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
167	0.02708	0.531	b3705	yidC	-10.20	0.088356	85 -- 115	24 -- 58	membrane protein insertase	_____________84____________________________________116\n_____________\|_____________________________________\|\n5'-CGC...GGUUU__A____UAAA_____GU_________U_________AACGC...CCC-3'\n______________GG_GUGA____AGGCA________UGG_UGACGGUGA\n______________\|\|_\|\|:\|____\|\|:\|\|________\|\|:_\|\|\|\|\|\|\|:\|\n______________CC_CAUU____UCUGU________ACU_ACUGCCAUU\n3'-UUU...UUUAU__C____UG_______AAGUCUUU___U_________AUUUA...UCG-5'\n_____________\|_____________________________________\|\n_____________59____________________________________23\n	109 -- 115	24 -- 30	-23.9536 kcal/mol	7.45063 kcal/mol	6.30019 kcal/mol	84 116@LB@ \| \|@LB@5'-CGC...GGUUU A UAAA GU U AACGC...CCC-3'@LB@ GG GUGA AGGCA UGG UGACGGUGA@LB@ \|\| \|\|:\| \|\|:\|\| \|\|: \|\|\|\|\|\|\|:\|@LB@ CC CAUU UCUGU ACU ACUGCCAUU@LB@3'-UUU...UUUAU C UG AAGUCUUU U AUUUA...UCG-5'@LB@ \| \|@LB@ 59 23@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -23.9536 kcal/mol@LB@Unfolding Energy - mRNA 7.45063 kcal/mol@LB@Unfolding Energy - sRNA 6.30019 kcal/mol@LB@@LB@Position - mRNA 85 -- 115@LB@Position - sRNA 24 -- 58@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 24 -- 30@LB@
87	0.01323	0.4992	b1951	rcsA	-11.40	0.049597	149 -- 196	25 -- 65	transcriptional regulator of colanic acid capsular biosynthesis	_____________148______________________________________________197\n_____________\|________________________________________________\|\n5'-GUU...CAUGA_______UUCA______G___AUUAU____ACGCAU_______G____UGCCA...UUG-3'\n______________UGAAAUA____GGUAAG_GGA_____CGUU______UGAGUGA_GGUA\n______________\|\|\|\|\|\|\|____\|\|\|\|\|:_:\|\|_____\|:\|\|______\|\|\|:\|\|\|_\|\|\|\|\n______________ACUUUAU____CCAUUU_UCU_____GUAA______ACUUACU_CCAU\n3'-UUU...GGCCA_______CC________G____________GUCUUU_______G____UAUUU...UCG-5'\n_____________\|________________________________________________\|\n_____________66_______________________________________________24\n	149 -- 155	59 -- 65	-29.5865 kcal/mol	10.9819 kcal/mol	7.2015 kcal/mol	148 197@LB@ \| \|@LB@5'-GUU...CAUGA UUCA G AUUAU ACGCAU G UGCCA...UUG-3'@LB@ UGAAAUA GGUAAG GGA CGUU UGAGUGA GGUA@LB@ \|\|\|\|\|\|\| \|\|\|\|\|: :\|\| \|:\|\| \|\|\|:\|\|\| \|\|\|\|@LB@ ACUUUAU CCAUUU UCU GUAA ACUUACU CCAU@LB@3'-UUU...GGCCA CC G GUCUUU G UAUUU...UCG-5'@LB@ \| \|@LB@ 66 24@LB@@LB@@LB@Energy -11.40 kcal/mol@LB@Hybridization Energy -29.5865 kcal/mol@LB@Unfolding Energy - mRNA 10.9819 kcal/mol@LB@Unfolding Energy - sRNA 7.2015 kcal/mol@LB@@LB@Position - mRNA 149 -- 196@LB@Position - sRNA 25 -- 65@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 59 -- 65@LB@
