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
42	0.001686	0.1293	b2733	mutS	-6.21	0.172669	203 -- 222	25 -- 42	methyl-directed mismatch repair protein	_____________202__________________223\n_____________\|____________________\|\n5'-GAU...CCCAU______AA_________U__ACGCC...UGG-3'\n______________GAGUGC__UAGAAAAUU_CG\n______________:\|\|::\|__\|\|:\|\|\|\|\|\|_\|\|\n______________UUCGUG__AUUUUUUAA_GC\n3'-UUU...CGUUC______A_____________AAUGU...CAA-5'\n_____________\|____________________\|\n_____________43___________________24\n	213 -- 219	27 -- 33	-10.4027 kcal/mol	2.54535 kcal/mol	1.64855 kcal/mol	202 223@LB@ \| \|@LB@5'-GAU...CCCAU AA U ACGCC...UGG-3'@LB@ GAGUGC UAGAAAAUU CG@LB@ :\|\|::\| \|\|:\|\|\|\|\|\| \|\|@LB@ UUCGUG AUUUUUUAA GC@LB@3'-UUU...CGUUC A AAUGU...CAA-5'@LB@ \| \|@LB@ 43 24@LB@@LB@@LB@Energy -6.21 kcal/mol@LB@Hybridization Energy -10.4027 kcal/mol@LB@Unfolding Energy - mRNA 2.54535 kcal/mol@LB@Unfolding Energy - sRNA 1.64855 kcal/mol@LB@@LB@Position - mRNA 203 -- 222@LB@Position - sRNA 25 -- 42@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 27 -- 33@LB@
113	0.009602	0.2693	b3237	argR	-14.05	0.000763	205 -- 250	27 -- 60	l-arginine-responsive arginine metabolism regulon transcriptional regulator	_____________204_____________________________________________251\n_____________\|_______________________________________________\|\n5'-ACA...UAUGC______CG____________AGAACUAGUUAA___________C___ACUUA...UGC-3'\n______________GAAGCU__GC_UAAGCAAGA____________AGCAUUUAAAG_AUU\n______________\|\|\|:\|\|__\|\|_\|\|\|\|\|\|\|\|\|____________\|\|\|\|:\|\|\|\|\|:_\|\|\|\n______________CUUUGA__CG_AUUCGUUCU____________UCGUGAAUUUU_UAA\n3'-UUU...CCCUA______A___A________________________________U___GCAAU...CAA-5'\n_____________\|_______________________________________________\|\n_____________61______________________________________________26\n	238 -- 244	33 -- 39	-28.1986 kcal/mol	7.87477 kcal/mol	6.27096 kcal/mol	204 251@LB@ \| \|@LB@5'-ACA...UAUGC CG AGAACUAGUUAA C ACUUA...UGC-3'@LB@ GAAGCU GC UAAGCAAGA AGCAUUUAAAG AUU@LB@ \|\|\|:\|\| \|\| \|\|\|\|\|\|\|\|\| \|\|\|\|:\|\|\|\|\|: \|\|\|@LB@ CUUUGA CG AUUCGUUCU UCGUGAAUUUU UAA@LB@3'-UUU...CCCUA A A U GCAAU...CAA-5'@LB@ \| \|@LB@ 61 26@LB@@LB@@LB@Energy -14.05 kcal/mol@LB@Hybridization Energy -28.1986 kcal/mol@LB@Unfolding Energy - mRNA 7.87477 kcal/mol@LB@Unfolding Energy - sRNA 6.27096 kcal/mol@LB@@LB@Position - mRNA 205 -- 250@LB@Position - sRNA 27 -- 60@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 33 -- 39@LB@
