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
98	0.009835	0.3104	b1213	ychQ	-13.77	0.026325	164 -- 179	6 -- 23	SIRB family inner membrane protein	_____________163________________180\n_____________\|__________________\|\n5'-GAC...CUAUG__________________AACGC...AUC-3'\n______________GUGAUAACGA__GCGCGU\n______________:\|\|\|\|\|\|\|:\|__\|\|\|\|\|\|\n______________UACUAUUGUU__CGCGCA\n3'-UUU...CCUAC__________UA______GAAAG-5'\n_____________\|__________________\|\n_____________24_________________5\n	167 -- 173	14 -- 20	-20.3809 kcal/mol	4.08318 kcal/mol	2.52311 kcal/mol	163 180@LB@ \| \|@LB@5'-GAC...CUAUG AACGC...AUC-3'@LB@ GUGAUAACGA GCGCGU@LB@ :\|\|\|\|\|\|\|:\| \|\|\|\|\|\|@LB@ UACUAUUGUU CGCGCA@LB@3'-UUU...CCUAC UA GAAAG-5'@LB@ \| \|@LB@ 24 5@LB@@LB@@LB@Energy -13.77 kcal/mol@LB@Hybridization Energy -20.3809 kcal/mol@LB@Unfolding Energy - mRNA 4.08318 kcal/mol@LB@Unfolding Energy - sRNA 2.52311 kcal/mol@LB@@LB@Position - mRNA 164 -- 179@LB@Position - sRNA 6 -- 23@LB@Position Seed - mRNA 167 -- 173@LB@Position Seed - sRNA 14 -- 20@LB@
75	0.006972	0.3087	b4348	hsdS	-13.63	0.027959	190 -- 211	7 -- 29	specificity determinant for hsdM and hsdR	_____________189_____________________212\n_____________\|_______________________\|\n5'-CUG...UUGGU_______A_____________G_GAAAU...UAA-3'\n______________GGGGUGA_GG_AAUGAGUGCG_G\n______________\|\|\|:\|\|\|_\|:_\|\|::\|:\|\|\|\|_\|\n______________CCCUACU_CU_UUGUUUACGC_C\n3'-UUU...UAAGU_______A__A__________G_AGAAAG-5'\n_____________\|_______________________\|\n_____________30______________________6\n	203 -- 209	9 -- 15	-24.9713 kcal/mol	3.9222 kcal/mol	7.41901 kcal/mol	189 212@LB@ \| \|@LB@5'-CUG...UUGGU A G GAAAU...UAA-3'@LB@ GGGGUGA GG AAUGAGUGCG G@LB@ \|\|\|:\|\|\| \|: \|\|::\|:\|\|\|\| \|@LB@ CCCUACU CU UUGUUUACGC C@LB@3'-UUU...UAAGU A A G AGAAAG-5'@LB@ \| \|@LB@ 30 6@LB@@LB@@LB@Energy -13.63 kcal/mol@LB@Hybridization Energy -24.9713 kcal/mol@LB@Unfolding Energy - mRNA 3.9222 kcal/mol@LB@Unfolding Energy - sRNA 7.41901 kcal/mol@LB@@LB@Position - mRNA 190 -- 211@LB@Position - sRNA 7 -- 29@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 9 -- 15@LB@
176	0.01748	0.3104	b0435	bolA	-9.78	0.131850	202 -- 220	4 -- 22	stationary-phase morphogene transcriptional repressor for mreB; also regulator for dacA dacC and ampC	_____________201_________________221\n_____________\|___________________\|\n5'-UGA...UUUCA________C___A___GA_AGAAG...CCG-3'\n______________UGAUGAUA_GUG_GCG__U\n______________\|\|\|\|:\|:\|_:\|\|_\|\|\|__\|\n______________ACUAUUGU_UAC_CGC__A\n3'-UUU...CUACU________U___G___AG_AAG-5'\n_____________\|___________________\|\n_____________23__________________3\n	203 -- 209	15 -- 21	-14.8727 kcal/mol	3.8346 kcal/mol	1.2572 kcal/mol	201 221@LB@ \| \|@LB@5'-UGA...UUUCA C A GA AGAAG...CCG-3'@LB@ UGAUGAUA GUG GCG U@LB@ \|\|\|\|:\|:\| :\|\| \|\|\| \|@LB@ ACUAUUGU UAC CGC A@LB@3'-UUU...CUACU U G AG AAG-5'@LB@ \| \|@LB@ 23 3@LB@@LB@@LB@Energy -9.78 kcal/mol@LB@Hybridization Energy -14.8727 kcal/mol@LB@Unfolding Energy - mRNA 3.8346 kcal/mol@LB@Unfolding Energy - sRNA 1.2572 kcal/mol@LB@@LB@Position - mRNA 202 -- 220@LB@Position - sRNA 4 -- 22@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 15 -- 21@LB@