148	0.02477	0.526	b2262	menB	-9.56	0.118602	261 -- 300	25 -- 56	dihydroxynaphthoic acid synthetase	_____________260______________________________________300\n_____________\|________________________________________\|\n5'-CGU...CCGAA___UUCGA__________UU_____AAAUCCACC_______-3'\n______________GGU_____GGACAUUC_G__AUGAA_________GACGGUA\n______________\|\|\|_____:\|\|\|\|\|\|\|_\|__\|\|\|\|\|_________\|\|\|\|\|\|\|\n______________CCA_____UCUGUAAG_C__UACUU_________CUGCCAU\n3'-UUU...UAUCC___UUUG_________U_UU_____A_______________UAUUU...UCG-5'\n_____________\|_________________________________________\|\n_____________57________________________________________24\n	294 -- 300	25 -- 31	-24.8577 kcal/mol	9.0019 kcal/mol	6.29869 kcal/mol	260 300@LB@ \| \|@LB@5'-CGU...CCGAA UUCGA UU AAAUCCACC -3'@LB@ GGU GGACAUUC G AUGAA GACGGUA@LB@ \|\|\| :\|\|\|\|\|\|\| \| \|\|\|\|\| \|\|\|\|\|\|\|@LB@ CCA UCUGUAAG C UACUU CUGCCAU@LB@3'-UUU...UAUCC UUUG U UU A UAUUU...UCG-5'@LB@ \| \|@LB@ 57 24@LB@@LB@@LB@Energy -9.56 kcal/mol@LB@Hybridization Energy -24.8577 kcal/mol@LB@Unfolding Energy - mRNA 9.0019 kcal/mol@LB@Unfolding Energy - sRNA 6.29869 kcal/mol@LB@@LB@Position - mRNA 261 -- 300@LB@Position - sRNA 25 -- 56@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 25 -- 31@LB@
197	0.03325	0.554	b4139	aspA	-12.92	0.022631	26 -- 66	25 -- 59	aspartate ammonia-lyase	_____________25_________________________________________67\n_____________\|__________________________________________\|\n5'-GAU...AAUUA________AA__C____C__________UCCAG__U______GAAAU...ACU-3'\n______________AGGGGUAA__AC_GACA_UUA_AAGUGA_____AU_ACGGUA\n______________\|\|\|\|\|\|\|\|__\|\|_\|\|\|\|_\|:\|_\|\|:\|\|\|_____\|\|_\|\|\|\|\|\|\n______________UCCCCAUU__UG_CUGU_AGU_UUUACU_____UA_UGCCAU\n3'-UUU...CUUUA____________U____A___C_____________C______UAUUU...UCG-5'\n_____________\|__________________________________________\|\n_____________60_________________________________________24\n	27 -- 33	52 -- 58	-28.0294 kcal/mol	8.80617 kcal/mol	6.29893 kcal/mol	25 67@LB@ \| \|@LB@5'-GAU...AAUUA AA C C UCCAG U GAAAU...ACU-3'@LB@ AGGGGUAA AC GACA UUA AAGUGA AU ACGGUA@LB@ \|\|\|\|\|\|\|\| \|\| \|\|\|\| \|:\| \|\|:\|\|\| \|\| \|\|\|\|\|\|@LB@ UCCCCAUU UG CUGU AGU UUUACU UA UGCCAU@LB@3'-UUU...CUUUA U A C C UAUUU...UCG-5'@LB@ \| \|@LB@ 60 24@LB@@LB@@LB@Energy -12.92 kcal/mol@LB@Hybridization Energy -28.0294 kcal/mol@LB@Unfolding Energy - mRNA 8.80617 kcal/mol@LB@Unfolding Energy - sRNA 6.29893 kcal/mol@LB@@LB@Position - mRNA 26 -- 66@LB@Position - sRNA 25 -- 59@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 52 -- 58@LB@
