Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
144	0.008344	0.2033	b3159	yhbV	-10.12	0.132236	144 -- 228	15 -- 82	U32 peptidase family protein		_____________143______________________________________________________________________________________229\n_____________\|________________________________________________________________________________________\|\n5'-GUG...AUGUC__AA_____G__AACCAC__________AUAUCA________GGCA_______AAA___AUGAAAUAUUCCUU_______________GGUAC...AUC-3'\n______________CG__GGCAC_CA______UCUUGGC_GC______CCGUAAAU____GUGA_GA___GCA______________AGGGC_CAGUGCUGU\n______________\|\|__::\|\|\|_\|\|______\|\|\|\|\|\|\|_\|\|______\|\|\|\|\|\|\|\|____:\|\|\|_\|\|___:\|\|______________\|\|\|\|\|_\|\|\|::\|\|\|\|\n______________GC__UUGUG_GU______AGAACCG_CG______GGCAUUUA____UACU_CU___UGU______________UCCCG_GUCGUGACA\n3'-UUU...AUGAC__GG________CCCUUU_______A__C_____________AUAA____A__CAA______________________U_________AAAAG...GUG-5'\n_____________\|________________________________________________________________________________________\|\n_____________83_______________________________________________________________________________________14\n	177 -- 183	48 -- 54	-52.1529 kcal/mol	19.8598 kcal/mol	22.1763 kcal/mol	143 229@LB@ \| \|@LB@5'-GUG...AUGUC AA G AACCAC AUAUCA GGCA AAA AUGAAAUAUUCCUU GGUAC...AUC-3'@LB@ CG GGCAC CA UCUUGGC GC CCGUAAAU GUGA GA GCA AGGGC CAGUGCUGU@LB@ \|\| ::\|\|\| \|\| \|\|\|\|\|\|\| \|\| \|\|\|\|\|\|\|\| :\|\|\| \|\| :\|\| \|\|\|\|\| \|\|\|::\|\|\|\|@LB@ GC UUGUG GU AGAACCG CG GGCAUUUA UACU CU UGU UCCCG GUCGUGACA@LB@3'-UUU...AUGAC GG CCCUUU A C AUAA A CAA U AAAAG...GUG-5'@LB@ \| \|@LB@ 83 14@LB@@LB@@LB@Energy -10.12 kcal/mol@LB@Hybridization Energy -52.1529 kcal/mol@LB@Unfolding Energy - mRNA 19.8598 kcal/mol@LB@Unfolding Energy - sRNA 22.1763 kcal/mol@LB@@LB@Position - mRNA 144 -- 228@LB@Position - sRNA 15 -- 82@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 48 -- 54@LB@
193	0.01192	0.2159	b2453	eutG	-10.04	0.136932	27 -- 40	17 -- 30	ethanol dehydrogenase involved in ethanolamine utilization; aldehyde reductase		_____________26_____________41\n_____________\|______________\|\n5'-GGC...UAUUG_______G______ACUGA...GUC-3'\n______________AAGGGCA_GGCAUU\n______________\|\|\|\|\|\|\|_:\|\|\|:\|\n______________UUCCCGU_UCGUGA\n3'-UUU...CAAUG_______G______CAAAA...GUG-5'\n_____________\|______________\|\n_____________31_____________16\n	27 -- 33	24 -- 30	-21.9245 kcal/mol	3.17394 kcal/mol	8.71417 kcal/mol	26 41@LB@ \| \|@LB@5'-GGC...UAUUG G ACUGA...GUC-3'@LB@ AAGGGCA GGCAUU@LB@ \|\|\|\|\|\|\| :\|\|\|:\|@LB@ UUCCCGU UCGUGA@LB@3'-UUU...CAAUG G CAAAA...GUG-5'@LB@ \| \|@LB@ 31 16@LB@@LB@@LB@Energy -10.04 kcal/mol@LB@Hybridization Energy -21.9245 kcal/mol@LB@Unfolding Energy - mRNA 3.17394 kcal/mol@LB@Unfolding Energy - sRNA 8.71417 kcal/mol@LB@@LB@Position - mRNA 27 -- 40@LB@Position - sRNA 17 -- 30@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 24 -- 30@LB@
