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
85	0.005692	0.2157	b4052	dnaB	-8.38	0.047402	89 -- 103	26 -- 40	replicative DNA helicase	_____________88______________104\n_____________\|_______________\|\n5'-UGC...CCACC_______U_______AAUUC...CGG-3'\n______________GUGCUUG_GAAAUUC\n______________\|::\|\|\|:_:\|\|\|\|\|\|\n______________CGUGAAU_UUUUAAG\n3'-UUU...UUCUU_______U_______CAAUG...CAA-5'\n_____________\|_______________\|\n_____________41______________25\n	97 -- 103	26 -- 32	-13.045 kcal/mol	3.01413 kcal/mol	1.64811 kcal/mol	88 104@LB@ \| \|@LB@5'-UGC...CCACC U AAUUC...CGG-3'@LB@ GUGCUUG GAAAUUC@LB@ \|::\|\|\|: :\|\|\|\|\|\|@LB@ CGUGAAU UUUUAAG@LB@3'-UUU...UUCUU U CAAUG...CAA-5'@LB@ \| \|@LB@ 41 25@LB@@LB@@LB@Energy -8.38 kcal/mol@LB@Hybridization Energy -13.045 kcal/mol@LB@Unfolding Energy - mRNA 3.01413 kcal/mol@LB@Unfolding Energy - sRNA 1.64811 kcal/mol@LB@@LB@Position - mRNA 89 -- 103@LB@Position - sRNA 26 -- 40@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 26 -- 32@LB@
84	0.005596	0.2146	b4065	yjcE	-5.39	0.265673	197 -- 210	9 -- 22	putative cation/proton antiporter	_____________196____________211\n_____________\|______________\|\n5'-UAU...AGGGA____AU________UCUUC...UGC-3'\n______________ACGC__GGAAAUCU\n______________\|\|:\|__\|\|\|\|\|\|\|\|\n______________UGUG__CCUUUAGA\n3'-UUU...AGCAA____GU________CUACACAA-5'\n_____________\|______________\|\n_____________23_____________8\n	203 -- 209	10 -- 16	-15.8377 kcal/mol	2.89158 kcal/mol	7.5588 kcal/mol	196 211@LB@ \| \|@LB@5'-UAU...AGGGA AU UCUUC...UGC-3'@LB@ ACGC GGAAAUCU@LB@ \|\|:\| \|\|\|\|\|\|\|\|@LB@ UGUG CCUUUAGA@LB@3'-UUU...AGCAA GU CUACACAA-5'@LB@ \| \|@LB@ 23 8@LB@@LB@@LB@Energy -5.39 kcal/mol@LB@Hybridization Energy -15.8377 kcal/mol@LB@Unfolding Energy - mRNA 2.89158 kcal/mol@LB@Unfolding Energy - sRNA 7.5588 kcal/mol@LB@@LB@Position - mRNA 197 -- 210@LB@Position - sRNA 9 -- 22@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 10 -- 16@LB@
61	0.003184	0.1645	b4112	basS	-6.79	0.124428	7 -- 41	10 -- 54	sensory histidine kinase in two-component regulatory system with BasR	_____________6______________________________________________42\n_____________\|______________________________________________\|\n_____5'-GGUUAA____CA_______C___C_____________GU_____________CUCUA...UAU-3'\n______________UGCU__AAGCAGG_AGU____________CG__GCAUCGGGAAAUU\n______________\|\|\|\|__\|\|\|\|\|:\|_\|\|:____________\|\|__:\|\|:\|:\|\|\|\|\|\|:\n______________ACGA__UUCGUUC_UCG____________GC__UGUGGUCCUUUAG\n3'-UUU...UUUGA____A________U___UGAAUUUUUUAA__AA_____________ACUAC...CAA-5'\n_____________\|______________________________________________\|\n_____________55_____________________________________________9\n	35 -- 41	10 -- 16	-31.3926 kcal/mol	10.7631 kcal/mol	13.8372 kcal/mol	6 42@LB@ \| \|@LB@ 5'-GGUUAA CA C C GU CUCUA...UAU-3'@LB@ UGCU AAGCAGG AGU CG GCAUCGGGAAAUU@LB@ \|\|\|\| \|\|\|\|\|:\| \|\|: \|\| :\|\|:\|:\|\|\|\|\|\|:@LB@ ACGA UUCGUUC UCG GC UGUGGUCCUUUAG@LB@3'-UUU...UUUGA A U UGAAUUUUUUAA AA ACUAC...CAA-5'@LB@ \| \|@LB@ 55 9@LB@@LB@@LB@Energy -6.79 kcal/mol@LB@Hybridization Energy -31.3926 kcal/mol@LB@Unfolding Energy - mRNA 10.7631 kcal/mol@LB@Unfolding Energy - sRNA 13.8372 kcal/mol@LB@@LB@Position - mRNA 7 -- 41@LB@Position - sRNA 10 -- 54@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 10 -- 16@LB@