145	0.01456	0.3231	b1529	marC	-5.50	0.250589	206 -- 227	39 -- 59	UPF0056 family inner membrane protein	_____________205____________________228\n_____________\|______________________\|\n5'-UGG...AUGUU__________A______UU___CUGGG...GCA-3'\n______________AGAUUUGUUU_AAGCAA__GGC\n______________\|:\|:\|\|\|:\|\|_\|\|\|\|\|\|__:\|\|\n______________UUUGAACGAA_UUCGUU__UCG\n3'-UUU...CCUAC_________________CU___UGAAU...CAA-5'\n_____________\|______________________\|\n_____________60_____________________38\n	207 -- 213	52 -- 58	-17.1508 kcal/mol	5.49588 kcal/mol	6.15149 kcal/mol	205 228@LB@ \| \|@LB@5'-UGG...AUGUU A UU CUGGG...GCA-3'@LB@ AGAUUUGUUU AAGCAA GGC@LB@ \|:\|:\|\|\|:\|\| \|\|\|\|\|\| :\|\|@LB@ UUUGAACGAA UUCGUU UCG@LB@3'-UUU...CCUAC CU UGAAU...CAA-5'@LB@ \| \|@LB@ 60 38@LB@@LB@@LB@Energy -5.50 kcal/mol@LB@Hybridization Energy -17.1508 kcal/mol@LB@Unfolding Energy - mRNA 5.49588 kcal/mol@LB@Unfolding Energy - sRNA 6.15149 kcal/mol@LB@@LB@Position - mRNA 206 -- 227@LB@Position - sRNA 39 -- 59@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 52 -- 58@LB@
52	0.002466	0.1527	b3527	yhjJ	-8.40	0.046956	207 -- 220	25 -- 41	putative periplasmic M16 family chaperone	_____________206_______________221\n_____________\|_________________\|\n5'-CUC...UGCAG_________________ACUUU...GGC-3'\n______________GGCAC___AAAAAUUCG\n______________:\|\|\|\|___\|\|\|\|\|\|\|\|\|\n______________UCGUG___UUUUUAAGC\n3'-UUU...GUUCU_____AAU_________AAUGU...CAA-5'\n_____________\|_________________\|\n_____________42________________24\n	214 -- 220	25 -- 31	-13.4116 kcal/mol	3.36563 kcal/mol	1.64839 kcal/mol	206 221@LB@ \| \|@LB@5'-CUC...UGCAG ACUUU...GGC-3'@LB@ GGCAC AAAAAUUCG@LB@ :\|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ UCGUG UUUUUAAGC@LB@3'-UUU...GUUCU AAU AAUGU...CAA-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -8.40 kcal/mol@LB@Hybridization Energy -13.4116 kcal/mol@LB@Unfolding Energy - mRNA 3.36563 kcal/mol@LB@Unfolding Energy - sRNA 1.64839 kcal/mol@LB@@LB@Position - mRNA 207 -- 220@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 25 -- 31@LB@
173	0.01972	0.3669	b3426	glpD	-5.91	0.203159	207 -- 224	3 -- 20	sn-glycerol-3-phosphate dehydrogenase aerobic FAD/NAD(P)-binding	_____________206_________________225\n_____________\|___________________\|\n5'-AAC...UGGAA____A_________U____AUAGG...AGG-3'\n______________ACCA__AGAUCUGA_UGUG\n______________\|\|\|\|__\|:\|\|\|\|\|\|_\|\|\|\|\n______________UGGU__UUUAGACU_ACAC\n3'-UUU...CAAUG____CC_____________AA-5'\n_____________\|___________________\|\n_____________21__________________2\n	213 -- 219	7 -- 13	-16.1802 kcal/mol	2.74973 kcal/mol	7.52321 kcal/mol	206 225@LB@ \| \|@LB@5'-AAC...UGGAA A U AUAGG...AGG-3'@LB@ ACCA AGAUCUGA UGUG@LB@ \|\|\|\| \|:\|\|\|\|\|\| \|\|\|\|@LB@ UGGU UUUAGACU ACAC@LB@3'-UUU...CAAUG CC AA-5'@LB@ \| \|@LB@ 21 2@LB@@LB@@LB@Energy -5.91 kcal/mol@LB@Hybridization Energy -16.1802 kcal/mol@LB@Unfolding Energy - mRNA 2.74973 kcal/mol@LB@Unfolding Energy - sRNA 7.52321 kcal/mol@LB@@LB@Position - mRNA 207 -- 224@LB@Position - sRNA 3 -- 20@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 7 -- 13@LB@
