Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
187	0.03332	0.5559	b2019	hisG	-10.76	0.077976	170 -- 191	15 -- 34	ATP phosphoribosyltransferase	_____________169____________________192\n_____________\|______________________\|\n5'-UUU...AUAAC_G_____ACA____U_______AAUAA...AUC-3'\n______________G_UUCAG___GGUU_AAAGAGG\n______________:_\|\|\|\|:___\|\|\|\|_\|\|\|\|\|\|\|\n______________U_AAGUU___CCAA_UUUCUCC\n3'-CGC...GUCAC_G_____C______U_______ACGGC...AAG-5'\n_____________\|______________________\|\n_____________35_____________________14\n	185 -- 191	15 -- 21	-17.0816 kcal/mol	2.9882 kcal/mol	3.33044 kcal/mol	169 192@LB@ \| \|@LB@5'-UUU...AUAAC G ACA U AAUAA...AUC-3'@LB@ G UUCAG GGUU AAAGAGG@LB@ : \|\|\|\|: \|\|\|\| \|\|\|\|\|\|\|@LB@ U AAGUU CCAA UUUCUCC@LB@3'-CGC...GUCAC G C U ACGGC...AAG-5'@LB@ \| \|@LB@ 35 14@LB@@LB@@LB@Energy -10.76 kcal/mol@LB@Hybridization Energy -17.0816 kcal/mol@LB@Unfolding Energy - mRNA 2.9882 kcal/mol@LB@Unfolding Energy - sRNA 3.33044 kcal/mol@LB@@LB@Position - mRNA 170 -- 191@LB@Position - sRNA 15 -- 34@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 15 -- 21@LB@
30	0.005373	0.5385	b1624	ydgJ	-10.76	0.078067	229 -- 247	61 -- 79	putative oxidoreductase	_____________228_________________248\n_____________\|___________________\|\n5'-GUA...GUUGA____G_A_______G____CAAAA...CGG-3'\n______________UUGG_U_UGGUUAU_CGAG\n______________\|\|\|\|_\|_\|:\|\|\|\|\|_\|\|\|\|\n______________AACC_A_AUCAAUA_GCUC\n3'-CGC...AGUGC____G_A_______A____AACUC...AAG-5'\n_____________\|___________________\|\n_____________80__________________60\n	236 -- 242	66 -- 72	-16.8363 kcal/mol	5.27817 kcal/mol	0.798019 kcal/mol	228 248@LB@ \| \|@LB@5'-GUA...GUUGA G A G CAAAA...CGG-3'@LB@ UUGG U UGGUUAU CGAG@LB@ \|\|\|\| \| \|:\|\|\|\|\| \|\|\|\|@LB@ AACC A AUCAAUA GCUC@LB@3'-CGC...AGUGC G A A AACUC...AAG-5'@LB@ \| \|@LB@ 80 60@LB@@LB@@LB@Energy -10.76 kcal/mol@LB@Hybridization Energy -16.8363 kcal/mol@LB@Unfolding Energy - mRNA 5.27817 kcal/mol@LB@Unfolding Energy - sRNA 0.798019 kcal/mol@LB@@LB@Position - mRNA 229 -- 247@LB@Position - sRNA 61 -- 79@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 66 -- 72@LB@
123	0.02095	0.5385	b2562	yfhL	-10.74	0.078719	174 -- 195	59 -- 77	putative 4Fe-4S cluster-containing protein	_____________173____________________196\n_____________\|______________________\|\n5'-AGC...CGCCC_____GU_______UGA_____UCCUU...UUA-3'\n______________GGUUU__GUUGUUU___GAGUU\n______________\|\|:\|\|__\|\|\|:\|\|:___\|\|\|\|\|\n______________CCGAA__CAAUAAG___CUCAA\n3'-CGC...UGCAA_____AU_______________CUCUU...AAG-5'\n_____________\|______________________\|\n_____________78_____________________58\n	