Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
169	0.02775	0.531	b2110	yehC	-5.87	0.481945	191 -- 199	20 -- 28	putative periplasmic pilin chaperone	_____________190_______200\n_____________\|_________\|\n5'-CAG...CUCCA_________CAUGG...CCG-3'\n______________GGUAAUAAA\n______________\|\|\|\|\|\|\|\|\|\n______________CCAUUAUUU\n3'-UUU...UACUG_________AUUUC...UCG-5'\n_____________\|_________\|\n_____________29________19\n	193 -- 199	20 -- 26	-7.96952 kcal/mol	1.36589 kcal/mol	0.737257 kcal/mol	190 200@LB@ \| \|@LB@5'-CAG...CUCCA CAUGG...CCG-3'@LB@ GGUAAUAAA@LB@ \|\|\|\|\|\|\|\|\|@LB@ CCAUUAUUU@LB@3'-UUU...UACUG AUUUC...UCG-5'@LB@ \| \|@LB@ 29 19@LB@@LB@@LB@Energy -5.87 kcal/mol@LB@Hybridization Energy -7.96952 kcal/mol@LB@Unfolding Energy - mRNA 1.36589 kcal/mol@LB@Unfolding Energy - sRNA 0.737257 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 20 -- 28@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 20 -- 26@LB@
137	0.02279	0.526	b1739	osmE	-8.84	0.162198	202 -- 246	21 -- 65	osmotically-inducible lipoprotein	_____________201____________________________________________247\n_____________\|______________________________________________\|\n5'-GAA...GAAUA____CA__AAUAU______A____U______C__C_______U___CCAUG...AGC-3'\n______________UGAA__AG_____GGCAGG_AUUC__GAGUG_AG_GGCGGUA_UAA\n______________\|\|\|\|__\|\|_____::\|\|\|:_\|\|\|\|__:\|:\|\|_\|:_\|:\|\|\|\|\|_\|\|\|\n______________ACUU__UC_____UUGUCU_UAAG__UUUAC_UU_CUGCCAU_AUU\n3'-UUU...GGCCA____UA__CCCAU______G____UC________A_______U___UAUUU...UCG-5'\n_____________\|______________________________________________\|\n_____________66_____________________________________________20\n	236 -- 242	25 -- 31	-25.0909 kcal/mol	9.03477 kcal/mol	7.21767 kcal/mol	201 247@LB@ \| \|@LB@5'-GAA...GAAUA CA AAUAU A U C C U CCAUG...AGC-3'@LB@ UGAA AG GGCAGG AUUC GAGUG AG GGCGGUA UAA@LB@ \|\|\|\| \|\| ::\|\|\|: \|\|\|\| :\|:\|\| \|: \|:\|\|\|\|\| \|\|\|@LB@ ACUU UC UUGUCU UAAG UUUAC UU CUGCCAU AUU@LB@3'-UUU...GGCCA UA CCCAU G UC A U UAUUU...UCG-5'@LB@ \| \|@LB@ 66 20@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -25.0909 kcal/mol@LB@Unfolding Energy - mRNA 9.03477 kcal/mol@LB@Unfolding Energy - sRNA 7.21767 kcal/mol@LB@@LB@Position - mRNA 202 -- 246@LB@Position - sRNA 21 -- 65@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 25 -- 31@LB@
144	0.02445	0.526	b3441	yhhY	-11.04	0.059403	187 -- 218	22 -- 53	aminoacyl nucleotide detoxifying acetyltransferase	_____________186________________________________219\n_____________\|__________________________________\|\n5'-CCC...CCCCA__GA_____A______________GAUA______CGCCA...UGC-3'\n______________AA__GGACA___AGGAAUGAGUGA____GUAAUA\n______________\|\|__:\|\|\|\|___\|\|:\|\|\|\|\|:\|\|\|____\|\|\|\|\|\|\n______________UU__UCUGU___UCUUUACUUACU____CAUUAU\n3'-UUU...CCCCA__UG_____AAG____________GC________UUAUU...UCG-5'\n_____________\|__________________________________\|\n_____________54_________________________________21\n	202 -- 208	30 -- 36	-22.9472 kcal/mol	5.59747 kcal/mol	6.31329 kcal/mol	186 219@LB@ \| \|@LB@5'-CCC...CCCCA GA A GAUA CGCCA...UGC-3'@LB@ AA GGACA AGGAAUGAGUGA GUAAUA@LB@ \|\| :\|\|\|\| \|\|:\|\|\|\|\|:\|\|\| \|\|\|\|\|\|@LB@ UU UCUGU UCUUUACUUACU CAUUAU@LB@3'-UUU...CCCCA UG AAG GC UUAUU...UCG-5'@LB@ \| \|@LB@ 54 21@LB@@LB@@LB@Energy -11.04 kcal/mol@LB@Hybridization Energy -22.9472 kcal/mol@LB@Unfolding Energy - mRNA 5.59747 kcal/mol@LB@Unfolding Energy - sRNA 6.31329 kcal/mol@LB@@LB@Position - mRNA 187 -- 218@LB@Position - sRNA 22 -- 53@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 30 -- 36@LB@
