Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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	Additional homologs
1	1.057e-08	3.724e-05	b0889	lrp	-13.58	0.012310	166 -- 227	21 -- 70	leucine-responsive global transcriptional regulator		_____________165_______________________________________________________________228\n_____________\|_________________________________________________________________\|\n5'-GUG...UCAGA___GAG____________AUAC__A_________AUAA___U__AUA___AGAA________G__AAAGA...AGC-3'\n______________CAG_____UAGGGAAGGA____AG_GAGACAAUA____UGG_AG___GCA____GCGCCC_U_GC\n______________\|\|\|_____:\|:::\|\|\|\|\|____\|\|_:\|\|\|\|\|\|\|\|____\|\|\|_\|\|___\|\|\|____:\|\|\|\|\|_\|_\|\|\n______________GUC_____GUUUUUUCCU____UC_UUCUGUUAU____ACC_UC___CGU____UGCGGG_A_CG\n3'-UUU...GAUAC___AUUAA________________A___________________G_______________U_G__AACUG...ACG-5'\n_____________\|_________________________________________________________________\|\n_____________71________________________________________________________________20\n	191 -- 197	41 -- 47	-39.3483 kcal/mol	8.89245 kcal/mol	16.878 kcal/mol	165 228@LB@ \| \|@LB@5'-GUG...UCAGA GAG AUAC A AUAA U AUA AGAA G AAAGA...AGC-3'@LB@ CAG UAGGGAAGGA AG GAGACAAUA UGG AG GCA GCGCCC U GC@LB@ \|\|\| :\|:::\|\|\|\|\| \|\| :\|\|\|\|\|\|\|\| \|\|\| \|\| \|\|\| :\|\|\|\|\| \| \|\|@LB@ GUC GUUUUUUCCU UC UUCUGUUAU ACC UC CGU UGCGGG A CG@LB@3'-UUU...GAUAC AUUAA A G U G AACUG...ACG-5'@LB@ \| \|@LB@ 71 20@LB@@LB@@LB@Energy -13.58 kcal/mol@LB@Hybridization Energy -39.3483 kcal/mol@LB@Unfolding Energy - mRNA 8.89245 kcal/mol@LB@Unfolding Energy - sRNA 16.878 kcal/mol@LB@@LB@Position - mRNA 166 -- 227@LB@Position - sRNA 21 -- 70@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 41 -- 47@LB@
2	4.208e-07	0.0007412	b2531	iscR	-21.46	0.000012	188 -- 264	2 -- 56	isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress- and iron starvation-inducible; autorepressor		_____________187___________________________________________________________________________265\n_____________\|_____________________________________________________________________________\|\n5'-AUG...UUUGA__U___________UG_GACUGACAUCUAAA______U_____GUGACCG__A______________C__A__U___AAGCG...AAC-3'\n______________GG_GAAGUAAGACA__A______________GGGCGC_AUGCC_______CA_UGCUUGACGUUGCG_UC_AC_CUG\n______________:\|_\|\|\|\|\|\|\|\|\|\|\|__\|______________\|:\|\|\|\|_\|:\|\|\|_______\|\|_:\|\|\|\|\|\|\|\|\|\|\|\|:_\|\|_\|\|_\|\|\|\n______________UC_CUUCAUUCUGU__U______________CUCGCG_UGCGG_______GU_GCGAACUGCAACGU_AG_UG_GAC\n3'-UUU...UUUUU______________UA_AC__________________U______________A______________A_________G-5'\n_____________\|_____________________________________________________________________________\|\n_____________57____________________________________________________________________________1\n	