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
185	0.01831	0.3104	b3164	pnp	-7.42	0.310961	131 -- 137	8 -- 14	polynucleotide phosphorylase/polyadenylase	_____________130_____138\n_____________\|_______\|\n5'-AGC...GCGAG_______AGAAG...UUA-3'\n______________GAUGCGC\n______________:\|\|\|\|\|\|\n______________UUACGCG\n3'-UUU...AUUGU_______CAGAAAG-5'\n_____________\|_______\|\n_____________15______7\n	131 -- 137	8 -- 14	-10.1419 kcal/mol	2.24272 kcal/mol	0.481462 kcal/mol	130 138@LB@ \| \|@LB@5'-AGC...GCGAG AGAAG...UUA-3'@LB@ GAUGCGC@LB@ :\|\|\|\|\|\|@LB@ UUACGCG@LB@3'-UUU...AUUGU CAGAAAG-5'@LB@ \| \|@LB@ 15 7@LB@@LB@@LB@Energy -7.42 kcal/mol@LB@Hybridization Energy -10.1419 kcal/mol@LB@Unfolding Energy - mRNA 2.24272 kcal/mol@LB@Unfolding Energy - sRNA 0.481462 kcal/mol@LB@@LB@Position - mRNA 131 -- 137@LB@Position - sRNA 8 -- 14@LB@Position Seed - mRNA 131 -- 137@LB@Position Seed - sRNA 8 -- 14@LB@
194	0.0191	0.3104	b2698	recX	-10.17	0.113250	93 -- 107	8 -- 22	regulatory protein for RecA	_____________92______________108\n_____________\|_______________\|\n5'-AAA...GUAGA__________G____AGCAG...GAC-3'\n______________UGAUAGCGAA_GCGU\n______________\|\|\|\|\|:\|:\|\|_\|\|\|:\n______________ACUAUUGUUU_CGCG\n3'-UUU...CUACU__________A____CAGAAAG-5'\n_____________\|_______________\|\n_____________23______________7\n	96 -- 102	13 -- 19	-16.2974 kcal/mol	4.88496 kcal/mol	1.23838 kcal/mol	92 108@LB@ \| \|@LB@5'-AAA...GUAGA G AGCAG...GAC-3'@LB@ UGAUAGCGAA GCGU@LB@ \|\|\|\|\|:\|:\|\| \|\|\|:@LB@ ACUAUUGUUU CGCG@LB@3'-UUU...CUACU A CAGAAAG-5'@LB@ \| \|@LB@ 23 7@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -16.2974 kcal/mol@LB@Unfolding Energy - mRNA 4.88496 kcal/mol@LB@Unfolding Energy - sRNA 1.23838 kcal/mol@LB@@LB@Position - mRNA 93 -- 107@LB@Position - sRNA 8 -- 22@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 13 -- 19@LB@
199	0.01944	0.3104	b3657	yicJ	-13.22	0.033173	129 -- 161	8 -- 45	putative transporter	_____________128_____________________________________162\n_____________\|_______________________________________\|\n5'-CAG...GAAUA_________CA_____________UU____A________UAUCG...UGU-3'\n______________UUCG_CUCU_____CAGGGAUGGU____AC_AAAUGCGU\n______________\|\|\|:_\|\|\|\|_____\|\|\|\|\|\|\|\|:\|____\|\|_\|\|\|\|\|\|\|:\n______________AAGU_GAGA_____GUCCCUACUA____UG_UUUACGCG\n3'-UUU...UUUUA____A____CUUAA__________CUAU___________CAGAAAG-5'\n_____________\|_______________________________________\|\n_____________46______________________________________7\n	155 -- 161	8 -- 14	-30.3918 kcal/mol	7.7216 kcal/mol	9.45195 kcal/mol	128 162@LB@ \| \|@LB@5'-CAG...GAAUA CA UU A UAUCG...UGU-3'@LB@ UUCG CUCU CAGGGAUGGU AC AAAUGCGU@LB@ \|\|\|: \|\|\|\| \|\|\|\|\|\|\|\|:\| \|\| \|\|\|\|\|\|\|:@LB@ AAGU GAGA GUCCCUACUA UG UUUACGCG@LB@3'-UUU...UUUUA A CUUAA CUAU CAGAAAG-5'@LB@ \| \|@LB@ 46 7@LB@@LB@@LB@Energy -13.22 kcal/mol@LB@Hybridization Energy -30.3918 kcal/mol@LB@Unfolding Energy - mRNA 7.7216 kcal/mol@LB@Unfolding Energy - sRNA 9.45195 kcal/mol@LB@@LB@Position - mRNA 129 -- 161@LB@Position - sRNA 8 -- 45@LB@Position Seed - mRNA 155 -- 161@LB@Position Seed - sRNA 8 -- 14@LB@
