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
161	0.006314	0.1377	b4099	phnI	-7.36	0.387929	194 -- 228	46 -- 79	ribophosphonate triphosphate synthase complex putative catalytic subunit	_____________193__________________________________229\n_____________\|____________________________________\|\n5'-AGC...GGAGG______G_____C__UGC___U_________C____AGGCG...GCG-3'\n______________UGUGCU_AUGUA_GU____CG_GAAAGGGGG_GAGA\n______________\|\|\|\|\|\|_\|\|\|:\|_\|\|____\|:_:\|\|\|\|\|::\|_:\|\|\|\n______________ACACGA_UACGU_CA____GU_UUUUCCUUC_UUCU\n3'-UUU...AGUUA_______________UUAA__U_________A____GUUAU...ACG-5'\n_____________\|____________________________________\|\n_____________80___________________________________45\n	217 -- 223	51 -- 57	-26.8268 kcal/mol	14.1464 kcal/mol	5.32077 kcal/mol	193 229@LB@ \| \|@LB@5'-AGC...GGAGG G C UGC U C AGGCG...GCG-3'@LB@ UGUGCU AUGUA GU CG GAAAGGGGG GAGA@LB@ \|\|\|\|\|\| \|\|\|:\| \|\| \|: :\|\|\|\|\|::\| :\|\|\|@LB@ ACACGA UACGU CA GU UUUUCCUUC UUCU@LB@3'-UUU...AGUUA UUAA U A GUUAU...ACG-5'@LB@ \| \|@LB@ 80 45@LB@@LB@@LB@Energy -7.36 kcal/mol@LB@Hybridization Energy -26.8268 kcal/mol@LB@Unfolding Energy - mRNA 14.1464 kcal/mol@LB@Unfolding Energy - sRNA 5.32077 kcal/mol@LB@@LB@Position - mRNA 194 -- 228@LB@Position - sRNA 46 -- 79@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 51 -- 57@LB@
9	1.504e-05	0.005627	b1189	dadA	-11.44	0.048458	195 -- 226	48 -- 78	D-amino acid dehydrogenase	_____________194_______________________________227\n_____________\|_________________________________\|\n5'-CCG...UCGGA__G_______G___UG____UACU_________UGUGG...CGG-3'\n______________GU_GCUAUGC_AGU___UCA____GGGAAGUGG\n______________\|\|_\|\|\|\|\|\|\|_\|\|\|___\|\|\|____:\|\|\|\|\|\|::\n______________CA_CGAUACG_UCA___AGU____UCCUUCAUU\n3'-UUU...GUUAA______________UUA___UUUU_________CUGUU...ACG-5'\n_____________\|_________________________________\|\n_____________79________________________________47\n	220 -- 226	48 -- 54	-26.7579 kcal/mol	10.7545 kcal/mol	4.57065 kcal/mol	194 227@LB@ \| \|@LB@5'-CCG...UCGGA G G UG UACU UGUGG...CGG-3'@LB@ GU GCUAUGC AGU UCA GGGAAGUGG@LB@ \|\| \|\|\|\|\|\|\| \|\|\| \|\|\| :\|\|\|\|\|\|::@LB@ CA CGAUACG UCA AGU UCCUUCAUU@LB@3'-UUU...GUUAA UUA UUUU CUGUU...ACG-5'@LB@ \| \|@LB@ 79 47@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -26.7579 kcal/mol@LB@Unfolding Energy - mRNA 10.7545 kcal/mol@LB@Unfolding Energy - sRNA 4.57065 kcal/mol@LB@@LB@Position - mRNA 195 -- 226@LB@Position - sRNA 48 -- 78@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 48 -- 54@LB@
