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
27	0.0001238	0.01616	b0081	mraZ	-12.77	0.021128	157 -- 196	45 -- 91	RsmH methytransferase inhibitor	_____________156_____________________________________________197\n_____________\|_______________________________________________\|\n5'-GAU...UUUCA___G____________GG_____A____GG___U_____________UGGCA...AAA-3'\n______________GUG_GA___AAUUGUG____GCA__AGU__GAA_AAGG_GGUGAGGC\n______________\|\|:_\|\|___\|\|\|\|\|\|\|____\|\|\|__\|:\|__:\|\|_\|\|\|\|_:\|\|:\|\|:\|\n______________CAU_CU___UUAACAC____CGU__UUA__UUU_UUCC_UCAUUCUG\n3'-UUU...CGCAG___G__UAG_______GAUA___CA___AG___U____U________UUAUA...ACG-5'\n_____________\|_______________________________________________\|\n_____________92______________________________________________44\n	190 -- 196	45 -- 51	-27.6686 kcal/mol	9.1766 kcal/mol	5.72765 kcal/mol	156 197@LB@ \| \|@LB@5'-GAU...UUUCA G GG A GG U UGGCA...AAA-3'@LB@ GUG GA AAUUGUG GCA AGU GAA AAGG GGUGAGGC@LB@ \|\|: \|\| \|\|\|\|\|\|\| \|\|\| \|:\| :\|\| \|\|\|\| :\|\|:\|\|:\|@LB@ CAU CU UUAACAC CGU UUA UUU UUCC UCAUUCUG@LB@3'-UUU...CGCAG G UAG GAUA CA AG U U UUAUA...ACG-5'@LB@ \| \|@LB@ 92 44@LB@@LB@@LB@Energy -12.77 kcal/mol@LB@Hybridization Energy -27.6686 kcal/mol@LB@Unfolding Energy - mRNA 9.1766 kcal/mol@LB@Unfolding Energy - sRNA 5.72765 kcal/mol@LB@@LB@Position - mRNA 157 -- 196@LB@Position - sRNA 45 -- 91@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 45 -- 51@LB@
79	0.001882	0.08273	b2219	atoS	-12.26	0.029240	6 -- 44	51 -- 94	sensory histidine kinase in two-component regulatory system with AtoC	_____________5_____________________________________________45\n_____________\|_____________________________________________\|\n______5'-UCAGG__________AA__A_____AA_______U__________C____CUCCG...AUA-3'\n______________GUUGUACGAA__GA____GC_____GGUA_UUCAAAGGGG_GAAG\n______________\|\|:\|\|\|\|\|\|\|__:\|____\|\|_____:\|\|\|_\|\|\|\|\|\|:::\|_\|\|\|\|\n______________CAGCAUGCUU__UU____CG_____UCAU_AAGUUUUUUC_CUUC\n3'-UUU...AGCCG__________AG__AACA__AUACG____U_______________AUUCU...ACG-5'\n_____________\|_____________________________________________\|\n_____________95____________________________________________50\n	9 -- 15	85 -- 91	-28.4119 kcal/mol	11.2894 kcal/mol	4.86774 kcal/mol	5 45@LB@ \| \|@LB@ 5'-UCAGG AA A AA U C CUCCG...AUA-3'@LB@ GUUGUACGAA GA GC GGUA UUCAAAGGGG GAAG@LB@ \|\|:\|\|\|\|\|\|\| :\| \|\| :\|\|\| \|\|\|\|\|\|:::\| \|\|\|\|@LB@ CAGCAUGCUU UU CG UCAU AAGUUUUUUC CUUC@LB@3'-UUU...AGCCG AG AACA AUACG U AUUCU...ACG-5'@LB@ \| \|@LB@ 95 50@LB@@LB@@LB@Energy -12.26 kcal/mol@LB@Hybridization Energy -28.4119 kcal/mol@LB@Unfolding Energy - mRNA 11.2894 kcal/mol@LB@Unfolding Energy - sRNA 4.86774 kcal/mol@LB@@LB@Position - mRNA 6 -- 44@LB@Position - sRNA 51 -- 94@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 85 -- 91@LB@
