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
61	0.002486	0.1417	b1487	ddpA	-13.46	0.049908	168 -- 192	43 -- 71	D D-dipeptide ABC transporter periplasmic binding protein	_____________167___________________________193\n_____________\|_____________________________\|\n5'-UCA...CCCUG________________CAG____A_____AAACU...UGA-3'\n______________GCACACAGCA___CGU____UUA_UCAGG\n______________:\|\|\|\|\|\|\|\|\|___\|\|\|____\|:\|_\|\|\|\|\|\n______________UGUGUGUCGU___GCA____AGU_AGUCC\n3'-UUU...UCUGA__________UAA___ACAA___G_____CCUAA...GCA-5'\n_____________\|_____________________________\|\n_____________72____________________________42\n	171 -- 177	62 -- 68	-25.043 kcal/mol	7.26137 kcal/mol	4.32409 kcal/mol	167 193@LB@ \| \|@LB@5'-UCA...CCCUG CAG A AAACU...UGA-3'@LB@ GCACACAGCA CGU UUA UCAGG@LB@ :\|\|\|\|\|\|\|\|\| \|\|\| \|:\| \|\|\|\|\|@LB@ UGUGUGUCGU GCA AGU AGUCC@LB@3'-UUU...UCUGA UAA ACAA G CCUAA...GCA-5'@LB@ \| \|@LB@ 72 42@LB@@LB@@LB@Energy -13.46 kcal/mol@LB@Hybridization Energy -25.043 kcal/mol@LB@Unfolding Energy - mRNA 7.26137 kcal/mol@LB@Unfolding Energy - sRNA 4.32409 kcal/mol@LB@@LB@Position - mRNA 168 -- 192@LB@Position - sRNA 43 -- 71@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 62 -- 68@LB@
64	0.002655	0.1417	b0876	ybjD	-10.33	0.215429	171 -- 200	39 -- 78	putative OLD family ATP-dependent endonuclease; DUF2813 family protein	_____________170________________________________________201\n_____________\|__________________________________________\|\n5'-CGU...GCGUA______AAGU_____________________UGG________AUGAU...GGG-3'\n______________AAGGAU____CACAUA___________UUUC____AGGGGAU\n______________\|\|:\|\|:____\|\|\|\|:\|___________\|\|\|\|____\|\|\|\|\|\|\|\n______________UUUCUG____GUGUGU___________AAAG____UCCCCUA\n3'-UUU...ACCCG______AU________CGUUAAGCAAC____UGAG_______AAGGU...GCA-5'\n_____________\|__________________________________________\|\n_____________79_________________________________________38\n	194 -- 200	39 -- 45	-20.0974 kcal/mol	4.99339 kcal/mol	4.77966 kcal/mol	170 201@LB@ \| \|@LB@5'-CGU...GCGUA AAGU UGG AUGAU...GGG-3'@LB@ AAGGAU CACAUA UUUC AGGGGAU@LB@ \|\|:\|\|: \|\|\|\|:\| \|\|\|\| \|\|\|\|\|\|\|@LB@ UUUCUG GUGUGU AAAG UCCCCUA@LB@3'-UUU...ACCCG AU CGUUAAGCAAC UGAG AAGGU...GCA-5'@LB@ \| \|@LB@ 79 38@LB@@LB@@LB@Energy -10.33 kcal/mol@LB@Hybridization Energy -20.0974 kcal/mol@LB@Unfolding Energy - mRNA 4.99339 kcal/mol@LB@Unfolding Energy - sRNA 4.77966 kcal/mol@LB@@LB@Position - mRNA 171 -- 200@LB@Position - sRNA 39 -- 78@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 39 -- 45@LB@
20	0.0001757	0.02926	b4175	hflC	-15.67	0.013919	175 -- 193	40 -- 75	HflB protease modulator specific for phage lambda cII repressor	_____________174__________________________________194\n_____________\|____________________________________\|\n5'-UUA...GUAAC____________________________________AAUAA...GUU-3'\n______________GACUAC___CAGCG______________UCAGGGGG\n______________\|\|\|\|\|\|___\|\|\|\|:______________\|\|\|\|\|\|\|:\n______________CUGAUG___GUCGU______________AGUCCCCU\n3'-UUU...CGUUU______UGU_____UAAGCAACAAAGUG________AAAGG...GCA-5'\n_____________\|____________________________________\|\n_____________76___________________________________39\n	