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
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@
195	0.01912	0.3104	b3910	yiiM	-10.43	0.102344	196 -- 205	9 -- 18	6-N-hydroxylaminopurine resistance protein	_____________195________206\n_____________\|__________\|\n5'-UAA...GAGGG__________AUAUC...UGC-3'\n______________AACAGAUGCG\n______________\|\|\|\|:\|\|\|\|\|\n______________UUGUUUACGC\n3'-UUU...UACUA__________GCAGAAAG-5'\n_____________\|__________\|\n_____________19_________8\n	199 -- 205	9 -- 15	-13.3675 kcal/mol	1.73119 kcal/mol	1.20319 kcal/mol	195 206@LB@ \| \|@LB@5'-UAA...GAGGG AUAUC...UGC-3'@LB@ AACAGAUGCG@LB@ \|\|\|\|:\|\|\|\|\|@LB@ UUGUUUACGC@LB@3'-UUU...UACUA GCAGAAAG-5'@LB@ \| \|@LB@ 19 8@LB@@LB@@LB@Energy -10.43 kcal/mol@LB@Hybridization Energy -13.3675 kcal/mol@LB@Unfolding Energy - mRNA 1.73119 kcal/mol@LB@Unfolding Energy - sRNA 1.20319 kcal/mol@LB@@LB@Position - mRNA 196 -- 205@LB@Position - sRNA 9 -- 18@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 9 -- 15@LB@
58	0.00518	0.3024	b4068	yjcH	-12.19	0.050580	228 -- 240	8 -- 21	DUF485 family inner membrane protein	_____________227____________241\n_____________\|______________\|\n5'-ACC...GGAUA__A___________AUUUC...UGC-3'\n______________GA_GAC_AAUGCGC\n______________\|\|_:\|\|_\|\|\|\|\|\|\|\n______________CU_UUG_UUACGCG\n3'-UUU...UACUA__A___U_______CAGAAAG-5'\n_____________\|______________\|\n_____________22_____________7\n	234 -- 240	8 -- 14	-14.481 kcal/mol	1.05266 kcal/mol	1.23638 kcal/mol	227 241@LB@ \| \|@LB@5'-ACC...GGAUA A AUUUC...UGC-3'@LB@ GA GAC AAUGCGC@LB@ \|\| :\|\| \|\|\|\|\|\|\|@LB@ CU UUG UUACGCG@LB@3'-UUU...UACUA A U CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -12.19 kcal/mol@LB@Hybridization Energy -14.481 kcal/mol@LB@Unfolding Energy - mRNA 1.05266 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 228 -- 240@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 8 -- 14@LB@
126	0.01241	0.3104	b4379	yjjW	-11.82	0.058804	207 -- 217	8 -- 18	putative pyruvate formate lyase activating enzyme	_____________206_________218\n_____________\|___________\|\n5'-CGG...UGAAC___________UUUAG...UGC-3'\n______________AGCAGAUGCGC\n______________\|:\|\|:\|\|\|\|\|\|\n______________UUGUUUACGCG\n3'-UUU...UACUA___________CAGAAAG-5'\n_____________\|___________\|\n_____________19__________7\n	211 -- 217	8 -- 14	-16.9543 kcal/mol	3.92931 kcal/mol	1.20363 kcal/mol	206 218@LB@ \| \|@LB@5'-CGG...UGAAC UUUAG...UGC-3'@LB@ AGCAGAUGCGC@LB@ \|:\|\|:\|\|\|\|\|\|@LB@ UUGUUUACGCG@LB@3'-UUU...UACUA CAGAAAG-5'@LB@ \| \|@LB@ 19 7@LB@@LB@@LB@Energy -11.82 kcal/mol@LB@Hybridization Energy -16.9543 kcal/mol@LB@Unfolding Energy - mRNA 3.92931 kcal/mol@LB@Unfolding Energy - sRNA 1.20363 kcal/mol@LB@@LB@Position - mRNA 207 -- 217@LB@Position - sRNA 8 -- 18@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 8 -- 14@LB@
110	0.01118	0.3104	b1726	yniB	-10.98	0.082506	169 -- 185	3 -- 23	putative inner membrane protein	_____________168___________________186\n_____________\|_____________________\|\n5'-AAG...ACUAA_____________________AAUCA...UGA-3'\n______________GUGA_AACGA___CGCGUCUU\n______________:\|\|\|_\|\|\|:\|___\|\|\|\|\|\|\|\|\n______________UACU_UUGUU___GCGCAGAA\n3'-UUU...CCUAC____A_____UAC________AG-5'\n_____________\|_____________________\|\n_____________24____________________2\n	179 -- 185	3 -- 9	-16.6558 kcal/mol	3.14383 kcal/mol	2.53367 kcal/mol	168 186@LB@ \| \|@LB@5'-AAG...ACUAA AAUCA...UGA-3'@LB@ GUGA AACGA CGCGUCUU@LB@ :\|\|\| \|\|\|:\| \|\|\|\|\|\|\|\|@LB@ UACU UUGUU GCGCAGAA@LB@3'-UUU...CCUAC A UAC AG-5'@LB@ \| \|@LB@ 24 2@LB@@LB@@LB@Energy -10.98 kcal/mol@LB@Hybridization Energy -16.6558 kcal/mol@LB@Unfolding Energy - mRNA 3.14383 kcal/mol@LB@Unfolding Energy - sRNA 2.53367 kcal/mol@LB@@LB@Position - mRNA 169 -- 185@LB@Position - sRNA 3 -- 23@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 3 -- 9@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@
