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
48	0.001595	0.1153	b4567	yjjZ	-9.54	0.291590	92 -- 131	37 -- 74	uncharacterized protein	_____________91_______________________________________132\n_____________\|________________________________________\|\n5'-CGG...UGAUU____AU_________AG___UACC__AUAG__A_______AUCUG...GGA-3'\n______________GCUA__CAUAGCGAU__GUU____CG____CA_GGGAUUU\n______________:\|\|\|__\|\|:\|\|\|:\|\|__\|\|\|____\|:____\|\|_\|\|\|\|\|\|\|\n______________UGAU__GUGUCGUUA__CAA____GU____GU_CCCUAAA\n3'-UUU...GUUUC____GU_________AG___CAAA__GA____C_______GGUAC...GCA-5'\n_____________\|________________________________________\|\n_____________75_______________________________________36\n	125 -- 131	37 -- 43	-26.8907 kcal/mol	12.5776 kcal/mol	4.77887 kcal/mol	91 132@LB@ \| \|@LB@5'-CGG...UGAUU AU AG UACC AUAG A AUCUG...GGA-3'@LB@ GCUA CAUAGCGAU GUU CG CA GGGAUUU@LB@ :\|\|\| \|\|:\|\|\|:\|\| \|\|\| \|: \|\| \|\|\|\|\|\|\|@LB@ UGAU GUGUCGUUA CAA GU GU CCCUAAA@LB@3'-UUU...GUUUC GU AG CAAA GA C GGUAC...GCA-5'@LB@ \| \|@LB@ 75 36@LB@@LB@@LB@Energy -9.54 kcal/mol@LB@Hybridization Energy -26.8907 kcal/mol@LB@Unfolding Energy - mRNA 12.5776 kcal/mol@LB@Unfolding Energy - sRNA 4.77887 kcal/mol@LB@@LB@Position - mRNA 92 -- 131@LB@Position - sRNA 37 -- 74@LB@Position Seed - mRNA 125 -- 131@LB@Position Seed - sRNA 37 -- 43@LB@
167	0.008121	0.1711	b2603	yfiR	-9.52	0.293133	262 -- 278	35 -- 51	putative periplasmic inhibitor of YfiN activity	_____________261_______________279\n_____________\|_________________\|\n5'-GUA...AAUAC_________A_CC____GACGU...GUA-3'\n______________UCGCUCAGG_G__UUCU\n______________\|\|:\|\|\|\|\|\|_\|__\|\|\|:\n______________AGUGAGUCC_C__AAGG\n3'-UUU...AACAA_________C_UA____UACGA...GCA-5'\n_____________\|_________________\|\n_____________52________________34\n	264 -- 270	43 -- 49	-18.1931 kcal/mol	6.80204 kcal/mol	1.87111 kcal/mol	261 279@LB@ \| \|@LB@5'-GUA...AAUAC A CC GACGU...GUA-3'@LB@ UCGCUCAGG G UUCU@LB@ \|\|:\|\|\|\|\|\| \| \|\|\|:@LB@ AGUGAGUCC C AAGG@LB@3'-UUU...AACAA C UA UACGA...GCA-5'@LB@ \| \|@LB@ 52 34@LB@@LB@@LB@Energy -9.52 kcal/mol@LB@Hybridization Energy -18.1931 kcal/mol@LB@Unfolding Energy - mRNA 6.80204 kcal/mol@LB@Unfolding Energy - sRNA 1.87111 kcal/mol@LB@@LB@Position - mRNA 262 -- 278@LB@Position - sRNA 35 -- 51@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 43 -- 49@LB@
150	0.006982	0.1638	b3581	sgbH	-9.48	0.297019	138 -- 176	34 -- 74	3-keto-L-gulonate 6-phosphate decarboxylase	_____________137________________________________________177\n_____________\|__________________________________________\|\n5'-UUU...UAUCA__GU_________UC__A___CCG__C_______C_______CGCCC...AAG-3'\n______________AC__UAU_CAGCA__UC_UUG___CA_UUCAGGG___UUUCA\n______________\|\|__:\|:_\|\|\|\|\|__\|\|_\|\|\|___\|\|_:\|\|\|\|\|\|___\|\|:\|\|\n______________UG__GUG_GUCGU__AG_AAC___GU_GAGUCCC___AAGGU\n3'-UUU...GUUUC__AU___U_____UA__C___AAA__________CUA_____ACGAA...GCA-5'\n_____________\|__________________________________________\|\n_____________75_________________________________________33\n	164 -- 170	42 -- 48	-24.4875 kcal/mol	10.188 kcal/mol	4.81599 kcal/mol	137 177@LB@ \| \|@LB@5'-UUU...UAUCA GU UC A CCG C C CGCCC...AAG-3'@LB@ AC UAU CAGCA UC UUG CA UUCAGGG UUUCA@LB@ \|\| :\|: \|\|\|\|\| \|\| \|\|\| \|\| :\|\|\|\|\|\| \|\|:\|\|@LB@ UG GUG GUCGU AG AAC GU GAGUCCC AAGGU@LB@3'-UUU...GUUUC AU U UA C AAA CUA ACGAA...GCA-5'@LB@ \| \|@LB@ 75 33@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -24.4875 kcal/mol@LB@Unfolding Energy - mRNA 10.188 kcal/mol@LB@Unfolding Energy - sRNA 4.81599 kcal/mol@LB@@LB@Position - mRNA 138 -- 176@LB@Position - sRNA 34 -- 74@LB@Position Seed - mRNA 164 -- 170@LB@Position Seed - sRNA 42 -- 48@LB@
