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	Additional homologs
111	0.004903	0.1545	b1735	chbR	-11.17	0.151186	109 -- 138	30 -- 50	repressor of chb operon for N N'-diacetylchitobiose utilization		_____________108____________________________139\n_____________\|______________________________\|\n5'-GAU...GUCCA________AUCAUUUAAU__CG________UGCGC...CUG-3'\n______________CGCUCAGG__________GA__UCCAUGCU\n______________\|:\|\|\|\|\|\|__________\|\|__\|\|\|\|\|\|\|\|\n______________GUGAGUCC__________CU__AGGUACGA\n3'-UUU...ACAAA________C___________AA________AUAUU...GCA-5'\n_____________\|______________________________\|\n_____________51_____________________________29\n	132 -- 138	30 -- 36	-23.5874 kcal/mol	7.28235 kcal/mol	5.13509 kcal/mol	108 139@LB@ \| \|@LB@5'-GAU...GUCCA AUCAUUUAAU CG UGCGC...CUG-3'@LB@ CGCUCAGG GA UCCAUGCU@LB@ \|:\|\|\|\|\|\| \|\| \|\|\|\|\|\|\|\|@LB@ GUGAGUCC CU AGGUACGA@LB@3'-UUU...ACAAA C AA AUAUU...GCA-5'@LB@ \| \|@LB@ 51 29@LB@@LB@@LB@Energy -11.17 kcal/mol@LB@Hybridization Energy -23.5874 kcal/mol@LB@Unfolding Energy - mRNA 7.28235 kcal/mol@LB@Unfolding Energy - sRNA 5.13509 kcal/mol@LB@@LB@Position - mRNA 109 -- 138@LB@Position - sRNA 30 -- 50@LB@Position Seed - mRNA 132 -- 138@LB@Position Seed - sRNA 30 -- 36@LB@
198	0.01016	0.1776	b1764	selD	-10.66	0.187945	118 -- 146	45 -- 71	selenophosphate synthase		_____________117___________________________147\n_____________\|_____________________________\|\n5'-UUU...AGCAA_G______G_____AGACACUC_______UCACU...AGC-3'\n______________A_GCGCAG_AAUUC________UCACUUA\n______________\|_:\|:\|\|\|_\|\|\|\|\|________\|\|\|\|\|:\|\n______________U_UGUGUC_UUAAG________AGUGAGU\n3'-UUU...UCUGA_G______G_____CAACAA_________CCCCU...GCA-5'\n_____________\|_____________________________\|\n_____________72____________________________44\n	140 -- 146	45 -- 51	-20.1282 kcal/mol	5.75637 kcal/mol	3.71323 kcal/mol	117 147@LB@ \| \|@LB@5'-UUU...AGCAA G G AGACACUC UCACU...AGC-3'@LB@ A GCGCAG AAUUC UCACUUA@LB@ \| :\|:\|\|\| \|\|\|\|\| \|\|\|\|\|:\|@LB@ U UGUGUC UUAAG AGUGAGU@LB@3'-UUU...UCUGA G G CAACAA CCCCU...GCA-5'@LB@ \| \|@LB@ 72 44@LB@@LB@@LB@Energy -10.66 kcal/mol@LB@Hybridization Energy -20.1282 kcal/mol@LB@Unfolding Energy - mRNA 5.75637 kcal/mol@LB@Unfolding Energy - sRNA 3.71323 kcal/mol@LB@@LB@Position - mRNA 118 -- 146@LB@Position - sRNA 45 -- 71@LB@Position Seed - mRNA 140 -- 146@LB@Position Seed - sRNA 45 -- 51@LB@
27	0.0003358	0.04376	b1784	yeaH	-12.48	0.082239	130 -- 197	41 -- 99	UPF0229 family protein		_____________129___________________________________________________________________198\n_____________\|_____________________________________________________________________\|\n5'-UGU...ACGAC___GAAC______CCUG___A_C_____CAC____GUA_________UGGCAAA___AG___G______CAUAU...CGA-3'\n______________AGC____CGUGGG____AGA_G_GGCAA___AGGC___GCAUACAGU_______UGU__UAC__GGGGG\n______________\|\|\|____\|\|\|\|\|\|____\|\|\|_\|_\|\|\|\|\|___\|\|:\|___:\|\|:\|\|\|\|:_______\|\|\|__:\|\|__:\|\|\|\|\n______________UCG____GCACCC____UCU_C_CCGUU___UCUG___UGUGUGUCG_______ACA__GUG__UCCCC\n_____3'-UUUUUU___GGUA_____________A______________A___________UUAAGCA___AA___AG_____UAAAG...GCA-5'\n_____________\|_____________________________________________________________________\|\n_____________100___________________________________________________________________40\n	