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
21	0.0001827	0.02926	b1937	fliE	-13.91	0.039102	192 -- 221	38 -- 77	flagellar basal-body component	_____________191________________________________________222\n_____________\|__________________________________________\|\n5'-CUG...UCCGG_____GAGA___U_______A_____________________GAAGG...GUU-3'\n______________GAGAC____AUG_CAGCGAU_____________CAGGGGAUU\n______________:\|\|\|\|____\|::_\|\|\|\|:\|\|_____________\|\|\|\|\|\|\|\|\|\n______________UUCUG____UGU_GUCGUUA_____________GUCCCCUAA\n3'-UUU...CCCGU_____AUG____________AGCAACAAAGUGA_________AGGUA...GCA-5'\n_____________\|__________________________________________\|\n_____________78_________________________________________37\n	215 -- 221	38 -- 44	-25.7557 kcal/mol	7.06678 kcal/mol	4.77969 kcal/mol	191 222@LB@ \| \|@LB@5'-CUG...UCCGG GAGA U A GAAGG...GUU-3'@LB@ GAGAC AUG CAGCGAU CAGGGGAUU@LB@ :\|\|\|\| \|:: \|\|\|\|:\|\| \|\|\|\|\|\|\|\|\|@LB@ UUCUG UGU GUCGUUA GUCCCCUAA@LB@3'-UUU...CCCGU AUG AGCAACAAAGUGA AGGUA...GCA-5'@LB@ \| \|@LB@ 78 37@LB@@LB@@LB@Energy -13.91 kcal/mol@LB@Hybridization Energy -25.7557 kcal/mol@LB@Unfolding Energy - mRNA 7.06678 kcal/mol@LB@Unfolding Energy - sRNA 4.77969 kcal/mol@LB@@LB@Position - mRNA 192 -- 221@LB@Position - sRNA 38 -- 77@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 38 -- 44@LB@
22	0.0001899	0.02926	b2562	yfhL	-14.77	0.023959	28 -- 42	42 -- 56	putative 4Fe-4S cluster-containing protein	_____________27______________43\n_____________\|_______________\|\n5'-AGC...UCUGC____CA_________AAUGU...UUA-3'\n______________UUGU__CGCUCAGGG\n______________\|\|\|\|__\|:\|\|\|\|\|\|\|\n______________AACA__GUGAGUCCC\n3'-UUU...UAAGC____AA_________CUAAA...GCA-5'\n_____________\|_______________\|\n_____________57______________41\n	36 -- 42	42 -- 48	-19.6539 kcal/mol	2.98712 kcal/mol	1.89561 kcal/mol	27 43@LB@ \| \|@LB@5'-AGC...UCUGC CA AAUGU...UUA-3'@LB@ UUGU CGCUCAGGG@LB@ \|\|\|\| \|:\|\|\|\|\|\|\|@LB@ AACA GUGAGUCCC@LB@3'-UUU...UAAGC AA CUAAA...GCA-5'@LB@ \| \|@LB@ 57 41@LB@@LB@@LB@Energy -14.77 kcal/mol@LB@Hybridization Energy -19.6539 kcal/mol@LB@Unfolding Energy - mRNA 2.98712 kcal/mol@LB@Unfolding Energy - sRNA 1.89561 kcal/mol@LB@@LB@Position - mRNA 28 -- 42@LB@Position - sRNA 42 -- 56@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 42 -- 48@LB@
23	0.0001955	0.02926	b3846	fadB	-13.56	0.047358	39 -- 83	35 -- 77	fused 3-hydroxybutyryl-CoA epimerase/delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase/enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase	_____________38________________________________________________84\n_____________\|_________________________________________________\|\n5'-AGU...ACCUU___U__C_____CUU____CA____________C___A_C_U_______GCCGA...CUG-3'\n______________AAG_CU_CGCAU___AGCA__UCGU____UCAU_CAG_G_G_GAUUUCU\n______________\|\|\|_\|\|_\|:\|\|:___\|\|\|\|__\|\|\|\|____\|\|\|:_\|\|\|_\|_\|_\|\|\|\|\|\|:\n______________UUC_GA_GUGUG___UCGU__AGCA____AGUG_GUC_C_C_CUAAAGG\n3'-UUU...CCCGU___U__U____________UA____ACAA____A_______________UACGA...GCA-5'\n_____________\|_________________________________________________\|\n_____________78________________________________________________34\n	