Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
186	0.02184	0.3768	b1256	ompW	-5.92	0.201836	13 -- 38	30 -- 57	outer membrane protein W		_____________12___________________________39\n_____________\|____________________________\|\n5'-GAC...UUAAU______GU______A_____________UUGAU...CUG-3'\n______________AUUUGC___AGCGA_AA_UAUUUAAAAA\n______________\|:\|\|\|\|___\|\|\|:\|_\|\|_:\|:\|\|\|\|\|\|\|\n______________UGAACG___UCGUU_UU_GUGAAUUUUU\n3'-UUU...UACUU______AAU_____C__C__________UAAGC...CAA-5'\n_____________\|____________________________\|\n_____________58___________________________29\n	32 -- 38	30 -- 36	-16.1426 kcal/mol	3.99952 kcal/mol	6.22352 kcal/mol	12 39@LB@ \| \|@LB@5'-GAC...UUAAU GU A UUGAU...CUG-3'@LB@ AUUUGC AGCGA AA UAUUUAAAAA@LB@ \|:\|\|\|\| \|\|\|:\| \|\| :\|:\|\|\|\|\|\|\|@LB@ UGAACG UCGUU UU GUGAAUUUUU@LB@3'-UUU...UACUU AAU C C UAAGC...CAA-5'@LB@ \| \|@LB@ 58 29@LB@@LB@@LB@Energy -5.92 kcal/mol@LB@Hybridization Energy -16.1426 kcal/mol@LB@Unfolding Energy - mRNA 3.99952 kcal/mol@LB@Unfolding Energy - sRNA 6.22352 kcal/mol@LB@@LB@Position - mRNA 13 -- 38@LB@Position - sRNA 30 -- 57@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 30 -- 36@LB@
93	0.006966	0.2379	b0436	tig	-6.81	0.123164	173 -- 190	25 -- 42	peptidyl-prolyl cis/trans isomerase (trigger factor)		_____________172________________191\n_____________\|__________________\|\n5'-UAC...UGACC_______GU__UUU____AGGUA...UCA-3'\n______________GAGCACU__GA___UUUG\n______________:\|\|\|\|\|\|__:\|___\|\|:\|\n______________UUCGUGA__UU___AAGC\n3'-UUU...CGUUC_______AU__UUU____AAUGU...CAA-5'\n_____________\|__________________\|\n_____________43_________________24\n	173 -- 179	36 -- 42	-10.673 kcal/mol	2.21437 kcal/mol	1.64855 kcal/mol	172 191@LB@ \| \|@LB@5'-UAC...UGACC GU UUU AGGUA...UCA-3'@LB@ GAGCACU GA UUUG@LB@ :\|\|\|\|\|\| :\| \|\|:\|@LB@ UUCGUGA UU AAGC@LB@3'-UUU...CGUUC AU UUU AAUGU...CAA-5'@LB@ \| \|@LB@ 43 24@LB@@LB@@LB@Energy -6.81 kcal/mol@LB@Hybridization Energy -10.673 kcal/mol@LB@Unfolding Energy - mRNA 2.21437 kcal/mol@LB@Unfolding Energy - sRNA 1.64855 kcal/mol@LB@@LB@Position - mRNA 173 -- 190@LB@Position - sRNA 25 -- 42@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 36 -- 42@LB@
137	0.01315	0.3087	b2239	glpQ	-7.04	0.107729	242 -- 248	36 -- 42	periplasmic glycerophosphodiester phosphodiesterase		_____________241_____249\n_____________\|_______\|\n5'-CGG...AUGAU_______AUAGU...UCA-3'\n______________GAGCACU\n______________:\|\|\|\|\|\|\n______________UUCGUGA\n3'-UUU...CGUUC_______AUUUU...CAA-5'\n_____________\|_______\|\n_____________43______35\n	242 -- 248	36 -- 42	-9.09813 kcal/mol	0.455964 kcal/mol	1.60154 kcal/mol	241 249@LB@ \| \|@LB@5'-CGG...AUGAU AUAGU...UCA-3'@LB@ GAGCACU@LB@ :\|\|\|\|\|\|@LB@ UUCGUGA@LB@3'-UUU...CGUUC AUUUU...CAA-5'@LB@ \| \|@LB@ 43 35@LB@@LB@@LB@Energy -7.04 kcal/mol@LB@Hybridization Energy -9.09813 kcal/mol@LB@Unfolding Energy - mRNA 0.455964 kcal/mol@LB@Unfolding Energy - sRNA 1.60154 kcal/mol@LB@@LB@Position - mRNA 242 -- 248@LB@Position - sRNA 36 -- 42@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 36 -- 42@LB@
