Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
83	0.007683	0.3104	b4244	pyrI	-7.62	0.290375	210 -- 222	10 -- 21	aspartate carbamoyltransferase regulatory subunit		_____________209___________223\n_____________\|_____________\|\n5'-UUC...CACAC__________U__AGGUU...UCA-3'\n______________GAUAAUAAAU_GC\n______________\|\|\|\|\|:\|\|\|\|_\|\|\n______________CUAUUGUUUA_CG\n3'-UUU...UACUA_____________CGCAG...AAG-5'\n_____________\|_____________\|\n_____________22____________9\n	213 -- 219	12 -- 18	-11.1174 kcal/mol	2.26673 kcal/mol	1.23076 kcal/mol	209 223@LB@ \| \|@LB@5'-UUC...CACAC U AGGUU...UCA-3'@LB@ GAUAAUAAAU GC@LB@ \|\|\|\|\|:\|\|\|\| \|\|@LB@ CUAUUGUUUA CG@LB@3'-UUU...UACUA CGCAG...AAG-5'@LB@ \| \|@LB@ 22 9@LB@@LB@@LB@Energy -7.62 kcal/mol@LB@Hybridization Energy -11.1174 kcal/mol@LB@Unfolding Energy - mRNA 2.26673 kcal/mol@LB@Unfolding Energy - sRNA 1.23076 kcal/mol@LB@@LB@Position - mRNA 210 -- 222@LB@Position - sRNA 10 -- 21@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 12 -- 18@LB@
90	0.009145	0.3104	b1079	flgH	-6.81	0.379144	179 -- 204	10 -- 38	flagellar protein of basal-body outer-membrane L ring		_____________178___________________________205\n_____________\|_____________________________\|\n5'-ACU...GUUUA____U___U____A_________C_____AAAAA...GGG-3'\n______________CUGA_UUU___GA_GAUGAUAGC__AUGC\n______________\|\|\|\|_\|\|:___\|\|_\|\|\|\|\|\|\|:\|__\|\|\|\|\n______________GACU_AAG___CU_CUACUAUUG__UACG\n3'-UUU...GUAGA____U___UCC__A_________UU____CGCAG...AAG-5'\n_____________\|_____________________________\|\n_____________39____________________________9\n	193 -- 199	16 -- 22	-21.1251 kcal/mol	4.97135 kcal/mol	9.34299 kcal/mol	178 205@LB@ \| \|@LB@5'-ACU...GUUUA U U A C AAAAA...GGG-3'@LB@ CUGA UUU GA GAUGAUAGC AUGC@LB@ \|\|\|\| \|\|: \|\| \|\|\|\|\|\|\|:\| \|\|\|\|@LB@ GACU AAG CU CUACUAUUG UACG@LB@3'-UUU...GUAGA U UCC A UU CGCAG...AAG-5'@LB@ \| \|@LB@ 39 9@LB@@LB@@LB@Energy -6.81 kcal/mol@LB@Hybridization Energy -21.1251 kcal/mol@LB@Unfolding Energy - mRNA 4.97135 kcal/mol@LB@Unfolding Energy - sRNA 9.34299 kcal/mol@LB@@LB@Position - mRNA 179 -- 204@LB@Position - sRNA 10 -- 38@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 16 -- 22@LB@
140	0.01344	0.3104	b2388	glk	-4.25	0.738023	201 -- 214	10 -- 20	glucokinase		_____________200____________215\n_____________\|______________\|\n5'-CUA...GAAGA_______AGU____AUUAG...AUU-3'\n______________AUGACAA___AUGC\n______________\|\|:\|\|\|\|___\|\|\|\|\n______________UAUUGUU___UACG\n3'-UUU...ACUAC______________CGCAG...AAG-5'\n_____________\|______________\|\n_____________21_____________9\n	201 -- 207	14 -- 20	-8.41213 kcal/mol	2.93934 kcal/mol	1.22774 