77 -- 83	35 -- 41	-27.7125 kcal/mol	9.35112 kcal/mol	4.80542 kcal/mol	38 84@LB@ \| \|@LB@5'-AGU...ACCUU U C CUU CA C A C U GCCGA...CUG-3'@LB@ AAG CU CGCAU AGCA UCGU UCAU CAG G G GAUUUCU@LB@ \|\|\| \|\| \|:\|\|: \|\|\|\| \|\|\|\| \|\|\|: \|\|\| \| \| \|\|\|\|\|\|:@LB@ UUC GA GUGUG UCGU AGCA AGUG GUC C C CUAAAGG@LB@3'-UUU...CCCGU U U UA ACAA A UACGA...GCA-5'@LB@ \| \|@LB@ 78 34@LB@@LB@@LB@Energy -13.56 kcal/mol@LB@Hybridization Energy -27.7125 kcal/mol@LB@Unfolding Energy - mRNA 9.35112 kcal/mol@LB@Unfolding Energy - sRNA 4.80542 kcal/mol@LB@@LB@Position - mRNA 39 -- 83@LB@Position - sRNA 35 -- 77@LB@Position Seed - mRNA 77 -- 83@LB@Position Seed - sRNA 35 -- 41@LB@
24	0.0002076	0.02926	b3459	panM	-18.00	0.002751	9 -- 48	38 -- 75	PanD autocleavage accelerator panothenate synthesis	_____________8___________________________________________49\n_____________\|___________________________________________\|\n___5'-AAAAUAAC_______A_G___GGAAU_____ACUA________________AUGCU...UUG-3'\n______________GGC_ACA_A_GGC_____AAUUC______UCAUUCAGGGGAUU\n______________\|:\|_\|\|\|_\|_:\|\|_____\|\|\|\|\|______\|\|\|:\|\|\|\|\|\|\|\|\|\|\n______________CUG_UGU_U_UCG_____UUAAG______AGUGAGUCCCCUAA\n3'-UUU...CGUUU___A___G_G_____________CAACAA______________AGGUA...GCA-5'\n_____________\|___________________________________________\|\n_____________76__________________________________________37\n	42 -- 48	38 -- 44	-31.5918 kcal/mol	8.81239 kcal/mol	4.77946 kcal/mol	8 49@LB@ \| \|@LB@ 5'-AAAAUAAC A G GGAAU ACUA AUGCU...UUG-3'@LB@ GGC ACA A GGC AAUUC UCAUUCAGGGGAUU@LB@ \|:\| \|\|\| \| :\|\| \|\|\|\|\| \|\|\|:\|\|\|\|\|\|\|\|\|\|@LB@ CUG UGU U UCG UUAAG AGUGAGUCCCCUAA@LB@3'-UUU...CGUUU A G G CAACAA AGGUA...GCA-5'@LB@ \| \|@LB@ 76 37@LB@@LB@@LB@Energy -18.00 kcal/mol@LB@Hybridization Energy -31.5918 kcal/mol@LB@Unfolding Energy - mRNA 8.81239 kcal/mol@LB@Unfolding Energy - sRNA 4.77946 kcal/mol@LB@@LB@Position - mRNA 9 -- 48@LB@Position - sRNA 38 -- 75@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 38 -- 44@LB@
25	0.0002079	0.02926	b4064	ghxP	-13.58	0.046769	115 -- 151	38 -- 73	guanine/hypoxanthine permease high affinity; guanine/hypoxanthine:H+ symporter	_____________114____________________________________152\n_____________\|______________________________________\|\n5'-UCG...CAAAC___GA_____G__GAUAAC________GG_________GUCCG...UAA-3'\n______________CUG___GCAG_AA______GUUUCGCU__CAGGGGAUU\n______________\|\|:___:\|\|\|_\|\|______\|\|\|\|\|:\|\|__\|\|\|\|\|\|\|\|\|\n______________GAU___UGUC_UU______CAAAGUGA__GUCCCCUAA\n3'-UUU...UUUCU___GUG____G__AAGCAA___________________AGGUA...GCA-5'\n_____________\|______________________________________\|\n_____________74_____________________________________37\n	145 -- 151	38 -- 44	-32.2199 kcal/mol	13.8672 kcal/mol	4.77333 kcal/mol	114 152@LB@ \| \|@LB@5'-UCG...CAAAC