185	0.03096	0.5492	b1686	menI	-12.09	0.035132	263 -- 300	22 -- 58	1 4-dihydroxy-2-naphthoyl-CoA hydrolase	_____________262____________________________________300\n_____________\|______________________________________\|\n5'-GGC...AUGGU_____UCCU_________CUU_____CAUAU________-3'\n______________GGGGU____GGAUAUUCG____UGAA_____UGGUGAUG\n______________\|\|\|\|\|____:\|\|:\|\|\|\|:____\|\|\|\|_____:\|\|\|:\|\|:\n______________CCCCA____UCUGUAAGU____ACUU_____GCCAUUAU\n3'-UUU...UUUAU_____UUUG_________CUUU____ACU__________UUAUU...UCG-5'\n_____________\|_______________________________________\|\n_____________59______________________________________21\n	294 -- 300	22 -- 28	-26.9755 kcal/mol	8.57608 kcal/mol	6.31389 kcal/mol	262 300@LB@ \| \|@LB@5'-GGC...AUGGU UCCU CUU CAUAU -3'@LB@ GGGGU GGAUAUUCG UGAA UGGUGAUG@LB@ \|\|\|\|\| :\|\|:\|\|\|\|: \|\|\|\| :\|\|\|:\|\|:@LB@ CCCCA UCUGUAAGU ACUU GCCAUUAU@LB@3'-UUU...UUUAU UUUG CUUU ACU UUAUU...UCG-5'@LB@ \| \|@LB@ 59 21@LB@@LB@@LB@Energy -12.09 kcal/mol@LB@Hybridization Energy -26.9755 kcal/mol@LB@Unfolding Energy - mRNA 8.57608 kcal/mol@LB@Unfolding Energy - sRNA 6.31389 kcal/mol@LB@@LB@Position - mRNA 263 -- 300@LB@Position - sRNA 22 -- 58@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 22 -- 28@LB@
32	0.003146	0.3086	b1553	rzpQ	-12.95	0.022283	187 -- 223	23 -- 60	Rz-like protein Qin prophage	_____________186______________________________________224\n_____________\|________________________________________\|\n5'-UAU...CCUGC______AUA______UGAA_____UAUUC___________UUUUC...GUG-3'\n______________UGGGGG___GAACAG____UCAGA________AUGGUGAU\n______________\|:\|\|\|\|___:\|\|\|\|\|____\|\|\|\|\|________\|:\|\|\|:\|\|\n______________AUCCCC___UUUGUC____AGUCU________UGCCAUUA\n3'-UUU...ACUUU______A________UGUA_____UUACUUAC________UUUAU...UCG-5'\n_____________\|________________________________________\|\n_____________61_______________________________________22\n	217 -- 223	23 -- 29	-27.4351 kcal/mol	8.1631 kcal/mol	6.31885 kcal/mol	186 224@LB@ \| \|@LB@5'-UAU...CCUGC AUA UGAA UAUUC UUUUC...GUG-3'@LB@ UGGGGG GAACAG UCAGA AUGGUGAU@LB@ \|:\|\|\|\| :\|\|\|\|\| \|\|\|\|\| \|:\|\|\|:\|\|@LB@ AUCCCC UUUGUC AGUCU UGCCAUUA@LB@3'-UUU...ACUUU A UGUA UUACUUAC UUUAU...UCG-5'@LB@ \| \|@LB@ 61 22@LB@@LB@@LB@Energy -12.95 kcal/mol@LB@Hybridization Energy -27.4351 kcal/mol@LB@Unfolding Energy - mRNA 8.1631 kcal/mol@LB@Unfolding Energy - sRNA 6.31885 kcal/mol@LB@@LB@Position - mRNA 187 -- 223@LB@Position - sRNA 23 -- 60@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 23 -- 29@LB@