39	0.003905	0.3287	b3541	dppD	-12.54	0.027771	124 -- 154	26 -- 56	dipeptide/heme ABC transporter ATPas	_____________123_______________________________155\n_____________\|_________________________________\|\n5'-UUU...CUGAC_______U________ACCU_____________CUGCG...GCG-3'\n______________GGU__GC_GGCAUUUA____GAUGGGUGACGGU\n______________\|\|\|__:\|_\|:\|\|\|\|:\|____:\|\|\|::\|\|\|\|\|\|\|\n______________CCA__UG_CUGUAAGU____UUACUUACUGCCA\n3'-UUU...UAUCC___UU__U________CU_______________UUAUU...UCG-5'\n_____________\|_________________________________\|\n_____________57________________________________25\n	148 -- 154	26 -- 32	-28.6535 kcal/mol	9.81942 kcal/mol	6.29593 kcal/mol	123 155@LB@ \| \|@LB@5'-UUU...CUGAC U ACCU CUGCG...GCG-3'@LB@ GGU GC GGCAUUUA GAUGGGUGACGGU@LB@ \|\|\| :\| \|:\|\|\|\|:\| :\|\|\|::\|\|\|\|\|\|\|@LB@ CCA UG CUGUAAGU UUACUUACUGCCA@LB@3'-UUU...UAUCC UU U CU UUAUU...UCG-5'@LB@ \| \|@LB@ 57 25@LB@@LB@@LB@Energy -12.54 kcal/mol@LB@Hybridization Energy -28.6535 kcal/mol@LB@Unfolding Energy - mRNA 9.81942 kcal/mol@LB@Unfolding Energy - sRNA 6.29593 kcal/mol@LB@@LB@Position - mRNA 124 -- 154@LB@Position - sRNA 26 -- 56@LB@Position Seed - mRNA 148 -- 154@LB@Position Seed - sRNA 26 -- 32@LB@
8	0.0001978	0.08119	b3391	hofQ	-22.13	0.000045	16 -- 73	27 -- 88	DNA catabolic putative fimbrial transporter	_____________15________________________________________________________________74\n_____________\|_________________________________________________________________\|\n5'-CUA...AUGGU___G__________C_____AU____GU_____AA____________AA_________C______GUGCA...UAG-3'\n______________AGG_CGAG_GCGAG_GCAUC__CGGU___AAUA_____AGACGGGCA___AGAAAUGG__GACGG\n______________\|::_\|\|\|:_\|\|\|\|\|_\|\|\|\|\|__\|\|\|\|___\|\|\|\|_____\|:\|\|:\|:\|\|___\|\|\|\|\|\|\|:__\|\|\|\|\|\n______________UUU_GCUU_CGCUC_CGUAG__GCCA___UUAU_____UUUGUCUGU___UCUUUACU__CUGCC\n______3'-UUUUU___G____A_________________ACU____CCCCA_________AAG________UA_____AUUAU...UCG-5'\n_____________\|_________________________________________________________________\|\n_____________89________________________________________________________________26\n	60 -- 66	35 -- 41	-51.8767 kcal/mol	10.3742 kcal/mol	19.3742 kcal/mol	15 74@LB@ \| \|@LB@5'-CUA...AUGGU G C AU GU AA AA C GUGCA...UAG-3'@LB@ AGG CGAG GCGAG GCAUC CGGU AAUA AGACGGGCA AGAAAUGG GACGG@LB@ \|:: \|\|\|: \|\|\|\|\| \|\|\|\|\| \|\|\|\| \|\|\|\| \|:\|\|:\|:\|\| \|\|\|\|\|\|\|: \|\|\|\|\|@LB@ UUU GCUU CGCUC CGUAG GCCA UUAU UUUGUCUGU UCUUUACU CUGCC@LB@ 3'-UUUUU G A ACU CCCCA AAG UA AUUAU...UCG-5'@LB@ \| \|@LB@ 89 26@LB@@LB@@LB@Energy -22.13 kcal/mol@LB@Hybridization Energy -51.8767 kcal/mol@LB@Unfolding Energy - mRNA 10.3742 kcal/mol@LB@Unfolding Energy - sRNA 19.3742 kcal/mol@LB@@LB@Position - mRNA 16 -- 73@LB@Position - sRNA 27 -- 88@LB@Position Seed - mRNA 60 -- 66@LB@Position Seed - sRNA 35 -- 41@LB@