119	0.004048	0.119	b3607	cysE	-9.06	0.179616	191 -- 204	40 -- 54	serine acetyltransferase	_____________190_____________205\n_____________\|_______________\|\n5'-CGG...CGUGU_______________CGUGU...CGA-3'\n______________GGAGUAAG_CAAUGU\n______________\|:\|\|\|\|\|\|_\|\|\|\|:\|\n______________CUUCAUUC_GUUAUA\n3'-UUU...UUUUC________U______CCUCG...ACG-5'\n_____________\|_______________\|\n_____________55______________39\n	192 -- 198	47 -- 53	-13.6491 kcal/mol	2.75521 kcal/mol	1.82942 kcal/mol	190 205@LB@ \| \|@LB@5'-CGG...CGUGU CGUGU...CGA-3'@LB@ GGAGUAAG CAAUGU@LB@ \|:\|\|\|\|\|\| \|\|\|\|:\|@LB@ CUUCAUUC GUUAUA@LB@3'-UUU...UUUUC U CCUCG...ACG-5'@LB@ \| \|@LB@ 55 39@LB@@LB@@LB@Energy -9.06 kcal/mol@LB@Hybridization Energy -13.6491 kcal/mol@LB@Unfolding Energy - mRNA 2.75521 kcal/mol@LB@Unfolding Energy - sRNA 1.82942 kcal/mol@LB@@LB@Position - mRNA 191 -- 204@LB@Position - sRNA 40 -- 54@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 47 -- 53@LB@
197	0.008895	0.1548	b2844	yqeF	-5.48	0.714940	222 -- 246	20 -- 39	short chain acyltransferase	_____________221_______________________247\n_____________\|_________________________\|\n5'-CCA...UUGUC_______UACG___A_______G__GCUUU...UCG-3'\n______________GGGGCGU____GAC_CCUAUCG_CU\n______________\|\|:\|\|\|:____:\|\|_\|\|:\|\|\|\|_\|\|\n______________CCUCGCG____UUG_GGGUAGC_GA\n3'-UUU...UUAUA______________C__________ACUGC...ACG-5'\n_____________\|_________________________\|\n_____________40________________________19\n	237 -- 243	22 -- 28	-25.7666 kcal/mol	8.11246 kcal/mol	12.1811 kcal/mol	221 247@LB@ \| \|@LB@5'-CCA...UUGUC UACG A G GCUUU...UCG-3'@LB@ GGGGCGU GAC CCUAUCG CU@LB@ \|\|:\|\|\|: :\|\| \|\|:\|\|\|\| \|\|@LB@ CCUCGCG UUG GGGUAGC GA@LB@3'-UUU...UUAUA C ACUGC...ACG-5'@LB@ \| \|@LB@ 40 19@LB@@LB@@LB@Energy -5.48 kcal/mol@LB@Hybridization Energy -25.7666 kcal/mol@LB@Unfolding Energy - mRNA 8.11246 kcal/mol@LB@Unfolding Energy - sRNA 12.1811 kcal/mol@LB@@LB@Position - mRNA 222 -- 246@LB@Position - sRNA 20 -- 39@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 22 -- 28@LB@
83	0.001966	0.08273	b1584	speG	-9.79	0.123144	169 -- 214	25 -- 77	spermidine N(1)-acetyltransferase	_____________168_____________________________________________________215\n_____________\|_______________________________________________________\|\n5'-UCU...UAACC__________________________U____G____CGUUAU___CA________CAGUG...GGU-3'\n______________UGUUAU____UGAUUUA____AGGAA_GUAA_GACA_______GC__AGCGCCCA\n______________\|\|:\|\|\|____\|:\|\|\|:\|____\|\|\|\|\|_\|\|\|\|_\|\|\|\|_______\|\|__\|:\|\|\|\|\|\|\n______________ACGAUA____AUUAAGU____UCCUU_CAUU_CUGU_______CG__UUGCGGGU\n3'-UUU...UUAAC______CGUC_______UUUU_______________UAUACCU__CG________AGCGA...ACG-5'\n_____________\|_______________________________________________________\|\n_____________78______________________________________________________24\n	