55	0.0007336	0.04699	b0585	fes	-14.13	0.008457	197 -- 228	46 -- 77	enterobactin/ferrienterobactin esterase	_____________196________________________________229\n_____________\|__________________________________\|\n5'-CAU...GGUUA__G____A___CG_________U___________GCUGG...GGU-3'\n______________UG_UGUG_CGG____UUAAAAG_AGGAAGUGAGA\n______________\|\|_\|:\|\|_\|:\|____\|:\|\|\|\|:_\|\|\|\|\|\|\|:\|\|\|\n______________AC_AUAC_GUC____AGUUUUU_UCCUUCAUUCU\n3'-UUU...UUAAC__G________AUUA___________________GUUAU...ACG-5'\n_____________\|__________________________________\|\n_____________78_________________________________45\n	222 -- 228	46 -- 52	-26.4508 kcal/mol	7.03406 kcal/mol	5.29333 kcal/mol	196 229@LB@ \| \|@LB@5'-CAU...GGUUA G A CG U GCUGG...GGU-3'@LB@ UG UGUG CGG UUAAAAG AGGAAGUGAGA@LB@ \|\| \|:\|\| \|:\| \|:\|\|\|\|: \|\|\|\|\|\|\|:\|\|\|@LB@ AC AUAC GUC AGUUUUU UCCUUCAUUCU@LB@3'-UUU...UUAAC G AUUA GUUAU...ACG-5'@LB@ \| \|@LB@ 78 45@LB@@LB@@LB@Energy -14.13 kcal/mol@LB@Hybridization Energy -26.4508 kcal/mol@LB@Unfolding Energy - mRNA 7.03406 kcal/mol@LB@Unfolding Energy - sRNA 5.29333 kcal/mol@LB@@LB@Position - mRNA 197 -- 228@LB@Position - sRNA 46 -- 77@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 46 -- 52@LB@
56	0.0007477	0.04704	b2777	queE	-11.99	0.034574	197 -- 232	45 -- 77	7-carboxy-7-deazaguanine synthase; queosine biosynthesis	_____________196___________________________________233\n_____________\|_____________________________________\|\n5'-AAU...GAGAA____________CC____UU__C_A__U__UCC____CCUGC...UUG-3'\n______________UGCUAUGCAGUA___CGA__AA_G_GA_GU___AGAC\n______________\|\|\|\|\|\|\|\|\|\|\|\|___\|:\|__\|\|_\|_\|\|_\|\|___\|\|\|\|\n______________ACGAUACGUCAU___GUU__UU_C_CU_CA___UCUG\n3'-UUU...UUAAC____________UAA___UU_______U__U______UUAUA...ACG-5'\n_____________\|_____________________________________\|\n_____________78____________________________________44\n	202 -- 208	66 -- 72	-23.7263 kcal/mol	6.13303 kcal/mol	5.60521 kcal/mol	196 233@LB@ \| \|@LB@5'-AAU...GAGAA CC UU C A U UCC CCUGC...UUG-3'@LB@ UGCUAUGCAGUA CGA AA G GA GU AGAC@LB@ \|\|\|\|\|\|\|\|\|\|\|\| \|:\| \|\| \| \|\| \|\| \|\|\|\|@LB@ ACGAUACGUCAU GUU UU C CU CA UCUG@LB@3'-UUU...UUAAC UAA UU U U UUAUA...ACG-5'@LB@ \| \|@LB@ 78 44@LB@@LB@@LB@Energy -11.99 kcal/mol@LB@Hybridization Energy -23.7263 kcal/mol@LB@Unfolding Energy - mRNA 6.13303 kcal/mol@LB@Unfolding Energy - sRNA 5.60521 kcal/mol@LB@@LB@Position - mRNA 197 -- 232@LB@Position - sRNA 45 -- 77@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 66 -- 72@LB@
175	0.007208	0.145	b1444	patD	-10.32	0.092173	197 -- 205	69 -- 77	gamma-aminobutyraldehyde dehydrogenase	_____________196_______206\n_____________\|_________\|\n5'-UCG...GAAUA_________ACAUA...UUG-3'\n______________UGCUAUGCA\n______________\|\|\|\|\|\|\|\|\|\n______________ACGAUACGU\n3'-UUU...UUAAC_________CAUUA...ACG-5'\n_____________\|_________\|\n_____________78________68\n	199 -- 205	69 -- 75	-13.9965 kcal/mol	1.91367 kcal/mol	1.75858 kcal/mol	196 206@LB@ \| \|@LB@5'-UCG...GAAUA ACAUA...UUG-3'@LB@ UGCUAUGCA@LB@ \|\|\|\|\|\|\|\|\|@LB@ ACGAUACGU@LB@3'-UUU...UUAAC CAUUA...ACG-5'@LB@ \| \|@LB@ 78 68@LB@@LB@@LB@Energy -10.32 kcal/mol@LB@Hybridization Energy -13.9965 kcal/mol@LB@Unfolding Energy - mRNA 1.91367 kcal/mol@LB@Unfolding Energy - sRNA 1.75858 kcal/mol@LB@@LB@Position - mRNA 197 -- 205@LB@Position - sRNA 69 -- 77@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 69 -- 75@LB@
