Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
61	0.001027	0.05816	b0443	fadM	-9.40	0.151451	193 -- 205	69 -- 81	long-chain acyl-CoA thioesterase III		_____________192___________206\n_____________\|_____________\|\n5'-GUU...AGGUU____C________AACAC...AUG-3'\n______________AUUG_GCUAUGCA\n______________\|\|\|\|_\|\|\|\|\|\|\|\|\n______________UAAC_CGAUACGU\n3'-UUU...UUAGU____A________CAUUA...ACG-5'\n_____________\|_____________\|\n_____________82____________68\n	199 -- 205	69 -- 75	-15.9471 kcal/mol	4.72824 kcal/mol	1.82028 kcal/mol	192 206@LB@ \| \|@LB@5'-GUU...AGGUU C AACAC...AUG-3'@LB@ AUUG GCUAUGCA@LB@ \|\|\|\| \|\|\|\|\|\|\|\|@LB@ UAAC CGAUACGU@LB@3'-UUU...UUAGU A CAUUA...ACG-5'@LB@ \| \|@LB@ 82 68@LB@@LB@@LB@Energy -9.40 kcal/mol@LB@Hybridization Energy -15.9471 kcal/mol@LB@Unfolding Energy - mRNA 4.72824 kcal/mol@LB@Unfolding Energy - sRNA 1.82028 kcal/mol@LB@@LB@Position - mRNA 193 -- 205@LB@Position - sRNA 69 -- 81@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 69 -- 75@LB@
89	0.002455	0.09689	b0466	ybaM	-10.99	0.063193	248 -- 263	68 -- 82	DUF2496 family protein		_____________247______________264\n_____________\|________________\|\n5'-GCA...GAUUU__________C__G__GAAAA...CGC-3'\n______________GAUUGUGCUG_UG_AG\n______________:\|\|\|\|\|\|\|\|:_\|\|_\|\|\n______________UUAACACGAU_AC_UC\n3'-UUU...CUUAG_____________G__AUUAA...ACG-5'\n_____________\|________________\|\n_____________83_______________67\n	251 -- 257	73 -- 79	-16.1643 kcal/mol	2.45269 kcal/mol	2.72435 kcal/mol	247 264@LB@ \| \|@LB@5'-GCA...GAUUU C G GAAAA...CGC-3'@LB@ GAUUGUGCUG UG AG@LB@ :\|\|\|\|\|\|\|\|: \|\| \|\|@LB@ UUAACACGAU AC UC@LB@3'-UUU...CUUAG G AUUAA...ACG-5'@LB@ \| \|@LB@ 83 67@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -16.1643 kcal/mol@LB@Unfolding Energy - mRNA 2.45269 kcal/mol@LB@Unfolding Energy - sRNA 2.72435 kcal/mol@LB@@LB@Position - mRNA 248 -- 263@LB@Position - sRNA 68 -- 82@LB@Position Seed - mRNA 251 -- 257@LB@Position Seed - sRNA 73 -- 79@LB@
105	0.003386	0.1114	b0517	allD	-12.14	0.031589	151 -- 204	43 -- 92	ureidoglycolate dehydrogenase	b0801	_____________150______________________________________________________205\n_____________\|________________________________________________________\|\n5'-AAA...UUCCC_______________CA__C____UUCACACCG___UU__________AC______AAAUC...UGG-3'\n______________UGUAUG__UUAAUUG__GU_AUGC_________UCG__AAAAAGGAAG__AGAUGA\n______________:\|\|\|:\|__\|:\|\|\|\|\|__\|:_\|\|\|\|_________\|\|:__\|\|\|\|\|\|\|\|\|\|__\|\|\|::\|\n______________GCAUGC__AGUUAAC__CG_UACG_________AGU__UUUUUCCUUC__UCUGUU\n3'-UUU...CCGCA______UU_______A___A____UCAUUA__________________AU______AUACC...ACG-5'\n_____________\|________________________________________________________\|\n_____________93_______________________________________________________42\n	190 -- 196	51 -- 57	-28.1957 kcal/mol	10.2009 kcal/mol	5.86211 kcal/mol	150 205@LB@ \| \|@LB@5'-AAA...UUCCC