93	0.009444	0.3104	b3822	recQ	-7.42	0.310549	176 -- 212	9 -- 45	ATP-dependent DNA helicase	_____________175____________________________________213\n_____________\|______________________________________\|\n5'-CGC...CUGUU________A__CAA__________AU______CAG___GAAGU...UUA-3'\n______________UUUAUUUC_GG___UC_GGGGUGA__GUGGCG___GCG\n______________\|\|:\|\|:\|\|_\|:___\|\|_\|\|\|:\|\|\|__:\|::\|:___\|\|\|\n______________AAGUAGAG_CU___AG_CCCUACU__UAUUGU___CGC\n3'-UUU...UUUUA________A__UA___U_______AC______UUA___GCAGAAAG-5'\n_____________\|______________________________________\|\n_____________46_____________________________________8\n	192 -- 198	23 -- 29	-25.6556 kcal/mol	8.78202 kcal/mol	9.45193 kcal/mol	175 213@LB@ \| \|@LB@5'-CGC...CUGUU A CAA AU CAG GAAGU...UUA-3'@LB@ UUUAUUUC GG UC GGGGUGA GUGGCG GCG@LB@ \|\|:\|\|:\|\| \|: \|\| \|\|\|:\|\|\| :\|::\|: \|\|\|@LB@ AAGUAGAG CU AG CCCUACU UAUUGU CGC@LB@3'-UUU...UUUUA A UA U AC UUA GCAGAAAG-5'@LB@ \| \|@LB@ 46 8@LB@@LB@@LB@Energy -7.42 kcal/mol@LB@Hybridization Energy -25.6556 kcal/mol@LB@Unfolding Energy - mRNA 8.78202 kcal/mol@LB@Unfolding Energy - sRNA 9.45193 kcal/mol@LB@@LB@Position - mRNA 176 -- 212@LB@Position - sRNA 9 -- 45@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 23 -- 29@LB@
125	0.01241	0.3104	b0002	thrA	-8.21	0.235915	191 -- 205	9 -- 21	Bifunctional aspartokinase/homoserine dehydrogenase 1	_____________190_____________206\n_____________\|_______________\|\n5'-CCA...AACGA________CC_____AGUGU...UGG-3'\n______________GGUAACAA__AUGCG\n______________\|:\|\|\|\|\|\|__\|\|\|\|\|\n______________CUAUUGUU__UACGC\n3'-UUU...UACUA_______________GCAGAAAG-5'\n_____________\|_______________\|\n_____________22______________8\n	192 -- 198	14 -- 20	-12.9357 kcal/mol	3.48482 kcal/mol	1.23627 kcal/mol	190 206@LB@ \| \|@LB@5'-CCA...AACGA CC AGUGU...UGG-3'@LB@ GGUAACAA AUGCG@LB@ \|:\|\|\|\|\|\| \|\|\|\|\|@LB@ CUAUUGUU UACGC@LB@3'-UUU...UACUA GCAGAAAG-5'@LB@ \| \|@LB@ 22 8@LB@@LB@@LB@Energy -8.21 kcal/mol@LB@Hybridization Energy -12.9357 kcal/mol@LB@Unfolding Energy - mRNA 3.48482 kcal/mol@LB@Unfolding Energy - sRNA 1.23627 kcal/mol@LB@@LB@Position - mRNA 191 -- 205@LB@Position - sRNA 9 -- 21@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 14 -- 20@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@
