Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
165	0.01591	0.3104	b4393	trpR	-12.13	0.051953	230 -- 246	5 -- 21	transcriptional repressor tryptophan-binding		_____________229_______________247\n_____________\|_________________\|\n5'-GAG...GCAGC_________ACA_____ACCAG...AUC-3'\n______________GAUGGCAGA___GCGUC\n______________\|\|\|::\|\|:\|___\|\|\|\|\|\n______________CUAUUGUUU___CGCAG\n3'-UUU...UACUA_________ACG_____AAAG-5'\n_____________\|_________________\|\n_____________22________________4\n	232 -- 238	13 -- 19	-18.7652 kcal/mol	5.38929 kcal/mol	1.24955 kcal/mol	229 247@LB@ \| \|@LB@5'-GAG...GCAGC ACA ACCAG...AUC-3'@LB@ GAUGGCAGA GCGUC@LB@ \|\|\|::\|\|:\| \|\|\|\|\|@LB@ CUAUUGUUU CGCAG@LB@3'-UUU...UACUA ACG AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -12.13 kcal/mol@LB@Hybridization Energy -18.7652 kcal/mol@LB@Unfolding Energy - mRNA 5.38929 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 230 -- 246@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 13 -- 19@LB@
99	0.009943	0.3104	b3405	ompR	-10.46	0.101388	231 -- 245	8 -- 21	response regulator in two-component regulatory system with EnvZ		_____________230_____________246\n_____________\|_______________\|\n5'-AAU...UGGUC________C______CUGCG...GCG-3'\n______________GAUGACGA_AUGCGC\n______________\|\|\|:\|\|:\|_\|\|\|\|\|\|\n______________CUAUUGUU_UACGCG\n3'-UUU...UACUA_______________CAGAAAG-5'\n_____________\|_______________\|\n_____________22______________7\n	232 -- 238	14 -- 20	-17.2341 kcal/mol	5.5408 kcal/mol	1.23638 kcal/mol	230 246@LB@ \| \|@LB@5'-AAU...UGGUC C CUGCG...GCG-3'@LB@ GAUGACGA AUGCGC@LB@ \|\|\|:\|\|:\| \|\|\|\|\|\|@LB@ CUAUUGUU UACGCG@LB@3'-UUU...UACUA CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -10.46 kcal/mol@LB@Hybridization Energy -17.2341 kcal/mol@LB@Unfolding Energy - mRNA 5.5408 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 231 -- 245@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 14 -- 20@LB@
117	0.01191	0.3104	b2137	yohF	-11.08	0.079147	231 -- 259	5 -- 35	putative oxidoreductase		_____________230_____________________________260\n_____________\|_______________________________\|\n5'-UAA...CCUCC___________C____CAAA___________AUUAC...GGC-3'\n______________GAUUCGGGGAU___GG____GAGUGCGCGUU\n______________:\|\|\|\|:\|\|\|\|\|___\|:____:\|:\|\|\|\|\|\|\|:\n______________UUAAGUCCCUA___CU____UUUACGCGCAG\n3'-UUU...GAGAC___________CUA__AUUG___________AAAG-5'\n_____________\|_______________________________\|\n_____________36______________________________4\n	253 -- 259	5 -- 11	-31.497 kcal/mol	11.2631 kcal/mol	9.15134 kcal/mol	230 260@LB@ \| \|@LB@5'-UAA...CCUCC C CAAA AUUAC...GGC-3'@LB@ GAUUCGGGGAU GG GAGUGCGCGUU@LB@ :\|\|\|\|:\|\|\|\|\| \|: :\|:\|\|\|\|\|\|\|:@LB@ UUAAGUCCCUA CU UUUACGCGCAG@LB@3'-UUU...GAGAC CUA AUUG AAAG-5'@LB@ \| \|@LB@ 36 4@LB@@LB@@LB@Energy -11.08 kcal/mol@LB@Hybridization Energy -31.497 kcal/mol@LB@Unfolding Energy - mRNA 11.2631 kcal/mol@LB@Unfolding Energy - sRNA 9.15134 kcal/mol@LB@@LB@Position - mRNA 231 -- 259@LB@Position - sRNA 5 -- 35@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 5 -- 11@LB@