107	0.004745	0.1538	b2413	cysZ	-9.47	0.298503	222 -- 238	58 -- 74	sulfate transporter sulfite inhibited	_____________221_______________239\n_____________\|_________________\|\n5'-ACC...CAUCU__CC_____________UUACU...UUU-3'\n______________GC__CACGCAGCGGUUU\n______________:\|__\|\|\|:\|\|\|\|::\|\|:\n______________UG__GUGUGUCGUUAAG\n3'-UUU...GUUUC__AU_____________CAACA...GCA-5'\n_____________\|_________________\|\n_____________75________________57\n	232 -- 238	58 -- 64	-18.5455 kcal/mol	5.77464 kcal/mol	3.3008 kcal/mol	221 239@LB@ \| \|@LB@5'-ACC...CAUCU CC UUACU...UUU-3'@LB@ GC CACGCAGCGGUUU@LB@ :\| \|\|\|:\|\|\|\|::\|\|:@LB@ UG GUGUGUCGUUAAG@LB@3'-UUU...GUUUC AU CAACA...GCA-5'@LB@ \| \|@LB@ 75 57@LB@@LB@@LB@Energy -9.47 kcal/mol@LB@Hybridization Energy -18.5455 kcal/mol@LB@Unfolding Energy - mRNA 5.77464 kcal/mol@LB@Unfolding Energy - sRNA 3.3008 kcal/mol@LB@@LB@Position - mRNA 222 -- 238@LB@Position - sRNA 58 -- 74@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 58 -- 64@LB@
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@
177	0.008834	0.1747	b0932	pepN	-9.31	0.316043	123 -- 145	58 -- 78	aminopeptidase N	_____________122_____________________146\n_____________\|_______________________\|\n5'-GUA...AAGAU_____UU_______GC_______ACGCA...AGA-3'\n______________GAAGA__CUGCAUA__GCGAUUU\n______________:\|\|\|\|__\|\|:\|\|:\|__\|\|:\|\|\|:\n______________UUUCU__GAUGUGU__CGUUAAG\n3'-UUU...ACCCG______________GU_______CAACA...GCA-5'\n_____________\|_______________________\|\n_____________79______________________57\n	139 -- 145	58 -- 64	-18.0038 kcal/mol	5.38317 kcal/mol	3.31018 kcal/mol	122 146@LB@ \| \|@LB@5'-GUA...AAGAU UU GC ACGCA...AGA-3'@LB@ GAAGA CUGCAUA GCGAUUU@LB@ :\|\|\|\| \|\|:\|\|:\| \|\|:\|\|\|:@LB@ UUUCU GAUGUGU CGUUAAG@LB@3'-UUU...ACCCG GU CAACA...GCA-5'@LB@ \| \|@LB@ 79 57@LB@@LB@@LB@Energy -9.31 kcal/mol@LB@Hybridization Energy -18.0038 kcal/mol@LB@Unfolding Energy - mRNA 5.38317 kcal/mol@LB@Unfolding Energy - sRNA 3.31018 kcal/mol@LB@@LB@Position - mRNA 123 -- 145@LB@Position - sRNA 58 -- 78@LB@Position Seed - mRNA 139 -- 145@LB@Position Seed - sRNA 58 -- 64@LB@
109	0.004772	0.1538	b2580	ung	-9.28	0.319241	25 -- 55	36 -- 70	uracil-DNA-glycosylase	_____________24__________________________________56\n_____________\|___________________________________\|\n5'-UCU...AAAAC______U___GUA____G_____AAAU________AUUGU...CCG-3'\n______________CACACA_CAA_____UG__UCGC_____GGAUUUU\n______________\|\|\|\|\|\|_\|\|\|_____\|\|__\|\|:\|_____\|\|\|\|\|\|:\n______________GUGUGU_GUU_____AC__AGUG_____CCUAAAG\n3'-UUU...CUGAU______C___AAGCA__AA____AGUCC_______GUACG...GCA-5'\n_____________\|___________________________________\|\n_____________71__________________________________35\n	49 -- 55	36 -- 42	-19.0861 kcal/mol	5.04532 kcal/mol	4.7591 kcal/mol	