139	0.0229	0.526	b3958	argC	-10.25	0.086580	11 -- 36	23 -- 56	N-acetyl-gamma-glutamylphosphate reductase NAD(P)-binding	_____________10___________________________________37\n_____________\|____________________________________\|\n5'-AUC...AGCGC_______CUC__________________________UUGUU...CUG-3'\n______________GGUAAAU___GAUA__________AAUGGCGGUAAU\n______________\|\|\|\|\|\|:___\|\|:\|__________\|\|\|\|:\|\|\|\|\|\|\|\n______________CCAUUUG___CUGU__________UUACUGCCAUUA\n3'-UUU...UAUCC_______U______AAGUCUUUAC____________UUUAU...UCG-5'\n_____________\|____________________________________\|\n_____________57___________________________________22\n	30 -- 36	23 -- 29	-21.8632 kcal/mol	5.30467 kcal/mol	6.31216 kcal/mol	10 37@LB@ \| \|@LB@5'-AUC...AGCGC CUC UUGUU...CUG-3'@LB@ GGUAAAU GAUA AAUGGCGGUAAU@LB@ \|\|\|\|\|\|: \|\|:\| \|\|\|\|:\|\|\|\|\|\|\|@LB@ CCAUUUG CUGU UUACUGCCAUUA@LB@3'-UUU...UAUCC U AAGUCUUUAC UUUAU...UCG-5'@LB@ \| \|@LB@ 57 22@LB@@LB@@LB@Energy -10.25 kcal/mol@LB@Hybridization Energy -21.8632 kcal/mol@LB@Unfolding Energy - mRNA 5.30467 kcal/mol@LB@Unfolding Energy - sRNA 6.31216 kcal/mol@LB@@LB@Position - mRNA 11 -- 36@LB@Position - sRNA 23 -- 56@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 23 -- 29@LB@
145	0.02447	0.526	b4518	ymdF	-10.96	0.061577	258 -- 296	23 -- 64	KGG family protein	_____________257________________________________________________297\n_____________\|__________________________________________________\|\n5'-UUU...CAUCA____C___UAAAAAA_________C___GC_____________G______UUCA-3'\n______________GAAG_AGG_______GGUGGACAG_ACA_____________GG_GGUAAU\n______________\|\|\|:_\|\|\|_______\|\|\|::\|\|\|\|_\|\|\|_____________\|:_\|\|\|\|\|\|\n______________CUUU_UCC_______CCAUUUGUC_UGU_____________CU_CCAUUA\n3'-UUU...GCCAA____A_______________________AAGUCUUUACUUA__G______UUUAU...UCG-5'\n_____________\|__________________________________________________\|\n_____________65_________________________________________________22\n	275 -- 281	48 -- 54	-22.543 kcal/mol	5.2615 kcal/mol	6.31898 kcal/mol	257 297@LB@ \| \|@LB@5'-UUU...CAUCA C UAAAAAA C GC G UUCA-3'@LB@ GAAG AGG GGUGGACAG ACA GG GGUAAU@LB@ \|\|\|: \|\|\| \|\|\|::\|\|\|\| \|\|\| \|: \|\|\|\|\|\|@LB@ CUUU UCC CCAUUUGUC UGU CU CCAUUA@LB@3'-UUU...GCCAA A AAGUCUUUACUUA G UUUAU...UCG-5'@LB@ \| \|@LB@ 65 22@LB@@LB@@LB@Energy -10.96 kcal/mol@LB@Hybridization Energy -22.543 kcal/mol@LB@Unfolding Energy - mRNA 5.2615 kcal/mol@LB@Unfolding Energy - sRNA 6.31898 kcal/mol@LB@@LB@Position - mRNA 258 -- 296@LB@Position - sRNA 23 -- 64@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 48 -- 54@LB@
16	0.0008012	0.1482	b2011	sbcB	-16.25	0.003318	186 -- 217	24 -- 52	exodeoxyribonuclease I; exonuclease I	_____________185______________________________218\n_____________\|________________________________\|\n5'-CCU...GAAAU_______UUAACCUAAU_______________GCAAC...CCA-3'\n______________AACGGAU__________GAUGAAUGACGGUAA\n______________\|\|\|:\|\|:__________:\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________UUGUCUG__________UUACUUACUGCCAUU\n3'-UUU...CCCAU_______UAAGUCU__________________AUUUA...UCG-5'\n_____________\|________________________________\|\n_____________53_______________________________23\n	211 -- 217	24 -- 30	-27.0341 kcal/mol	4.49086 kcal/mol	6.2974 