244 -- 250	14 -- 20	-58.8762 kcal/mol	20.5805 kcal/mol	16.8438 kcal/mol	187 265@LB@ \| \|@LB@5'-AUG...UUUGA U UG GACUGACAUCUAAA U GUGACCG A C A U AAGCG...AAC-3'@LB@ GG GAAGUAAGACA A GGGCGC AUGCC CA UGCUUGACGUUGCG UC AC CUG@LB@ :\| \|\|\|\|\|\|\|\|\|\|\| \| \|:\|\|\|\| \|:\|\|\| \|\| :\|\|\|\|\|\|\|\|\|\|\|\|: \|\| \|\| \|\|\|@LB@ UC CUUCAUUCUGU U CUCGCG UGCGG GU GCGAACUGCAACGU AG UG GAC@LB@3'-UUU...UUUUU UA AC U A A G-5'@LB@ \| \|@LB@ 57 1@LB@@LB@@LB@Energy -21.46 kcal/mol@LB@Hybridization Energy -58.8762 kcal/mol@LB@Unfolding Energy - mRNA 20.5805 kcal/mol@LB@Unfolding Energy - sRNA 16.8438 kcal/mol@LB@@LB@Position - mRNA 188 -- 264@LB@Position - sRNA 2 -- 56@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 14 -- 20@LB@
3	7.57e-07	0.0008889	b1763	topB	-11.97	0.035059	233 -- 258	1 -- 37	DNA topoisomerase III		_____________232___________________________________259\n_____________\|_____________________________________\|\n5'-UCU...AGUCU_____________________________________CCAAA...GUA-3'\n______________GGCGC_GCG_CCAUUGCU_GAUGU________CCUGC\n______________:\|\|\|\|_:\|\|_\|\|\|\|:\|\|\|_\|\|:\|\|________\|\|\|\|\|\n______________UCGCG_UGC_GGUAGCGA_CUGCA________GGACG\n3'-UUU...AUACC_____U___G________A_____ACGUAAGU_____-5'\n_____________\|____________________________________\|\n_____________38___________________________________1\n	242 -- 248	20 -- 26	-35.9728 kcal/mol	8.72127 kcal/mol	15.288 kcal/mol	232 259@LB@ \| \|@LB@5'-UCU...AGUCU CCAAA...GUA-3'@LB@ GGCGC GCG CCAUUGCU GAUGU CCUGC@LB@ :\|\|\|\| :\|\| \|\|\|\|:\|\|\| \|\|:\|\| \|\|\|\|\|@LB@ UCGCG UGC GGUAGCGA CUGCA GGACG@LB@3'-UUU...AUACC U G A ACGUAAGU -5'@LB@ \| \|@LB@ 38 1@LB@@LB@@LB@Energy -11.97 kcal/mol@LB@Hybridization Energy -35.9728 kcal/mol@LB@Unfolding Energy - mRNA 8.72127 kcal/mol@LB@Unfolding Energy - sRNA 15.288 kcal/mol@LB@@LB@Position - mRNA 233 -- 258@LB@Position - sRNA 1 -- 37@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 20 -- 26@LB@
4	1.28e-06	0.001128	b0884	infA	-17.67	0.000535	178 -- 264	1 -- 71	translation initiation factor IF-1		_____________177_______________________________________________________________________________________265\n_____________\|_________________________________________________________________________________________\|\n5'-UUU...UUACG________ACCCC______UUAGAUGGCCAA_____________U__AA_____G__A___________AA______CUAA____A___UCCGC...CUG-3'\n______________GUAGUGAU_____AGAGGA____________AG_AAGACAAUAU_GA__UGCAA_GU_CCGUU_CUUGA__CGUUGC____UACC_UGU\n______________\|:\|\|\|:\|\|_____\|:\|\|\|\|____________\|\|_\|\|\|\|\|\|\|\|\|\|_\|\|__:\|\|\|\|_\|:_\|\|:\|:_\|\|\|\|\|__\|\|\|\|\|\|____:\|\|\|_\|\|:\n______________CGUCAUUA_____UUUCCU____________UC_UUCUGUUAUA_CU__GCGUU_CG_GGUAG_GAACU__GCAACG____GUGG_ACG\n3'-UUU...CGAUA________AGUUU____________________A__________C__C______G________C_____________UAA_________-5'\n_____________\|________________________________________________________________________________________\|\n_____________72_______________________________________________________________________________________1\n	