181 -- 187	64 -- 70	-15.8972 kcal/mol	4.34594 kcal/mol	0.811926 kcal/mol	173 196@LB@ \| \|@LB@5'-AGC...CGCCC GU UGA UCCUU...UUA-3'@LB@ GGUUU GUUGUUU GAGUU@LB@ \|\|:\|\| \|\|\|:\|\|: \|\|\|\|\|@LB@ CCGAA CAAUAAG CUCAA@LB@3'-CGC...UGCAA AU CUCUU...AAG-5'@LB@ \| \|@LB@ 78 58@LB@@LB@@LB@Energy -10.74 kcal/mol@LB@Hybridization Energy -15.8972 kcal/mol@LB@Unfolding Energy - mRNA 4.34594 kcal/mol@LB@Unfolding Energy - sRNA 0.811926 kcal/mol@LB@@LB@Position - mRNA 174 -- 195@LB@Position - sRNA 59 -- 77@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 64 -- 70@LB@
114	0.01931	0.5385	b1951	rcsA	-10.71	0.079523	269 -- 285	16 -- 29	transcriptional regulator of colanic acid capsular biosynthesis	_____________268_______________286\n_____________\|_________________\|\n5'-GUU...AGUAG__________AAA____AAAUC...UUG-3'\n______________AGGGGUUAAA___AGAG\n______________\|:\|\|\|\|\|\|\|\|___\|\|\|\|\n______________UUCCCAAUUU___UCUC\n3'-CGC...UGAAG_________________CACGG...AAG-5'\n_____________\|_________________\|\n_____________30________________15\n	272 -- 278	20 -- 26	-15.5636 kcal/mol	1.76121 kcal/mol	3.08831 kcal/mol	268 286@LB@ \| \|@LB@5'-GUU...AGUAG AAA AAAUC...UUG-3'@LB@ AGGGGUUAAA AGAG@LB@ \|:\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UUCCCAAUUU UCUC@LB@3'-CGC...UGAAG CACGG...AAG-5'@LB@ \| \|@LB@ 30 15@LB@@LB@@LB@Energy -10.71 kcal/mol@LB@Hybridization Energy -15.5636 kcal/mol@LB@Unfolding Energy - mRNA 1.76121 kcal/mol@LB@Unfolding Energy - sRNA 3.08831 kcal/mol@LB@@LB@Position - mRNA 269 -- 285@LB@Position - sRNA 16 -- 29@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 20 -- 26@LB@
144	0.02429	0.5467	b3156	yhbS	-10.71	0.079718	207 -- 222	50 -- 67	GNAT family putative N-acetyltransferase	_____________206________________223\n_____________\|__________________\|\n5'-CCG...UGCUA__________________CCAUU...AUC-3'\n______________AUUCGAGU__AGAAAUUC\n______________\|\|\|\|\|\|\|\|__\|\|\|\|\|:\|\|\n______________UAAGCUCA__UCUUUGAG\n3'-CGC...AUCAA________AC________AGCUU...AAG-5'\n_____________\|__________________\|\n_____________68_________________49\n	216 -- 222	50 -- 56	-17.6544 kcal/mol	2.73618 kcal/mol	4.21029 kcal/mol	206 223@LB@ \| \|@LB@5'-CCG...UGCUA CCAUU...AUC-3'@LB@ AUUCGAGU AGAAAUUC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|:\|\|@LB@ UAAGCUCA UCUUUGAG@LB@3'-CGC...AUCAA AC AGCUU...AAG-5'@LB@ \| \|@LB@ 68 49@LB@@LB@@LB@Energy -10.71 kcal/mol@LB@Hybridization Energy -17.6544 kcal/mol@LB@Unfolding Energy - mRNA 2.73618 kcal/mol@LB@Unfolding Energy - sRNA 4.21029 kcal/mol@LB@@LB@Position - mRNA 207 -- 222@LB@Position - sRNA 50 -- 67@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 50 -- 56@LB@