GA G GAUAAC GG GUCCG...UAA-3'@LB@ CUG GCAG AA GUUUCGCU CAGGGGAUU@LB@ \|\|: :\|\|\| \|\| \|\|\|\|\|:\|\| \|\|\|\|\|\|\|\|\|@LB@ GAU UGUC UU CAAAGUGA GUCCCCUAA@LB@3'-UUU...UUUCU GUG G AAGCAA AGGUA...GCA-5'@LB@ \| \|@LB@ 74 37@LB@@LB@@LB@Energy -13.58 kcal/mol@LB@Hybridization Energy -32.2199 kcal/mol@LB@Unfolding Energy - mRNA 13.8672 kcal/mol@LB@Unfolding Energy - sRNA 4.77333 kcal/mol@LB@@LB@Position - mRNA 115 -- 151@LB@Position - sRNA 38 -- 73@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 38 -- 44@LB@
26	0.0002514	0.03403	b4551	yheV	-11.83	0.112444	191 -- 229	42 -- 77	DUF2387 family putative metal-binding protein	_____________190_____________________________________230\n_____________\|_______________________________________\|\n5'-AUC...GAGUA____G__A_G________C__AAAAC________GC___CGCAA...UUG-3'\n______________GAGG_UA_A_AUGGCAAU_CG_____GUUUUAUU__GGG\n______________:\|\|:_\|\|_\|_\|::\|\|\|\|\|_\|\|_____\|\|\|\|:\|:\|__\|\|\|\n______________UUCU_AU_U_UGUCGUUA_GC_____CAAAGUGA__CCC\n3'-UUU...CCCGU____G__G_G________A__AA___________GU___CUAAA...GCA-5'\n_____________\|_______________________________________\|\n_____________78______________________________________41\n	217 -- 223	48 -- 54	-24.6454 kcal/mol	8.05545 kcal/mol	4.7648 kcal/mol	190 230@LB@ \| \|@LB@5'-AUC...GAGUA G A G C AAAAC GC CGCAA...UUG-3'@LB@ GAGG UA A AUGGCAAU CG GUUUUAUU GGG@LB@ :\|\|: \|\| \| \|::\|\|\|\|\| \|\| \|\|\|\|:\|:\| \|\|\|@LB@ UUCU AU U UGUCGUUA GC CAAAGUGA CCC@LB@3'-UUU...CCCGU G G G A AA GU CUAAA...GCA-5'@LB@ \| \|@LB@ 78 41@LB@@LB@@LB@Energy -11.83 kcal/mol@LB@Hybridization Energy -24.6454 kcal/mol@LB@Unfolding Energy - mRNA 8.05545 kcal/mol@LB@Unfolding Energy - sRNA 4.7648 kcal/mol@LB@@LB@Position - mRNA 191 -- 229@LB@Position - sRNA 42 -- 77@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 48 -- 54@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@
28	0.0004009	0.04965	b3511	hdeD	-17.16	0.005105	126 -- 176	35 -- 75	acid-resistance membrane protein	_____________125__________________________________________________177\n_____________\|____________________________________________________\|\n5'-GAG...AAAUC________U_UUA__CG________G__AUAGAUUGAUAG____________UUCUU...UCG-3'\n______________GACUGCAU_C___GA__CGUU_UUU_GC____________CAGGGGAUUUUC\n______________\|\|\|\|:\|\|:_\|___:\|__\|\|\|\|_\|\|\|_:\|____________\|\|\|\|\|\|\|\|\|\|:\|\n______________CUGAUGUG_G___UU__GCAA_AAA_UG____________GUCCCCUAAAGG\n3'-UUU...CGUUU________U_UCG__AA____C___G__A_______________________UACGA...GCA-5'\n_____________\|____________________________________________________\|\n_____________76___________________________________________________34\n	170 -- 176	35 -- 41	-34.0299 kcal/mol	12.0619 kcal/mol	4.80541 kcal/mol	125 177@LB@ \| \|@LB@5'-GAG...AAAUC U UUA CG G AUAGAUUGAUAG UUCUU...UCG-3'@LB@ GACUGCAU C GA CGUU UUU GC CAGGGGAUUUUC@LB@ \|\|\|\|:\|\|: \| :\| \|\|\|\| \|\|\| :\| \|\|\|\|\|\|\|\|\|\|:\|@LB@ CUGAUGUG G UU GCAA AAA UG GUCCCCUAAAGG@LB@3'-UUU...CGUUU U UCG AA C G A UACGA...GCA-5'@LB@ \| \|@LB@ 76 34@LB@@LB@@LB@Energy -17.16 kcal/mol@LB@Hybridization Energy -34.0299 kcal/mol@LB@Unfolding Energy - mRNA 12.0619 kcal/mol@LB@Unfolding Energy - sRNA 4.80541 kcal/mol@LB@@LB@Position - mRNA 126 -- 176@LB@Position - sRNA 35 -- 75@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 35 -- 41@LB@