187 -- 193	40 -- 46	-24.7611 kcal/mol	4.31935 kcal/mol	4.77786 kcal/mol	174 194@LB@ \| \|@LB@5'-UUA...GUAAC AAUAA...GUU-3'@LB@ GACUAC CAGCG UCAGGGGG@LB@ \|\|\|\|\|\| \|\|\|\|: \|\|\|\|\|\|\|:@LB@ CUGAUG GUCGU AGUCCCCU@LB@3'-UUU...CGUUU UGU UAAGCAACAAAGUG AAAGG...GCA-5'@LB@ \| \|@LB@ 76 39@LB@@LB@@LB@Energy -15.67 kcal/mol@LB@Hybridization Energy -24.7611 kcal/mol@LB@Unfolding Energy - mRNA 4.31935 kcal/mol@LB@Unfolding Energy - sRNA 4.77786 kcal/mol@LB@@LB@Position - mRNA 175 -- 193@LB@Position - sRNA 40 -- 75@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 40 -- 46@LB@
37	0.0006599	0.0618	b3399	yrfG	-16.99	0.005777	176 -- 197	35 -- 56	GMP/IMP nucleotidase	_____________175____________________198\n_____________\|______________________\|\n5'-UAG...GCAAA___C_______U__A_______CUCAU...AGC-3'\n______________UUG_UUCACUC_GG_GAUUUCC\n______________\|\|\|_\|\|\|\|\|\|\|_\|\|_\|\|\|\|\|\|\|\n______________AAC_AAGUGAG_CC_CUAAAGG\n3'-UUU...UAAGC___A_______U__C_______UACGA...GCA-5'\n_____________\|______________________\|\n_____________57_____________________34\n	191 -- 197	35 -- 41	-24.095 kcal/mol	5.08619 kcal/mol	2.02101 kcal/mol	175 198@LB@ \| \|@LB@5'-UAG...GCAAA C U A CUCAU...AGC-3'@LB@ UUG UUCACUC GG GAUUUCC@LB@ \|\|\| \|\|\|\|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ AAC AAGUGAG CC CUAAAGG@LB@3'-UUU...UAAGC A U C UACGA...GCA-5'@LB@ \| \|@LB@ 57 34@LB@@LB@@LB@Energy -16.99 kcal/mol@LB@Hybridization Energy -24.095 kcal/mol@LB@Unfolding Energy - mRNA 5.08619 kcal/mol@LB@Unfolding Energy - sRNA 2.02101 kcal/mol@LB@@LB@Position - mRNA 176 -- 197@LB@Position - sRNA 35 -- 56@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 35 -- 41@LB@
70	0.002881	0.1417	b4144	yjeI	-14.17	0.033933	177 -- 235	31 -- 99	DUF4156 family lipoprotein	_____________176______________________________________________________________________236\n_____________\|________________________________________________________________________\|\n5'-GCA...CGUCC_________AUU________G__UA______________AA_______________CA______G__G____CGCGC...GCA-3'\n______________AGCUCAUUG______AUGGG_AA__AC_AUGCAC_GUAA__________UACUUAG__GGGAUU_UC_GUGC\n______________\|\|\|:\|\|\|:\|______\|\|\|\|\|_\|\|__\|\|_\|::\|\|\|_\|:\|\|__________:\|\|\|:\|\|__\|\|\|\|\|\|_\|\|_:\|\|\|\n______________UCGGGUAGC______UACCC_UU__UG_UGUGUG_CGUU__________GUGAGUC__CCCUAA_AG_UACG\n_____3'-UUUUUU_________ACCCUC_____G__UC__A______U____AAGCAACAAA__________________G____AAUAU...GCA-5'\n_____________\|________________________________________________________________________\|\n_____________100______________________________________________________________________30\n	213 -- 219	44 -- 50	-46.9384 kcal/mol	12.7048 kcal/mol	20.0691 kcal/mol	176 236@LB@ \| \|@LB@5'-GCA...CGUCC AUU G UA AA CA G G CGCGC...GCA-3'@LB@ AGCUCAUUG AUGGG AA AC AUGCAC GUAA UACUUAG GGGAUU UC GUGC@LB@ \|\|\|:\|\|\|:\| \|\|\|\|\| \|\| \|\| \|::\|\|\| \|:\|\| :\|\|\|:\|\| \|\|\|\|\|\| \|\| :\|\|\|@LB@ UCGGGUAGC UACCC UU UG UGUGUG CGUU GUGAGUC CCCUAA AG UACG@LB@ 3'-UUUUUU ACCCUC G UC A U AAGCAACAAA G AAUAU...GCA-5'@LB@ \| \|@LB@ 100 30@LB@@LB@@LB@Energy -14.17 kcal/mol@LB@Hybridization Energy -46.9384 kcal/mol@LB@Unfolding Energy - mRNA 12.7048 kcal/mol@LB@Unfolding Energy - sRNA 20.0691 kcal/mol@LB@@LB@Position - mRNA 177 -- 235@LB@Position - sRNA 31 -- 99@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 44 -- 50@LB@