131	0.01234	0.3033	b4139	aspA	-5.03	0.315570	237 -- 252	26 -- 41	aspartate ammonia-lyase	_____________236______________253\n_____________\|________________\|\n5'-GAU...UGUUG_____CA_________CAGCU...ACU-3'\n______________GGUAC__GGGAAGUUC\n______________:\|:\|\|__:::\|\|:\|\|\|\n______________UCGUG__UUUUUUAAG\n3'-UUU...GUUCU_____AA_________CAAUG...CAA-5'\n_____________\|________________\|\n_____________42_______________25\n	246 -- 252	26 -- 32	-10.8102 kcal/mol	4.127 kcal/mol	1.64829 kcal/mol	236 253@LB@ \| \|@LB@5'-GAU...UGUUG CA CAGCU...ACU-3'@LB@ GGUAC GGGAAGUUC@LB@ :\|:\|\| :::\|\|:\|\|\|@LB@ UCGUG UUUUUUAAG@LB@3'-UUU...GUUCU AA CAAUG...CAA-5'@LB@ \| \|@LB@ 42 25@LB@@LB@@LB@Energy -5.03 kcal/mol@LB@Hybridization Energy -10.8102 kcal/mol@LB@Unfolding Energy - mRNA 4.127 kcal/mol@LB@Unfolding Energy - sRNA 1.64829 kcal/mol@LB@@LB@Position - mRNA 237 -- 252@LB@Position - sRNA 26 -- 41@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 26 -- 32@LB@
125	0.01132	0.2916	b4152	frdC	-8.74	0.037729	137 -- 154	25 -- 41	fumarate reductase (anaerobic) membrane anchor subunit	_____________136________________155\n_____________\|__________________\|\n5'-AGA...AGCAG____AAG___________AAAGA...CGG-3'\n______________GGCA___UAGAAAGUUCG\n______________:\|\|\|___\|\|:\|\|\|:\|\|\|\|\n______________UCGU___AUUUUUUAAGC\n3'-UUU...GUUCU____GA____________AAUGU...CAA-5'\n_____________\|__________________\|\n_____________42_________________24\n	148 -- 154	25 -- 31	-13.3883 kcal/mol	3.00162 kcal/mol	1.64839 kcal/mol	136 155@LB@ \| \|@LB@5'-AGA...AGCAG AAG AAAGA...CGG-3'@LB@ GGCA UAGAAAGUUCG@LB@ :\|\|\| \|\|:\|\|\|:\|\|\|\|@LB@ UCGU AUUUUUUAAGC@LB@3'-UUU...GUUCU GA AAUGU...CAA-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -13.3883 kcal/mol@LB@Unfolding Energy - mRNA 3.00162 kcal/mol@LB@Unfolding Energy - sRNA 1.64839 kcal/mol@LB@@LB@Position - mRNA 137 -- 154@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 148 -- 154@LB@Position Seed - sRNA 25 -- 31@LB@
50	0.002273	0.1465	b4159	mscM	-6.32	0.162358	72 -- 90	16 -- 34	mechanosensitive channel protein miniconductance	_____________71__________________91\n_____________\|___________________\|\n5'-AAG...CUACC____CC_____________ACGCU...AGC-3'\n______________GAAA__UUUGUUACGCCAG\n______________:\|\|\|__\|\|:\|\|\|\|\|:\|\|\|\|\n______________UUUU__AAGCAAUGUGGUC\n3'-UUU...GUGAA____UU_____________CUUUA...CAA-5'\n_____________\|___________________\|\n_____________35__________________15\n	84 -- 90	16 -- 22	-19.9467 kcal/mol	4.98786 kcal/mol	8.63814 kcal/mol	71 91@LB@ \| \|@LB@5'-AAG...CUACC CC ACGCU...AGC-3'@LB@ GAAA UUUGUUACGCCAG@LB@ :\|\|\| \|\|:\|\|\|\|\|:\|\|\|\|@LB@ UUUU AAGCAAUGUGGUC@LB@3'-UUU...GUGAA UU CUUUA...CAA-5'@LB@ \| \|@LB@ 35 15@LB@@LB@@LB@Energy -6.32 kcal/mol@LB@Hybridization Energy -19.9467 kcal/mol@LB@Unfolding Energy - mRNA 4.98786 kcal/mol@LB@Unfolding Energy - sRNA 8.63814 kcal/mol@LB@@LB@Position - mRNA 72 -- 90@LB@Position - sRNA 16 -- 34@LB@Position Seed - mRNA 84 -- 90@LB@Position Seed - sRNA 16 -- 22@LB@