112	0.009574	0.2693	b2494	bepA	-6.13	0.179960	208 -- 220	29 -- 41	OM protein maintenance and assembly metalloprotease and chaperone periplasmic	_____________207___________221\n_____________\|_____________\|\n5'-UGA...GUUCA____G________AAACC...UGC-3'\n______________GGCA_UUGAAAAA\n______________:\|\|\|_\|\|:\|\|\|\|\|\n______________UCGU_AAUUUUUU\n3'-UUU...GUUCU____G________AAGCA...CAA-5'\n_____________\|_____________\|\n_____________42____________28\n	214 -- 220	29 -- 35	-11.3192 kcal/mol	3.5632 kcal/mol	1.62306 kcal/mol	207 221@LB@ \| \|@LB@5'-UGA...GUUCA G AAACC...UGC-3'@LB@ GGCA UUGAAAAA@LB@ :\|\|\| \|\|:\|\|\|\|\|@LB@ UCGU AAUUUUUU@LB@3'-UUU...GUUCU G AAGCA...CAA-5'@LB@ \| \|@LB@ 42 28@LB@@LB@@LB@Energy -6.13 kcal/mol@LB@Hybridization Energy -11.3192 kcal/mol@LB@Unfolding Energy - mRNA 3.5632 kcal/mol@LB@Unfolding Energy - sRNA 1.62306 kcal/mol@LB@@LB@Position - mRNA 208 -- 220@LB@Position - sRNA 29 -- 41@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 29 -- 35@LB@
194	0.02335	0.3864	b4182	yjfJ	-9.08	0.030148	209 -- 238	10 -- 37	PspA/IM30 family protein	_____________208____________________________239\n_____________\|______________________________\|\n5'-GAA...GGAAU____________AU______UG________GUUUA...AGC-3'\n______________UUUAAAAAGUUU__UUACGC__GGGAAAUC\n______________:\|\|\|\|\|\|\|:\|\|:__\|\|\|\|:\|__:\|\|\|\|\|\|\|\n______________GAAUUUUUUAAG__AAUGUG__UCCUUUAG\n3'-UUU...UUCGU____________C_______G_________ACUAC...CAA-5'\n_____________\|______________________________\|\n_____________38_____________________________9\n	232 -- 238	10 -- 16	-23.4786 kcal/mol	5.49388 kcal/mol	8.90309 kcal/mol	208 239@LB@ \| \|@LB@5'-GAA...GGAAU AU UG GUUUA...AGC-3'@LB@ UUUAAAAAGUUU UUACGC GGGAAAUC@LB@ :\|\|\|\|\|\|\|:\|\|: \|\|\|\|:\| :\|\|\|\|\|\|\|@LB@ GAAUUUUUUAAG AAUGUG UCCUUUAG@LB@3'-UUU...UUCGU C G ACUAC...CAA-5'@LB@ \| \|@LB@ 38 9@LB@@LB@@LB@Energy -9.08 kcal/mol@LB@Hybridization Energy -23.4786 kcal/mol@LB@Unfolding Energy - mRNA 5.49388 kcal/mol@LB@Unfolding Energy - sRNA 8.90309 kcal/mol@LB@@LB@Position - mRNA 209 -- 238@LB@Position - sRNA 10 -- 37@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 10 -- 16@LB@
6	4.032e-05	0.02042	b0889	lrp	-10.51	0.011361	210 -- 221	37 -- 48	leucine-responsive global transcriptional regulator	_____________209__________222\n_____________\|____________\|\n5'-GUG...UAGAU____________CCUGG...AGC-3'\n______________AGCAAGAAGCGC\n______________\|\|\|\|\|\|\|\|\|\|:\|\n______________UCGUUCUUCGUG\n3'-UUU...CGAAU____________AAUUU...CAA-5'\n_____________\|____________\|\n_____________49___________36\n	215 -- 221	37 -- 43	-19.5953 kcal/mol	3.24674 kcal/mol	5.83483 kcal/mol	