170 -- 176	63 -- 69	-48.2653 kcal/mol	18.2122 kcal/mol	17.5731 kcal/mol	129 198@LB@ \| \|@LB@5'-UGU...ACGAC GAAC CCUG A C CAC GUA UGGCAAA AG G CAUAU...CGA-3'@LB@ AGC CGUGGG AGA G GGCAA AGGC GCAUACAGU UGU UAC GGGGG@LB@ \|\|\| \|\|\|\|\|\| \|\|\| \| \|\|\|\|\| \|\|:\| :\|\|:\|\|\|\|: \|\|\| :\|\| :\|\|\|\|@LB@ UCG GCACCC UCU C CCGUU UCUG UGUGUGUCG ACA GUG UCCCC@LB@ 3'-UUUUUU GGUA A A UUAAGCA AA AG UAAAG...GCA-5'@LB@ \| \|@LB@ 100 40@LB@@LB@@LB@Energy -12.48 kcal/mol@LB@Hybridization Energy -48.2653 kcal/mol@LB@Unfolding Energy - mRNA 18.2122 kcal/mol@LB@Unfolding Energy - sRNA 17.5731 kcal/mol@LB@@LB@Position - mRNA 130 -- 197@LB@Position - sRNA 41 -- 99@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 63 -- 69@LB@
94	0.004209	0.1538	b1798	leuE	-8.23	0.450453	21 -- 61	47 -- 73	leucine efflux protein		_____________20_________________________________________62\n_____________\|__________________________________________\|\n5'-UGC...AAUUU____________U____CC_AGCACUACCCGAAUU_______GGAGC...AAA-3'\n______________UUACGC_CAGUA_UUUG__G_______________UUUCACU\n______________:\|\|\|:\|_\|\|\|:\|_\|\|:\|__\|_______________\|\|\|\|\|\|\|\n______________GAUGUG_GUCGU_AAGC__C_______________AAAGUGA\n3'-UUU...UUUCU______U_____U____AA_______________________GUCCC...GCA-5'\n_____________\|__________________________________________\|\n_____________74_________________________________________46\n	55 -- 61	47 -- 53	-16.3548 kcal/mol	4.43937 kcal/mol	3.69006 kcal/mol	20 62@LB@ \| \|@LB@5'-UGC...AAUUU U CC AGCACUACCCGAAUU GGAGC...AAA-3'@LB@ UUACGC CAGUA UUUG G UUUCACU@LB@ :\|\|\|:\| \|\|\|:\| \|\|:\| \| \|\|\|\|\|\|\|@LB@ GAUGUG GUCGU AAGC C AAAGUGA@LB@3'-UUU...UUUCU U U AA GUCCC...GCA-5'@LB@ \| \|@LB@ 74 46@LB@@LB@@LB@Energy -8.23 kcal/mol@LB@Hybridization Energy -16.3548 kcal/mol@LB@Unfolding Energy - mRNA 4.43937 kcal/mol@LB@Unfolding Energy - sRNA 3.69006 kcal/mol@LB@@LB@Position - mRNA 21 -- 61@LB@Position - sRNA 47 -- 73@LB@Position Seed - mRNA 55 -- 61@LB@Position Seed - sRNA 47 -- 53@LB@
52	0.001789	0.121	b1799	dmlR	-11.56	0.127346	72 -- 108	34 -- 68	transcriptional activator of dmlA	b3060	_____________71_______________________________________109\n_____________\|________________________________________\|\n5'-CGC...GGGAU_________ACGCA_______________UU_____C___CUUCC...CGG-3'\n______________CGCAGCAAU_____UCGU__UUUCA_UCA__GGGUU_UCA\n______________\|:\|\|\|\|\|\|\|_____\|\|\|\|__\|\|\|\|\|_\|\|\|__\|\|:\|\|_:\|\|\n______________GUGUCGUUA_____AGCA__AAAGU_AGU__CCUAA_GGU\n3'-UUU...GAUGU__________________AC_____G___CC_____A___ACGAA...GCA-5'\n_____________\|________________________________________\|\n_____________69_______________________________________33\n	74 -- 80	60 -- 66	-24.8584 kcal/mol	8.52016 kcal/mol	4.78423 kcal/mol	71 109@LB@ \| \|@LB@5'-CGC...GGGAU ACGCA UU C CUUCC...CGG-3'@LB@ CGCAGCAAU UCGU UUUCA UCA GGGUU UCA@LB@ \|:\|\|\|\|\|\|\| \|\|\|\| \|\|\|\|\| \|\|\| \|\|:\|\| :\|\|@LB@ GUGUCGUUA AGCA AAAGU AGU CCUAA GGU@LB@3'-UUU...GAUGU AC G CC A ACGAA...GCA-5'@LB@ \| \|@LB@ 69 33@LB@@LB@@LB@Energy -11.56 kcal/mol@LB@Hybridization Energy -24.8584 kcal/mol@LB@Unfolding Energy - mRNA 8.52016 kcal/mol@LB@Unfolding Energy - sRNA 4.78423 kcal/mol@LB@@LB@Position - mRNA 72 -- 108@LB@Position - sRNA 34 -- 68@LB@Position Seed - mRNA 74 -- 80@LB@Position Seed - sRNA 60 -- 66@LB@
