Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
151	0.007209	0.1668	b0968	yccX	-9.35	0.311742	266 -- 274	62 -- 70	weak acylphosphatase		_____________265_______275\n_____________\|_________\|\n5'-GGC...UACAC_________CGAAG...CCG-3'\n______________CACACAGUA\n______________\|\|\|\|\|\|\|:\|\n______________GUGUGUCGU\n3'-UUU...CUGAU_________UAAGC...GCA-5'\n_____________\|_________\|\n_____________71________61\n	268 -- 274	62 -- 68	-13.335 kcal/mol	0.836274 kcal/mol	3.14945 kcal/mol	265 275@LB@ \| \|@LB@5'-GGC...UACAC CGAAG...CCG-3'@LB@ CACACAGUA@LB@ \|\|\|\|\|\|\|:\|@LB@ GUGUGUCGU@LB@3'-UUU...CUGAU UAAGC...GCA-5'@LB@ \| \|@LB@ 71 61@LB@@LB@@LB@Energy -9.35 kcal/mol@LB@Hybridization Energy -13.335 kcal/mol@LB@Unfolding Energy - mRNA 0.836274 kcal/mol@LB@Unfolding Energy - sRNA 3.14945 kcal/mol@LB@@LB@Position - mRNA 266 -- 274@LB@Position - sRNA 62 -- 70@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 62 -- 68@LB@
152	0.007399	0.1668	b0591	entS	-13.87	0.039944	258 -- 287	45 -- 70	enterobactin exporter iron-regulated		_____________257____________________________288\n_____________\|______________________________\|\n5'-AAU...CGUUU_________UUCC___CUC______U____AUUGU...UGG-3'\n______________CGCGCAGUA____UCG___GUUUCA_CUCA\n______________\|:\|:\|\|\|:\|____\|\|\|___\|\|\|\|\|\|_\|\|\|\|\n______________GUGUGUCGU____AGC___CAAAGU_GAGU\n3'-UUU...CUGAU_________UA_____AA____________CCCCU...GCA-5'\n_____________\|______________________________\|\n_____________71_____________________________44\n	260 -- 266	62 -- 68	-23.1768 kcal/mol	5.59312 kcal/mol	3.71317 kcal/mol	257 288@LB@ \| \|@LB@5'-AAU...CGUUU UUCC CUC U AUUGU...UGG-3'@LB@ CGCGCAGUA UCG GUUUCA CUCA@LB@ \|:\|:\|\|\|:\| \|\|\| \|\|\|\|\|\| \|\|\|\|@LB@ GUGUGUCGU AGC CAAAGU GAGU@LB@3'-UUU...CUGAU UA AA CCCCU...GCA-5'@LB@ \| \|@LB@ 71 44@LB@@LB@@LB@Energy -13.87 kcal/mol@LB@Hybridization Energy -23.1768 kcal/mol@LB@Unfolding Energy - mRNA 5.59312 kcal/mol@LB@Unfolding Energy - sRNA 3.71317 kcal/mol@LB@@LB@Position - mRNA 258 -- 287@LB@Position - sRNA 45 -- 70@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 62 -- 68@LB@
153	0.007486	0.1668	b1732	katE	-14.34	0.030774	245 -- 275	42 -- 74	catalase HPII heme d-containing		_____________244___________________________________276\n_____________\|_____________________________________\|\n5'-UGG...UCACC________AUUC______AG__AA_____________AUGGA...ACG-3'\n______________ACUACACG____CAGCGA__CG_______AC_CGGGG\n______________\|\|\|\|\|\|\|:____\|\|\|\|:\|__\|\|_______\|\|_\|:\|\|\|\n______________UGAUGUGU____GUCGUU__GC_______UG_GUCCC\n3'-UUU...GUUUC__________________AA__AACAAAG__A_____CUAAA...GCA-5'\n_____________\|_____________________________________\|\n_____________75____________________________________41\n	246 -- 252	67 -- 73	-24.7059 kcal/mol	5.60497 kcal/mol	4.7632 kcal/mol	244 276@LB@ \| \|@LB@5'-UGG...UCACC AUUC AG AA AUGGA...ACG-3'@LB@ ACUACACG CAGCGA CG AC CGGGG@LB@ \|\|\|\|\|\|\|: \|\|\|\|:\| \|\| \|\| \|:\|\|\|@LB@ UGAUGUGU GUCGUU GC UG GUCCC@LB@3'-UUU...GUUUC AA AACAAAG A CUAAA...GCA-5'@LB@ \| \|@LB@ 75 41@LB@@LB@@LB@Energy -14.34 kcal/mol@LB@Hybridization Energy -24.7059 kcal/mol@LB@Unfolding Energy - mRNA 5.60497 kcal/mol@LB@Unfolding Energy - sRNA 4.7632 kcal/mol@LB@@LB@Position - mRNA 245 -- 275@LB@Position - sRNA 42 -- 74@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 67 -- 73@LB@
154	0.007512	0.1668	b2180	yejF	-18.70	0.001576	262 -- 293	44 -- 72	microcin C ABC transporter ATPase		_____________261______________________________294\n_____________\|________________________________\|\n5'-GAC...AACCG_____________CAA__A_________A___AUUGAGG-3'\n______________UACGUACAGUAGU___UG_UGUUUCACU_CAG\n______________\|\|\|::\|\|\|\|:\|:\|___:\|_\|\|\|\|\|\|\|\|\|_\|\|\|\n______________AUGUGUGUCGUUA___GC_ACAAAGUGA_GUC\n3'-UUU...UUCUG_____________A____A_____________CCCUA...GCA-5'\n_____________\|________________________________\|\n_____________73_______________________________43\n	283 -- 289	47 -- 53	-27.8629 kcal/mol	5.03502 kcal/mol	4.12429 kcal/mol	261 294@LB@ \| \|@LB@5'-GAC...AACCG CAA A A AUUGAGG-3'@LB@ UACGUACAGUAGU UG UGUUUCACU CAG@LB@ \|\|\|::\|\|\|\|:\|:\| :\| \|\|\|\|\|\|\|\|\| \|\|\|@LB@ AUGUGUGUCGUUA GC ACAAAGUGA GUC@LB@3'-UUU...UUCUG A A CCCUA...GCA-5'@LB@ \| \|@LB@ 73 43@LB@@LB@@LB@Energy -18.70 kcal/mol@LB@Hybridization Energy -27.8629 kcal/mol@LB@Unfolding Energy - mRNA 5.03502 kcal/mol@LB@Unfolding Energy - sRNA 4.12429 kcal/mol@LB@@LB@Position - mRNA 262 -- 293@LB@Position - sRNA 44 -- 72@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 47 -- 53@LB@
155	0.007577	0.1668	b4364	yjjP	-9.15	0.334468	166 -- 178	62 -- 74	DUF1212 family inner membrane protein		_____________165___________179\n_____________\|_____________\|\n5'-UCA...UCUGA__A__________CGUCU...UUU-3'\n______________AC_AUACGCAGCA\n______________\|\|_\|:\|\|:\|\|\|\|\|\n______________UG_UGUGUGUCGU\n3'-UUU...GUUUC__A__________UAAGC...GCA-5'\n_____________\|_____________\|\n_____________75____________61\n	172 -- 178	62 -- 68	-14.8746 kcal/mol	2.48219 kcal/mol	3.24359 kcal/mol	165 179@LB@ \| \|@LB@5'-UCA...UCUGA A CGUCU...UUU-3'@LB@ AC AUACGCAGCA@LB@ \|\| \|:\|\|:\|\|\|\|\|@LB@ UG UGUGUGUCGU@LB@3'-UUU...GUUUC A UAAGC...GCA-5'@LB@ \| \|@LB@ 75 61@LB@@LB@@LB@Energy -9.15 kcal/mol@LB@Hybridization Energy -14.8746 kcal/mol@LB@Unfolding Energy - mRNA 2.48219 kcal/mol@LB@Unfolding Energy - sRNA 3.24359 kcal/mol@LB@@LB@Position - mRNA 166 -- 178@LB@Position - sRNA 62 -- 74@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 62 -- 68@LB@
