@LB@3'-AUU...CAGAC AUGGA...AUG-5'@LB@ \| \|@LB@ 32 16@LB@@LB@@LB@Energy -9.56 kcal/mol@LB@Hybridization Energy -17.0326 kcal/mol@LB@Unfolding Energy - mRNA 3.22818 kcal/mol@LB@Unfolding Energy - sRNA 4.26586 kcal/mol@LB@@LB@Position - mRNA 197 -- 211@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 18 -- 24@LB@
121	0.004045	0.1176	b1738	chbB	-6.64	0.311906	2 -- 15	34 -- 50	N N'-diacetylchitobiose-specific enzyme IIB component of PTS	_____________1_________________16\n_____________\|_________________\|\n__________5'-A_________________AUAAC...CGG-3'\n______________AUGUGAAG___AGGGUC\n______________\|:\|\|\|\|\|\|___\|:\|\|\|\|\n______________UGCACUUC___UUCCAG\n3'-AUU...GCUAA________AUU______ACUUU...AUG-5'\n_____________\|_________________\|\n_____________51________________33\n	3 -- 9	43 -- 49	-17.276 kcal/mol	2.8636 kcal/mol	7.69543 kcal/mol	1 16@LB@ \| \|@LB@ 5'-A AUAAC...CGG-3'@LB@ AUGUGAAG AGGGUC@LB@ \|:\|\|\|\|\|\| \|:\|\|\|\|@LB@ UGCACUUC UUCCAG@LB@3'-AUU...GCUAA AUU ACUUU...AUG-5'@LB@ \| \|@LB@ 51 33@LB@@LB@@LB@Energy -6.64 kcal/mol@LB@Hybridization Energy -17.276 kcal/mol@LB@Unfolding Energy - mRNA 2.8636 kcal/mol@LB@Unfolding Energy - sRNA 7.69543 kcal/mol@LB@@LB@Position - mRNA 2 -- 15@LB@Position - sRNA 34 -- 50@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 43 -- 49@LB@
47	0.0005047	0.03778	b1888	cheA	-10.26	0.037926	179 -- 191	53 -- 66	fused chemotactic sensory histidine kinase in two-component regulatory system with CheB and CheY: sensory histidine kinase/signal sensing protein	_____________178____________192\n_____________\|______________\|\n5'-GAU...UGCCA______________GGUGA...AAG-3'\n______________UCAGCCGAA_CCGA\n______________\|\|\|\|\|\|:\|\|_\|\|\|\|\n______________AGUCGGUUU_GGCU\n3'-AUU...UUAUA_________A____AAUGC...AUG-5'\n_____________\|______________\|\n_____________67_____________52\n	181 -- 187	58 -- 64	-19.401 kcal/mol	2.99348 kcal/mol	6.16775 kcal/mol	178 192@LB@ \| \|@LB@5'-GAU...UGCCA GGUGA...AAG-3'@LB@ UCAGCCGAA CCGA@LB@ \|\|\|\|\|\|:\|\| \|\|\|\|@LB@ AGUCGGUUU GGCU@LB@3'-AUU...UUAUA A AAUGC...AUG-5'@LB@ \| \|@LB@ 67 52@LB@@LB@@LB@Energy -10.26 kcal/mol@LB@Hybridization Energy -19.401 kcal/mol@LB@Unfolding Energy - mRNA 2.99348 kcal/mol@LB@Unfolding Energy - sRNA 6.16775 kcal/mol@LB@@LB@Position - mRNA 179 -- 191@LB@Position - sRNA 53 -- 66@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 58 -- 64@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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