171	0.01687	0.3104	b1512	lsrR	-11.43	0.068975	231 -- 262	7 -- 31	lsr operon transcriptional repressor	b4295	_____________230______________________________263\n_____________\|________________________________\|\n5'-GCU...CAGAA______AUGUG___A__AG_______C_____GAUCG...AGA-3'\n______________CAGGGA_____UGA_GA__AACAGGU_GCGCG\n______________\|\|\|\|\|\|_____\|\|\|_\|\|__\|\|\|\|::\|_\|\|\|\|\|\n______________GUCCCU_____ACU_CU__UUGUUUA_CGCGC\n3'-UUU...CUUAA______________A__A______________AGAAAG-5'\n_____________\|________________________________\|\n_____________32_______________________________6\n	250 -- 256	12 -- 18	-27.0439 kcal/mol	7.86672 kcal/mol	7.75103 kcal/mol	230 263@LB@ \| \|@LB@5'-GCU...CAGAA AUGUG A AG C GAUCG...AGA-3'@LB@ CAGGGA UGA GA AACAGGU GCGCG@LB@ \|\|\|\|\|\| \|\|\| \|\| \|\|\|\|::\| \|\|\|\|\|@LB@ GUCCCU ACU CU UUGUUUA CGCGC@LB@3'-UUU...CUUAA A A AGAAAG-5'@LB@ \| \|@LB@ 32 6@LB@@LB@@LB@Energy -11.43 kcal/mol@LB@Hybridization Energy -27.0439 kcal/mol@LB@Unfolding Energy - mRNA 7.86672 kcal/mol@LB@Unfolding Energy - sRNA 7.75103 kcal/mol@LB@@LB@Position - mRNA 231 -- 262@LB@Position - sRNA 7 -- 31@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 12 -- 18@LB@
68	0.006348	0.3087	b1202	ycgV	-6.40	0.429936	233 -- 244	4 -- 18	putative adhesin	b2647	_____________232_____________245\n_____________\|_______________\|\n5'-ACU...ACCAA_______________CGCUG...UUG-3'\n______________AGCAGAU___CGUCU\n______________\|:\|\|:\|\|___\|\|\|\|\|\n______________UUGUUUA___GCAGA\n3'-UUU...UACUA_______CGC_____AAG-5'\n_____________\|_______________\|\n_____________19______________3\n	233 -- 239	12 -- 18	-9.8712 kcal/mol	2.23703 kcal/mol	1.22995 kcal/mol	232 245@LB@ \| \|@LB@5'-ACU...ACCAA CGCUG...UUG-3'@LB@ AGCAGAU CGUCU@LB@ \|:\|\|:\|\| \|\|\|\|\|@LB@ UUGUUUA GCAGA@LB@3'-UUU...UACUA CGC AAG-5'@LB@ \| \|@LB@ 19 3@LB@@LB@@LB@Energy -6.40 kcal/mol@LB@Hybridization Energy -9.8712 kcal/mol@LB@Unfolding Energy - mRNA 2.23703 kcal/mol@LB@Unfolding Energy - sRNA 1.22995 kcal/mol@LB@@LB@Position - mRNA 233 -- 244@LB@Position - sRNA 4 -- 18@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 12 -- 18@LB@
153	0.0145	0.3104	b3866	yihI	-12.31	0.048207	234 -- 252	5 -- 21	activator of Der GTPase		_____________233_________________253\n_____________\|___________________\|\n5'-GAA...GCAAA___CAU_____A_______GAAAA...GUC-3'\n______________GGU___GCAAA_GCGCGUC\n______________\|:\|___:\|\|\|\|_\|\|\|\|\|\|\|\n______________CUA___UGUUU_CGCGCAG\n3'-UUU...UACUA___U_______A_______AAAG-5'\n_____________\|___________________\|\n_____________22__________________4\n	246 -- 252	5 -- 11	-18.8767 kcal/mol	5.31745 kcal/mol	1.24955 kcal/mol	233 253@LB@ \| \|@LB@5'-GAA...GCAAA CAU A GAAAA...GUC-3'@LB@ GGU GCAAA GCGCGUC@LB@ \|:\| :\|\|\|\| \|\|\|\|\|\|\|@LB@ CUA UGUUU CGCGCAG@LB@3'-UUU...UACUA U A AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -12.31 kcal/mol@LB@Hybridization Energy -18.8767 kcal/mol@LB@Unfolding Energy - mRNA 5.31745 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 234 -- 252@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 5 -- 11@LB@
18	0.00061	0.1147	b2126	yehU	-11.17	0.076396	235 -- 252	1 -- 18	inner membrane putative sensory kinase in two-component system with YehT		_____________234________________253\n_____________\|__________________\|\n5'-GUC...GCUUC__________________UAGUC...UAA-3'\n______________AGCAGAUGUGCGUUUUUU\n______________\|:\|\|:\|\|\|:\|\|\|\|:\|\|\|:\n______________UUGUUUACGCGCAGAAAG\n3'-UUU...UACUA__________________-5'\n_____________\|_________________\|\n_____________19________________1\n	246 -- 252	1 -- 7	-22.3117 kcal/mol	9.89973 kcal/mol	1.24077 kcal/mol	234 253@LB@ \| \|@LB@5'-GUC...GCUUC UAGUC...UAA-3'@LB@ AGCAGAUGUGCGUUUUUU@LB@ \|:\|\|:\|\|\|:\|\|\|\|:\|\|\|:@LB@ UUGUUUACGCGCAGAAAG@LB@3'-UUU...UACUA -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -11.17 kcal/mol@LB@Hybridization Energy -22.3117 kcal/mol@LB@Unfolding Energy - mRNA 9.89973 kcal/mol@LB@Unfolding Energy - sRNA 1.24077 kcal/mol@LB@@LB@Position - mRNA 235 -- 252@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 1 -- 7@LB@