54	0.01077	0.5385	b1820	yobD	-10.70	0.079862	85 -- 97	73 -- 84	UPF0266 family inner membrane protein	_____________84____________98\n_____________\|_____________\|\n5'-ACC...GUGGA___U_________CUUCG...CCC-3'\n______________UCA_CGUUGGCUU\n______________\|\|\|_\|\|\|\|\|\|\|\|\|\n______________AGU_GCAACCGAA\n3'-CGC...UUUCA_____________AUCAA...AAG-5'\n_____________\|_____________\|\n_____________85____________72\n	91 -- 97	73 -- 79	-16.3135 kcal/mol	5.10116 kcal/mol	0.508835 kcal/mol	84 98@LB@ \| \|@LB@5'-ACC...GUGGA U CUUCG...CCC-3'@LB@ UCA CGUUGGCUU@LB@ \|\|\| \|\|\|\|\|\|\|\|\|@LB@ AGU GCAACCGAA@LB@3'-CGC...UUUCA AUCAA...AAG-5'@LB@ \| \|@LB@ 85 72@LB@@LB@@LB@Energy -10.70 kcal/mol@LB@Hybridization Energy -16.3135 kcal/mol@LB@Unfolding Energy - mRNA 5.10116 kcal/mol@LB@Unfolding Energy - sRNA 0.508835 kcal/mol@LB@@LB@Position - mRNA 85 -- 97@LB@Position - sRNA 73 -- 84@LB@Position Seed - mRNA 91 -- 97@LB@Position Seed - sRNA 73 -- 79@LB@
62	0.01254	0.5385	b0027	lspA	-10.68	0.080768	51 -- 66	75 -- 90	prolipoprotein signal peptidase (signal peptidase II)	_____________50________________67\n_____________\|_________________\|\n5'-UAU...GGGCU______________A__AAAGC...ACU-3'\n______________GAAAG_UCGCGUUG_GU\n______________:\|\|\|\|_\|\|:\|\|\|\|\|_\|:\n______________UUUUC_AGUGCAAC_CG\n3'-CGC...AGGCG_____A___________AAAUC...AAG-5'\n_____________\|_________________\|\n_____________91________________74\n	57 -- 63	77 -- 83	-15.4073 kcal/mol	4.21469 kcal/mol	0.517251 kcal/mol	50 67@LB@ \| \|@LB@5'-UAU...GGGCU A AAAGC...ACU-3'@LB@ GAAAG UCGCGUUG GU@LB@ :\|\|\|\| \|\|:\|\|\|\|\| \|:@LB@ UUUUC AGUGCAAC CG@LB@3'-CGC...AGGCG A AAAUC...AAG-5'@LB@ \| \|@LB@ 91 74@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -15.4073 kcal/mol@LB@Unfolding Energy - mRNA 4.21469 kcal/mol@LB@Unfolding Energy - sRNA 0.517251 kcal/mol@LB@@LB@Position - mRNA 51 -- 66@LB@Position - sRNA 75 -- 90@LB@Position Seed - mRNA 57 -- 63@LB@Position Seed - sRNA 77 -- 83@LB@
23	0.004272	0.5385	b3315	rplV	-10.64	0.081808	245 -- 278	60 -- 90	50S ribosomal subunit protein L22	_____________244________________________________279\n_____________\|__________________________________\|\n5'-CGC...GCUCA__________C___UU___GACCUG_____C___AAGAA...UGG-3'\n______________GAAGGUUCGC_UUG__GCU______AUUCG_GGU\n______________:\|\|:\|\|\|\|:\|_\|\|\|__\|\|\|______\|\|\|\|\|_:\|\|\n______________UUUUCAAGUG_AAC__CGA______UAAGC_UCA\n3'-CGC...AGGCG__________C________AAUCAA_________ACUCU...AAG-5'\n_____________\|__________________________________\|\n_____________91_________________________________59\n	