156	0.007591	0.1668	b1044	ymdA	-16.39	0.008687	226 -- 252	46 -- 73	uncharacterized protein		_____________225__________________________253\n_____________\|____________________________\|\n5'-UGA...CUCUC______U____________U________UUAUU...UUU-3'\n______________UUAUGC_CGGCAGUUUGUU_UUUC_CUU\n______________:\|\|::\|_\|:\|\|\|:\|\|:\|\|\|_\|\|\|\|_\|\|:\n______________GAUGUG_GUCGUUAAGCAA_AAAG_GAG\n3'-UUU...UUUCU______U____________C____U___UCCCC...GCA-5'\n_____________\|____________________________\|\n_____________74___________________________45\n	236 -- 242	57 -- 63	-24.6333 kcal/mol	4.51706 kcal/mol	3.72492 kcal/mol	225 253@LB@ \| \|@LB@5'-UGA...CUCUC U U UUAUU...UUU-3'@LB@ UUAUGC CGGCAGUUUGUU UUUC CUU@LB@ :\|\|::\| \|:\|\|\|:\|\|:\|\|\| \|\|\|\| \|\|:@LB@ GAUGUG GUCGUUAAGCAA AAAG GAG@LB@3'-UUU...UUUCU U C U UCCCC...GCA-5'@LB@ \| \|@LB@ 74 45@LB@@LB@@LB@Energy -16.39 kcal/mol@LB@Hybridization Energy -24.6333 kcal/mol@LB@Unfolding Energy - mRNA 4.51706 kcal/mol@LB@Unfolding Energy - sRNA 3.72492 kcal/mol@LB@@LB@Position - mRNA 226 -- 252@LB@Position - sRNA 46 -- 73@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 57 -- 63@LB@
157	0.007641	0.1668	b3154	yhbP	-10.32	0.216043	188 -- 213	45 -- 78	UPF0306 family protein		_____________187________________________________214\n_____________\|__________________________________\|\n5'-AAA...GUAUA_____GA____________GGAAA__________UCGCC...UUU-3'\n______________AAAGA______ACAGCAAU_________CACUCA\n______________\|\|\|\|\|______\|\|\|\|\|\|\|\|_________\|\|\|\|\|\|\n______________UUUCU______UGUCGUUA_________GUGAGU\n3'-UUU...ACCCG_____GAUGUG________AGCAACAAA______CCCCU...GCA-5'\n_____________\|__________________________________\|\n_____________79_________________________________44\n	196 -- 202	60 -- 66	-17.2265 kcal/mol	3.1682 kcal/mol	3.741 kcal/mol	187 214@LB@ \| \|@LB@5'-AAA...GUAUA GA GGAAA UCGCC...UUU-3'@LB@ AAAGA ACAGCAAU CACUCA@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ UUUCU UGUCGUUA GUGAGU@LB@3'-UUU...ACCCG GAUGUG AGCAACAAA CCCCU...GCA-5'@LB@ \| \|@LB@ 79 44@LB@@LB@@LB@Energy -10.32 kcal/mol@LB@Hybridization Energy -17.2265 kcal/mol@LB@Unfolding Energy - mRNA 3.1682 kcal/mol@LB@Unfolding Energy - sRNA 3.741 kcal/mol@LB@@LB@Position - mRNA 188 -- 213@LB@Position - sRNA 45 -- 78@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 60 -- 66@LB@
158	0.007677	0.1668	b1267	yciO	-9.92	0.252655	228 -- 242	61 -- 75	putative RNA binding protein		_____________227_____________243\n_____________\|_______________\|\n5'-GCG...AUCCU___A__C________CGUCU...CAA-3'\n______________GAU_AC_CACAGCAA\n______________\|\|:_\|\|_\|\|\|\|\|\|\|\|\n______________CUG_UG_GUGUCGUU\n3'-UUU...CGUUU___A__U________AAGCA...GCA-5'\n_____________\|_______________\|\n_____________76______________60\n	236 -- 242	61 -- 67	-14.6343 kcal/mol	1.46218 kcal/mol	3.25399 kcal/mol	227 243@LB@ \| \|@LB@5'-GCG...AUCCU A C CGUCU...CAA-3'@LB@ GAU AC CACAGCAA@LB@ \|\|: \|\| \|\|\|\|\|\|\|\|@LB@ CUG UG GUGUCGUU@LB@3'-UUU...CGUUU A U AAGCA...GCA-5'@LB@ \| \|@LB@ 76 60@LB@@LB@@LB@Energy -9.92 kcal/mol@LB@Hybridization Energy -14.6343 kcal/mol@LB@Unfolding Energy - mRNA 1.46218 kcal/mol@LB@Unfolding Energy - sRNA 3.25399 kcal/mol@LB@@LB@Position - mRNA 228 -- 242@LB@Position - sRNA 61 -- 75@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 61 -- 67@LB@
