Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
150	0.02489	0.526	b2088	insE1	-9.25	0.136086	235 -- 276	1 -- 55	IS3 transposase A	b0298 b0373 b0540 b1027	_____________234_____________________________________________________277\n_____________\|_______________________________________________________\|\n5'-ACC...ACCCC_______________CC_______UU__C____________CCC___________UUGCU...CUG-3'\n______________GUAAACAG_CAUUCG____UGAAU__CG______AGUGAAG____UGA____AGC\n______________\|\|\|\|\|\|\|\|_\|\|\|\|\|:____\|\|\|\|\|__\|\|______\|:\|:\|\|\|____\|\|\|____\|\|\|\n______________CAUUUGUC_GUAAGU____ACUUA__GC______UUAUUUC____ACU____UCG\n3'-UUU...AUCCC________U______CUUU_____CU__CAUUAU_______AAUU___ACUA___-5'\n_____________\|______________________________________________________\|\n_____________56_____________________________________________________1\n	261 -- 267	15 -- 21	-23.7484 kcal/mol	8.16492 kcal/mol	6.33758 kcal/mol	234 277@LB@ \| \|@LB@5'-ACC...ACCCC CC UU C CCC UUGCU...CUG-3'@LB@ GUAAACAG CAUUCG UGAAU CG AGUGAAG UGA AGC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|: \|\|\|\|\| \|\| \|:\|:\|\|\| \|\|\| \|\|\|@LB@ CAUUUGUC GUAAGU ACUUA GC UUAUUUC ACU UCG@LB@3'-UUU...AUCCC U CUUU CU CAUUAU AAUU ACUA -5'@LB@ \| \|@LB@ 56 1@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -23.7484 kcal/mol@LB@Unfolding Energy - mRNA 8.16492 kcal/mol@LB@Unfolding Energy - sRNA 6.33758 kcal/mol@LB@@LB@Position - mRNA 235 -- 276@LB@Position - sRNA 1 -- 55@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 15 -- 21@LB@
151	0.02491	0.526	b3575	yiaK	-7.81	0.245984	13 -- 22	1 -- 10	2 3-diketo-L-gulonate reductase NADH-dependent		_____________12_________23\n_____________\|__________\|\n5'-UUU...CGUCC__________GCAAA...UCG-3'\n______________UGAUGGUAGC\n______________\|\|\|\|\|:\|\|\|\|\n______________ACUACUAUCG\n3'-UUU...CAAUU__________-5'\n_____________\|_________\|\n_____________11________1\n	16 -- 22	1 -- 7	-14.2362 kcal/mol	6.39652 kcal/mol	0.0255427 kcal/mol	12 23@LB@ \| \|@LB@5'-UUU...CGUCC GCAAA...UCG-3'@LB@ UGAUGGUAGC@LB@ \|\|\|\|\|:\|\|\|\|@LB@ ACUACUAUCG@LB@3'-UUU...CAAUU -5'@LB@ \| \|@LB@ 11 1@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -14.2362 kcal/mol@LB@Unfolding Energy - mRNA 6.39652 kcal/mol@LB@Unfolding Energy - sRNA 0.0255427 kcal/mol@LB@@LB@Position - mRNA 13 -- 22@LB@Position - sRNA 1 -- 10@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 1 -- 7@LB@
153	0.02513	0.526	b2745	truD	-9.91	0.100940	94 -- 116	1 -- 24	tRNA(Glu) pseudouridine(13) synthase		_____________93_______________________117\n_____________\|________________________\|\n5'-AAC...GCCAU________U_____C_____A___CACUA...UGG-3'\n______________AUGGAUGA_GUUAA__GUGA_AGC\n______________\|\|::\|\|:\|_\|\|\|\|\|__:\|\|\|_\|\|\|\n______________UAUUUAUU_CAAUU__UACU_UCG\n3'-UUU...GCCAU________U_____AC____A___-5'\n_____________\|_______________________\|\n_____________25______________________1\n	95 -- 101	17 -- 23	-14.0384 kcal/mol	4.01581 kcal/mol	0.108605 kcal/mol	93 117@LB@ \| \|@LB@5'-AAC...GCCAU U C A CACUA...UGG-3'@LB@ AUGGAUGA GUUAA GUGA AGC@LB@ \|\|::\|\|:\| \|\|\|\|\| :\|\|\| \|\|\|@LB@ UAUUUAUU CAAUU UACU UCG@LB@3'-UUU...GCCAU U AC A -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -9.91 kcal/mol@LB@Hybridization Energy -14.0384 kcal/mol@LB@Unfolding Energy - mRNA 4.01581 kcal/mol@LB@Unfolding Energy - sRNA 0.108605 kcal/mol@LB@@LB@Position - mRNA 94 -- 116@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 17 -- 23@LB@
158	0.0258	0.526	b3738	atpB	-11.34	0.051140	75 -- 89	1 -- 15	F0 sector of membrane-bound ATP synthase subunit a		_____________74______________90\n_____________\|_______________\|\n5'-CAU...UUGGU____C__________GUUGG...ACC-3'\n______________GUUA_UGGUGGUGGC\n______________\|\|\|\|_\|\|:\|\|:\|:\|\|\n______________CAAU_ACUACUAUCG\n3'-UUU...UAUUU____U__________-5'\n_____________\|______________\|\n_____________16_____________1\n	83 -- 89	1 -- 7	-16.9836 kcal/mol	5.59496 kcal/mol	0.0474282 kcal/mol	74 90@LB@ \| \|@LB@5'-CAU...UUGGU C GUUGG...ACC-3'@LB@ GUUA UGGUGGUGGC@LB@ \|\|\|\| \|\|:\|\|:\|:\|\|@LB@ CAAU ACUACUAUCG@LB@3'-UUU...UAUUU U -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -11.34 kcal/mol@LB@Hybridization Energy -16.9836 kcal/mol@LB@Unfolding Energy - mRNA 5.59496 kcal/mol@LB@Unfolding Energy - sRNA 0.0474282 kcal/mol@LB@@LB@Position - mRNA 75 -- 89@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 83 -- 89@LB@Position Seed - sRNA 1 -- 7@LB@
159	0.02583	0.526	b2572	rseA	-12.83	0.023837	184 -- 236	1 -- 63	anti-sigma factor		_____________183_____________________________________________________________237\n_____________\|_______________________________________________________________\|\n5'-UCC...AUACU_____A_____U________G__________CA__UUUCCGCU____________________GAAAC...GGG-3'\n______________GGAUA_GGGUA__UAGGCAU_CAGAAA_GAA__AC______________UUAAUGG__AUGGC\n______________::\|\|\|_\|\|\|\|\|__:\|\|:\|\|\|_\|\|\|\|\|\|_\|\|\|__\|\|______________\|\|\|\|\|\|:__\|\|:\|\|\n______________UUUAU_CCCAU__GUCUGUA_GUCUUU_CUU__UG______________AAUUACU__UAUCG\n3'-UUU...CCAAC_____C_____UU_______A______A___AC__CCAUUAUUUAUUUC_______AC_____-5'\n_____________\|______________________________________________________________\|\n_____________64_____________________________________________________________1\n	225 -- 231	8 -- 14	-31.1691 kcal/mol	11.9981 kcal/mol	6.344 kcal/mol	183 237@LB@ \| \|@LB@5'-UCC...AUACU A U G CA UUUCCGCU GAAAC...GGG-3'@LB@ GGAUA GGGUA UAGGCAU CAGAAA GAA AC UUAAUGG AUGGC@LB@ ::\|\|\| \|\|\|\|\| :\|\|:\|\|\| \|\|\|\|\|\| \|\|\| \|\| \|\|\|\|\|\|: \|\|:\|\|@LB@ UUUAU CCCAU GUCUGUA GUCUUU CUU UG AAUUACU UAUCG@LB@3'-UUU...CCAAC C UU A A AC CCAUUAUUUAUUUC AC -5'@LB@ \| \|@LB@ 64 1@LB@@LB@@LB@Energy -12.83 kcal/mol@LB@Hybridization Energy -31.1691 kcal/mol@LB@Unfolding Energy - mRNA 11.9981 kcal/mol@LB@Unfolding Energy - sRNA 6.344 kcal/mol@LB@@LB@Position - mRNA 184 -- 236@LB@Position - sRNA 1 -- 63@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 8 -- 14@LB@