29	0.0004091	0.04965	b0958	sulA	-15.92	0.011809	212 -- 243	48 -- 76	SOS cell division inhibitor	_____________211______________________________244\n_____________\|________________________________\|\n5'-AUA...ACUUC____________UC__UC_____C___C____CCGCA...UCA-3'\n______________AGGCUAUGCACA__GU__UUCGU_GUU_UCAU\n______________\|\|:\|\|\|::\|\|\|\|__\|:__\|\|\|\|\|_\|\|\|_\|\|\|:\n______________UCUGAUGUGUGU__CG__AAGCA_CAA_AGUG\n3'-UUU...CCGUU________________UU_____A________AGUCC...GCA-5'\n_____________\|________________________________\|\n_____________77_______________________________47\n	217 -- 223	65 -- 71	-24.9625 kcal/mol	5.35271 kcal/mol	3.68714 kcal/mol	211 244@LB@ \| \|@LB@5'-AUA...ACUUC UC UC C C CCGCA...UCA-3'@LB@ AGGCUAUGCACA GU UUCGU GUU UCAU@LB@ \|\|:\|\|\|::\|\|\|\| \|: \|\|\|\|\| \|\|\| \|\|\|:@LB@ UCUGAUGUGUGU CG AAGCA CAA AGUG@LB@3'-UUU...CCGUU UU A AGUCC...GCA-5'@LB@ \| \|@LB@ 77 47@LB@@LB@@LB@Energy -15.92 kcal/mol@LB@Hybridization Energy -24.9625 kcal/mol@LB@Unfolding Energy - mRNA 5.35271 kcal/mol@LB@Unfolding Energy - sRNA 3.68714 kcal/mol@LB@@LB@Position - mRNA 212 -- 243@LB@Position - sRNA 48 -- 76@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 65 -- 71@LB@
30	0.0004324	0.05073	b3364	tsgA	-16.38	0.008733	203 -- 236	38 -- 75	putative transporter	_____________202_____________________________________237\n_____________\|_______________________________________\|\n5'-CCA...AUCAU___________________CAUCAA______CAU_____AGCUU...AUA-3'\n______________GACUA___ACAGCAAU_CG_______GCUCA___GGAUU\n______________\|\|\|\|\|___\|\|\|\|\|\|\|\|_\|\|_______:\|\|\|\|___\|\|\|\|\|\n______________CUGAU___UGUCGUUA_GC_______UGAGU___CCUAA\n3'-UUU...CGUUU_____GUG________A__AACAAAG_____CC______AGGUA...GCA-5'\n_____________\|_______________________________________\|\n_____________76______________________________________37\n	209 -- 215	60 -- 66	-26.4683 kcal/mol	5.30565 kcal/mol	4.77946 kcal/mol	202 237@LB@ \| \|@LB@5'-CCA...AUCAU CAUCAA CAU AGCUU...AUA-3'@LB@ GACUA ACAGCAAU CG GCUCA GGAUU@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\| \|\| :\|\|\|\| \|\|\|\|\|@LB@ CUGAU UGUCGUUA GC UGAGU CCUAA@LB@3'-UUU...CGUUU GUG A AACAAAG CC AGGUA...GCA-5'@LB@ \| \|@LB@ 76 37@LB@@LB@@LB@Energy -16.38 kcal/mol@LB@Hybridization Energy -26.4683 kcal/mol@LB@Unfolding Energy - mRNA 5.30565 kcal/mol@LB@Unfolding Energy - sRNA 4.77946 kcal/mol@LB@@LB@Position - mRNA 203 -- 236@LB@Position - sRNA 38 -- 75@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 60 -- 66@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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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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