CA C UUCACACCG UU AC AAAUC...UGG-3'@LB@ UGUAUG UUAAUUG GU AUGC UCG AAAAAGGAAG AGAUGA@LB@ :\|\|\|:\| \|:\|\|\|\|\| \|: \|\|\|\| \|\|: \|\|\|\|\|\|\|\|\|\| \|\|\|::\|@LB@ GCAUGC AGUUAAC CG UACG AGU UUUUUCCUUC UCUGUU@LB@3'-UUU...CCGCA UU A A UCAUUA AU AUACC...ACG-5'@LB@ \| \|@LB@ 93 42@LB@@LB@@LB@Energy -12.14 kcal/mol@LB@Hybridization Energy -28.1957 kcal/mol@LB@Unfolding Energy - mRNA 10.2009 kcal/mol@LB@Unfolding Energy - sRNA 5.86211 kcal/mol@LB@@LB@Position - mRNA 151 -- 204@LB@Position - sRNA 43 -- 92@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 51 -- 57@LB@
126	0.004539	0.1258	b0546	ybcM	-11.00	0.062763	188 -- 220	45 -- 91	DLP12 prophage; putative DNA-binding transcriptional regulator	b1499 b0564 b3515 b4116 b0566 b3516	_____________187_____________________________________________221\n_____________\|_______________________________________________\|\n5'-GCU...AUAAA___G__UGA__GUA_________A_______________________UAACU...GUC-3'\n______________GUA_GG___GA___UGCUG_GCA______________GAGGUAAGAC\n______________\|\|\|_\|:___:\|___\|\|\|\|:_\|\|\|______________\|\|:\|\|\|\|\|\|\|\n______________CAU_CU___UU___ACGAU_CGU______________CUUCAUUCUG\n3'-UUU...CGCAG___G__UAG__AAC_____A___CAUUAAGUUUUUUC__________UUAUA...ACG-5'\n_____________\|_______________________________________________\|\n_____________92______________________________________________44\n	214 -- 220	45 -- 51	-23.4531 kcal/mol	6.72952 kcal/mol	5.72765 kcal/mol	187 221@LB@ \| \|@LB@5'-GCU...AUAAA G UGA GUA A UAACU...GUC-3'@LB@ GUA GG GA UGCUG GCA GAGGUAAGAC@LB@ \|\|\| \|: :\| \|\|\|\|: \|\|\| \|\|:\|\|\|\|\|\|\|@LB@ CAU CU UU ACGAU CGU CUUCAUUCUG@LB@3'-UUU...CGCAG G UAG AAC A CAUUAAGUUUUUUC UUAUA...ACG-5'@LB@ \| \|@LB@ 92 44@LB@@LB@@LB@Energy -11.00 kcal/mol@LB@Hybridization Energy -23.4531 kcal/mol@LB@Unfolding Energy - mRNA 6.72952 kcal/mol@LB@Unfolding Energy - sRNA 5.72765 kcal/mol@LB@@LB@Position - mRNA 188 -- 220@LB@Position - sRNA 45 -- 91@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 45 -- 51@LB@
55	0.0007336	0.04699	b0585	fes	-14.13	0.008457	197 -- 228	46 -- 77	enterobactin/ferrienterobactin esterase		_____________196________________________________229\n_____________\|__________________________________\|\n5'-CAU...GGUUA__G____A___CG_________U___________GCUGG...GGU-3'\n______________UG_UGUG_CGG____UUAAAAG_AGGAAGUGAGA\n______________\|\|_\|:\|\|_\|:\|____\|:\|\|\|\|:_\|\|\|\|\|\|\|:\|\|\|\n______________AC_AUAC_GUC____AGUUUUU_UCCUUCAUUCU\n3'-UUU...UUAAC__G________AUUA___________________GUUAU...ACG-5'\n_____________\|__________________________________\|\n_____________78_________________________________45\n	222 -- 228	46 -- 52	-26.4508 kcal/mol	7.03406 kcal/mol	5.29333 kcal/mol	196 229@LB@ \| \|@LB@5'-CAU...GGUUA G A CG U GCUGG...GGU-3'@LB@ UG UGUG CGG UUAAAAG AGGAAGUGAGA@LB@ \|\| \|:\|\| \|:\| \|:\|\|\|\|: \|\|\|\|\|\|\|:\|\|\|@LB@ AC AUAC GUC AGUUUUU UCCUUCAUUCU@LB@3'-UUU...UUAAC G AUUA GUUAU...ACG-5'@LB@ \| \|@LB@ 78 45@LB@@LB@@LB@Energy -14.13 kcal/mol@LB@Hybridization Energy -26.4508 kcal/mol@LB@Unfolding Energy - mRNA 7.03406 kcal/mol@LB@Unfolding Energy - sRNA 5.29333 kcal/mol@LB@@LB@Position - mRNA 197 -- 228@LB@Position - sRNA 46 -- 77@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 46 -- 52@LB@