12	2.043e-05	0.005627	b3935	priA	-14.36	0.007166	198 -- 229	1 -- 34	Primosome factor n' (replication factor Y)	_____________197________________________________230\n_____________\|__________________________________\|\n5'-GAA...AUGAU__U___________CC________C______C__UCCGC...GCG-3'\n______________GC_AUGCCCGUUGC___ACGUUGC__UUGCC_GU\n______________\|\|_\|:\|\|\|\|:\|:\|\|___\|\|\|\|\|\|\|__\|::\|\|_\|:\n______________CG_UGCGGGUAGCG___UGCAACG__AGUGG_CG\n3'-UUU...CCUCG__U___________AAC_______UA_____A__-5'\n_____________\|_________________________________\|\n_____________35________________________________1\n	214 -- 220	11 -- 17	-36.548 kcal/mol	6.92453 kcal/mol	15.2664 kcal/mol	197 230@LB@ \| \|@LB@5'-GAA...AUGAU U CC C C UCCGC...GCG-3'@LB@ GC AUGCCCGUUGC ACGUUGC UUGCC GU@LB@ \|\| \|:\|\|\|\|:\|:\|\| \|\|\|\|\|\|\| \|::\|\| \|:@LB@ CG UGCGGGUAGCG UGCAACG AGUGG CG@LB@3'-UUU...CCUCG U AAC UA A -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -14.36 kcal/mol@LB@Hybridization Energy -36.548 kcal/mol@LB@Unfolding Energy - mRNA 6.92453 kcal/mol@LB@Unfolding Energy - sRNA 15.2664 kcal/mol@LB@@LB@Position - mRNA 198 -- 229@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 11 -- 17@LB@
26	0.000123	0.01616	b3280	yrdB	-11.55	0.045184	198 -- 244	43 -- 92	DUF1488 family protein	_____________197__________________________________________________245\n_____________\|____________________________________________________\|\n5'-CCA...UUGUC__CG______________C__C____UUC_____C_____AG__________GAAUA...GCG-3'\n______________CG__UGAAUCAG____GC_AU_CAGU____CGGA_AGGGA__AGUGGGACGA\n______________\|\|__:\|\|\|\|\|\|:____\|\|_\|\|_\|\|\|\|____\|::\|_\|:\|\|\|__\|\|\|::\|\|\|:\|\n______________GC__GCUUAGUU____CG_UA_GUCA____GUUU_UUCCU__UCAUUCUGUU\n3'-UUU...CCGCA__AU________AACA__A__C____UUAA____U_________________AUACC...ACG-5'\n_____________\|____________________________________________________\|\n_____________93___________________________________________________42\n	238 -- 244	43 -- 49	-31.3697 kcal/mol	13.9577 kcal/mol	5.86211 kcal/mol	197 245@LB@ \| \|@LB@5'-CCA...UUGUC CG C C UUC C AG GAAUA...GCG-3'@LB@ CG UGAAUCAG GC AU CAGU CGGA AGGGA AGUGGGACGA@LB@ \|\| :\|\|\|\|\|\|: \|\| \|\| \|\|\|\| \|::\| \|:\|\|\| \|\|\|::\|\|\|:\|@LB@ GC GCUUAGUU CG UA GUCA GUUU UUCCU UCAUUCUGUU@LB@3'-UUU...CCGCA AU AACA A C UUAA U AUACC...ACG-5'@LB@ \| \|@LB@ 93 42@LB@@LB@@LB@Energy -11.55 kcal/mol@LB@Hybridization Energy -31.3697 kcal/mol@LB@Unfolding Energy - mRNA 13.9577 kcal/mol@LB@Unfolding Energy - sRNA 5.86211 kcal/mol@LB@@LB@Position - mRNA 198 -- 244@LB@Position - sRNA 43 -- 92@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 43 -- 49@LB@