171	0.008374	0.1723	b4485	ytfR	-15.31	0.017344	177 -- 203	32 -- 71	putative sugar ABC transporter ATPase	_____________176_______________________________________204\n_____________\|_________________________________________\|\n5'-CCU...UGGGA_____________________A___________AA______ACGAC...GCC-3'\n______________GCACGC____________UUU_CAC_CGGGGGA___CCAUG\n______________:\|\|\|:\|____________\|\|\|_\|\|\|_\|:\|\|\|\|\|___\|\|\|\|\|\n______________UGUGUG____________AAA_GUG_GUCCCCU___GGUAC\n3'-UUU...UCUGA______UCGUUAAGCAAC_______A_______AAA_____GAAUA...GCA-5'\n_____________\|_________________________________________\|\n_____________72________________________________________31\n	190 -- 196	40 -- 46	-27.8319 kcal/mol	5.2959 kcal/mol	7.22604 kcal/mol	176 204@LB@ \| \|@LB@5'-CCU...UGGGA A AA ACGAC...GCC-3'@LB@ GCACGC UUU CAC CGGGGGA CCAUG@LB@ :\|\|\|:\| \|\|\| \|\|\| \|:\|\|\|\|\| \|\|\|\|\|@LB@ UGUGUG AAA GUG GUCCCCU GGUAC@LB@3'-UUU...UCUGA UCGUUAAGCAAC A AAA GAAUA...GCA-5'@LB@ \| \|@LB@ 72 31@LB@@LB@@LB@Energy -15.31 kcal/mol@LB@Hybridization Energy -27.8319 kcal/mol@LB@Unfolding Energy - mRNA 5.2959 kcal/mol@LB@Unfolding Energy - sRNA 7.22604 kcal/mol@LB@@LB@Position - mRNA 177 -- 203@LB@Position - sRNA 32 -- 71@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 40 -- 46@LB@
170	0.008354	0.1723	b3294	rplQ	-12.86	0.068031	178 -- 204	31 -- 54	50S ribosomal subunit protein L17	_____________177_________________________205\n_____________\|___________________________\|\n5'-UAU...UUAAG________G__AA____AAGG______GCCAU...UCA-3'\n______________GUUUUACU_AG__GGAU____UCAUGC\n______________\|\|\|\|:\|\|\|_\|\|__\|\|\|\|____:\|\|\|\|\|\n______________CAAAGUGA_UC__CCUA____GGUACG\n3'-UUU...AGCAA________G__C_____AA________AAUAU...GCA-5'\n_____________\|___________________________\|\n_____________55__________________________30\n	179 -- 185	47 -- 53	-21.6424 kcal/mol	4.376 kcal/mol	4.40484 kcal/mol	177 205@LB@ \| \|@LB@5'-UAU...UUAAG G AA AAGG GCCAU...UCA-3'@LB@ GUUUUACU AG GGAU UCAUGC@LB@ \|\|\|\|:\|\|\| \|\| \|\|\|\| :\|\|\|\|\|@LB@ CAAAGUGA UC CCUA GGUACG@LB@3'-UUU...AGCAA G C AA AAUAU...GCA-5'@LB@ \| \|@LB@ 55 30@LB@@LB@@LB@Energy -12.86 kcal/mol@LB@Hybridization Energy -21.6424 kcal/mol@LB@Unfolding Energy - mRNA 4.376 kcal/mol@LB@Unfolding Energy - sRNA 4.40484 kcal/mol@LB@@LB@Position - mRNA 178 -- 204@LB@Position - sRNA 31 -- 54@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 47 -- 53@LB@