107	0.01107	0.3104	b0723	sdhA	-7.08	0.348281	169 -- 200	7 -- 42	succinate dehydrogenase flavoprotein subunit	_____________168__________________________________201\n_____________\|____________________________________\|\n5'-GGU...ACGUG____A________UU_______UG____________AUGAA...GUG-3'\n______________AUUU_UGGAUUCG___GUGGUG_____GGGUGUGUG\n______________\|\|:\|_\|\|:\|\|\|\|:___:\|\|:\|\|_____:::\|\|:\|:\|\n______________UAGA_ACUUAAGU___UACUAC_____UUUACGCGC\n3'-UUU...UAAAG____G________CCC______UAUUG_________AGAAAG-5'\n_____________\|____________________________________\|\n_____________43___________________________________6\n	194 -- 200	7 -- 13	-22.2639 kcal/mol	5.75915 kcal/mol	9.42962 kcal/mol	168 201@LB@ \| \|@LB@5'-GGU...ACGUG A UU UG AUGAA...GUG-3'@LB@ AUUU UGGAUUCG GUGGUG GGGUGUGUG@LB@ \|\|:\| \|\|:\|\|\|\|: :\|\|:\|\| :::\|\|:\|:\|@LB@ UAGA ACUUAAGU UACUAC UUUACGCGC@LB@3'-UUU...UAAAG G CCC UAUUG AGAAAG-5'@LB@ \| \|@LB@ 43 6@LB@@LB@@LB@Energy -7.08 kcal/mol@LB@Hybridization Energy -22.2639 kcal/mol@LB@Unfolding Energy - mRNA 5.75915 kcal/mol@LB@Unfolding Energy - sRNA 9.42962 kcal/mol@LB@@LB@Position - mRNA 169 -- 200@LB@Position - sRNA 7 -- 42@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 7 -- 13@LB@
145	0.01404	0.3104	b0721	sdhC	-10.79	0.088833	202 -- 215	9 -- 22	succinate dehydrogenase membrane subunit binds cytochrome b556	_____________201____________216\n_____________\|______________\|\n5'-UCC...AUUCA______G_______AAAAA...CCG-3'\n______________UGAUAA_AAAUGUG\n______________\|\|\|\|\|\|_\|\|\|\|\|:\|\n______________ACUAUU_UUUACGC\n3'-UUU...CUACU______G_______GCAGAAAG-5'\n_____________\|______________\|\n_____________23_____________8\n	209 -- 215	9 -- 15	-14.1232 kcal/mol	2.09271 kcal/mol	1.23827 kcal/mol	201 216@LB@ \| \|@LB@5'-UCC...AUUCA G AAAAA...CCG-3'@LB@ UGAUAA AAAUGUG@LB@ \|\|\|\|\|\| \|\|\|\|\|:\|@LB@ ACUAUU UUUACGC@LB@3'-UUU...CUACU G GCAGAAAG-5'@LB@ \| \|@LB@ 23 8@LB@@LB@@LB@Energy -10.79 kcal/mol@LB@Hybridization Energy -14.1232 kcal/mol@LB@Unfolding Energy - mRNA 2.09271 kcal/mol@LB@Unfolding Energy - sRNA 1.23827 kcal/mol@LB@@LB@Position - mRNA 202 -- 215@LB@Position - sRNA 9 -- 22@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 9 -- 15@LB@
142	0.01346	0.3104	b0729	sucD	-11.71	0.061414	39 -- 57	3 -- 21	succinyl-CoA synthetase NAD(P)-binding alpha subunit	_____________38__________________58\n_____________\|___________________\|\n5'-GUU...GGCGC_________A___G__G__AACGU...CUA-3'\n______________GGUAGCAGA_GUG_GU_UU\n______________\|:\|\|:\|\|:\|_\|:\|_\|\|_\|\|\n______________CUAUUGUUU_CGC_CA_AA\n3'-UUU...UACUA_________A___G__G__AG-5'\n_____________\|___________________\|\n_____________22__________________2\n	41 -- 47	13 -- 19	-17.4316 kcal/mol	4.46052 kcal/mol	1.257 kcal/mol	38 58@LB@ \| \|@LB@5'-GUU...GGCGC A G G AACGU...CUA-3'@LB@ GGUAGCAGA GUG GU UU@LB@ \|:\|\|:\|\|:\| \|:\| \|\| \|\|@LB@ CUAUUGUUU CGC CA AA@LB@3'-UUU...UACUA A G G AG-5'@LB@ \| \|@LB@ 22 2@LB@@LB@@LB@Energy -11.71 kcal/mol@LB@Hybridization Energy -17.4316 kcal/mol@LB@Unfolding Energy - mRNA 4.46052 kcal/mol@LB@Unfolding Energy - sRNA 1.257 kcal/mol@LB@@LB@Position - mRNA 39 -- 57@LB@Position - sRNA 3 -- 21@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 13 -- 19@LB@