36	0.002407	0.2206	b2550	yphH	-13.17	0.033778	238 -- 251	7 -- 20	putative DNA-binding transcriptional regulator		_____________237____________252\n_____________\|______________\|\n5'-AGG...CCACC______________AUUCU...UGG-3'\n______________AUAACAAAUGCGUG\n______________\|\|\|\|\|\|\|\|\|\|\|\|:\|\n______________UAUUGUUUACGCGC\n3'-UUU...ACUAC______________AGAAAG-5'\n_____________\|______________\|\n_____________21_____________6\n	245 -- 251	7 -- 13	-19.0929 kcal/mol	4.67933 kcal/mol	1.23906 kcal/mol	237 252@LB@ \| \|@LB@5'-AGG...CCACC AUUCU...UGG-3'@LB@ AUAACAAAUGCGUG@LB@ \|\|\|\|\|\|\|\|\|\|\|\|:\|@LB@ UAUUGUUUACGCGC@LB@3'-UUU...ACUAC AGAAAG-5'@LB@ \| \|@LB@ 21 6@LB@@LB@@LB@Energy -13.17 kcal/mol@LB@Hybridization Energy -19.0929 kcal/mol@LB@Unfolding Energy - mRNA 4.67933 kcal/mol@LB@Unfolding Energy - sRNA 1.23906 kcal/mol@LB@@LB@Position - mRNA 238 -- 251@LB@Position - sRNA 7 -- 20@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 7 -- 13@LB@
183	0.01807	0.3104	b1508	hipB	-7.23	0.331427	238 -- 247	10 -- 19	antitoxin of HipAB toxin-antitoxin system	b1299 b1434	_____________237________248\n_____________\|__________\|\n5'-AUG...GCAAU__________AAUGA...AAA-3'\n______________UGGCGAAUGC\n______________\|::\|:\|\|\|\|\|\n______________AUUGUUUACG\n3'-UUU...CUACU__________CGCAG...AAG-5'\n_____________\|__________\|\n_____________20_________9\n	241 -- 247	10 -- 16	-11.7956 kcal/mol	3.36082 kcal/mol	1.20833 kcal/mol	237 248@LB@ \| \|@LB@5'-AUG...GCAAU AAUGA...AAA-3'@LB@ UGGCGAAUGC@LB@ \|::\|:\|\|\|\|\|@LB@ AUUGUUUACG@LB@3'-UUU...CUACU CGCAG...AAG-5'@LB@ \| \|@LB@ 20 9@LB@@LB@@LB@Energy -7.23 kcal/mol@LB@Hybridization Energy -11.7956 kcal/mol@LB@Unfolding Energy - mRNA 3.36082 kcal/mol@LB@Unfolding Energy - sRNA 1.20833 kcal/mol@LB@@LB@Position - mRNA 238 -- 247@LB@Position - sRNA 10 -- 19@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 10 -- 16@LB@
89	0.009028	0.3104	b0529	folD	-8.62	0.203566	239 -- 251	4 -- 17	bifunctional 5 10-methylene-tetrahydrofolate dehydrogenase/ 5 10-methylene-tetrahydrofolate cyclohydrolase		_____________238____________252\n_____________\|______________\|\n5'-CAA...GCGCA______________GAAGU...CAC-3'\n______________GCAGGUGCGC_UCU\n______________:\|\|::\|\|\|\|\|_\|\|\|\n______________UGUUUACGCG_AGA\n3'-UUU...ACUAU__________C___AAG-5'\n_____________\|______________\|\n_____________18_____________3\n	242 -- 248	8 -- 14	-17.587 kcal/mol	7.73476 kcal/mol	1.22888 kcal/mol	238 252@LB@ \| \|@LB@5'-CAA...GCGCA GAAGU...CAC-3'@LB@ GCAGGUGCGC UCU@LB@ :\|\|::\|\|\|\|\| \|\|\|@LB@ UGUUUACGCG AGA@LB@3'-UUU...ACUAU C AAG-5'@LB@ \| \|@LB@ 18 3@LB@@LB@@LB@Energy -8.62 kcal/mol@LB@Hybridization Energy -17.587 kcal/mol@LB@Unfolding Energy - mRNA 7.73476 kcal/mol@LB@Unfolding Energy - sRNA 1.22888 kcal/mol@LB@@LB@Position - mRNA 239 -- 251@LB@Position - sRNA 4 -- 17@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 8 -- 14@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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service.

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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