165	0.02655	0.526	b2388	glk	-7.68	0.259430	184 -- 233	1 -- 52	glucokinase		_____________183_____________________________________________________234\n_____________\|_______________________________________________________\|\n5'-CUA...ACUUU______G__GUU_____________AAA___UGCAUU_____C_______UG___GGCAC...AUU-3'\n______________AGCGGA_CA____GAA__GAAUGAC___GUA________AGU_GGUGAUG__GGC\n______________\|:\|:\|\|_\|\|____\|\|\|__\|\|\|\|\|\|\|___\|\|\|________\|\|\|_::\|\|\|\|\|__:\|\|\n______________UUGUCU_GU____CUU__CUUACUG___CAU________UCA_UUACUAC__UCG\n3'-UUU...CCCAU_________AAGU___UA_______C_____UAUUUAUU___A_______UA___-5'\n_____________\|______________________________________________________\|\n_____________53_____________________________________________________1\n	222 -- 228	6 -- 12	-28.455 kcal/mol	14.4434 kcal/mol	6.33555 kcal/mol	183 234@LB@ \| \|@LB@5'-CUA...ACUUU G GUU AAA UGCAUU C UG GGCAC...AUU-3'@LB@ AGCGGA CA GAA GAAUGAC GUA AGU GGUGAUG GGC@LB@ \|:\|:\|\| \|\| \|\|\| \|\|\|\|\|\|\| \|\|\| \|\|\| ::\|\|\|\|\| :\|\|@LB@ UUGUCU GU CUU CUUACUG CAU UCA UUACUAC UCG@LB@3'-UUU...CCCAU AAGU UA C UAUUUAUU A UA -5'@LB@ \| \|@LB@ 53 1@LB@@LB@@LB@Energy -7.68 kcal/mol@LB@Hybridization Energy -28.455 kcal/mol@LB@Unfolding Energy - mRNA 14.4434 kcal/mol@LB@Unfolding Energy - sRNA 6.33555 kcal/mol@LB@@LB@Position - mRNA 184 -- 233@LB@Position - sRNA 1 -- 52@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 6 -- 12@LB@
166	0.02659	0.526	b1580	rspB	-9.76	0.108040	184 -- 209	1 -- 29	putative Zn-dependent NAD(P)-binding oxidoreductase		_____________183___________________________210\n_____________\|_____________________________\|\n5'-AUG...GGAAC______G_______A_______AA_____AUAUU...UUG-3'\n______________UGGUAA_GAGUAAG__UAAUGA____AGC\n______________:\|\|\|\|\|_:\|:\|\|\|:__\|\|\|\|\|\|____\|\|\|\n______________GCCAUU_UUUAUUU__AUUACU____UCG\n3'-UUU...UUACU______A_______CA______ACUA___-5'\n_____________\|____________________________\|\n_____________30___________________________1\n	191 -- 197	16 -- 22	-16.0836 kcal/mol	4.192 kcal/mol	2.12711 kcal/mol	183 210@LB@ \| \|@LB@5'-AUG...GGAAC G A AA AUAUU...UUG-3'@LB@ UGGUAA GAGUAAG UAAUGA AGC@LB@ :\|\|\|\|\| :\|:\|\|\|: \|\|\|\|\|\| \|\|\|@LB@ GCCAUU UUUAUUU AUUACU UCG@LB@3'-UUU...UUACU A CA ACUA -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -9.76 kcal/mol@LB@Hybridization Energy -16.0836 kcal/mol@LB@Unfolding Energy - mRNA 4.192 kcal/mol@LB@Unfolding Energy - sRNA 2.12711 kcal/mol@LB@@LB@Position - mRNA 184 -- 209@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 16 -- 22@LB@