105	0.01074	0.3104	b3791	wecE	-13.91	0.024834	1 -- 12	7 -- 18	TDP-4-oxo-6-deoxy-D-glucose transaminase	______________1___________13\n______________\|___________\|\n___________5'-____________AAUUG...CCC-3'\n______________GACAGAUGCGCG\n______________:\|\|\|:\|\|\|\|\|\|\|\n______________UUGUUUACGCGC\n3'-UUU...UACUA____________AGAAAG-5'\n_____________\|____________\|\n_____________19___________6\n	6 -- 12	7 -- 13	-19.4696 kcal/mol	4.34626 kcal/mol	1.20891 kcal/mol	1 13@LB@ \| \|@LB@ 5'- AAUUG...CCC-3'@LB@ GACAGAUGCGCG@LB@ :\|\|\|:\|\|\|\|\|\|\|@LB@ UUGUUUACGCGC@LB@3'-UUU...UACUA AGAAAG-5'@LB@ \| \|@LB@ 19 6@LB@@LB@@LB@Energy -13.91 kcal/mol@LB@Hybridization Energy -19.4696 kcal/mol@LB@Unfolding Energy - mRNA 4.34626 kcal/mol@LB@Unfolding Energy - sRNA 1.20891 kcal/mol@LB@@LB@Position - mRNA 1 -- 12@LB@Position - sRNA 7 -- 18@LB@Position Seed - mRNA 6 -- 12@LB@Position Seed - sRNA 7 -- 13@LB@
53	0.004896	0.3024	b3790	wecD	-9.15	0.167607	125 -- 139	7 -- 21	TDP-fucosamine acetyltransferase	_____________124_____________140\n_____________\|_______________\|\n5'-CUG...GGCUC_________G_____AAGCG...UGA-3'\n______________GAUGACGAG_GUGUG\n______________\|\|\|:\|\|:\|:_\|:\|:\|\n______________CUAUUGUUU_CGCGC\n3'-UUU...UACUA_________A_____AGAAAG-5'\n_____________\|_______________\|\n_____________22______________6\n	126 -- 132	14 -- 20	-15.9636 kcal/mol	5.57309 kcal/mol	1.24179 kcal/mol	124 140@LB@ \| \|@LB@5'-CUG...GGCUC G AAGCG...UGA-3'@LB@ GAUGACGAG GUGUG@LB@ \|\|\|:\|\|:\|: \|:\|:\|@LB@ CUAUUGUUU CGCGC@LB@3'-UUU...UACUA A AGAAAG-5'@LB@ \| \|@LB@ 22 6@LB@@LB@@LB@Energy -9.15 kcal/mol@LB@Hybridization Energy -15.9636 kcal/mol@LB@Unfolding Energy - mRNA 5.57309 kcal/mol@LB@Unfolding Energy - sRNA 1.24179 kcal/mol@LB@@LB@Position - mRNA 125 -- 139@LB@Position - sRNA 7 -- 21@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 14 -- 20@LB@
193	0.01896	0.3104	b3181	greA	-10.36	0.105339	194 -- 204	10 -- 20	transcript cleavage factor	_____________193_________205\n_____________\|___________\|\n5'-CGC...GAGGU___________AAGCU...UCG-3'\n______________AUAACAAAUGC\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________UAUUGUUUACG\n3'-UUU...ACUAC___________CGCAG...AAG-5'\n_____________\|___________\|\n_____________21__________9\n	198 -- 204	10 -- 16	-13.1767 kcal/mol	1.58941 kcal/mol	1.22774 kcal/mol	193 205@LB@ \| \|@LB@5'-CGC...GAGGU AAGCU...UCG-3'@LB@ AUAACAAAUGC@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ UAUUGUUUACG@LB@3'-UUU...ACUAC CGCAG...AAG-5'@LB@ \| \|@LB@ 21 9@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -13.1767 kcal/mol@LB@Unfolding Energy - mRNA 1.58941 kcal/mol@LB@Unfolding Energy - sRNA 1.22774 kcal/mol@LB@@LB@Position - mRNA 194 -- 204@LB@Position - sRNA 10 -- 20@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 10 -- 16@LB@
189	0.01853	0.3104	b3743	asnC	-7.74	0.278830	255 -- 266	5 -- 18	transcriptional activator of asnA; autorepressor	_____________254____________267\n_____________\|______________\|\n5'-AUU...UAAUG______________ACCGC...GCG-3'\n______________GGC_AAUGCGCG_C\n______________::\|_\|\|\|\|\|\|\|\|_\|\n______________UUG_UUACGCGC_G\n3'-UUU...UACUA___U________A_AAAG-5'\n_____________\|______________\|\n_____________19_____________4\n	259 -- 265	7 -- 13	-14.4034 kcal/mol	5.44099 kcal/mol	1.2243 kcal/mol	254 267@LB@ \| \|@LB@5'-AUU...UAAUG ACCGC...GCG-3'@LB@ GGC AAUGCGCG C@LB@ ::\| \|\|\|\|\|\|\|\| \|@LB@ UUG UUACGCGC G@LB@3'-UUU...UACUA U A AAAG-5'@LB@ \| \|@LB@ 19 4@LB@@LB@@LB@Energy -7.74 kcal/mol@LB@Hybridization Energy -14.4034 kcal/mol@LB@Unfolding Energy - mRNA 5.44099 kcal/mol@LB@Unfolding Energy - sRNA 1.2243 kcal/mol@LB@@LB@Position - mRNA 255 -- 266@LB@Position - sRNA 5 -- 18@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 7 -- 13@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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