11	0.0004411	0.1198	b3154	yhbP	-10.16	0.129625	138 -- 186	18 -- 75	UPF0306 family protein		_____________137_________________________________________________________187\n_____________\|___________________________________________________________\|\n5'-AAA...AAGAA_______U____AUC_U________CAU______________GU_____CC________AAAAG...UUU-3'\n______________ACCAGGG__GUC___G_CUGCGUCG___GUUA________AG___CAGG__CACAGUAU\n______________\|\|\|\|\|\|\|__:\|\|___\|_\|\|\|\|\|:\|\|___:\|\|\|________\|\|___\|\|:\|__\|\|\|\|\|:\|:\n______________UGGUCCC__UAG___C_GACGCGGC___UAAU________UC___GUUC__GUGUCGUG\n3'-UUU...GGUUG_______UU___AAC__________AUU____AAUACUAC__AAU____CC________ACAAA...GUG-5'\n_____________\|___________________________________________________________\|\n_____________76__________________________________________________________17\n	155 -- 161	52 -- 58	-41.8924 kcal/mol	11.5669 kcal/mol	20.1571 kcal/mol	137 187@LB@ \| \|@LB@5'-AAA...AAGAA U AUC U CAU GU CC AAAAG...UUU-3'@LB@ ACCAGGG GUC G CUGCGUCG GUUA AG CAGG CACAGUAU@LB@ \|\|\|\|\|\|\| :\|\| \| \|\|\|\|\|:\|\| :\|\|\| \|\| \|\|:\| \|\|\|\|\|:\|:@LB@ UGGUCCC UAG C GACGCGGC UAAU UC GUUC GUGUCGUG@LB@3'-UUU...GGUUG UU AAC AUU AAUACUAC AAU CC ACAAA...GUG-5'@LB@ \| \|@LB@ 76 17@LB@@LB@@LB@Energy -10.16 kcal/mol@LB@Hybridization Energy -41.8924 kcal/mol@LB@Unfolding Energy - mRNA 11.5669 kcal/mol@LB@Unfolding Energy - sRNA 20.1571 kcal/mol@LB@@LB@Position - mRNA 138 -- 186@LB@Position - sRNA 18 -- 75@LB@Position Seed - mRNA 155 -- 161@LB@Position Seed - sRNA 52 -- 58@LB@
160	0.009416	0.2062	b2095	gatZ	-8.10	0.305092	155 -- 170	18 -- 33	D-tagatose 1 6-bisphosphate aldolase 2 subunit	b3132	_____________154______________171\n_____________\|________________\|\n5'-AAU...GUGGC__________G_____AACGC...UUG-3'\n______________UGCGAGGGCA_GGCAU\n______________\|:\|:\|\|\|\|\|\|_:\|\|\|:\n______________AUGUUCCCGU_UCGUG\n3'-UUU...ACUCA__________G_____ACAAA...GUG-5'\n_____________\|________________\|\n_____________34_______________17\n	158 -- 164	24 -- 30	-26.3287 kcal/mol	9.40457 kcal/mol	8.82204 kcal/mol	154 171@LB@ \| \|@LB@5'-AAU...GUGGC G AACGC...UUG-3'@LB@ UGCGAGGGCA GGCAU@LB@ \|:\|:\|\|\|\|\|\| :\|\|\|:@LB@ AUGUUCCCGU UCGUG@LB@3'-UUU...ACUCA G ACAAA...GUG-5'@LB@ \| \|@LB@ 34 17@LB@@LB@@LB@Energy -8.10 kcal/mol@LB@Hybridization Energy -26.3287 kcal/mol@LB@Unfolding Energy - mRNA 9.40457 kcal/mol@LB@Unfolding Energy - sRNA 8.82204 kcal/mol@LB@@LB@Position - mRNA 155 -- 170@LB@Position - sRNA 18 -- 33@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 24 -- 30@LB@
164	0.009677	0.2068	b1956	yedQ	-11.74	0.064514	187 -- 209	18 -- 41	putative membrane-anchored diguanylate cyclase		_____________186______________________210\n_____________\|________________________\|\n5'-GAG...CAGGU________CGUC____________GAGAC...UAU-3'\n______________UGG_GAGU____AGGGUGCAGCAC\n______________\|\|:_\|\|\|\|____\|\|\|\|::\|\|\|\|\|\|\n______________ACU_CUCA____UCCCGUGUCGUG\n3'-UUU...AUAAU___A____AUGU____________ACAAA...GUG-5'\n_____________\|________________________\|\n_____________42_______________________17\n	203 -- 209	18 -- 24	-27.1151 