59	0.0009764	0.05816	b0593	entC	-14.06	0.008887	219 -- 262	19 -- 57	isochorismate synthase 1		_____________218____________________________________________263\n_____________\|______________________________________________\|\n5'-GGC...UGGCU_________CAGC____C______CAACACUU______A_______UUUCU...CAG-3'\n______________GAGGAAGUA____AGAC___AUGG________GCGCCC_AUCGCUU\n______________:\|\|\|\|\|\|\|\|____\|\|\|\|___\|\|\|\|________:\|\|\|\|\|_\|\|\|\|\|\|\|\n______________UUCCUUCAU____UCUG___UACC________UGCGGG_UAGCGAA\n3'-UUU...GUUUU_________________UUA____UCGCGU________________CUGCA...ACG-5'\n_____________\|______________________________________________\|\n_____________58_____________________________________________18\n	256 -- 262	19 -- 25	-38.3486 kcal/mol	10.4998 kcal/mol	13.7965 kcal/mol	218 263@LB@ \| \|@LB@5'-GGC...UGGCU CAGC C CAACACUU A UUUCU...CAG-3'@LB@ GAGGAAGUA AGAC AUGG GCGCCC AUCGCUU@LB@ :\|\|\|\|\|\|\|\| \|\|\|\| \|\|\|\| :\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UUCCUUCAU UCUG UACC UGCGGG UAGCGAA@LB@3'-UUU...GUUUU UUA UCGCGU CUGCA...ACG-5'@LB@ \| \|@LB@ 58 18@LB@@LB@@LB@Energy -14.06 kcal/mol@LB@Hybridization Energy -38.3486 kcal/mol@LB@Unfolding Energy - mRNA 10.4998 kcal/mol@LB@Unfolding Energy - sRNA 13.7965 kcal/mol@LB@@LB@Position - mRNA 219 -- 262@LB@Position - sRNA 19 -- 57@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 19 -- 25@LB@
69	0.001222	0.06239	b0699	ybfA	-13.19	0.016050	183 -- 205	37 -- 62	DUF2517 family protein		_____________182________________________206\n_____________\|__________________________\|\n5'-AUG...AGAUA____________AAA___________ACUCU...GGA-3'\n______________CAAAAGGGGGAG______AGUAUGGA\n______________\|\|\|\|\|::\|\|:\|\|______\|:\|\|\|\|\|\|\n______________GUUUUUUCCUUC______UUAUACCU\n3'-UUU...AUUAA____________AUUCUG________CGCGU...ACG-5'\n_____________\|__________________________\|\n_____________63_________________________36\n	199 -- 205	37 -- 43	-21.7 kcal/mol	3.27833 kcal/mol	5.2343 kcal/mol	182 206@LB@ \| \|@LB@5'-AUG...AGAUA AAA ACUCU...GGA-3'@LB@ CAAAAGGGGGAG AGUAUGGA@LB@ \|\|\|\|\|::\|\|:\|\| \|:\|\|\|\|\|\|@LB@ GUUUUUUCCUUC UUAUACCU@LB@3'-UUU...AUUAA AUUCUG CGCGU...ACG-5'@LB@ \| \|@LB@ 63 36@LB@@LB@@LB@Energy -13.19 kcal/mol@LB@Hybridization Energy -21.7 kcal/mol@LB@Unfolding Energy - mRNA 3.27833 kcal/mol@LB@Unfolding Energy - sRNA 5.2343 kcal/mol@LB@@LB@Position - mRNA 183 -- 205@LB@Position - sRNA 37 -- 62@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 37 -- 43@LB@