79	0.00332	0.1462	b1845	ptrB	-10.90	0.169644	42 -- 70	35 -- 70	protease II		_____________41____________________________________71\n_____________\|_____________________________________\|\n5'-UCU...AGAAU________C_____AA____________CU_______UCUGU...AGC-3'\n______________CGCACAGC_AUUUG__________CAGG__GAUUUUC\n______________\|:\|\|\|\|\|\|_\|\|\|:\|__________\|\|\|\|__\|\|\|\|\|:\|\n______________GUGUGUCG_UAAGC__________GUCC__CUAAAGG\n3'-UUU...CUGAU________U_____AACAAAGUGA____C________UACGA...GCA-5'\n_____________\|_____________________________________\|\n_____________71____________________________________34\n	64 -- 70	35 -- 41	-24.5069 kcal/mol	8.82337 kcal/mol	4.7817 kcal/mol	41 71@LB@ \| \|@LB@5'-UCU...AGAAU C AA CU UCUGU...AGC-3'@LB@ CGCACAGC AUUUG CAGG GAUUUUC@LB@ \|:\|\|\|\|\|\| \|\|\|:\| \|\|\|\| \|\|\|\|\|:\|@LB@ GUGUGUCG UAAGC GUCC CUAAAGG@LB@3'-UUU...CUGAU U AACAAAGUGA C UACGA...GCA-5'@LB@ \| \|@LB@ 71 34@LB@@LB@@LB@Energy -10.90 kcal/mol@LB@Hybridization Energy -24.5069 kcal/mol@LB@Unfolding Energy - mRNA 8.82337 kcal/mol@LB@Unfolding Energy - sRNA 4.7817 kcal/mol@LB@@LB@Position - mRNA 42 -- 70@LB@Position - sRNA 35 -- 70@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 35 -- 41@LB@
7	1.819e-05	0.009142	b1849	purT	-22.68	0.000026	168 -- 199	33 -- 74	phosphoribosylglycinamide formyltransferase 2		_____________167________________________________________200\n_____________\|__________________________________________\|\n5'-UUU...UUUAU________________AA__________________A_____UAUGA...GUC-3'\n______________ACUGCGCGCGG_AAUU___________UCAGGGGAU_UUCGU\n______________\|\|\|:\|:\|:\|:\|_\|\|\|\|___________\|\|\|\|\|\|\|\|\|_\|:\|:\|\n______________UGAUGUGUGUC_UUAA___________AGUCCCCUA_AGGUA\n3'-UUU...GUUUC___________G____GCAACAAAGUG_________A_____CGAAU...GCA-5'\n_____________\|__________________________________________\|\n_____________75_________________________________________32\n	187 -- 193	39 -- 45	-34.2979 kcal/mol	6.80622 kcal/mol	4.81602 kcal/mol	167 200@LB@ \| \|@LB@5'-UUU...UUUAU AA A UAUGA...GUC-3'@LB@ ACUGCGCGCGG AAUU UCAGGGGAU UUCGU@LB@ \|\|\|:\|:\|:\|:\| \|\|\|\| \|\|\|\|\|\|\|\|\| \|:\|:\|@LB@ UGAUGUGUGUC UUAA AGUCCCCUA AGGUA@LB@3'-UUU...GUUUC G GCAACAAAGUG A CGAAU...GCA-5'@LB@ \| \|@LB@ 75 32@LB@@LB@@LB@Energy -22.68 kcal/mol@LB@Hybridization Energy -34.2979 kcal/mol@LB@Unfolding Energy - mRNA 6.80622 kcal/mol@LB@Unfolding Energy - sRNA 4.81602 kcal/mol@LB@@LB@Position - mRNA 168 -- 199@LB@Position - sRNA 33 -- 74@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 39 -- 45@LB@
17	0.0001292	0.02674	b1854	pykA	-13.69	0.043994	133 -- 157	36 -- 68	pyruvate kinase II		_____________132_______________________________158\n_____________\|_________________________________\|\n5'-GAA...GCCAU______________A__________________AUGUU...ACG-3'\n______________CGCGGC_____GUU_UUUCAUUC___GGAUUUC\n______________\|:\|:\|\|_____\|\|\|_\|\|\|\|\|:\|\|___\|\|\|\|\|\|\|\n______________GUGUCG_____CAA_AAAGUGAG___CCUAAAG\n3'-UUU...GAUGU______UUAAG___C________UCC_______GUACG...GCA-5'\n_____________\|_________________________________\|\n_____________69________________________________35\n	