209 222@LB@ \| \|@LB@5'-GUG...UAGAU CCUGG...AGC-3'@LB@ AGCAAGAAGCGC@LB@ \|\|\|\|\|\|\|\|\|\|:\|@LB@ UCGUUCUUCGUG@LB@3'-UUU...CGAAU AAUUU...CAA-5'@LB@ \| \|@LB@ 49 36@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -19.5953 kcal/mol@LB@Unfolding Energy - mRNA 3.24674 kcal/mol@LB@Unfolding Energy - sRNA 5.83483 kcal/mol@LB@@LB@Position - mRNA 210 -- 221@LB@Position - sRNA 37 -- 48@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 37 -- 43@LB@
121	0.01057	0.2813	b0452	tesB	-8.75	0.037433	210 -- 223	26 -- 40	acyl-CoA thioesterase 2	_____________209_____________224\n_____________\|_______________\|\n5'-CAA...GUCAG_______________ACUGA...AGG-3'\n______________GCGC_UAAAAAAUUU\n______________\|\|:\|_\|\|\|\|\|\|\|\|\|:\n______________CGUG_AUUUUUUAAG\n3'-UUU...UUCUU____A__________CAAUG...CAA-5'\n_____________\|_______________\|\n_____________41______________25\n	217 -- 223	26 -- 32	-10.9054 kcal/mol	0.50684 kcal/mol	1.64811 kcal/mol	209 224@LB@ \| \|@LB@5'-CAA...GUCAG ACUGA...AGG-3'@LB@ GCGC UAAAAAAUUU@LB@ \|\|:\| \|\|\|\|\|\|\|\|\|:@LB@ CGUG AUUUUUUAAG@LB@3'-UUU...UUCUU A CAAUG...CAA-5'@LB@ \| \|@LB@ 41 25@LB@@LB@@LB@Energy -8.75 kcal/mol@LB@Hybridization Energy -10.9054 kcal/mol@LB@Unfolding Energy - mRNA 0.50684 kcal/mol@LB@Unfolding Energy - sRNA 1.64811 kcal/mol@LB@@LB@Position - mRNA 210 -- 223@LB@Position - sRNA 26 -- 40@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 26 -- 32@LB@
29	0.000834	0.09021	b2798	ygdG	-11.41	0.005967	211 -- 245	24 -- 57	Ssb-binding protein misidentified as ExoIX	_____________210_________________________________246\n_____________\|___________________________________\|\n5'-CCA...UGUUC_________UUGUC__U_____GAAUCUU______CGCAU...UCG-3'\n______________AUUUGCUUA_____GA_GCACU_______AUUCGU\n______________\|:\|\|\|\|\|\|\|_____\|\|_\|\|\|\|\|_______\|\|\|\|\|\|\n______________UGAACGAAU_____CU_CGUGA_______UAAGCA\n3'-UUU...UACUU_________UCGUU__U_____AUUUUU_______AUGUG...CAA-5'\n_____________\|___________________________________\|\n_____________58__________________________________23\n	213 -- 219	49 -- 55	-23.2646 kcal/mol	5.57825 kcal/mol	6.27607 kcal/mol	210 246@LB@ \| \|@LB@5'-CCA...UGUUC UUGUC U GAAUCUU CGCAU...UCG-3'@LB@ AUUUGCUUA GA GCACU AUUCGU@LB@ \|:\|\|\|\|\|\|\| \|\| \|\|\|\|\| \|\|\|\|\|\|@LB@ UGAACGAAU CU CGUGA UAAGCA@LB@3'-UUU...UACUU UCGUU U AUUUUU AUGUG...CAA-5'@LB@ \| \|@LB@ 58 23@LB@@LB@@LB@Energy -11.41 kcal/mol@LB@Hybridization Energy -23.2646 kcal/mol@LB@Unfolding Energy - mRNA 5.57825 kcal/mol@LB@Unfolding Energy - sRNA 6.27607 kcal/mol@LB@@LB@Position - mRNA 211 -- 245@LB@Position - sRNA 24 -- 57@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 49 -- 55@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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