kcal/mol	185 218@LB@ \| \|@LB@5'-CCU...GAAAU UUAACCUAAU GCAAC...CCA-3'@LB@ AACGGAU GAUGAAUGACGGUAA@LB@ \|\|\|:\|\|: :\|\|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ UUGUCUG UUACUUACUGCCAUU@LB@3'-UUU...CCCAU UAAGUCU AUUUA...UCG-5'@LB@ \| \|@LB@ 53 23@LB@@LB@@LB@Energy -16.25 kcal/mol@LB@Hybridization Energy -27.0341 kcal/mol@LB@Unfolding Energy - mRNA 4.49086 kcal/mol@LB@Unfolding Energy - sRNA 6.2974 kcal/mol@LB@@LB@Position - mRNA 186 -- 217@LB@Position - sRNA 24 -- 52@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 24 -- 30@LB@
91	0.01489	0.5059	b3805	hemC	-12.98	0.021909	168 -- 195	24 -- 52	hydroxymethylbilane synthase	_____________167___________________________196\n_____________\|_____________________________\|\n5'-AAA...GUUAG_______CA_____UGAU___________CAAGC...GCC-3'\n______________GAUGGAC___CGGA____AAUGACGGUAA\n______________:\|::\|\|\|___\|:\|\|____\|\|\|\|\|\|\|\|\|\|\|\n______________UUGUCUG___GUCU____UUACUGCCAUU\n3'-UUU...CCCAU_______UAA____UUAC___________AUUUA...UCG-5'\n_____________\|_____________________________\|\n_____________53____________________________23\n	189 -- 195	24 -- 30	-23.6136 kcal/mol	4.33145 kcal/mol	6.2974 kcal/mol	167 196@LB@ \| \|@LB@5'-AAA...GUUAG CA UGAU CAAGC...GCC-3'@LB@ GAUGGAC CGGA AAUGACGGUAA@LB@ :\|::\|\|\| \|:\|\| \|\|\|\|\|\|\|\|\|\|\|@LB@ UUGUCUG GUCU UUACUGCCAUU@LB@3'-UUU...CCCAU UAA UUAC AUUUA...UCG-5'@LB@ \| \|@LB@ 53 23@LB@@LB@@LB@Energy -12.98 kcal/mol@LB@Hybridization Energy -23.6136 kcal/mol@LB@Unfolding Energy - mRNA 4.33145 kcal/mol@LB@Unfolding Energy - sRNA 6.2974 kcal/mol@LB@@LB@Position - mRNA 168 -- 195@LB@Position - sRNA 24 -- 52@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 24 -- 30@LB@
155	0.02521	0.526	b4208	cycA	-8.71	0.171102	175 -- 207	24 -- 51	D-alanine/D-serine/glycine transporter	_____________174________________________________208\n_____________\|__________________________________\|\n5'-AUU...ACAAC_______GGUA__________AAAAAC_______AUCAG...UUG-3'\n______________ACAGACA____CAGGAA_GAA______AUGGUAG\n______________\|\|\|\|\|\|\|____\|\|\|:\|\|_\|\|\|______\|:\|\|\|\|:\n______________UGUCUGU____GUCUUU_CUU______UGCCAUU\n3'-UUU...CCAUU_______AA________A___AC___________AUUUA...UCG-5'\n_____________\|__________________________________\|\n_____________52_________________________________23\n	201 -- 207	24 -- 30	-19.5671 kcal/mol	4.55835 kcal/mol	6.29692 kcal/mol	174 208@LB@ \| \|@LB@5'-AUU...ACAAC GGUA AAAAAC AUCAG...UUG-3'@LB@ ACAGACA CAGGAA GAA AUGGUAG@LB@ \|\|\|\|\|\|\| \|\|\|:\|\| \|\|\| \|:\|\|\|\|:@LB@ UGUCUGU GUCUUU CUU UGCCAUU@LB@3'-UUU...CCAUU AA A AC AUUUA...UCG-5'@LB@ \| \|@LB@ 52 23@LB@@LB@@LB@Energy -8.71 kcal/mol@LB@Hybridization Energy -19.5671 kcal/mol@LB@Unfolding Energy - mRNA 4.55835 kcal/mol@LB@Unfolding Energy - sRNA 6.29692 kcal/mol@LB@@LB@Position - mRNA 175 -- 207@LB@Position - sRNA 24 -- 51@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 24 -- 30@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:

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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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