214 -- 220	40 -- 46	-55.7119 kcal/mol	17.4656 kcal/mol	20.5786 kcal/mol	177 265@LB@ \| \|@LB@5'-UUU...UUACG ACCCC UUAGAUGGCCAA U AA G A AA CUAA A UCCGC...CUG-3'@LB@ GUAGUGAU AGAGGA AG AAGACAAUAU GA UGCAA GU CCGUU CUUGA CGUUGC UACC UGU@LB@ \|:\|\|\|:\|\| \|:\|\|\|\| \|\| \|\|\|\|\|\|\|\|\|\| \|\| :\|\|\|\| \|: \|\|:\|: \|\|\|\|\| \|\|\|\|\|\| :\|\|\| \|\|:@LB@ CGUCAUUA UUUCCU UC UUCUGUUAUA CU GCGUU CG GGUAG GAACU GCAACG GUGG ACG@LB@3'-UUU...CGAUA AGUUU A C C G C UAA -5'@LB@ \| \|@LB@ 72 1@LB@@LB@@LB@Energy -17.67 kcal/mol@LB@Hybridization Energy -55.7119 kcal/mol@LB@Unfolding Energy - mRNA 17.4656 kcal/mol@LB@Unfolding Energy - sRNA 20.5786 kcal/mol@LB@@LB@Position - mRNA 178 -- 264@LB@Position - sRNA 1 -- 71@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 40 -- 46@LB@
5	2.521e-06	0.001776	b3365	nirB	-15.77	0.002536	156 -- 206	35 -- 88	nitrite reductase large subunit NAD(P)H-binding		_____________155____________________________________________________207\n_____________\|______________________________________________________\|\n5'-AUC...GUUGC_______UUAA__G__G_________________A__UC_______AAAU____AAAGU...UUA-3'\n______________UGAAUCG_____G_UA_GCGGUAAU__AGAAAAG_AA__GAGGCAA____GAGC\n______________:\|\|\|\|\|:_____\|_\|\|_\|\|:\|\|\|\|\|__\|:\|\|\|\|\|_\|\|__:\|\|:\|\|\|____\|\|\|\|\n______________GCUUAGU_____C_AU_CGUCAUUA__UUUUUUC_UU__UUCUGUU____CUCG\n3'-UUU...AGCAU_______UAACA_G__A________AG_______C__CA_______AUAC____CGUUG...ACG-5'\n_____________\|______________________________________________________\|\n_____________89_____________________________________________________34\n	192 -- 198	43 -- 49	-31.7984 kcal/mol	7.74851 kcal/mol	8.27555 kcal/mol	155 207@LB@ \| \|@LB@5'-AUC...GUUGC UUAA G G A UC AAAU AAAGU...UUA-3'@LB@ UGAAUCG G UA GCGGUAAU AGAAAAG AA GAGGCAA GAGC@LB@ :\|\|\|\|\|: \| \|\| \|\|:\|\|\|\|\| \|:\|\|\|\|\| \|\| :\|\|:\|\|\| \|\|\|\|@LB@ GCUUAGU C AU CGUCAUUA UUUUUUC UU UUCUGUU CUCG@LB@3'-UUU...AGCAU UAACA G A AG C CA AUAC CGUUG...ACG-5'@LB@ \| \|@LB@ 89 34@LB@@LB@@LB@Energy -15.77 kcal/mol@LB@Hybridization Energy -31.7984 kcal/mol@LB@Unfolding Energy - mRNA 7.74851 kcal/mol@LB@Unfolding Energy - sRNA 8.27555 kcal/mol@LB@@LB@Position - mRNA 156 -- 206@LB@Position - sRNA 35 -- 88@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 43 -- 49@LB@