14	0.0005823	0.1358	b4348	hsdS	-17.02	0.002033	190 -- 210	27 -- 58	specificity determinant for hsdM and hsdR	_____________189______________________________211\n_____________\|________________________________\|\n5'-CUG...UUGGU________________________________GGAAA...UAA-3'\n______________GGGGUGA__________AGGAAUGAGUG_CGG\n______________\|\|\|\|\|:\|__________\|\|:\|\|\|\|\|:\|\|_\|\|\|\n______________CCCCAUU__________UCUUUACUUAC_GCC\n3'-UUU...UUUAU_______UGUCUGUAAG___________U___AUUAU...UCG-5'\n_____________\|________________________________\|\n_____________59_______________________________26\n	190 -- 196	52 -- 58	-27.0928 kcal/mol	3.78881 kcal/mol	6.28755 kcal/mol	189 211@LB@ \| \|@LB@5'-CUG...UUGGU GGAAA...UAA-3'@LB@ GGGGUGA AGGAAUGAGUG CGG@LB@ \|\|\|\|\|:\| \|\|:\|\|\|\|\|:\|\| \|\|\|@LB@ CCCCAUU UCUUUACUUAC GCC@LB@3'-UUU...UUUAU UGUCUGUAAG U AUUAU...UCG-5'@LB@ \| \|@LB@ 59 26@LB@@LB@@LB@Energy -17.02 kcal/mol@LB@Hybridization Energy -27.0928 kcal/mol@LB@Unfolding Energy - mRNA 3.78881 kcal/mol@LB@Unfolding Energy - sRNA 6.28755 kcal/mol@LB@@LB@Position - mRNA 190 -- 210@LB@Position - sRNA 27 -- 58@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 52 -- 58@LB@
21	0.001002	0.1516	b4045	yjbJ	-13.25	0.018991	259 -- 290	28 -- 62	stress-induced protein UPF0337 family	_____________258__________________________________291\n_____________\|____________________________________\|\n5'-CGU...AGAGC_______C_____U___CGAU________U______AUCAU...AAG-3'\n______________AAUGGGG__AAAC_GAC_______GAUGA_AUGACG\n______________\|\|\|:\|\|\|__\|\|\|\|_\|\|\|_______:\|\|\|\|_\|\|\|\|\|\|\n______________UUAUCCC__UUUG_CUG_______UUACU_UACUGC\n3'-UUU...CAACU_______CA____U___UAAGUCU____________CAUUA...UCG-5'\n_____________\|____________________________________\|\n_____________63___________________________________27\n	259 -- 265	56 -- 62	-23.7721 kcal/mol	4.22826 kcal/mol	6.29418 kcal/mol	258 291@LB@ \| \|@LB@5'-CGU...AGAGC C U CGAU U AUCAU...AAG-3'@LB@ AAUGGGG AAAC GAC GAUGA AUGACG@LB@ \|\|\|:\|\|\| \|\|\|\| \|\|\| :\|\|\|\| \|\|\|\|\|\|@LB@ UUAUCCC UUUG CUG UUACU UACUGC@LB@3'-UUU...CAACU CA U UAAGUCU CAUUA...UCG-5'@LB@ \| \|@LB@ 63 27@LB@@LB@@LB@Energy -13.25 kcal/mol@LB@Hybridization Energy -23.7721 kcal/mol@LB@Unfolding Energy - mRNA 4.22826 kcal/mol@LB@Unfolding Energy - sRNA 6.29418 kcal/mol@LB@@LB@Position - mRNA 259 -- 290@LB@Position - sRNA 28 -- 62@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 56 -- 62@LB@