156	0.01673	0.3455	b0740	tolB	-6.75	0.127692	202 -- 229	33 -- 61	periplasmic protein		_____________201____________________________230\n_____________\|______________________________\|\n5'-UCC...UAUGA______AG__A_________U_________UUUUC...CCG-3'\n______________UGAAGC__GC_UUA__CGAG_AGCAUUUGG\n______________\|\|\|\|:\|__\|\|_\|\|\|__\|:\|\|_\|\|\|\|:\|\|::\n______________ACUUUG__CG_AAU__GUUC_UCGUGAAUU\n3'-UUU...GCCCU______AA______UC____U_________UUUUA...CAA-5'\n_____________\|______________________________\|\n_____________62_____________________________32\n	222 -- 228	34 -- 40	-20.0945 kcal/mol	5.97693 kcal/mol	7.37029 kcal/mol	201 230@LB@ \| \|@LB@5'-UCC...UAUGA AG A U UUUUC...CCG-3'@LB@ UGAAGC GC UUA CGAG AGCAUUUGG@LB@ \|\|\|\|:\| \|\| \|\|\| \|:\|\| \|\|\|\|:\|\|::@LB@ ACUUUG CG AAU GUUC UCGUGAAUU@LB@3'-UUU...GCCCU AA UC U UUUUA...CAA-5'@LB@ \| \|@LB@ 62 32@LB@@LB@@LB@Energy -6.75 kcal/mol@LB@Hybridization Energy -20.0945 kcal/mol@LB@Unfolding Energy - mRNA 5.97693 kcal/mol@LB@Unfolding Energy - sRNA 7.37029 kcal/mol@LB@@LB@Position - mRNA 202 -- 229@LB@Position - sRNA 33 -- 61@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 34 -- 40@LB@
140	0.01344	0.3093	b0426	yajQ	-3.92	0.510019	240 -- 246	37 -- 43	phage Phi6 host factor ATP/GTP binding protein		_____________239_____247\n_____________\|_______\|\n5'-UAA...UUCAG_______GUAAC...GUA-3'\n______________GAAGCAC\n______________\|\|\|\|\|\|\|\n______________CUUCGUG\n3'-UUU...UCGUU_______AAUUU...CAA-5'\n_____________\|_______\|\n_____________44______36\n	240 -- 246	37 -- 43	-10.1802 kcal/mol	2.59742 kcal/mol	3.6595 kcal/mol	239 247@LB@ \| \|@LB@5'-UAA...UUCAG GUAAC...GUA-3'@LB@ GAAGCAC@LB@ \|\|\|\|\|\|\|@LB@ CUUCGUG@LB@3'-UUU...UCGUU AAUUU...CAA-5'@LB@ \| \|@LB@ 44 36@LB@@LB@@LB@Energy -3.92 kcal/mol@LB@Hybridization Energy -10.1802 kcal/mol@LB@Unfolding Energy - mRNA 2.59742 kcal/mol@LB@Unfolding Energy - sRNA 3.6595 kcal/mol@LB@@LB@Position - mRNA 240 -- 246@LB@Position - sRNA 37 -- 43@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 37 -- 43@LB@
167	0.01879	0.3614	b4383	deoB	-8.94	0.033088	90 -- 118	37 -- 59	phosphopentomutase		_____________89____________________________119\n_____________\|_____________________________\|\n5'-AGG...CAAUU________CGAUA_____CC__A______ACCAA...AUA-3'\n______________AAACUUGC_____AAGCA__GG_AAGCAC\n______________\|\|\|\|\|\|\|\|_____\|\|\|\|\|__:\|_\|\|\|\|\|\|\n______________UUUGAACG_____UUCGU__UC_UUCGUG\n3'-UUU...CCUAC________AA___________________AAUUU...CAA-5'\n_____________\|_____________________________\|\n_____________60____________________________36\n	91 -- 97	52 -- 58	-21.3309 kcal/mol	6.14475 kcal/mol	6.24627 kcal/mol	89 119@LB@ \| \|@LB@5'-AGG...CAAUU CGAUA CC A ACCAA...AUA-3'@LB@ AAACUUGC AAGCA GG AAGCAC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\| :\| \|\|\|\|\|\|@LB@ UUUGAACG UUCGU UC UUCGUG@LB@3'-UUU...CCUAC AA AAUUU...CAA-5'@LB@ \| \|@LB@ 60 36@LB@@LB@@LB@Energy -8.94 kcal/mol@LB@Hybridization Energy -21.3309 kcal/mol@LB@Unfolding Energy - mRNA 6.14475 kcal/mol@LB@Unfolding Energy - sRNA 6.24627 kcal/mol@LB@@LB@Position - mRNA 90 -- 118@LB@Position - sRNA 37 -- 59@LB@Position Seed - mRNA 91 -- 97@LB@Position Seed - sRNA 52 -- 58@LB@
16	0.0003675	0.07398	b0566	envY	-6.67	0.133095	149 -- 159	37 -- 47	porin thermoregulatory transcriptional activator	b1499 b0564 b3515 b4116 b3516	_____________148_________160\n_____________\|___________\|\n5'-GGC...CUCAU___________AGAUC...ACU-3'\n______________GCAGGAAGCAU\n______________\|\|\|:\|\|\|\|\|\|:\n______________CGUUCUUCGUG\n3'-UUU...GAAUU___________AAUUU...CAA-5'\n_____________\|___________\|\n_____________48__________36\n	153 -- 159	37 -- 43	-16.6622 kcal/mol	4.74809 kcal/mol	5.23944 kcal/mol	148 160@LB@ \| \|@LB@5'-GGC...CUCAU AGAUC...ACU-3'@LB@ GCAGGAAGCAU@LB@ \|\|\|:\|\|\|\|\|\|:@LB@ CGUUCUUCGUG@LB@3'-UUU...GAAUU AAUUU...CAA-5'@LB@ \| \|@LB@ 48 36@LB@@LB@@LB@Energy -6.67 kcal/mol@LB@Hybridization Energy -16.6622 kcal/mol@LB@Unfolding Energy - mRNA 4.74809 kcal/mol@LB@Unfolding Energy - sRNA 5.23944 kcal/mol@LB@@LB@Position - mRNA 149 -- 159@LB@Position - sRNA 37 -- 47@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 37 -- 43@LB@