159	0.007688	0.1668	b0454	ybaZ	-17.74	0.003345	226 -- 245	34 -- 52	excision repair protein alkyltransferase-like protein ATL		_____________225__________________246\n_____________\|____________________\|\n5'-AGG...GCGAC__________C_UU______GAUUA...UUC-3'\n______________UUCACUCGGG_G__UUUCCA\n______________\|\|\|\|\|\|\|:\|\|_\|__\|\|\|\|\|\|\n______________AAGUGAGUCC_C__AAAGGU\n3'-UUU...CAACA____________CU______ACGAA...GCA-5'\n_____________\|____________________\|\n_____________53___________________33\n	229 -- 235	43 -- 49	-23.7092 kcal/mol	4.0826 kcal/mol	1.88482 kcal/mol	225 246@LB@ \| \|@LB@5'-AGG...GCGAC C UU GAUUA...UUC-3'@LB@ UUCACUCGGG G UUUCCA@LB@ \|\|\|\|\|\|\|:\|\| \| \|\|\|\|\|\|@LB@ AAGUGAGUCC C AAAGGU@LB@3'-UUU...CAACA CU ACGAA...GCA-5'@LB@ \| \|@LB@ 53 33@LB@@LB@@LB@Energy -17.74 kcal/mol@LB@Hybridization Energy -23.7092 kcal/mol@LB@Unfolding Energy - mRNA 4.0826 kcal/mol@LB@Unfolding Energy - sRNA 1.88482 kcal/mol@LB@@LB@Position - mRNA 226 -- 245@LB@Position - sRNA 34 -- 52@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 43 -- 49@LB@
160	0.007693	0.1668	b1671	ydhX	-11.21	0.148807	210 -- 235	39 -- 74	putative 4Fe-4S ferridoxin-type protein; FNR Nar NarP-regulated protein; putative subunit of YdhYVWXUT oxidoreductase complex	b4072	_____________209__________________________________236\n_____________\|____________________________________\|\n5'-CAC...CCUUC___CG________________________U______GGGAA...AGG-3'\n______________ACU__ACGCA__AAUUUGU________UC_GGGGAU\n______________\|\|\|__\|\|:\|\|__\|\|\|\|:\|\|________\|\|_\|\|\|\|\|\|\n______________UGA__UGUGU__UUAAGCA________AG_CCCCUA\n3'-UUU...GUUUC___UG_____CG_______ACAAAGUG__U______AAGGU...GCA-5'\n_____________\|____________________________________\|\n_____________75___________________________________38\n	220 -- 226	56 -- 62	-21.5478 kcal/mol	5.56457 kcal/mol	4.77831 kcal/mol	209 236@LB@ \| \|@LB@5'-CAC...CCUUC CG U GGGAA...AGG-3'@LB@ ACU ACGCA AAUUUGU UC GGGGAU@LB@ \|\|\| \|\|:\|\| \|\|\|\|:\|\| \|\| \|\|\|\|\|\|@LB@ UGA UGUGU UUAAGCA AG CCCCUA@LB@3'-UUU...GUUUC UG CG ACAAAGUG U AAGGU...GCA-5'@LB@ \| \|@LB@ 75 38@LB@@LB@@LB@Energy -11.21 kcal/mol@LB@Hybridization Energy -21.5478 kcal/mol@LB@Unfolding Energy - mRNA 5.56457 kcal/mol@LB@Unfolding Energy - sRNA 4.77831 kcal/mol@LB@@LB@Position - mRNA 210 -- 235@LB@Position - sRNA 39 -- 74@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 56 -- 62@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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