Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
23	0.0008148	0.1243	b2573	rpoE	-12.22	0.112158	248 -- 284	1 -- 24	RNA polymerase sigma E factor		_____________247___________________________________285\n_____________\|_____________________________________\|\n5'-ACA...CAGAA____G______AAGCCUUUAACUUACU_______C__UAUCA...UGG-3'\n______________GGGA_AUCAGA________________GGUAGUG_GC\n______________\|\|\|\|_\|\|\|\|:\|________________:\|:\|\|\|\|_\|\|\n______________CCCU_UAGUUU________________UCGUCAC_CG\n3'-UUU...UUUAC____G______CUUU______________________-5'\n_____________\|____________________________________\|\n_____________25___________________________________1\n	275 -- 281	3 -- 9	-22.4239 kcal/mol	7.75978 kcal/mol	2.44282 kcal/mol	247 285@LB@ \| \|@LB@5'-ACA...CAGAA G AAGCCUUUAACUUACU C UAUCA...UGG-3'@LB@ GGGA AUCAGA GGUAGUG GC@LB@ \|\|\|\| \|\|\|\|:\| :\|:\|\|\|\| \|\|@LB@ CCCU UAGUUU UCGUCAC CG@LB@3'-UUU...UUUAC G CUUU -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -12.22 kcal/mol@LB@Hybridization Energy -22.4239 kcal/mol@LB@Unfolding Energy - mRNA 7.75978 kcal/mol@LB@Unfolding Energy - sRNA 2.44282 kcal/mol@LB@@LB@Position - mRNA 248 -- 284@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 3 -- 9@LB@
17	0.0006839	0.1243	b1247	oppF	-10.96	0.191014	264 -- 288	1 -- 22	oligopeptide ABC transporter ATPase		_____________263________________________289\n_____________\|__________________________\|\n5'-GCG...ACUUU__A________U____AAAC______UCUGG...CGC-3'\n______________GA_AUCAAAGA__GGC____AGUGGU\n______________\|\|_\|\|\|\|\|\|\|\|__:\|\|____\|\|\|\|\|:\n______________CU_UAGUUUCU__UCG____UCACCG\n3'-UUU...UACCC__G________UU_____________-5'\n_____________\|_________________________\|\n_____________23________________________1\n	268 -- 274	12 -- 18	-19.2479 kcal/mol	6.74487 kcal/mol	1.54023 kcal/mol	263 289@LB@ \| \|@LB@5'-GCG...ACUUU A U AAAC UCUGG...CGC-3'@LB@ GA AUCAAAGA GGC AGUGGU@LB@ \|\| \|\|\|\|\|\|\|\| :\|\| \|\|\|\|\|:@LB@ CU UAGUUUCU UCG UCACCG@LB@3'-UUU...UACCC G UU -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -10.96 kcal/mol@LB@Hybridization Energy -19.2479 kcal/mol@LB@Unfolding Energy - mRNA 6.74487 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 264 -- 288@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 12 -- 18@LB@
19	0.000738	0.1243	b1508	hipB	-18.00	0.004180	266 -- 295	1 -- 32	antitoxin of HipAB toxin-antitoxin system	b1299 b1434	_____________265________________________________296\n_____________\|__________________________________\|\n5'-AUG...CGCCA_________CU___________C___________GAAAA-3'\n______________GCAAAAUGG__GGACG_CAGAG__GAGC__UGGC\n______________:\|\|\|\|\|\|\|\|__\|\|\|\|:_\|\|:\|\|__:\|\|\|__\|\|\|\|\n______________UGUUUUACC__CCUGU_GUUUC__UUCG__ACCG\n3'-UUU...CGAGG________________A_____UU____UC____-5'\n_____________\|_________________________________\|\n_____________33________________________________1\n	268 -- 274	24 -- 30	-30.0826 kcal/mol	9.54799 kcal/mol	2.53929 kcal/mol	265 296@LB@ \| \|@LB@5'-AUG...CGCCA CU C GAAAA-3'@LB@ GCAAAAUGG GGACG CAGAG GAGC UGGC@LB@ :\|\|\|\|\|\|\|\| \|\|\|\|: \|\|:\|\| :\|\|\| \|\|\|\|@LB@ UGUUUUACC CCUGU GUUUC UUCG ACCG@LB@3'-UUU...CGAGG A UU UC -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -18.00 kcal/mol@LB@Hybridization Energy -30.0826 kcal/mol@LB@Unfolding Energy - mRNA 9.54799 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 266 -- 295@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 24 -- 30@LB@