kcal/mol	6.50018 kcal/mol	8.87585 kcal/mol	186 210@LB@ \| \|@LB@5'-GAG...CAGGU CGUC GAGAC...UAU-3'@LB@ UGG GAGU AGGGUGCAGCAC@LB@ \|\|: \|\|\|\| \|\|\|\|::\|\|\|\|\|\|@LB@ ACU CUCA UCCCGUGUCGUG@LB@3'-UUU...AUAAU A AUGU ACAAA...GUG-5'@LB@ \| \|@LB@ 42 17@LB@@LB@@LB@Energy -11.74 kcal/mol@LB@Hybridization Energy -27.1151 kcal/mol@LB@Unfolding Energy - mRNA 6.50018 kcal/mol@LB@Unfolding Energy - sRNA 8.87585 kcal/mol@LB@@LB@Position - mRNA 187 -- 209@LB@Position - sRNA 18 -- 41@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 18 -- 24@LB@
143	0.008308	0.2033	b2049	cpsB	-11.81	0.062535	184 -- 242	25 -- 78	mannose-1-phosphate guanyltransferase		_____________183_______________________________________________________________243\n_____________\|_________________________________________________________________\|\n5'-ACA...UAAAU____U_______U____A_______A________CUCUAUCCA__________________U___UCCGG...GCC-3'\n______________GAUA_UCGGGGA_AAUU_UGGC_GC_GUCG_AAA_________GUUGUGAUG____GCAGG_GGC\n______________:\|:\|_:\|:\|\|\|\|_\|\|\|:_\|\|\|\|_\|\|_\|:\|\|_\|\|\|_________:\|\|:\|\|\|\|\|____:\|\|:\|_\|\|\|\n______________UUGU_GGUCCCU_UUAG_ACCG_CG_CGGC_UUU_________UAAUACUAC____UGUUC_CCG\n3'-UUU...CGCGG_________________A____A_______A___AA________________UCAA_________UGUCG...GUG-5'\n_____________\|_________________________________________________________________\|\n_____________79________________________________________________________________24\n	227 -- 233	37 -- 43	-41.0645 kcal/mol	15.3492 kcal/mol	13.8987 kcal/mol	183 243@LB@ \| \|@LB@5'-ACA...UAAAU U U A A CUCUAUCCA U UCCGG...GCC-3'@LB@ GAUA UCGGGGA AAUU UGGC GC GUCG AAA GUUGUGAUG GCAGG GGC@LB@ :\|:\| :\|:\|\|\|\| \|\|\|: \|\|\|\| \|\| \|:\|\| \|\|\| :\|\|:\|\|\|\|\| :\|\|:\| \|\|\|@LB@ UUGU GGUCCCU UUAG ACCG CG CGGC UUU UAAUACUAC UGUUC CCG@LB@3'-UUU...CGCGG A A A AA UCAA UGUCG...GUG-5'@LB@ \| \|@LB@ 79 24@LB@@LB@@LB@Energy -11.81 kcal/mol@LB@Hybridization Energy -41.0645 kcal/mol@LB@Unfolding Energy - mRNA 15.3492 kcal/mol@LB@Unfolding Energy - sRNA 13.8987 kcal/mol@LB@@LB@Position - mRNA 184 -- 242@LB@Position - sRNA 25 -- 78@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 37 -- 43@LB@
149	0.008735	0.2059	b3088	alx	-8.37	0.274530	278 -- 288	25 -- 35	putative membrane-bound redox modulator		_____________277_________289\n_____________\|___________\|\n5'-GGG...CUGUU___________GUCGU...CAC-3'\n______________GUUGCAGGGGC\n______________\|\|\|:\|\|:\|\|\|\|\n______________CAAUGUUCCCG\n3'-UUU...CUACU___________UGUCG...GUG-5'\n_____________\|___________\|\n_____________36__________24\n	282 -- 288	25 -- 31	-18.295 kcal/mol	6.20791 kcal/mol	3.71635 kcal/mol	277 289@LB@ \| \|@LB@5'-GGG...CUGUU GUCGU...CAC-3'@LB@ GUUGCAGGGGC@LB@ \|\|\|:\|\|:\|\|\|\|@LB@ CAAUGUUCCCG@LB@3'-UUU...CUACU UGUCG...GUG-5'@LB@ \| \|@LB@ 36 24@LB@@LB@@LB@Energy -8.37 kcal/mol@LB@Hybridization Energy -18.295 kcal/mol@LB@Unfolding Energy - mRNA 6.20791 kcal/mol@LB@Unfolding Energy - sRNA 3.71635 kcal/mol@LB@@LB@Position - mRNA 278 -- 288@LB@Position - sRNA 25 -- 35@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 25 -- 31@LB@