168	0.02737	0.531	b1385	feaB	-11.89	0.038862	180 -- 210	1 -- 28	phenylacetaldehyde dehydrogenase		_____________179_____________________________211\n_____________\|_______________________________\|\n5'-UUG...CACUG_____AU_______AAA________CAG___CGCAU...GUG-3'\n______________GGUAA__AAUAAGG___AGUGAUGA___AGC\n______________\|\|\|\|\|__\|\|\|\|\|:\|___\|:\|\|\|\|\|\|___\|\|\|\n______________CCAUU__UUAUUUC___UUACUACU___UCG\n3'-UUU...UACUG_____AU_______AA_________A_____-5'\n_____________\|______________________________\|\n_____________29_____________________________1\n	198 -- 204	5 -- 11	-19.4278 kcal/mol	6.77275 kcal/mol	0.766821 kcal/mol	179 211@LB@ \| \|@LB@5'-UUG...CACUG AU AAA CAG CGCAU...GUG-3'@LB@ GGUAA AAUAAGG AGUGAUGA AGC@LB@ \|\|\|\|\| \|\|\|\|\|:\| \|:\|\|\|\|\|\| \|\|\|@LB@ CCAUU UUAUUUC UUACUACU UCG@LB@3'-UUU...UACUG AU AA A -5'@LB@ \| \|@LB@ 29 1@LB@@LB@@LB@Energy -11.89 kcal/mol@LB@Hybridization Energy -19.4278 kcal/mol@LB@Unfolding Energy - mRNA 6.77275 kcal/mol@LB@Unfolding Energy - sRNA 0.766821 kcal/mol@LB@@LB@Position - mRNA 180 -- 210@LB@Position - sRNA 1 -- 28@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 5 -- 11@LB@
173	0.02817	0.531	b0952	pqiC	-7.60	0.267291	63 -- 71	1 -- 9	DUF330 family putative lipoprotein		_____________62________72\n_____________\|_________\|\n5'-ACG...AACAA_________GGAUA...GCG-3'\n______________GAUGGUGGC\n______________\|\|\|\|:\|:\|\|\n______________CUACUAUCG\n3'-UUU...AAUUA_________-5'\n_____________\|________\|\n_____________10_______1\n	65 -- 71	1 -- 7	-13.4268 kcal/mol	5.80912 kcal/mol	0.0200155 kcal/mol	62 72@LB@ \| \|@LB@5'-ACG...AACAA GGAUA...GCG-3'@LB@ GAUGGUGGC@LB@ \|\|\|\|:\|:\|\|@LB@ CUACUAUCG@LB@3'-UUU...AAUUA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -7.60 kcal/mol@LB@Hybridization Energy -13.4268 kcal/mol@LB@Unfolding Energy - mRNA 5.80912 kcal/mol@LB@Unfolding Energy - sRNA 0.0200155 kcal/mol@LB@@LB@Position - mRNA 63 -- 71@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 1 -- 7@LB@
177	0.02886	0.5353	b2206	napA	-7.95	0.233634	77 -- 89	1 -- 13	nitrate reductase periplasmic large subunit		_____________76____________90\n_____________\|_____________\|\n5'-GAC...GAUUG_________A___AGAAG...UUG-3'\n______________UGGUGGUGG_AGC\n______________\|::\|\|:\|\|:_\|\|\|\n______________AUUACUACU_UCG\n3'-UUU...UUUCA_________A___-5'\n_____________\|____________\|\n_____________14___________1\n	79 -- 85	5 -- 11	-12.9311 kcal/mol	4.9403 kcal/mol	0.0446954 kcal/mol	76 90@LB@ \| \|@LB@5'-GAC...GAUUG A AGAAG...UUG-3'@LB@ UGGUGGUGG AGC@LB@ \|::\|\|:\|\|: \|\|\|@LB@ AUUACUACU UCG@LB@3'-UUU...UUUCA A -5'@LB@ \| \|@LB@ 14 1@LB@@LB@@LB@Energy -7.95 kcal/mol@LB@Hybridization Energy -12.9311 kcal/mol@LB@Unfolding Energy - mRNA 4.9403 kcal/mol@LB@Unfolding Energy - sRNA 0.0446954 kcal/mol@LB@@LB@Position - mRNA 77 -- 89@LB@Position - sRNA 1 -- 13@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 5 -- 11@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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service.

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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