26	0.001009	0.1361	b3731	atpC	-14.21	0.042680	144 -- 160	2 -- 20	F1 sector of membrane-bound ATP synthase epsilon subunit		_____________143_________________161\n_____________\|___________________\|\n5'-UCC...GGUUC______________U____AAAAA...UGG-3'\n______________CAUCGAAGA__AGC_GUGG\n______________\|\|\|\|:\|\|\|\|__\|\|\|_\|\|\|\|\n______________GUAGUUUCU__UCG_CACC\n3'-UUU...CCCCU_________UU___U____G-5'\n_____________\|___________________\|\n_____________21__________________1\n	146 -- 152	12 -- 18	-19.7705 kcal/mol	4.1055 kcal/mol	1.45839 kcal/mol	143 161@LB@ \| \|@LB@5'-UCC...GGUUC U AAAAA...UGG-3'@LB@ CAUCGAAGA AGC GUGG@LB@ \|\|\|\|:\|\|\|\| \|\|\| \|\|\|\|@LB@ GUAGUUUCU UCG CACC@LB@3'-UUU...CCCCU UU U G-5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -14.21 kcal/mol@LB@Hybridization Energy -19.7705 kcal/mol@LB@Unfolding Energy - mRNA 4.1055 kcal/mol@LB@Unfolding Energy - sRNA 1.45839 kcal/mol@LB@@LB@Position - mRNA 144 -- 160@LB@Position - sRNA 2 -- 20@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 12 -- 18@LB@
25	0.0009834	0.1361	b3733	atpG	-13.27	0.068654	183 -- 205	1 -- 22	F1 sector of membrane-bound ATP synthase gamma subunit		_____________182_____________________206\n_____________\|_______________________\|\n5'-GGC...CGCAA________________UCA____CGGCG...GUA-3'\n______________GGCAUUGAGGAGAAGC___UGGC\n______________\|:\|\|\|::\|:\|\|:\|\|\|\|___\|\|\|\|\n______________CUGUAGUUUCUUUUCG___ACCG\n3'-UUU...UACCC________________UC_____-5'\n_____________\|______________________\|\n_____________23_____________________1\n	192 -- 198	7 -- 13	-25.5897 kcal/mol	10.7799 kcal/mol	1.54023 kcal/mol	182 206@LB@ \| \|@LB@5'-GGC...CGCAA UCA CGGCG...GUA-3'@LB@ GGCAUUGAGGAGAAGC UGGC@LB@ \|:\|\|\|::\|:\|\|:\|\|\|\| \|\|\|\|@LB@ CUGUAGUUUCUUUUCG ACCG@LB@3'-UUU...UACCC UC -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -13.27 kcal/mol@LB@Hybridization Energy -25.5897 kcal/mol@LB@Unfolding Energy - mRNA 10.7799 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 183 -- 205@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 7 -- 13@LB@
24	0.0009771	0.1361	b4295	yjhU	-16.20	0.013710	198 -- 226	5 -- 30	putative DNA-binding transcriptional regulator; KpLE2 phage-like element	b1512	_____________197___________________________227\n_____________\|_____________________________\|\n5'-GUA...AUACA_______AUA__G______C___C_____CCUGU...UUG-3'\n______________AAAGUGG___GA_AUCAAA_AAA_AGCAG\n______________\|\|\|:\|\|\|___\|\|_\|\|\|\|\|\|_\|\|\|_\|\|\|\|\|\n______________UUUUACC___CU_UAGUUU_UUU_UCGUC\n3'-UUU...AGGUG_______C____G______C_________ACCG-5'\n_____________\|_____________________________\|\n_____________31____________________________4\n	198 -- 204	24 -- 30	-21.4023 kcal/mol	2.69702 kcal/mol	2.50278 kcal/mol	197 227@LB@ \| \|@LB@5'-GUA...AUACA AUA G C C CCUGU...UUG-3'@LB@ AAAGUGG GA AUCAAA AAA AGCAG@LB@ \|\|\|:\|\|\| \|\| \|\|\|\|\|\| \|\|\| \|\|\|\|\|@LB@ UUUUACC CU UAGUUU UUU UCGUC@LB@3'-UUU...AGGUG C G C ACCG-5'@LB@ \| \|@LB@ 31 4@LB@@LB@@LB@Energy -16.20 kcal/mol@LB@Hybridization Energy -21.4023 kcal/mol@LB@Unfolding Energy - mRNA 2.69702 kcal/mol@LB@Unfolding Energy - sRNA 2.50278 kcal/mol@LB@@LB@Position - mRNA 198 -- 226@LB@Position - sRNA 5 -- 30@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 24 -- 30@LB@
28	0.001242	0.1512	b0879	macB	-8.34	0.466885	135 -- 159	1 -- 22	macrolide ABC transporter peremase/ATPase		_____________134_________________________160\n_____________\|___________________________\|\n5'-AAU...GUUGA__U_________GCUU___________GAUGA...CGG-3'\n______________GA_UGUCAAAGG____GAAGC_G_GGC\n______________\|\|_::\|\|\|\|\|\|:____:\|\|\|\|_\|_\|\|\|\n______________CU_GUAGUUUCU____UUUCG_C_CCG\n3'-UUU...UACCC_____________________U_A___-5'\n_____________\|__________________________\|\n_____________23_________________________1\n	140 -- 146	12 -- 18	-17.2972 kcal/mol	7.41924 kcal/mol	1.54023 kcal/mol	134 160@LB@ \| \|@LB@5'-AAU...GUUGA U GCUU GAUGA...CGG-3'@LB@ GA UGUCAAAGG GAAGC G GGC@LB@ \|\| ::\|\|\|\|\|\|: :\|\|\|\| \| \|\|\|@LB@ CU GUAGUUUCU UUUCG C CCG@LB@3'-UUU...UACCC U A -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -8.34 kcal/mol@LB@Hybridization Energy -17.2972 kcal/mol@LB@Unfolding Energy - mRNA 7.41924 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 135 -- 159@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 140 -- 146@LB@Position Seed - sRNA 12 -- 18@LB@