135	0.006184	0.1605	b0637	rsfS	-13.92	0.038847	179 -- 195	40 -- 56	ribosomal silencing factor	_____________178_______________196\n_____________\|_________________\|\n5'-AUU...UCUAU___A_____C_______AAAAC...UCA-3'\n______________UUG_UUCAC_CAGGGGG\n______________\|\|\|_\|\|\|\|\|_\|\|\|\|\|\|:\n______________AAC_AAGUG_GUCCCCU\n3'-UUU...UAAGC___A_____A_______AAAGG...GCA-5'\n_____________\|_________________\|\n_____________57________________39\n	189 -- 195	40 -- 46	-20.5369 kcal/mol	4.69018 kcal/mol	1.92548 kcal/mol	178 196@LB@ \| \|@LB@5'-AUU...UCUAU A C AAAAC...UCA-3'@LB@ UUG UUCAC CAGGGGG@LB@ \|\|\| \|\|\|\|\| \|\|\|\|\|\|:@LB@ AAC AAGUG GUCCCCU@LB@3'-UUU...UAAGC A A AAAGG...GCA-5'@LB@ \| \|@LB@ 57 39@LB@@LB@@LB@Energy -13.92 kcal/mol@LB@Hybridization Energy -20.5369 kcal/mol@LB@Unfolding Energy - mRNA 4.69018 kcal/mol@LB@Unfolding Energy - sRNA 1.92548 kcal/mol@LB@@LB@Position - mRNA 179 -- 195@LB@Position - sRNA 40 -- 56@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 40 -- 46@LB@
73	0.00298	0.1437	b0474	adk	-13.48	0.049381	180 -- 198	34 -- 50	adenylate kinase	_____________179_________________199\n_____________\|___________________\|\n5'-ACC...CGACA_____UA____________CAAUG...AUA-3'\n______________CAUUU__AGGGGAUUUUCG\n______________\|\|:\|:__\|\|\|\|\|\|\|\|\|:\|:\n______________GUGAG__UCCCCUAAAGGU\n3'-UUU...ACAAA___________________ACGAA...GCA-5'\n_____________\|___________________\|\n_____________51__________________33\n	191 -- 197	35 -- 41	-19.9961 kcal/mol	4.64453 kcal/mol	1.87382 kcal/mol	179 199@LB@ \| \|@LB@5'-ACC...CGACA UA CAAUG...AUA-3'@LB@ CAUUU AGGGGAUUUUCG@LB@ \|\|:\|: \|\|\|\|\|\|\|\|\|:\|:@LB@ GUGAG UCCCCUAAAGGU@LB@3'-UUU...ACAAA ACGAA...GCA-5'@LB@ \| \|@LB@ 51 33@LB@@LB@@LB@Energy -13.48 kcal/mol@LB@Hybridization Energy -19.9961 kcal/mol@LB@Unfolding Energy - mRNA 4.64453 kcal/mol@LB@Unfolding Energy - sRNA 1.87382 kcal/mol@LB@@LB@Position - mRNA 180 -- 198@LB@Position - sRNA 34 -- 50@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 35 -- 41@LB@
174	0.008627	0.1745	b1926	fliT	-7.57	0.540698	180 -- 211	31 -- 53	putative flagellar synthesis and assembly chaperone	_____________179______________________________212\n_____________\|________________________________\|\n5'-GUG...CCUUC___G_______ACCCAGUCU___GAA______ACCGC...UCA-3'\n______________UUU_AUUCAGG_________GAU___CCAUGC\n______________\|\|\|_\|:\|\|\|\|\|_________\|\|\|___\|\|\|\|\|\|\n______________AAA_UGAGUCC_________CUA___GGUACG\n3'-UUU...GCAAC___G_______C___________AA_______AAUAU...GCA-5'\n_____________\|________________________________\|\n_____________54_______________________________30\n	184 -- 190	43 -- 49	-18.5651 kcal/mol	6.60729 kcal/mol	4.38339 kcal/mol	179 212@LB@ \| \|@LB@5'-GUG...CCUUC G ACCCAGUCU GAA ACCGC...UCA-3'@LB@ UUU AUUCAGG GAU CCAUGC@LB@ \|\|\| \|:\|\|\|\|\| \|\|\| \|\|\|\|\|\|@LB@ AAA UGAGUCC CUA GGUACG@LB@3'-UUU...GCAAC G C AA AAUAU...GCA-5'@LB@ \| \|@LB@ 54 30@LB@@LB@@LB@Energy -7.57 kcal/mol@LB@Hybridization Energy -18.5651 kcal/mol@LB@Unfolding Energy - mRNA 6.60729 kcal/mol@LB@Unfolding Energy - sRNA 4.38339 kcal/mol@LB@@LB@Position - mRNA 180 -- 211@LB@Position - sRNA 31 -- 53@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 43 -- 49@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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