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@
177	0.01751	0.3104	b2900	yqfB	-9.18	0.165418	52 -- 70	1 -- 17	UPF0267 family protein	_____________51__________________71\n_____________\|___________________\|\n5'-UUC...ACGUC________U__GCC_____CCGCC...UCA-3'\n______________ACAAAUGC_CG___CUUUU\n______________\|\|\|\|\|\|\|\|_\|\|___\|\|\|\|:\n______________UGUUUACG_GC___GAAAG\n3'-UUU...ACUAU________C__A_______-5'\n_____________\|__________________\|\n_____________18_________________1\n	53 -- 59	10 -- 16	-13.5578 kcal/mol	3.13415 kcal/mol	1.23994 kcal/mol	51 71@LB@ \| \|@LB@5'-UUC...ACGUC U GCC CCGCC...UCA-3'@LB@ ACAAAUGC CG CUUUU@LB@ \|\|\|\|\|\|\|\| \|\| \|\|\|\|:@LB@ UGUUUACG GC GAAAG@LB@3'-UUU...ACUAU C A -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -9.18 kcal/mol@LB@Hybridization Energy -13.5578 kcal/mol@LB@Unfolding Energy - mRNA 3.13415 kcal/mol@LB@Unfolding Energy - sRNA 1.23994 kcal/mol@LB@@LB@Position - mRNA 52 -- 70@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 10 -- 16@LB@
111	0.01125	0.3104	b0102	zapD	-10.07	0.117779	99 -- 113	8 -- 22	FtsZ stabilizer	_____________98______________114\n_____________\|_______________\|\n5'-ACC...GUCAU_________CG____ACCGG...CCA-3'\n______________UGAUAAUAA__GCGC\n______________\|\|\|\|\|\|:\|\|__\|\|\|\|\n______________ACUAUUGUU__CGCG\n3'-UUU...CUACU_________UA____CAGAAAG-5'\n_____________\|_______________\|\n_____________23______________7\n	101 -- 107	14 -- 20	-15.8633 kcal/mol	4.55182 kcal/mol	1.23838 kcal/mol	98 114@LB@ \| \|@LB@5'-ACC...GUCAU CG ACCGG...CCA-3'@LB@ UGAUAAUAA GCGC@LB@ \|\|\|\|\|\|:\|\| \|\|\|\|@LB@ ACUAUUGUU CGCG@LB@3'-UUU...CUACU UA CAGAAAG-5'@LB@ \| \|@LB@ 23 7@LB@@LB@@LB@Energy -10.07 kcal/mol@LB@Hybridization Energy -15.8633 kcal/mol@LB@Unfolding Energy - mRNA 4.55182 kcal/mol@LB@Unfolding Energy - sRNA 1.23838 kcal/mol@LB@@LB@Position - mRNA 99 -- 113@LB@Position - sRNA 8 -- 22@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 14 -- 20@LB@
50	0.004415	0.299	b0752	zitB	-14.03	0.023662	243 -- 258	5 -- 21	zinc efflux system	_____________242_______________259\n_____________\|_________________\|\n5'-CGC...CAGAA____________U____GCUUG...UGG-3'\n______________GAUAAUAA_UGC_CGUC\n______________\|\|\|\|\|:\|\|_\|\|\|_\|\|\|\|\n______________CUAUUGUU_ACG_GCAG\n3'-UUU...UACUA________U___C____AAAG-5'\n_____________\|_________________\|\n_____________22________________4\n	244 -- 250	14 -- 20	-17.36 kcal/mol	2.08049 kcal/mol	1.24955 kcal/mol	242 259@LB@ \| \|@LB@5'-CGC...CAGAA U GCUUG...UGG-3'@LB@ GAUAAUAA UGC CGUC@LB@ \|\|\|\|\|:\|\| \|\|\| \|\|\|\|@LB@ CUAUUGUU ACG GCAG@LB@3'-UUU...UACUA U C AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -14.03 kcal/mol@LB@Hybridization Energy -17.36 kcal/mol@LB@Unfolding Energy - mRNA 2.08049 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 243 -- 258@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 14 -- 20@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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