142	0.01375	0.3119	b4166	queG	-9.76	0.019130	257 -- 284	36 -- 60	epoxyqueuosine reductase cobalamine-stimulated; queosine biosynthesis	_____________256__________________________285\n_____________\|____________________________\|\n5'-CGC...GGGCU______GG____UC______U_______ACCGA...UCA-3'\n______________GGAACU__GCUU__AGCAGG_AGGUAUU\n______________\|:\|\|\|\|__\|\|\|\|__\|\|\|\|:\|_\|:\|:\|:\|\n______________CUUUGA__CGAA__UCGUUC_UUCGUGA\n3'-UUU...CCCUA______A_____U_______________AUUUU...CAA-5'\n_____________\|____________________________\|\n_____________61___________________________35\n	278 -- 284	36 -- 42	-22.8123 kcal/mol	6.80174 kcal/mol	6.24973 kcal/mol	256 285@LB@ \| \|@LB@5'-CGC...GGGCU GG UC U ACCGA...UCA-3'@LB@ GGAACU GCUU AGCAGG AGGUAUU@LB@ \|:\|\|\|\| \|\|\|\| \|\|\|\|:\| \|:\|:\|:\|@LB@ CUUUGA CGAA UCGUUC UUCGUGA@LB@3'-UUU...CCCUA A U AUUUU...CAA-5'@LB@ \| \|@LB@ 61 35@LB@@LB@@LB@Energy -9.76 kcal/mol@LB@Hybridization Energy -22.8123 kcal/mol@LB@Unfolding Energy - mRNA 6.80174 kcal/mol@LB@Unfolding Energy - sRNA 6.24973 kcal/mol@LB@@LB@Position - mRNA 257 -- 284@LB@Position - sRNA 36 -- 60@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 36 -- 42@LB@
98	0.007325	0.239	b4171	miaA	-8.40	0.046782	42 -- 58	5 -- 24	delta(2)-isopentenylpyrophosphate tRNA-adenosine transferase	_____________41___________________59\n_____________\|____________________\|\n5'-GAA...GUGGA____________________AGCGA...UUU-3'\n______________UUGCAC___GAAAUCUGAUG\n______________\|\|:\|\|\|___\|\|\|\|\|\|\|\|\|\|\|\n______________AAUGUG___CUUUAGACUAC\n3'-UUU...UAAGC______GUC___________ACAA-5'\n_____________\|____________________\|\n_____________25___________________4\n	52 -- 58	5 -- 11	-19.996 kcal/mol	4.00751 kcal/mol	7.58501 kcal/mol	41 59@LB@ \| \|@LB@5'-GAA...GUGGA AGCGA...UUU-3'@LB@ UUGCAC GAAAUCUGAUG@LB@ \|\|:\|\|\| \|\|\|\|\|\|\|\|\|\|\|@LB@ AAUGUG CUUUAGACUAC@LB@3'-UUU...UAAGC GUC ACAA-5'@LB@ \| \|@LB@ 25 4@LB@@LB@@LB@Energy -8.40 kcal/mol@LB@Hybridization Energy -19.996 kcal/mol@LB@Unfolding Energy - mRNA 4.00751 kcal/mol@LB@Unfolding Energy - sRNA 7.58501 kcal/mol@LB@@LB@Position - mRNA 42 -- 58@LB@Position - sRNA 5 -- 24@LB@Position Seed - mRNA 52 -- 58@LB@Position Seed - sRNA 5 -- 11@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@
14	0.0002995	0.06692	b4195	ulaC	-9.74	0.019405	182 -- 212	24 -- 54	L-ascorbate-specific enzyme IIA component of PTS	_____________181_______________________________213\n_____________\|_________________________________\|\n5'-GCG...CAGGA___G__________C____CAU_______A___GAUUC...UGG-3'\n______________UGU__AAGUAAGGA_GCGC____GAAAUU_CGU\n______________\|\|:__\|\|\|:\|\|\|:\|_\|\|:\|____:\|\|\|\|\|_\|\|\|\n______________ACG__UUCGUUCUU_CGUG____UUUUAA_GCA\n3'-UUU...UUUGA___AA______________AAUU__________AUGUG...CAA-5'\n_____________\|_________________________________\|\n_____________55________________________________23\n	187 -- 193	42 -- 48	-22.0137 kcal/mol	6.00518 kcal/mol	6.26866 kcal/mol	181 213@LB@ \| \|@LB@5'-GCG...CAGGA G C CAU A GAUUC...UGG-3'@LB@ UGU AAGUAAGGA GCGC GAAAUU CGU@LB@ \|\|: \|\|\|:\|\|\|:\| \|\|:\| :\|\|\|\|\| \|\|\|@LB@ ACG UUCGUUCUU CGUG UUUUAA GCA@LB@3'-UUU...UUUGA AA AAUU AUGUG...CAA-5'@LB@ \| \|@LB@ 55 23@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -22.0137 kcal/mol@LB@Unfolding Energy - mRNA 6.00518 kcal/mol@LB@Unfolding Energy - sRNA 6.26866 kcal/mol@LB@@LB@Position - mRNA 182 -- 212@LB@Position - sRNA 24 -- 54@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 42 -- 48@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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