Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
125	0.02442	0.6177	b3181	greA	-6.11	0.239901	243 -- 260	40 -- 56	transcript cleavage factor	_____________242_________________261\n_____________\|___________________\|\n5'-CGC...AAUUA__________CU_______CUGAA...UCG-3'\n______________CG_CGAAGAG__GGAUUUU\n______________\|\|_\|:\|\|\|\|\|__\|:\|\|\|\|:\n______________GC_GUUUCUC__CUUAAAG\n3'-UUU...ACCGG__A________________UAAAA...ACA-5'\n_____________\|___________________\|\n_____________57__________________39\n	245 -- 251	47 -- 53	-12.1125 kcal/mol	4.98158 kcal/mol	1.02557 kcal/mol	242 261@LB@ \| \|@LB@5'-CGC...AAUUA CU CUGAA...UCG-3'@LB@ CG CGAAGAG GGAUUUU@LB@ \|\| \|:\|\|\|\|\| \|:\|\|\|\|:@LB@ GC GUUUCUC CUUAAAG@LB@3'-UUU...ACCGG A UAAAA...ACA-5'@LB@ \| \|@LB@ 57 39@LB@@LB@@LB@Energy -6.11 kcal/mol@LB@Hybridization Energy -12.1125 kcal/mol@LB@Unfolding Energy - mRNA 4.98158 kcal/mol@LB@Unfolding Energy - sRNA 1.02557 kcal/mol@LB@@LB@Position - mRNA 243 -- 260@LB@Position - sRNA 40 -- 56@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 47 -- 53@LB@
126	0.02445	0.6177	b4364	yjjP	-5.95	0.256190	188 -- 200	42 -- 53	DUF1212 family inner membrane protein	_____________187___________201\n_____________\|_____________\|\n5'-UCA...UAUGA_______C_____AUGCA...UUU-3'\n______________CAAAGGG_GAGUU\n______________\|\|\|\|\|:\|_\|\|:\|\|\n______________GUUUCUC_CUUAA\n3'-UUU...GGGCA_____________AGUAA...ACA-5'\n_____________\|_____________\|\n_____________54____________41\n	188 -- 194	47 -- 53	-11.6429 kcal/mol	4.76073 kcal/mol	0.933904 kcal/mol	187 201@LB@ \| \|@LB@5'-UCA...UAUGA C AUGCA...UUU-3'@LB@ CAAAGGG GAGUU@LB@ \|\|\|\|\|:\| \|\|:\|\|@LB@ GUUUCUC CUUAA@LB@3'-UUU...GGGCA AGUAA...ACA-5'@LB@ \| \|@LB@ 54 41@LB@@LB@@LB@Energy -5.95 kcal/mol@LB@Hybridization Energy -11.6429 kcal/mol@LB@Unfolding Energy - mRNA 4.76073 kcal/mol@LB@Unfolding Energy - sRNA 0.933904 kcal/mol@LB@@LB@Position - mRNA 188 -- 200@LB@Position - sRNA 42 -- 53@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 47 -- 53@LB@
127	0.0247	0.6177	b3306	rpsH	-8.61	0.078593	53 -- 64	46 -- 57	30S ribosomal subunit protein S8	_____________52___________65\n_____________\|____________\|\n5'-AGC...CGCUG________C___UCGUC...AAG-3'\n______________CCGUCAAA_AGG\n______________\|\|\|\|\|\|\|\|_\|\|\|\n______________GGCAGUUU_UCC\n3'-UUU...AACCG________C___UUAAA...ACA-5'\n_____________\|____________\|\n_____________58___________45\n	54 -- 60	50 -- 56	-14.2597 kcal/mol	2.91134 kcal/mol	2.7365 kcal/mol	52 65@LB@ \| \|@LB@5'-AGC...CGCUG C UCGUC...AAG-3'@LB@ CCGUCAAA AGG@LB@ \|\|\|\|\|\|\|\| \|\|\|@LB@ GGCAGUUU UCC@LB@3'-UUU...AACCG C UUAAA...ACA-5'@LB@ \| \|@LB@ 58 45@LB@@LB@@LB@Energy -8.61 kcal/mol@LB@Hybridization Energy -14.2597 kcal/mol@LB@Unfolding Energy - mRNA 2.91134 kcal/mol@LB@Unfolding Energy - sRNA 2.7365 kcal/mol@LB@@LB@Position - mRNA 53 -- 64@LB@Position - sRNA 46 -- 57@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 50 -- 56@LB@