62	0.001027	0.05816	b0717	ybgP	-6.75	0.488398	48 -- 57	53 -- 62	putative periplasmic pilin chaperone	b3047	_____________47_________58\n_____________\|__________\|\n5'-GCG...GUUGG__________CAUGC...CCA-3'\n______________CGAGGAAGGA\n______________\|:\|::\|\|\|\|\|\n______________GUUUUUUCCU\n3'-UUU...AUUAA__________UCAUU...ACG-5'\n_____________\|__________\|\n_____________63_________52\n	51 -- 57	53 -- 59	-10.1576 kcal/mol	0.982686 kcal/mol	2.4254 kcal/mol	47 58@LB@ \| \|@LB@5'-GCG...GUUGG CAUGC...CCA-3'@LB@ CGAGGAAGGA@LB@ \|:\|::\|\|\|\|\|@LB@ GUUUUUUCCU@LB@3'-UUU...AUUAA UCAUU...ACG-5'@LB@ \| \|@LB@ 63 52@LB@@LB@@LB@Energy -6.75 kcal/mol@LB@Hybridization Energy -10.1576 kcal/mol@LB@Unfolding Energy - mRNA 0.982686 kcal/mol@LB@Unfolding Energy - sRNA 2.4254 kcal/mol@LB@@LB@Position - mRNA 48 -- 57@LB@Position - sRNA 53 -- 62@LB@Position Seed - mRNA 51 -- 57@LB@Position Seed - sRNA 53 -- 59@LB@
18	4.045e-05	0.007917	b0723	sdhA	-14.73	0.005501	172 -- 195	67 -- 90	succinate dehydrogenase flavoprotein subunit		_____________171______________________196\n_____________\|________________________\|\n5'-GGU...UGAUU________C______G____G___GUGUG...GUG-3'\n______________UAUGGAUU_GUUGUG_UGUG_GGU\n______________\|\|:\|:\|\|:_:\|\|\|\|\|_\|:\|\|_:\|\|\n______________AUGCUUAG_UAACAC_AUAC_UCA\n3'-UUU...GCAGC________U______G____G___UUAAG...ACG-5'\n_____________\|________________________\|\n_____________91_______________________66\n	173 -- 179	83 -- 89	-23.9499 kcal/mol	4.69238 kcal/mol	4.5307 kcal/mol	171 196@LB@ \| \|@LB@5'-GGU...UGAUU C G G GUGUG...GUG-3'@LB@ UAUGGAUU GUUGUG UGUG GGU@LB@ \|\|:\|:\|\|: :\|\|\|\|\| \|:\|\| :\|\|@LB@ AUGCUUAG UAACAC AUAC UCA@LB@3'-UUU...GCAGC U G G UUAAG...ACG-5'@LB@ \| \|@LB@ 91 66@LB@@LB@@LB@Energy -14.73 kcal/mol@LB@Hybridization Energy -23.9499 kcal/mol@LB@Unfolding Energy - mRNA 4.69238 kcal/mol@LB@Unfolding Energy - sRNA 4.5307 kcal/mol@LB@@LB@Position - mRNA 172 -- 195@LB@Position - sRNA 67 -- 90@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 83 -- 89@LB@
164	0.006461	0.1377	b0864	artP	-11.21	0.055481	74 -- 84	70 -- 80	arginine ABC transporter ATPase		_____________73__________85\n_____________\|___________\|\n5'-AAA...UUAUU___________UUAUU...UAC-3'\n______________UUGUGCUAUGU\n______________\|\|\|\|\|\|\|\|\|\|:\n______________AACACGAUACG\n3'-UUU...UAGUU___________UCAUU...ACG-5'\n_____________\|___________\|\n_____________81__________69\n	78 -- 84	70 -- 76	-15.8897 kcal/mol	2.86206 kcal/mol	1.81863 kcal/mol	73 85@LB@ \| \|@LB@5'-AAA...UUAUU UUAUU...UAC-3'@LB@ UUGUGCUAUGU@LB@ \|\|\|\|\|\|\|\|\|\|:@LB@ AACACGAUACG@LB@3'-UUU...UAGUU UCAUU...ACG-5'@LB@ \| \|@LB@ 81 69@LB@@LB@@LB@Energy -11.21 kcal/mol@LB@Hybridization Energy -15.8897 kcal/mol@LB@Unfolding Energy - mRNA 2.86206 kcal/mol@LB@Unfolding Energy - sRNA 1.81863 kcal/mol@LB@@LB@Position - mRNA 74 -- 84@LB@Position - sRNA 70 -- 80@LB@Position Seed - mRNA 78 -- 84@LB@Position Seed - sRNA 70 -- 76@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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