6	5.595e-06	0.003285	b2048	cpsG	-15.91	0.002276	49 -- 82	20 -- 54	phosphomannomutase		_____________48__________________________________83\n_____________\|___________________________________\|\n5'-GGG...AUCUC_________________U____UU___GG______ACGGA...GCG-3'\n______________GAAG_AGGAUGAUGUGG_GCGU__CGC__AUCGCU\n______________\|\|\|\|_\|:\|\|::\|\|:\|\|\|_\|\|\|:__\|\|\|__\|\|\|\|\|\|\n______________CUUC_UUCUGUUAUACC_CGCG__GCG__UAGCGA\n3'-UUU...UUUUC____A____________U____UU___GG______ACUGC...ACG-5'\n_____________\|___________________________________\|\n_____________55__________________________________19\n	54 -- 60	42 -- 48	-40.4755 kcal/mol	10.8622 kcal/mol	13.7092 kcal/mol	48 83@LB@ \| \|@LB@5'-GGG...AUCUC U UU GG ACGGA...GCG-3'@LB@ GAAG AGGAUGAUGUGG GCGU CGC AUCGCU@LB@ \|\|\|\| \|:\|\|::\|\|:\|\|\| \|\|\|: \|\|\| \|\|\|\|\|\|@LB@ CUUC UUCUGUUAUACC CGCG GCG UAGCGA@LB@3'-UUU...UUUUC A U UU GG ACUGC...ACG-5'@LB@ \| \|@LB@ 55 19@LB@@LB@@LB@Energy -15.91 kcal/mol@LB@Hybridization Energy -40.4755 kcal/mol@LB@Unfolding Energy - mRNA 10.8622 kcal/mol@LB@Unfolding Energy - sRNA 13.7092 kcal/mol@LB@@LB@Position - mRNA 49 -- 82@LB@Position - sRNA 20 -- 54@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 42 -- 48@LB@
7	8.167e-06	0.003921	b1531	marA	-12.70	0.022098	183 -- 204	40 -- 62	multiple antibiotic resistance transcriptional regulator		_____________182_____________________205\n_____________\|_______________________\|\n5'-AAG...GUAAA______________U________CCAGA...AGC-3'\n______________CAAAAAA_GAGGUA_GACGAUGU\n______________\|\|\|\|\|\|\|_\|\|:\|\|\|_\|\|\|:\|\|:\|\n______________GUUUUUU_CUUCAU_CUGUUAUA\n3'-UUU...AUUAA_______C______U________CCUCG...ACG-5'\n_____________\|_______________________\|\n_____________63______________________39\n	198 -- 204	40 -- 46	-19.9636 kcal/mol	3.18051 kcal/mol	4.08673 kcal/mol	182 205@LB@ \| \|@LB@5'-AAG...GUAAA U CCAGA...AGC-3'@LB@ CAAAAAA GAGGUA GACGAUGU@LB@ \|\|\|\|\|\|\| \|\|:\|\|\| \|\|\|:\|\|:\|@LB@ GUUUUUU CUUCAU CUGUUAUA@LB@3'-UUU...AUUAA C U CCUCG...ACG-5'@LB@ \| \|@LB@ 63 39@LB@@LB@@LB@Energy -12.70 kcal/mol@LB@Hybridization Energy -19.9636 kcal/mol@LB@Unfolding Energy - mRNA 3.18051 kcal/mol@LB@Unfolding Energy - sRNA 4.08673 kcal/mol@LB@@LB@Position - mRNA 183 -- 204@LB@Position - sRNA 40 -- 62@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 40 -- 46@LB@
8	8.903e-06	0.003921	b1654	grxD	-12.06	0.033180	187 -- 203	41 -- 57	glutaredoxin-4		_____________186_____________________204\n_____________\|_______________________\|\n5'-AAA...AGUUU_______C_______________ACCAC...CUG-3'\n______________GAGGAAG_AAGACAAU___GAGC\n______________:\|\|\|\|\|\|_\|\|\|\|\|\|\|\|___\|\|\|\|\n______________UUCCUUC_UUCUGUUA___CUCG\n3'-UUU...GUUUU_______A________UAC____CGUUG...ACG-5'\n_____________\|_______________________\|\n_____________58______________________40\n	196 -- 202	42 -- 48	-22.6133 kcal/mol	5.89741 kcal/mol	4.1846 kcal/mol	186 204@LB@ \| \|@LB@5'-AAA...AGUUU C ACCAC...CUG-3'@LB@ GAGGAAG AAGACAAU GAGC@LB@ :\|\|\|\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|@LB@ UUCCUUC UUCUGUUA CUCG@LB@3'-UUU...GUUUU A UAC CGUUG...ACG-5'@LB@ \| \|@LB@ 58 40@LB@@LB@@LB@Energy -12.06 kcal/mol@LB@Hybridization Energy -22.6133 kcal/mol@LB@Unfolding Energy - mRNA 5.89741 kcal/mol@LB@Unfolding Energy - sRNA 4.1846 kcal/mol@LB@@LB@Position - mRNA 187 -- 203@LB@Position - sRNA 41 -- 57@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 42 -- 48@LB@
9	1.504e-05	0.005627	b1189	dadA	-11.44	0.048458	195 -- 226	48 -- 78	D-amino acid dehydrogenase		_____________194_______________________________227\n_____________\|_________________________________\|\n5'-CCG...UCGGA__G_______G___UG____UACU_________UGUGG...CGG-3'\n______________GU_GCUAUGC_AGU___UCA____GGGAAGUGG\n______________\|\|_\|\|\|\|\|\|\|_\|\|\|___\|\|\|____:\|\|\|\|\|\|::\n______________CA_CGAUACG_UCA___AGU____UCCUUCAUU\n3'-UUU...GUUAA______________UUA___UUUU_________CUGUU...ACG-5'\n_____________\|_________________________________\|\n_____________79________________________________47\n	220 -- 226	48 -- 54	-26.7579 kcal/mol	10.7545 kcal/mol	4.57065 kcal/mol	194 227@LB@ \| \|@LB@5'-CCG...UCGGA G G UG UACU UGUGG...CGG-3'@LB@ GU GCUAUGC AGU UCA GGGAAGUGG@LB@ \|\| \|\|\|\|\|\|\| \|\|\| \|\|\| :\|\|\|\|\|\|::@LB@ CA CGAUACG UCA AGU UCCUUCAUU@LB@3'-UUU...GUUAA UUA UUUU CUGUU...ACG-5'@LB@ \| \|@LB@ 79 47@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -26.7579 kcal/mol@LB@Unfolding Energy - mRNA 10.7545 kcal/mol@LB@Unfolding Energy - sRNA 4.57065 kcal/mol@LB@@LB@Position - mRNA 195 -- 226@LB@Position - sRNA 48 -- 78@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 48 -- 54@LB@
10	1.762e-05	0.005627	b1112	bhsA	-13.86	0.010205	165 -- 186	1 -- 22	biofilm cell surface and signaling protein	b0806 b0802	_____________164_____________________187\n_____________\|_______________________\|\n5'-UAA...UAAUU________AC_U___________AUAAG...AAC-3'\n______________GCUUG_CG__G_CAUUCAUCUGC\n______________\|\|\|\|\|_\|\|__\|_\|\|\|\|\|\|:\|\|\|\|\n______________CGAAC_GC__C_GUAAGUGGACG\n3'-UUU...GGUAG_____U__AA_____________-5'\n_____________\|______________________\|\n_____________23_____________________1\n	180 -- 186	1 -- 7	-25.8922 kcal/mol	3.94114 kcal/mol	8.09964 kcal/mol	164 187@LB@ \| \|@LB@5'-UAA...UAAUU AC U AUAAG...AAC-3'@LB@ GCUUG CG G CAUUCAUCUGC@LB@ \|\|\|\|\| \|\| \| \|\|\|\|\|\|:\|\|\|\|@LB@ CGAAC GC C GUAAGUGGACG@LB@3'-UUU...GGUAG U AA -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -13.86 kcal/mol@LB@Hybridization Energy -25.8922 kcal/mol@LB@Unfolding Energy - mRNA 3.94114 kcal/mol@LB@Unfolding Energy - sRNA 8.09964 kcal/mol@LB@@LB@Position - mRNA 165 -- 186@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 1 -- 7@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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