139	0.00529	0.1336	b3211	yhcC	-9.14	0.172713	199 -- 227	39 -- 75	putative Fe-S oxidoreductase Radical SAM superfamily protein	_____________198___________________________________228\n_____________\|_____________________________________\|\n5'-UGC...UCAGA_________UA________UU________U_______UUUGG...GCC-3'\n______________UUAUGCAGU____CAGAAA________AG_CAAUAUG\n______________:\|\|\|\|\|\|\|\|____\|\|:\|\|\|________\|\|_\|\|\|\|\|\|\|\n______________GAUACGUCA____GUUUUU________UC_GUUAUAC\n3'-UUU...AACAC_________UUAA______UCCUUCAU__U_______CUCGC...ACG-5'\n_____________\|_____________________________________\|\n_____________76____________________________________38\n	221 -- 227	39 -- 45	-19.1659 kcal/mol	3.3824 kcal/mol	6.6377 kcal/mol	198 228@LB@ \| \|@LB@5'-UGC...UCAGA UA UU U UUUGG...GCC-3'@LB@ UUAUGCAGU CAGAAA AG CAAUAUG@LB@ :\|\|\|\|\|\|\|\| \|\|:\|\|\| \|\| \|\|\|\|\|\|\|@LB@ GAUACGUCA GUUUUU UC GUUAUAC@LB@3'-UUU...AACAC UUAA UCCUUCAU U CUCGC...ACG-5'@LB@ \| \|@LB@ 76 38@LB@@LB@@LB@Energy -9.14 kcal/mol@LB@Hybridization Energy -19.1659 kcal/mol@LB@Unfolding Energy - mRNA 3.3824 kcal/mol@LB@Unfolding Energy - sRNA 6.6377 kcal/mol@LB@@LB@Position - mRNA 199 -- 227@LB@Position - sRNA 39 -- 75@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 39 -- 45@LB@
191	0.008524	0.1548	b3203	hpf	-8.75	0.209451	199 -- 206	68 -- 75	ribosome hibernation promoting factor HPF; stabilizes 100S dimers	_____________198______207\n_____________\|________\|\n5'-GAU...AGACA________CUCAA...GAA-3'\n______________CUAUGCAG\n______________\|\|\|\|\|\|\|\|\n______________GAUACGUC\n3'-UUU...AACAC________AUUAA...ACG-5'\n_____________\|________\|\n_____________76_______67\n	200 -- 206	68 -- 74	-11.4515 kcal/mol	0.966058 kcal/mol	1.73443 kcal/mol	198 207@LB@ \| \|@LB@5'-GAU...AGACA CUCAA...GAA-3'@LB@ CUAUGCAG@LB@ \|\|\|\|\|\|\|\|@LB@ GAUACGUC@LB@3'-UUU...AACAC AUUAA...ACG-5'@LB@ \| \|@LB@ 76 67@LB@@LB@@LB@Energy -8.75 kcal/mol@LB@Hybridization Energy -11.4515 kcal/mol@LB@Unfolding Energy - mRNA 0.966058 kcal/mol@LB@Unfolding Energy - sRNA 1.73443 kcal/mol@LB@@LB@Position - mRNA 199 -- 206@LB@Position - sRNA 68 -- 75@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 68 -- 74@LB@
53	0.0006788	0.04512	b3949	frwC	-10.17	0.100438	200 -- 218	68 -- 90	putative enzyme IIC component of PTS	_____________199_____________________219\n_____________\|_______________________\|\n5'-UUG...CAGCU_______G_______________AUCCU...UGG-3'\n______________UAUGAAU_AGUUG____GUGCAG\n______________\|\|:\|\|\|\|_\|:\|\|\|____:\|\|\|\|\|\n______________AUGCUUA_UUAAC____UACGUC\n3'-UUU...GCAGC_______G_____ACGA______AUUAA...ACG-5'\n_____________\|_______________________\|\n_____________91______________________67\n	200 -- 206	84 -- 90	-18.2816 kcal/mol	3.60123 kcal/mol	4.51505 kcal/mol	199 219@LB@ \| \|@LB@5'-UUG...CAGCU G AUCCU...UGG-3'@LB@ UAUGAAU AGUUG GUGCAG@LB@ \|\|:\|\|\|\| \|:\|\|\| :\|\|\|\|\|@LB@ AUGCUUA UUAAC UACGUC@LB@3'-UUU...GCAGC G ACGA AUUAA...ACG-5'@LB@ \| \|@LB@ 91 67@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -18.2816 kcal/mol@LB@Unfolding Energy - mRNA 3.60123 kcal/mol@LB@Unfolding Energy - sRNA 4.51505 kcal/mol@LB@@LB@Position - mRNA 200 -- 218@LB@Position - sRNA 68 -- 90@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 84 -- 90@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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