24 56@LB@ \| \|@LB@5'-UCU...AAAAC U GUA G AAAU AUUGU...CCG-3'@LB@ CACACA CAA UG UCGC GGAUUUU@LB@ \|\|\|\|\|\| \|\|\| \|\| \|\|:\| \|\|\|\|\|\|:@LB@ GUGUGU GUU AC AGUG CCUAAAG@LB@3'-UUU...CUGAU C AAGCA AA AGUCC GUACG...GCA-5'@LB@ \| \|@LB@ 71 35@LB@@LB@@LB@Energy -9.28 kcal/mol@LB@Hybridization Energy -19.0861 kcal/mol@LB@Unfolding Energy - mRNA 5.04532 kcal/mol@LB@Unfolding Energy - sRNA 4.7591 kcal/mol@LB@@LB@Position - mRNA 25 -- 55@LB@Position - sRNA 36 -- 70@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 36 -- 42@LB@
166	0.008074	0.1711	b2158	yeiH	-9.26	0.321503	233 -- 257	41 -- 72	UPF0324 family inner membrane protein	_____________232_______________________________258\n_____________\|_________________________________\|\n5'-CAC...CAUCG_____UG_____________________C____UUAGC...GUG-3'\n______________UACAC__UGGCA________UUUUAUUC_GGGG\n______________\|\|\|\|\|__::\|\|\|________\|\|\|:\|:\|\|_\|\|\|\|\n______________AUGUG__GUCGU________AAAGUGAG_CCCC\n3'-UUU...UUCUG_____U______UAAGCAAC________U____UAAAG...GCA-5'\n_____________\|_________________________________\|\n_____________73________________________________40\n	246 -- 252	46 -- 52	-21.8619 kcal/mol	7.84401 kcal/mol	4.75632 kcal/mol	232 258@LB@ \| \|@LB@5'-CAC...CAUCG UG C UUAGC...GUG-3'@LB@ UACAC UGGCA UUUUAUUC GGGG@LB@ \|\|\|\|\| ::\|\|\| \|\|\|:\|:\|\| \|\|\|\|@LB@ AUGUG GUCGU AAAGUGAG CCCC@LB@3'-UUU...UUCUG U UAAGCAAC U UAAAG...GCA-5'@LB@ \| \|@LB@ 73 40@LB@@LB@@LB@Energy -9.26 kcal/mol@LB@Hybridization Energy -21.8619 kcal/mol@LB@Unfolding Energy - mRNA 7.84401 kcal/mol@LB@Unfolding Energy - sRNA 4.75632 kcal/mol@LB@@LB@Position - mRNA 233 -- 257@LB@Position - sRNA 41 -- 72@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 46 -- 52@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@
117	0.005152	0.155	b2235	nrdB	-9.05	0.346139	190 -- 222	48 -- 77	ribonucleoside-diphosphate reductase 1 beta subunit ferritin-like protein	_____________189_______________________________223\n_____________\|_________________________________\|\n5'-UCC...CCAAC_____AC__U_______UAUACCACCU______AGACG...AAU-3'\n______________AGGAC__AC_CAUGGCA__________UUUCAC\n______________\|:\|\|\|__\|\|_\|\|::\|\|\|__________\|\|\|\|\|\|\n______________UUCUG__UG_GUGUCGU__________AAAGUG\n3'-UUU...CCCGU_____A___U_______UAAGCAAC________AGUCC...GCA-5'\n_____________\|_________________________________\|\n_____________78________________________________47\n	200 -- 206	62 -- 68	-18.188 kcal/mol	5.45206 kcal/mol	3.68729 kcal/mol	189 223@LB@ \| \|@LB@5'-UCC...CCAAC AC U UAUACCACCU AGACG...AAU-3'@LB@ AGGAC AC CAUGGCA UUUCAC@LB@ \|:\|\|\| \|\| \|\|::\|\|\| \|\|\|\|\|\|@LB@ UUCUG UG GUGUCGU AAAGUG@LB@3'-UUU...CCCGU A U UAAGCAAC AGUCC...GCA-5'@LB@ \| \|@LB@ 78 47@LB@@LB@@LB@Energy -9.05 kcal/mol@LB@Hybridization Energy -18.188 kcal/mol@LB@Unfolding Energy - mRNA 5.45206 kcal/mol@LB@Unfolding Energy - sRNA 3.68729 kcal/mol@LB@@LB@Position - mRNA 190 -- 222@LB@Position - sRNA 48 -- 77@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 62 -- 68@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)

Job resubmission

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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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