50	0.005695	0.3739	b1086	rluC	-13.13	0.020232	139 -- 168	28 -- 55	23S rRNA pseudouridine(955 2504 2580) synthase	_____________138____________________________169\n_____________\|______________________________\|\n5'-UCC...CAAAA_______UAA____AG_A____________CGAAU...UAC-3'\n______________GUAAAUA___GCAU__A_AAAUGAGUGGCG\n______________\|\|\|\|\|:\|___:\|\|\|__\|_\|\|\|\|\|\|:\|\|:\|\|\n______________CAUUUGU___UGUA__U_UUUACUUACUGC\n3'-UUU...AUCCC_______C______AG_C____________CAUUA...UCG-5'\n_____________\|______________________________\|\n_____________56_____________________________27\n	161 -- 167	29 -- 35	-21.8911 kcal/mol	2.47099 kcal/mol	6.28725 kcal/mol	138 169@LB@ \| \|@LB@5'-UCC...CAAAA UAA AG A CGAAU...UAC-3'@LB@ GUAAAUA GCAU A AAAUGAGUGGCG@LB@ \|\|\|\|\|:\| :\|\|\| \| \|\|\|\|\|\|:\|\|:\|\|@LB@ CAUUUGU UGUA U UUUACUUACUGC@LB@3'-UUU...AUCCC C AG C CAUUA...UCG-5'@LB@ \| \|@LB@ 56 27@LB@@LB@@LB@Energy -13.13 kcal/mol@LB@Hybridization Energy -21.8911 kcal/mol@LB@Unfolding Energy - mRNA 2.47099 kcal/mol@LB@Unfolding Energy - sRNA 6.28725 kcal/mol@LB@@LB@Position - mRNA 139 -- 168@LB@Position - sRNA 28 -- 55@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 29 -- 35@LB@
72	0.01058	0.4523	b3458	livK	-8.91	0.157650	183 -- 215	28 -- 63	leucine transporter subunit	_____________182___________________________________216\n_____________\|_____________________________________\|\n5'-UGU...AUCAC________AUUUUU____UAU______CG________AAAAC...CGA-3'\n______________GAAUGGGG_______GAC_____GAAA__GAAUG_CG\n______________:\|\|\|:\|\|\|_______\|\|\|_____\|\|\|\|__\|\|\|\|\|_\|\|\n______________UUUAUCCC_______CUG_____CUUU__CUUAC_GC\n3'-UUU...CCAAC________CAUUUGU___UAAGU____A______U__CAUUA...UCG-5'\n_____________\|_____________________________________\|\n_____________64____________________________________27\n	184 -- 190	56 -- 62	-20.644 kcal/mol	5.44449 kcal/mol	6.29422 kcal/mol	182 216@LB@ \| \|@LB@5'-UGU...AUCAC AUUUUU UAU CG AAAAC...CGA-3'@LB@ GAAUGGGG GAC GAAA GAAUG CG@LB@ :\|\|\|:\|\|\| \|\|\| \|\|\|\| \|\|\|\|\| \|\|@LB@ UUUAUCCC CUG CUUU CUUAC GC@LB@3'-UUU...CCAAC CAUUUGU UAAGU A U CAUUA...UCG-5'@LB@ \| \|@LB@ 64 27@LB@@LB@@LB@Energy -8.91 kcal/mol@LB@Hybridization Energy -20.644 kcal/mol@LB@Unfolding Energy - mRNA 5.44449 kcal/mol@LB@Unfolding Energy - sRNA 6.29422 kcal/mol@LB@@LB@Position - mRNA 183 -- 215@LB@Position - sRNA 28 -- 63@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 56 -- 62@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)

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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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