kcal/mol	200 215@LB@ \| \|@LB@5'-CUA...GAAGA AGU AUUAG...AUU-3'@LB@ AUGACAA AUGC@LB@ \|\|:\|\|\|\| \|\|\|\|@LB@ UAUUGUU UACG@LB@3'-UUU...ACUAC CGCAG...AAG-5'@LB@ \| \|@LB@ 21 9@LB@@LB@@LB@Energy -4.25 kcal/mol@LB@Hybridization Energy -8.41213 kcal/mol@LB@Unfolding Energy - mRNA 2.93934 kcal/mol@LB@Unfolding Energy - sRNA 1.22774 kcal/mol@LB@@LB@Position - mRNA 201 -- 214@LB@Position - sRNA 10 -- 20@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 14 -- 20@LB@
182	0.01795	0.3104	b0403	malZ	-8.22	0.235274	180 -- 211	10 -- 46	maltodextrin glucosidase		_____________179_____________________________________212\n_____________\|_______________________________________\|\n5'-UUU...CAGAU_______A_____________AAUU______U_______AUGGC...AGC-3'\n______________UUUCAUC________CAGGGG____AUGAUG_UAAAUGC\n______________\|\|\|\|\|\|\|________\|\|\|\|\|:____\|\|\|\|\|:_:\|\|\|\|\|\|\n______________AAAGUAG________GUCCCU____UACUAU_GUUUACG\n3'-UUU...GUUUU_______AGACUUAA______AC________U_______CGCAG...AAG-5'\n_____________\|_______________________________________\|\n_____________47______________________________________9\n	205 -- 211	10 -- 16	-25.6812 kcal/mol	8.00905 kcal/mol	9.44998 kcal/mol	179 212@LB@ \| \|@LB@5'-UUU...CAGAU A AAUU U AUGGC...AGC-3'@LB@ UUUCAUC CAGGGG AUGAUG UAAAUGC@LB@ \|\|\|\|\|\|\| \|\|\|\|\|: \|\|\|\|\|: :\|\|\|\|\|\|@LB@ AAAGUAG GUCCCU UACUAU GUUUACG@LB@3'-UUU...GUUUU AGACUUAA AC U CGCAG...AAG-5'@LB@ \| \|@LB@ 47 9@LB@@LB@@LB@Energy -8.22 kcal/mol@LB@Hybridization Energy -25.6812 kcal/mol@LB@Unfolding Energy - mRNA 8.00905 kcal/mol@LB@Unfolding Energy - sRNA 9.44998 kcal/mol@LB@@LB@Position - mRNA 180 -- 211@LB@Position - sRNA 10 -- 46@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 10 -- 16@LB@
183	0.01807	0.3104	b1508	hipB	-7.23	0.331427	238 -- 247	10 -- 19	antitoxin of HipAB toxin-antitoxin system	b1299 b1434	_____________237________248\n_____________\|__________\|\n5'-AUG...GCAAU__________AAUGA...AAA-3'\n______________UGGCGAAUGC\n______________\|::\|:\|\|\|\|\|\n______________AUUGUUUACG\n3'-UUU...CUACU__________CGCAG...AAG-5'\n_____________\|__________\|\n_____________20_________9\n	241 -- 247	10 -- 16	-11.7956 kcal/mol	3.36082 kcal/mol	1.20833 kcal/mol	237 248@LB@ \| \|@LB@5'-AUG...GCAAU AAUGA...AAA-3'@LB@ UGGCGAAUGC@LB@ \|::\|:\|\|\|\|\|@LB@ AUUGUUUACG@LB@3'-UUU...CUACU CGCAG...AAG-5'@LB@ \| \|@LB@ 20 9@LB@@LB@@LB@Energy -7.23 kcal/mol@LB@Hybridization Energy -11.7956 kcal/mol@LB@Unfolding Energy - mRNA 3.36082 kcal/mol@LB@Unfolding Energy - sRNA 1.20833 kcal/mol@LB@@LB@Position - mRNA 238 -- 247@LB@Position - sRNA 10 -- 19@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 10 -- 16@LB@