248 -- 254	81 -- 87	-21.0379 kcal/mol	8.68511 kcal/mol	1.70935 kcal/mol	244 279@LB@ \| \|@LB@5'-CGC...GCUCA C UU GACCUG C AAGAA...UGG-3'@LB@ GAAGGUUCGC UUG GCU AUUCG GGU@LB@ :\|\|:\|\|\|\|:\| \|\|\| \|\|\| \|\|\|\|\| :\|\|@LB@ UUUUCAAGUG AAC CGA UAAGC UCA@LB@3'-CGC...AGGCG C AAUCAA ACUCU...AAG-5'@LB@ \| \|@LB@ 91 59@LB@@LB@@LB@Energy -10.64 kcal/mol@LB@Hybridization Energy -21.0379 kcal/mol@LB@Unfolding Energy - mRNA 8.68511 kcal/mol@LB@Unfolding Energy - sRNA 1.70935 kcal/mol@LB@@LB@Position - mRNA 245 -- 278@LB@Position - sRNA 60 -- 90@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 81 -- 87@LB@
61	0.01179	0.5385	b3748	rbsD	-10.58	0.083988	129 -- 141	72 -- 84	D-ribose pyranase	_____________128___________142\n_____________\|_____________\|\n5'-GGU...UAACG_____A_______CCCAA...UCC-3'\n______________UCACG_UGGUUUU\n______________\|\|\|\|\|_\|\|\|:\|\|\|\n______________AGUGC_ACCGAAA\n3'-CGC...UUUCA_____A_______UCAAU...AAG-5'\n_____________\|_____________\|\n_____________85____________71\n	135 -- 141	72 -- 78	-14.1499 kcal/mol	3.06287 kcal/mol	0.509125 kcal/mol	128 142@LB@ \| \|@LB@5'-GGU...UAACG A CCCAA...UCC-3'@LB@ UCACG UGGUUUU@LB@ \|\|\|\|\| \|\|\|:\|\|\|@LB@ AGUGC ACCGAAA@LB@3'-CGC...UUUCA A UCAAU...AAG-5'@LB@ \| \|@LB@ 85 71@LB@@LB@@LB@Energy -10.58 kcal/mol@LB@Hybridization Energy -14.1499 kcal/mol@LB@Unfolding Energy - mRNA 3.06287 kcal/mol@LB@Unfolding Energy - sRNA 0.509125 kcal/mol@LB@@LB@Position - mRNA 129 -- 141@LB@Position - sRNA 72 -- 84@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 72 -- 78@LB@
66	0.01284	0.5385	b1645	ydhK	-10.57	0.084210	155 -- 164	75 -- 84	putative efflux protein (PET) component of YdhJK efflux pump	_____________154________165\n_____________\|__________\|\n5'-CAG...CGAUG__________GUCGG...UGG-3'\n______________UCACGUUGGU\n______________\|\|\|\|\|\|\|\|\|:\n______________AGUGCAACCG\n3'-CGC...UUUCA__________AAAUC...AAG-5'\n_____________\|__________\|\n_____________85_________74\n	158 -- 164	75 -- 81	-15.7281 kcal/mol	4.6508 kcal/mol	0.505918 kcal/mol	154 165@LB@ \| \|@LB@5'-CAG...CGAUG GUCGG...UGG-3'@LB@ UCACGUUGGU@LB@ \|\|\|\|\|\|\|\|\|:@LB@ AGUGCAACCG@LB@3'-CGC...UUUCA AAAUC...AAG-5'@LB@ \| \|@LB@ 85 74@LB@@LB@@LB@Energy -10.57 kcal/mol@LB@Hybridization Energy -15.7281 kcal/mol@LB@Unfolding Energy - mRNA 4.6508 kcal/mol@LB@Unfolding Energy - sRNA 0.505918 kcal/mol@LB@@LB@Position - mRNA 155 -- 164@LB@Position - sRNA 75 -- 84@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 75 -- 81@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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