81	0.004478	0.1855	b3327	gspF	-8.77	0.233220	243 -- 251	26 -- 34	general secretory pathway component cryptic		_____________242_______252\n_____________\|_________\|\n5'-AUG...AAAAA_________AUCAU...AAG-3'\n______________UUGCAAGGG\n______________\|\|:\|\|\|\|\|\|\n______________AAUGUUCCC\n3'-UUU...UACUC_________GUGUC...GUG-5'\n_____________\|_________\|\n_____________35________25\n	245 -- 251	26 -- 32	-12.3281 kcal/mol	0.874927 kcal/mol	2.67841 kcal/mol	242 252@LB@ \| \|@LB@5'-AUG...AAAAA AUCAU...AAG-3'@LB@ UUGCAAGGG@LB@ \|\|:\|\|\|\|\|\|@LB@ AAUGUUCCC@LB@3'-UUU...UACUC GUGUC...GUG-5'@LB@ \| \|@LB@ 35 25@LB@@LB@@LB@Energy -8.77 kcal/mol@LB@Hybridization Energy -12.3281 kcal/mol@LB@Unfolding Energy - mRNA 0.874927 kcal/mol@LB@Unfolding Energy - sRNA 2.67841 kcal/mol@LB@@LB@Position - mRNA 243 -- 251@LB@Position - sRNA 26 -- 34@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 26 -- 32@LB@
163	0.009572	0.2068	b4126	yjdI	-8.84	0.226749	182 -- 194	26 -- 41	putative 4Fe-4S mono-cluster protein		_____________181______________195\n_____________\|________________\|\n5'-UAG...CAUAC_______A________AAGGU...GCG-3'\n______________UGAUGAG____GAGGG\n______________\|\|\|\|\|\|\|____:\|\|\|\|\n______________ACUACUC____UUCCC\n3'-UUU...AUAAU_______AAUG_____GUGUC...GUG-5'\n_____________\|________________\|\n_____________42_______________25\n	182 -- 188	35 -- 41	-13.4129 kcal/mol	1.87738 kcal/mol	2.69216 kcal/mol	181 195@LB@ \| \|@LB@5'-UAG...CAUAC A AAGGU...GCG-3'@LB@ UGAUGAG GAGGG@LB@ \|\|\|\|\|\|\| :\|\|\|\|@LB@ ACUACUC UUCCC@LB@3'-UUU...AUAAU AAUG GUGUC...GUG-5'@LB@ \| \|@LB@ 42 25@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -13.4129 kcal/mol@LB@Unfolding Energy - mRNA 1.87738 kcal/mol@LB@Unfolding Energy - sRNA 2.69216 kcal/mol@LB@@LB@Position - mRNA 182 -- 194@LB@Position - sRNA 26 -- 41@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 35 -- 41@LB@
195	0.01197	0.2159	b0738	tolR	-7.83	0.338188	180 -- 193	26 -- 40	membrane spanning protein in TolA-TolQ-TolR complex		_____________179_____________194\n_____________\|_______________\|\n5'-UGG...UUAGC______CA_______GUAAG...UGG-3'\n______________GA_GAG__ACAAGGG\n______________\|\|_\|\|\|__\|\|\|\|\|\|\|\n______________CU_CUC__UGUUCCC\n3'-UUU...UAAUA__A___AA_______GUGUC...GUG-5'\n_____________\|_______________\|\n_____________41______________25\n	187 -- 193	26 -- 32	-14.5104 kcal/mol	3.98616 kcal/mol	2.69022 kcal/mol	179 194@LB@ \| \|@LB@5'-UGG...UUAGC CA GUAAG...UGG-3'@LB@ GA GAG ACAAGGG@LB@ \|\| \|\|\| \|\|\|\|\|\|\|@LB@ CU CUC UGUUCCC@LB@3'-UUU...UAAUA A AA GUGUC...GUG-5'@LB@ \| \|@LB@ 41 25@LB@@LB@@LB@Energy -7.83 kcal/mol@LB@Hybridization Energy -14.5104 kcal/mol@LB@Unfolding Energy - mRNA 3.98616 kcal/mol@LB@Unfolding Energy - sRNA 2.69022 kcal/mol@LB@@LB@Position - mRNA 180 -- 193@LB@Position - sRNA 26 -- 40@LB@Position Seed - mRNA 187 -- 193@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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