193	0.01896	0.3104	b3181	greA	-10.36	0.105339	194 -- 204	10 -- 20	transcript cleavage factor		_____________193_________205\n_____________\|___________\|\n5'-CGC...GAGGU___________AAGCU...UCG-3'\n______________AUAACAAAUGC\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________UAUUGUUUACG\n3'-UUU...ACUAC___________CGCAG...AAG-5'\n_____________\|___________\|\n_____________21__________9\n	198 -- 204	10 -- 16	-13.1767 kcal/mol	1.58941 kcal/mol	1.22774 kcal/mol	193 205@LB@ \| \|@LB@5'-CGC...GAGGU AAGCU...UCG-3'@LB@ AUAACAAAUGC@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ UAUUGUUUACG@LB@3'-UUU...ACUAC CGCAG...AAG-5'@LB@ \| \|@LB@ 21 9@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -13.1767 kcal/mol@LB@Unfolding Energy - mRNA 1.58941 kcal/mol@LB@Unfolding Energy - sRNA 1.22774 kcal/mol@LB@@LB@Position - mRNA 194 -- 204@LB@Position - sRNA 10 -- 20@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 10 -- 16@LB@
152	0.01445	0.3104	b0385	yaiC	-12.21	0.050169	39 -- 67	12 -- 42	diguanylate cyclase cellulose regualtor		_____________38_______________________________68\n_____________\|________________________________\|\n5'-CAA...CAACA_______________U______C_________UUAUG...CCG-3'\n______________AUCUCUGAA___AGG_GAUGAU_GUAAUAAGU\n______________\|\|\|\|\|\|\|\|\|___\|\|\|_\|\|\|\|\|\|_:\|\|\|:\|\|:\|\n______________UAGAGACUU___UCC_CUACUA_UAUUGUUUA\n3'-UUU...UAAAG_________AAG__________C_________CGCGC...AAG-5'\n_____________\|________________________________\|\n_____________43_______________________________11\n	40 -- 46	35 -- 41	-28.8147 kcal/mol	7.19368 kcal/mol	9.40905 kcal/mol	38 68@LB@ \| \|@LB@5'-CAA...CAACA U C UUAUG...CCG-3'@LB@ AUCUCUGAA AGG GAUGAU GUAAUAAGU@LB@ \|\|\|\|\|\|\|\|\| \|\|\| \|\|\|\|\|\| :\|\|\|:\|\|:\|@LB@ UAGAGACUU UCC CUACUA UAUUGUUUA@LB@3'-UUU...UAAAG AAG C CGCGC...AAG-5'@LB@ \| \|@LB@ 43 11@LB@@LB@@LB@Energy -12.21 kcal/mol@LB@Hybridization Energy -28.8147 kcal/mol@LB@Unfolding Energy - mRNA 7.19368 kcal/mol@LB@Unfolding Energy - sRNA 9.40905 kcal/mol@LB@@LB@Position - mRNA 39 -- 67@LB@Position - sRNA 12 -- 42@LB@Position Seed - mRNA 40 -- 46@LB@Position Seed - sRNA 35 -- 41@LB@
188	0.0185	0.3104	b3364	tsgA	-7.52	0.300608	282 -- 299	12 -- 29	putative transporter		_____________281________________300\n_____________\|__________________\|\n5'-CCA...UCACC_____________G____A-3'\n______________GGGAUGGUGAUGG_AAAU\n______________\|\|\|\|\|\|:\|\|\|\|::_\|\|\|\|\n______________CCCUACUACUAUU_UUUA\n3'-UUU...UAAGU_____________G____CGCGC...AAG-5'\n_____________\|__________________\|\n_____________30_________________11\n	282 -- 288	23 -- 29	-23.3156 kcal/mol	8.39977 kcal/mol	7.39774 kcal/mol	281 300@LB@ \| \|@LB@5'-CCA...UCACC G A-3'@LB@ GGGAUGGUGAUGG AAAU@LB@ \|\|\|\|\|\|:\|\|\|\|:: \|\|\|\|@LB@ CCCUACUACUAUU UUUA@LB@3'-UUU...UAAGU G CGCGC...AAG-5'@LB@ \| \|@LB@ 30 11@LB@@LB@@LB@Energy -7.52 kcal/mol@LB@Hybridization Energy -23.3156 kcal/mol@LB@Unfolding Energy - mRNA 8.39977 kcal/mol@LB@Unfolding Energy - sRNA 7.39774 kcal/mol@LB@@LB@Position - mRNA 282 -- 299@LB@Position - sRNA 12 -- 29@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 23 -- 29@LB@
162	0.01506	0.3104	b0871	poxB	-6.02	0.481603	228 -- 255	23 -- 53	pyruvate dehydrogenase thiamine triphosphate-binding FAD-binding		_____________227_______________________________256\n_____________\|_________________________________\|\n5'-CCG...AUAUC_____________________CGG_________AACGC...GUG-3'\n______________GCCAAAA___CA_CUC_GAAU___CAGGGGUGA\n______________\|\|\|\|\|\|\|___\|\|_\|\|\|_\|\|\|\|___\|\|\|\|\|:\|\|\|\n______________CGGUUUU___GU_GAG_CUUA___GUCCCUACU\n3'-UUU...CUCAC_______AAA__A___A____A___________ACUAU...AAG-5'\n_____________\|_________________________________\|\n_____________54________________________________22\n	249 -- 255	23 -- 29	-28.0165 kcal/mol	6.84512 kcal/mol	15.1535 kcal/mol	227 256@LB@ \| \|@LB@5'-CCG...AUAUC CGG AACGC...GUG-3'@LB@ GCCAAAA CA CUC GAAU CAGGGGUGA@LB@ \|\|\|\|\|\|\| \|\| \|\|\| \|\|\|\| \|\|\|\|\|:\|\|\|@LB@ CGGUUUU GU GAG CUUA GUCCCUACU@LB@3'-UUU...CUCAC AAA A A A ACUAU...AAG-5'@LB@ \| \|@LB@ 54 22@LB@@LB@@LB@Energy -6.02 kcal/mol@LB@Hybridization Energy -28.0165 kcal/mol@LB@Unfolding Energy - mRNA 6.84512 kcal/mol@LB@Unfolding Energy - sRNA 15.1535 kcal/mol@LB@@LB@Position - mRNA 228 -- 255@LB@Position - sRNA 23 -- 53@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 23 -- 29@LB@
76	0.007084	0.3087	b4214	cysQ	-5.34	0.578728	11 -- 17	26 -- 32	3'(2') 5'-bisphosphate nucleotidase		_____________10______18\n_____________\|_______\|\n5'-AAC...AAUCA_______CAUCC...ACA-3'\n______________UCAGGGA\n______________\|\|\|\|\|\|\|\n______________AGUCCCU\n3'-UUU...ACUUA_______ACUAC...AAG-5'\n_____________\|_______\|\n_____________33______25\n	11 -- 17	26 -- 32	-11.6237 kcal/mol	0.931861 kcal/mol	5.35475 kcal/mol	10 18@LB@ \| \|@LB@5'-AAC...AAUCA CAUCC...ACA-3'@LB@ UCAGGGA@LB@ \|\|\|\|\|\|\|@LB@ AGUCCCU@LB@3'-UUU...ACUUA ACUAC...AAG-5'@LB@ \| \|@LB@ 33 25@LB@@LB@@LB@Energy -5.34 kcal/mol@LB@Hybridization Energy -11.6237 kcal/mol@LB@Unfolding Energy - mRNA 0.931861 kcal/mol@LB@Unfolding Energy - sRNA 5.35475 kcal/mol@LB@@LB@Position - mRNA 11 -- 17@LB@Position - sRNA 26 -- 32@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 26 -- 32@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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