183	0.02165	0.3768	b4201	priB	-4.41	0.419305	289 -- 298	45 -- 54	primosomal protein N		_____________288________299\n_____________\|__________\|\n5'-AGG...GUUCG__________UC-3'\n______________UGCUUGAGCA\n______________\|\|\|\|\|:\|\|\|\|\n______________ACGAAUUCGU\n3'-UUU...UUUGA__________UCUUC...CAA-5'\n_____________\|__________\|\n_____________55_________44\n	290 -- 296	47 -- 53	-14.7774 kcal/mol	4.46723 kcal/mol	5.90361 kcal/mol	288 299@LB@ \| \|@LB@5'-AGG...GUUCG UC-3'@LB@ UGCUUGAGCA@LB@ \|\|\|\|\|:\|\|\|\|@LB@ ACGAAUUCGU@LB@3'-UUU...UUUGA UCUUC...CAA-5'@LB@ \| \|@LB@ 55 44@LB@@LB@@LB@Energy -4.41 kcal/mol@LB@Hybridization Energy -14.7774 kcal/mol@LB@Unfolding Energy - mRNA 4.46723 kcal/mol@LB@Unfolding Energy - sRNA 5.90361 kcal/mol@LB@@LB@Position - mRNA 289 -- 298@LB@Position - sRNA 45 -- 54@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 47 -- 53@LB@
166	0.01873	0.3614	b0473	htpG	-6.61	0.137913	119 -- 133	26 -- 39	protein refolding molecular co-chaperone Hsp90 Hsp70-dependent; heat-shock protein; ATPase		_____________118_____________134\n_____________\|_______________\|\n5'-UCA...GCUCU_________UU____UCCCU...GUG-3'\n______________CGCUUGAAA__AUUC\n______________\|:\|\|\|:\|\|\|__\|\|\|\|\n______________GUGAAUUUU__UAAG\n3'-UUU...UCUUC_________U_____CAAUG...CAA-5'\n_____________\|_______________\|\n_____________40______________25\n	121 -- 127	31 -- 37	-10.0825 kcal/mol	1.82368 kcal/mol	1.64668 kcal/mol	118 134@LB@ \| \|@LB@5'-UCA...GCUCU UU UCCCU...GUG-3'@LB@ CGCUUGAAA AUUC@LB@ \|:\|\|\|:\|\|\| \|\|\|\|@LB@ GUGAAUUUU UAAG@LB@3'-UUU...UCUUC U CAAUG...CAA-5'@LB@ \| \|@LB@ 40 25@LB@@LB@@LB@Energy -6.61 kcal/mol@LB@Hybridization Energy -10.0825 kcal/mol@LB@Unfolding Energy - mRNA 1.82368 kcal/mol@LB@Unfolding Energy - sRNA 1.64668 kcal/mol@LB@@LB@Position - mRNA 119 -- 133@LB@Position - sRNA 26 -- 39@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 31 -- 37@LB@
62	0.00332	0.1645	b1305	pspB	-5.29	0.278747	189 -- 201	34 -- 46	psp operon transcription co-activator		_____________188___________202\n_____________\|_____________\|\n5'-AUU...UCGUC_____________UGAGC...GUG-3'\n______________UAAGGAGUACUUA\n______________:\|\|\|:\|\|:\|\|\|\|\|\n______________GUUCUUCGUGAAU\n3'-UUU...AAUUC_____________UUUUU...CAA-5'\n_____________\|_____________\|\n_____________47____________33\n	195 -- 201	34 -- 40	-14.7021 kcal/mol	3.41245 kcal/mol	5.99897 kcal/mol	188 202@LB@ \| \|@LB@5'-AUU...UCGUC UGAGC...GUG-3'@LB@ UAAGGAGUACUUA@LB@ :\|\|\|:\|\|:\|\|\|\|\|@LB@ GUUCUUCGUGAAU@LB@3'-UUU...AAUUC UUUUU...CAA-5'@LB@ \| \|@LB@ 47 33@LB@@LB@@LB@Energy -5.29 kcal/mol@LB@Hybridization Energy -14.7021 kcal/mol@LB@Unfolding Energy - mRNA 3.41245 kcal/mol@LB@Unfolding Energy - sRNA 5.99897 kcal/mol@LB@@LB@Position - mRNA 189 -- 201@LB@Position - sRNA 34 -- 46@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 34 -- 40@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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