208 -- 214	25 -- 31	-32.6914 kcal/mol	9.23779 kcal/mol	13.6641 kcal/mol	168 215@LB@ \| \|@LB@5'-UCU...UAACC U G CGUUAU CA CAGUG...GGU-3'@LB@ UGUUAU UGAUUUA AGGAA GUAA GACA GC AGCGCCCA@LB@ \|\|:\|\|\| \|:\|\|\|:\| \|\|\|\|\| \|\|\|\| \|\|\|\| \|\| \|:\|\|\|\|\|\|@LB@ ACGAUA AUUAAGU UCCUU CAUU CUGU CG UUGCGGGU@LB@3'-UUU...UUAAC CGUC UUUU UAUACCU CG AGCGA...ACG-5'@LB@ \| \|@LB@ 78 24@LB@@LB@@LB@Energy -9.79 kcal/mol@LB@Hybridization Energy -32.6914 kcal/mol@LB@Unfolding Energy - mRNA 9.23779 kcal/mol@LB@Unfolding Energy - sRNA 13.6641 kcal/mol@LB@@LB@Position - mRNA 169 -- 214@LB@Position - sRNA 25 -- 77@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 25 -- 31@LB@
100	0.003303	0.1114	b1126	potA	-10.42	0.087379	73 -- 89	61 -- 76	spermidine/putrescine ABC transporter ATPase	_____________72________________90\n_____________\|_________________\|\n5'-CAA...AUAAA____A_C__________CAACA...UUC-3'\n______________GCUA_G_CAGUAAUUCA\n______________\|\|\|\|_\|_\|\|\|\|\|\|\|\|\|\|\n______________CGAU_C_GUCAUUAAGU\n3'-UUU...UAACA____A____________UUUUU...ACG-5'\n_____________\|_________________\|\n_____________77________________60\n	83 -- 89	61 -- 67	-17.6149 kcal/mol	3.71554 kcal/mol	3.47887 kcal/mol	72 90@LB@ \| \|@LB@5'-CAA...AUAAA A C CAACA...UUC-3'@LB@ GCUA G CAGUAAUUCA@LB@ \|\|\|\| \| \|\|\|\|\|\|\|\|\|\|@LB@ CGAU C GUCAUUAAGU@LB@3'-UUU...UAACA A UUUUU...ACG-5'@LB@ \| \|@LB@ 77 60@LB@@LB@@LB@Energy -10.42 kcal/mol@LB@Hybridization Energy -17.6149 kcal/mol@LB@Unfolding Energy - mRNA 3.71554 kcal/mol@LB@Unfolding Energy - sRNA 3.47887 kcal/mol@LB@@LB@Position - mRNA 73 -- 89@LB@Position - sRNA 61 -- 76@LB@Position Seed - mRNA 83 -- 89@LB@Position Seed - sRNA 61 -- 67@LB@
123	0.004425	0.1258	b2535	csiE	-7.63	0.347411	1 -- 40	5 -- 36	stationary phase inducible protein	______________1_______________________________________41\n______________\|_______________________________________\|\n___________5'-__AG___UAA____UGA_____A_C___AUAAU_______AAAAC...UGG-3'\n______________GC__AAC___CCCA___UCGCU_G_ACG_____CAUUCAC\n______________\|\|__\|\|\|___\|\|\|\|___\|\|\|\|\|_\|_\|\|\|_____\|\|\|\|\|\|\|\n______________CG__UUG___GGGU___AGCGA_C_UGC_____GUAAGUG\n3'-UUU...UACCU__CG___C______________A_____AAC_________GACG-5'\n_____________\|________________________________________\|\n_____________37_______________________________________4\n	34 -- 40	5 -- 11	-25.9316 kcal/mol	3.04784 kcal/mol	15.2569 kcal/mol	1 41@LB@ \| \|@LB@ 5'- AG UAA UGA A C AUAAU