29	0.00125	0.1512	b2499	purM	-15.92	0.016248	173 -- 203	3 -- 34	phosphoribosylaminoimidazole synthetase		_____________172____________________________________204\n_____________\|______________________________________\|\n5'-UAU...UUCUA_______UAACGC________CC_______________ACCGA...CGC-3'\n______________CCGCAAG______GUGGGGAC_________AAGCAGUG\n______________\|\|:\|\|\|:______:\|\|\|\|\|\|\|_________\|\|\|\|\|\|\|\|\n______________GGUGUUU______UACCCCUG_________UUCGUCAC\n3'-UUU...CCCGA_____________________UAGUUUCUU________CG-5'\n_____________\|______________________________________\|\n_____________35_____________________________________2\n	197 -- 203	3 -- 9	-29.7141 kcal/mol	9.52212 kcal/mol	4.26884 kcal/mol	172 204@LB@ \| \|@LB@5'-UAU...UUCUA UAACGC CC ACCGA...CGC-3'@LB@ CCGCAAG GUGGGGAC AAGCAGUG@LB@ \|\|:\|\|\|: :\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ GGUGUUU UACCCCUG UUCGUCAC@LB@3'-UUU...CCCGA UAGUUUCUU CG-5'@LB@ \| \|@LB@ 35 2@LB@@LB@@LB@Energy -15.92 kcal/mol@LB@Hybridization Energy -29.7141 kcal/mol@LB@Unfolding Energy - mRNA 9.52212 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 173 -- 203@LB@Position - sRNA 3 -- 34@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 3 -- 9@LB@
27	0.001238	0.1512	b4045	yjbJ	-9.99	0.275707	259 -- 267	19 -- 28	stress-induced protein UPF0337 family		_____________258________268\n_____________\|__________\|\n5'-CGU...AGAGC__________AACUG...AAG-3'\n______________AAUGGGG_CA\n______________\|\|\|\|\|\|\|_\|\|\n______________UUACCCC_GU\n3'-UUU...GUGUU_______U__AGUUU...CCG-5'\n_____________\|__________\|\n_____________29_________18\n	259 -- 265	22 -- 28	-11.8839 kcal/mol	1.24365 kcal/mol	0.649553 kcal/mol	258 268@LB@ \| \|@LB@5'-CGU...AGAGC AACUG...AAG-3'@LB@ AAUGGGG CA@LB@ \|\|\|\|\|\|\| \|\|@LB@ UUACCCC GU@LB@3'-UUU...GUGUU U AGUUU...CCG-5'@LB@ \| \|@LB@ 29 18@LB@@LB@@LB@Energy -9.99 kcal/mol@LB@Hybridization Energy -11.8839 kcal/mol@LB@Unfolding Energy - mRNA 1.24365 kcal/mol@LB@Unfolding Energy - sRNA 0.649553 kcal/mol@LB@@LB@Position - mRNA 259 -- 267@LB@Position - sRNA 19 -- 28@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 22 -- 28@LB@
31	0.001481	0.1635	b3468	yhhN	-14.35	0.039524	32 -- 52	1 -- 21	TMEM86 family putative inner membrane protein		_____________31____________________53\n_____________\|_____________________\|\n5'-CGA...UGAUA___A__________A______UUGCU...UAA-3'\n______________ACA_UAAAGAAAAG_GGUGGU\n______________\|\|\|_:\|\|\|\|\|\|\|\|\|_:\|\|\|\|:\n______________UGU_GUUUCUUUUC_UCACCG\n3'-UUU...ACCCC___A__________G______-5'\n_____________\|____________________\|\n_____________22___________________1\n	39 -- 45	8 -- 14	-21.1877 kcal/mol	5.32481 kcal/mol	1.51103 kcal/mol	31 53@LB@ \| \|@LB@5'-CGA...UGAUA A A UUGCU...UAA-3'@LB@ ACA UAAAGAAAAG GGUGGU@LB@ \|\|\| :\|\|\|\|\|\|\|\|\| :\|\|\|\|:@LB@ UGU GUUUCUUUUC UCACCG@LB@3'-UUU...ACCCC A G -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -14.35 kcal/mol@LB@Hybridization Energy -21.1877 kcal/mol@LB@Unfolding Energy - mRNA 5.32481 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 32 -- 52@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 8 -- 14@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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