168	0.01645	0.3104	b3720	bglH	-8.64	0.202347	15 -- 28	9 -- 22	carbohydrate-specific outer membrane porin cryptic	_____________14_____________29\n_____________\|______________\|\n5'-AUU...GAUCG_________UG___AAGGA...GCC-3'\n______________UGAUGAUAA__GCG\n______________\|\|\|\|:\|:\|\|__\|\|\|\n______________ACUAUUGUU__CGC\n3'-UUU...CUACU_________UA___GCAGAAAG-5'\n_____________\|______________\|\n_____________23_____________8\n	17 -- 23	14 -- 20	-13.7208 kcal/mol	3.8428 kcal/mol	1.23827 kcal/mol	14 29@LB@ \| \|@LB@5'-AUU...GAUCG UG AAGGA...GCC-3'@LB@ UGAUGAUAA GCG@LB@ \|\|\|\|:\|:\|\| \|\|\|@LB@ ACUAUUGUU CGC@LB@3'-UUU...CUACU UA GCAGAAAG-5'@LB@ \| \|@LB@ 23 8@LB@@LB@@LB@Energy -8.64 kcal/mol@LB@Hybridization Energy -13.7208 kcal/mol@LB@Unfolding Energy - mRNA 3.8428 kcal/mol@LB@Unfolding Energy - sRNA 1.23827 kcal/mol@LB@@LB@Position - mRNA 15 -- 28@LB@Position - sRNA 9 -- 22@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 14 -- 20@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@
35	0.002165	0.2094	b2714	ascG	-14.61	0.018547	188 -- 213	10 -- 30	asc operon transcriptional repressor; prpBC operon repressor	_____________187________________________214\n_____________\|__________________________\|\n5'-AAA...UGUAA________AAA_________CG____UGGAA...AAG-3'\n______________AGGGAUGA___UGAUGACGA__AUGC\n______________\|\|\|\|\|\|\|\|___\|\|\|\|:\|\|:\|__\|\|\|\|\n______________UCCCUACU___ACUAUUGUU__UACG\n3'-UUU...UUAAG__________________________CGCAG...AAG-5'\n_____________\|__________________________\|\n_____________31_________________________9\n	201 -- 207	14 -- 20	-25.4703 kcal/mol	3.44882 kcal/mol	7.41066 kcal/mol	187 214@LB@ \| \|@LB@5'-AAA...UGUAA AAA CG UGGAA...AAG-3'@LB@ AGGGAUGA UGAUGACGA AUGC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|:\|\|:\| \|\|\|\|@LB@ UCCCUACU ACUAUUGUU UACG@LB@3'-UUU...UUAAG CGCAG...AAG-5'@LB@ \| \|@LB@ 31 9@LB@@LB@@LB@Energy -14.61 kcal/mol@LB@Hybridization Energy -25.4703 kcal/mol@LB@Unfolding Energy - mRNA 3.44882 kcal/mol@LB@Unfolding Energy - sRNA 7.41066 kcal/mol@LB@@LB@Position - mRNA 188 -- 213@LB@Position - sRNA 10 -- 30@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 14 -- 20@LB@
38	0.002512	0.2224	b0436	tig	-7.88	0.265562	192 -- 204	10 -- 21	peptidyl-prolyl cis/trans isomerase (trigger factor)	_____________191___________205\n_____________\|_____________\|\n5'-UAC...UUUGA_______A_____AAGUU...UCA-3'\n______________GGUAACA_GAUGC\n______________\|:\|\|\|\|\|_:\|\|\|\|\n______________CUAUUGU_UUACG\n3'-UUU...UACUA_____________CGCAG...AAG-5'\n_____________\|_____________\|\n_____________22____________9\n	192 -- 198	15 -- 21	-12.2618 kcal/mol	3.15229 kcal/mol	1.23076 kcal/mol	191 205@LB@ \| \|@LB@5'-UAC...UUUGA A AAGUU...UCA-3'@LB@ GGUAACA GAUGC@LB@ \|:\|\|\|\|\| :\|\|\|\|@LB@ CUAUUGU UUACG@LB@3'-UUU...UACUA CGCAG...AAG-5'@LB@ \| \|@LB@ 22 9@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -12.2618 kcal/mol@LB@Unfolding Energy - mRNA 3.15229 kcal/mol@LB@Unfolding Energy - sRNA 1.23076 kcal/mol@LB@@LB@Position - mRNA 192 -- 204@LB@Position - sRNA 10 -- 21@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 15 -- 21@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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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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