AAAAC...UGG-3'@LB@ GC AAC CCCA UCGCU G ACG CAUUCAC@LB@ \|\| \|\|\| \|\|\|\| \|\|\|\|\| \| \|\|\| \|\|\|\|\|\|\|@LB@ CG UUG GGGU AGCGA C UGC GUAAGUG@LB@3'-UUU...UACCU CG C A AAC GACG-5'@LB@ \| \|@LB@ 37 4@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -25.9316 kcal/mol@LB@Unfolding Energy - mRNA 3.04784 kcal/mol@LB@Unfolding Energy - sRNA 15.2569 kcal/mol@LB@@LB@Position - mRNA 1 -- 40@LB@Position - sRNA 5 -- 36@LB@Position Seed - mRNA 34 -- 40@LB@Position Seed - sRNA 5 -- 11@LB@
179	0.007631	0.1495	b3229	sspA	-8.36	0.252415	276 -- 298	54 -- 83	stringent starvation protein A phage P1 late gene activator RNAP-associated acid-resistance protein inactive glutathione S-transferase homolog	_____________275_____________________________299\n_____________\|_______________________________\|\n5'-CCA...AGGUC__C____________________________UG-3'\n______________CG_AUUGUGCUG_GC_______UGAGAAAGG\n______________\|:_\|\|\|\|\|\|\|\|:_\|\|_______::\|:\|\|\|\|\|\n______________GU_UAACACGAU_CG_______GUUUUUUCC\n3'-UUU...GCUUA____________A__UCAUUAA_________UUCAU...ACG-5'\n_____________\|_______________________________\|\n_____________84______________________________53\n	292 -- 298	54 -- 60	-18.0489 kcal/mol	5.94535 kcal/mol	3.74667 kcal/mol	275 299@LB@ \| \|@LB@5'-CCA...AGGUC C UG-3'@LB@ CG AUUGUGCUG GC UGAGAAAGG@LB@ \|: \|\|\|\|\|\|\|\|: \|\| ::\|:\|\|\|\|\|@LB@ GU UAACACGAU CG GUUUUUUCC@LB@3'-UUU...GCUUA A UCAUUAA UUCAU...ACG-5'@LB@ \| \|@LB@ 84 53@LB@@LB@@LB@Energy -8.36 kcal/mol@LB@Hybridization Energy -18.0489 kcal/mol@LB@Unfolding Energy - mRNA 5.94535 kcal/mol@LB@Unfolding Energy - sRNA 3.74667 kcal/mol@LB@@LB@Position - mRNA 276 -- 298@LB@Position - sRNA 54 -- 83@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 54 -- 60@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@
82	0.001946	0.08273	b2661	gabD	-10.13	0.102437	19 -- 25	1 -- 7	succinate-semialdehyde dehydrogenase I NADP-dependent	_____________18______26\n_____________\|_______\|\n5'-CAC...AUCCA_______AAUGC...CGG-3'\n______________CACCUGC\n______________\|\|\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	19 -- 25	1 -- 7	-13.7555 kcal/mol	1.28845 kcal/mol	2.34039 kcal/mol	18 26@LB@ \| \|@LB@5'-CAC...AUCCA AAUGC...CGG-3'@LB@ CACCUGC@LB@ \|\|\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -10.13 kcal/mol@LB@Hybridization Energy -13.7555 kcal/mol@LB@Unfolding Energy - mRNA 1.28845 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 19 -- 25@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 1 -- 7@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

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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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