128	0.02532	0.6177	b3642	pyrE	-8.06	0.101423	72 -- 92	43 -- 68	orotate phosphoribosyltransferase	_____________71_________________________93\n_____________\|__________________________\|\n5'-CGG...CUUGU_G___C____________________CGAAU...AUU-3'\n______________U_GCU__UGGCCCG____AGGGGAAU\n______________\|_\|\|\|__\|\|\|\|\|\|\|____\|\|:\|\|\|\|\|\n______________A_CGA__ACCGGGC____UCUCCUUA\n3'-UUU...GUUAU_G___UA_______AGUU________AAGUA...ACA-5'\n_____________\|__________________________\|\n_____________69_________________________42\n	86 -- 92	43 -- 49	-26.5136 kcal/mol	7.12642 kcal/mol	11.3306 kcal/mol	71 93@LB@ \| \|@LB@5'-CGG...CUUGU G C CGAAU...AUU-3'@LB@ U GCU UGGCCCG AGGGGAAU@LB@ \| \|\|\| \|\|\|\|\|\|\| \|\|:\|\|\|\|\|@LB@ A CGA ACCGGGC UCUCCUUA@LB@3'-UUU...GUUAU G UA AGUU AAGUA...ACA-5'@LB@ \| \|@LB@ 69 42@LB@@LB@@LB@Energy -8.06 kcal/mol@LB@Hybridization Energy -26.5136 kcal/mol@LB@Unfolding Energy - mRNA 7.12642 kcal/mol@LB@Unfolding Energy - sRNA 11.3306 kcal/mol@LB@@LB@Position - mRNA 72 -- 92@LB@Position - sRNA 43 -- 68@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 43 -- 49@LB@
129	0.02539	0.6177	b0129	yadI	-10.21	0.037333	124 -- 136	40 -- 52	putative PTS Enzyme IIA	_____________123___________137\n_____________\|_____________\|\n5'-CUG...UUGGG_____________GACGG...UGA-3'\n______________GGAGAGGAGUUUU\n______________::\|\|\|\|\|\|:\|\|\|:\n______________UUUCUCCUUAAAG\n3'-UUU...GGCAG_____________UAAAA...ACA-5'\n_____________\|_____________\|\n_____________53____________39\n	130 -- 136	40 -- 46	-14.8894 kcal/mol	3.74683 kcal/mol	0.936082 kcal/mol	123 137@LB@ \| \|@LB@5'-CUG...UUGGG GACGG...UGA-3'@LB@ GGAGAGGAGUUUU@LB@ ::\|\|\|\|\|\|:\|\|\|:@LB@ UUUCUCCUUAAAG@LB@3'-UUU...GGCAG UAAAA...ACA-5'@LB@ \| \|@LB@ 53 39@LB@@LB@@LB@Energy -10.21 kcal/mol@LB@Hybridization Energy -14.8894 kcal/mol@LB@Unfolding Energy - mRNA 3.74683 kcal/mol@LB@Unfolding Energy - sRNA 0.936082 kcal/mol@LB@@LB@Position - mRNA 124 -- 136@LB@Position - sRNA 40 -- 52@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 40 -- 46@LB@
130	0.02541	0.6177	b4365	yjjQ	-8.08	0.100207	263 -- 277	38 -- 55	putative transcriptional regulator	_____________262_________________278\n_____________\|___________________\|\n5'-AGG...GCAGG___A_______________GAGGA...AUG-3'\n______________GUU_AAAGAGG____UCAU\n______________\|\|:_\|\|\|\|\|\|\|____\|\|\|\|\n______________CAG_UUUCUCC____AGUA\n3'-UUU...CCGGG___________UUAA____AAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________37\n	267 -- 273	46 -- 52	-10.7142 kcal/mol	1.46087 kcal/mol	1.17036 kcal/mol	262 278@LB@ \| \|@LB@5'-AGG...GCAGG A GAGGA...AUG-3'@LB@ GUU AAAGAGG UCAU@LB@ \|\|: \|\|\|\|\|\|\| \|\|\|\|@LB@ CAG UUUCUCC AGUA@LB@3'-UUU...CCGGG UUAA AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -10.7142 kcal/mol@LB@Unfolding Energy - mRNA 1.46087 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 263 -- 277@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 46 -- 52@LB@
131	0.02569	0.6177	b0848	ybjM	-8.44	0.085177	187 -- 197	44 -- 55	inner membrane protein	_____________186__________198\n_____________\|____________\|\n5'-GAA...GCAGU____________CGAGU...GGG-3'\n______________GUC_AGGAGGAA\n______________\|\|\|_\|:\|\|\|\|\|\|\n______________CAG_UUCUCCUU\n3'-UUU...CCGGG___U________AAAGU...ACA-5'\n_____________\|____________\|\n_____________56___________43\n	191 -- 197	44 -- 50	-13.6185 kcal/mol	4.23971 kcal/mol	0.941432 kcal/mol	186 198@LB@ \| \|@LB@5'-GAA...GCAGU CGAGU...GGG-3'@LB@ GUC AGGAGGAA@LB@ \|\|\| \|:\|\|\|\|\|\|@LB@ CAG UUCUCCUU@LB@3'-UUU...CCGGG U AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -8.44 kcal/mol@LB@Hybridization Energy -13.6185 kcal/mol@LB@Unfolding Energy - mRNA 4.23971 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 187 -- 197@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 44 -- 50@LB@