151 -- 157	36 -- 42	-24.2432 kcal/mol	5.79946 kcal/mol	4.75078 kcal/mol	132 158@LB@ \| \|@LB@5'-GAA...GCCAU A AUGUU...ACG-3'@LB@ CGCGGC GUU UUUCAUUC GGAUUUC@LB@ \|:\|:\|\| \|\|\| \|\|\|\|\|:\|\| \|\|\|\|\|\|\|@LB@ GUGUCG CAA AAAGUGAG CCUAAAG@LB@3'-UUU...GAUGU UUAAG C UCC GUACG...GCA-5'@LB@ \| \|@LB@ 69 35@LB@@LB@@LB@Energy -13.69 kcal/mol@LB@Hybridization Energy -24.2432 kcal/mol@LB@Unfolding Energy - mRNA 5.79946 kcal/mol@LB@Unfolding Energy - sRNA 4.75078 kcal/mol@LB@@LB@Position - mRNA 133 -- 157@LB@Position - sRNA 36 -- 68@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 36 -- 42@LB@
147	0.006785	0.1624	b1920	fliY	-15.06	0.020217	159 -- 198	40 -- 75	cystine transporter subunit		_____________158______________________________________199\n_____________\|________________________________________\|\n5'-CCA...ACAAU____C_____U____ACAGACAUAACAA_________U__AUAUG...UGC-3'\n______________GGCU_UACAC_GCAA_____________CAUUCGGGG_GA\n______________\|:\|\|_:\|\|\|\|_\|\|\|\|_____________\|\|:\|\|:\|\|\|_\|\|\n______________CUGA_GUGUG_CGUU_____________GUGAGUCCC_CU\n3'-UUU...CGUUU____U_____U____AAGCAACAAA_______________AAAGG...GCA-5'\n_____________\|________________________________________\|\n_____________76_______________________________________39\n	189 -- 195	42 -- 48	-27.6268 kcal/mol	7.79206 kcal/mol	4.77786 kcal/mol	158 199@LB@ \| \|@LB@5'-CCA...ACAAU C U ACAGACAUAACAA U AUAUG...UGC-3'@LB@ GGCU UACAC GCAA CAUUCGGGG GA@LB@ \|:\|\| :\|\|\|\| \|\|\|\| \|\|:\|\|:\|\|\| \|\|@LB@ CUGA GUGUG CGUU GUGAGUCCC CU@LB@3'-UUU...CGUUU U U AAGCAACAAA AAAGG...GCA-5'@LB@ \| \|@LB@ 76 39@LB@@LB@@LB@Energy -15.06 kcal/mol@LB@Hybridization Energy -27.6268 kcal/mol@LB@Unfolding Energy - mRNA 7.79206 kcal/mol@LB@Unfolding Energy - sRNA 4.77786 kcal/mol@LB@@LB@Position - mRNA 159 -- 198@LB@Position - sRNA 40 -- 75@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 42 -- 48@LB@
13	0.0001005	0.0245	b1921	fliZ	-13.92	0.038869	246 -- 263	63 -- 78	RpoS antagonist; putative regulator of FliA activity		_____________245________________264\n_____________\|__________________\|\n5'-UGC...AUCUU_______UUAA_______CAGAC...AUC-3'\n______________AAAGACU____ACACAGC\n______________\|\|\|\|\|\|\|____\|\|\|\|\|\|\|\n______________UUUCUGA____UGUGUCG\n3'-UUU...ACCCG_______UG_________UUAAG...GCA-5'\n_____________\|__________________\|\n_____________79_________________62\n	257 -- 263	63 -- 69	-17.8578 kcal/mol	0.69523 kcal/mol	3.24195 kcal/mol	245 264@LB@ \| \|@LB@5'-UGC...AUCUU UUAA CAGAC...AUC-3'@LB@ AAAGACU ACACAGC@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UUUCUGA UGUGUCG@LB@3'-UUU...ACCCG UG UUAAG...GCA-5'@LB@ \| \|@LB@ 79 62@LB@@LB@@LB@Energy -13.92 kcal/mol@LB@Hybridization Energy -17.8578 kcal/mol@LB@Unfolding Energy - mRNA 0.69523 kcal/mol@LB@Unfolding Energy - sRNA 3.24195 kcal/mol@LB@@LB@Position - mRNA 246 -- 263@LB@Position - sRNA 63 -- 78@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 63 -- 69@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

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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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