132	0.02588	0.6177	b3180	yhbY	-5.98	0.252347	290 -- 297	46 -- 53	RNA binding protein associated with pre-50S ribosomal subunits	_____________289______298\n_____________\|________\|\n5'-CUG...UUGAC________UGC-3'\n______________CGAAGGGG\n______________\|:\|\|\|:\|\|\n______________GUUUCUCC\n3'-UUU...GGGCA________UUAAA...ACA-5'\n_____________\|________\|\n_____________54_______45\n	291 -- 297	46 -- 52	-10.2464 kcal/mol	3.35117 kcal/mol	0.910679 kcal/mol	289 298@LB@ \| \|@LB@5'-CUG...UUGAC UGC-3'@LB@ CGAAGGGG@LB@ \|:\|\|\|:\|\|@LB@ GUUUCUCC@LB@3'-UUU...GGGCA UUAAA...ACA-5'@LB@ \| \|@LB@ 54 45@LB@@LB@@LB@Energy -5.98 kcal/mol@LB@Hybridization Energy -10.2464 kcal/mol@LB@Unfolding Energy - mRNA 3.35117 kcal/mol@LB@Unfolding Energy - sRNA 0.910679 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 46 -- 53@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 46 -- 52@LB@
133	0.02604	0.6177	b0876	ybjD	-5.23	0.342712	179 -- 199	45 -- 55	putative OLD family ATP-dependent endonuclease; DUF2813 family protein	_____________178___________________200\n_____________\|_____________________\|\n5'-CGU...GAUAA____CAUAUUUCUG_______UAUGA...GGG-3'\n______________GUCA__________GAGGGGA\n______________\|\|\|\|__________:\|\|:\|\|\|\n______________CAGU__________UUCUCCU\n3'-UUU...CCGGG_____________________UAAAG...ACA-5'\n_____________\|_____________________\|\n_____________56____________________44\n	193 -- 199	45 -- 51	-10.7419 kcal/mol	4.58374 kcal/mol	0.930875 kcal/mol	178 200@LB@ \| \|@LB@5'-CGU...GAUAA CAUAUUUCUG UAUGA...GGG-3'@LB@ GUCA GAGGGGA@LB@ \|\|\|\| :\|\|:\|\|\|@LB@ CAGU UUCUCCU@LB@3'-UUU...CCGGG UAAAG...ACA-5'@LB@ \| \|@LB@ 56 44@LB@@LB@@LB@Energy -5.23 kcal/mol@LB@Hybridization Energy -10.7419 kcal/mol@LB@Unfolding Energy - mRNA 4.58374 kcal/mol@LB@Unfolding Energy - sRNA 0.930875 kcal/mol@LB@@LB@Position - mRNA 179 -- 199@LB@Position - sRNA 45 -- 55@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 45 -- 51@LB@
134	0.02619	0.6177	b1126	potA	-9.47	0.052791	285 -- 299	37 -- 55	spermidine/putrescine ABC transporter ATPase	_____________284_________________300\n_____________\|___________________\|\n5'-CAA...UUGAU_GU________________C-3'\n______________G__AAAGAGG____UCAUU\n______________\|__\|\|\|\|\|\|\|____\|\|\|\|\|\n______________C__UUUCUCC____AGUAA\n3'-UUU...CCGGG_AG_______UUAA_____AAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________36\n	288 -- 294	46 -- 52	-11.4861 kcal/mol	0.840334 kcal/mol	1.17789 kcal/mol	284 300@LB@ \| \|@LB@5'-CAA...UUGAU GU C-3'@LB@ G AAAGAGG UCAUU@LB@ \| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ C UUUCUCC AGUAA@LB@3'-UUU...CCGGG AG UUAA AAAAA...ACA-5'@LB@ \| \|@LB@ 56 36@LB@@LB@@LB@Energy -9.47 kcal/mol@LB@Hybridization Energy -11.4861 kcal/mol@LB@Unfolding Energy - mRNA 0.840334 kcal/mol@LB@Unfolding Energy - sRNA 1.17789 kcal/mol@LB@@LB@Position - mRNA 285 -- 299@LB@Position - sRNA 37 -- 55@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 46 -- 52@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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