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
83	0.0117	0.4626	b1071	flgM	-8.58	0.180603	153 -- 179	1 -- 25	anti-sigma factor for FliA (sigma 28)	_____________152_________________________180\n_____________\|___________________________\|\n5'-CCA...UUGCC__________CAACAC_____AAA___GCCCU...CAA-3'\n______________GAUAAAUAAG______AUGAU___AGC\n______________:\|\|\|\|\|\|\|\|:______\|\|\|\|\|___\|\|\|\n______________UUAUUUAUUU______UACUA___UCG\n3'-UUU...UGCCA__________CAAU_______CUA___-5'\n_____________\|__________________________\|\n_____________26_________________________1\n	156 -- 162	16 -- 22	-10.1551 kcal/mol	1.46038 kcal/mol	0.112205 kcal/mol	152 180@LB@ \| \|@LB@5'-CCA...UUGCC CAACAC AAA GCCCU...CAA-3'@LB@ GAUAAAUAAG AUGAU AGC@LB@ :\|\|\|\|\|\|\|\|: \|\|\|\|\| \|\|\|@LB@ UUAUUUAUUU UACUA UCG@LB@3'-UUU...UGCCA CAAU CUA -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -8.58 kcal/mol@LB@Hybridization Energy -10.1551 kcal/mol@LB@Unfolding Energy - mRNA 1.46038 kcal/mol@LB@Unfolding Energy - sRNA 0.112205 kcal/mol@LB@@LB@Position - mRNA 153 -- 179@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 16 -- 22@LB@
52	0.0063	0.3902	b1473	yddG	-8.84	0.162012	257 -- 264	2 -- 9	aromatic amino acid exporter	_____________256______265\n_____________\|________\|\n5'-GCG...AGCAC________GAUUG...CGG-3'\n______________GAUGGUAG\n______________\|\|\|\|:\|\|\|\n______________CUACUAUC\n3'-UUU...AAUUA________G-5'\n_____________\|________\|\n_____________10_______1\n	258 -- 264	2 -- 8	-10.1209 kcal/mol	1.26064 kcal/mol	0.0191352 kcal/mol	256 265@LB@ \| \|@LB@5'-GCG...AGCAC GAUUG...CGG-3'@LB@ GAUGGUAG@LB@ \|\|\|\|:\|\|\|@LB@ CUACUAUC@LB@3'-UUU...AAUUA G-5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -10.1209 kcal/mol@LB@Unfolding Energy - mRNA 1.26064 kcal/mol@LB@Unfolding Energy - sRNA 0.0191352 kcal/mol@LB@@LB@Position - mRNA 257 -- 264@LB@Position - sRNA 2 -- 9@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 2 -- 8@LB@
95	0.01574	0.5059	b2714	ascG	-10.13	0.091468	184 -- 220	14 -- 55	asc operon transcriptional repressor; prpBC operon repressor	_____________183________________________________________221\n_____________\|__________________________________________\|\n5'-AAA...UGCGU_____G_____________AU_______AC____CUG_____GGCGA...AAG-3'\n______________GUAAA_GGAU_____GAAA__GAUGACG__GAUG___GAAGU\n______________\|\|\|\|\|_:\|\|:_____\|\|\|\|__:\|\|\|\|\|\|__:\|\|:___:\|\|\|\|\n______________CAUUU_UCUG_____CUUU__UUACUGC__UUAU___UUUCA\n3'-UUU...AUCCC_____G____UAAGU____AC_______CA____UUA_____AUUAC...UCG-5'\n_____________\|__________________________________________\|\n_____________56_________________________________________13\n	200 -- 206	28 -- 34	-22.7561 kcal/mol	6.30192 kcal/mol	6.32604 kcal/mol	183 221@LB@ \| \|@LB@5'-AAA...UGCGU G AU AC CUG GGCGA...AAG-3'@LB@ GUAAA GGAU GAAA GAUGACG GAUG GAAGU@LB@ \|\|\|\|\| :\|\|: \|\|\|\| :\|\|\|\|\|\| :\|\|: :\|\|\|\|@LB@ CAUUU UCUG CUUU UUACUGC UUAU UUUCA@LB@3'-UUU...AUCCC G UAAGU AC CA UUA AUUAC...UCG-5'@LB@ \| \|@LB@ 56 13@LB@@LB@@LB@Energy -10.13 kcal/mol@LB@Hybridization Energy -22.7561 kcal/mol@LB@Unfolding Energy - mRNA 6.30192 kcal/mol@LB@Unfolding Energy - sRNA 6.32604 kcal/mol@LB@@LB@Position - mRNA 184 -- 220@LB@Position - sRNA 14 -- 55@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 28 -- 34@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@
25	0.00149	0.1957	b4244	pyrI	-16.22	0.003374	188 -- 229	11 -- 59	aspartate carbamoyltransferase regulatory subunit	_____________187_________________________________________________230\n_____________\|___________________________________________________\|\n5'-UUC...CUGUA__________________________CAC___A________UGC_______AGCUA...UCA-3'\n______________AGGGG_AAAUAGA________GAUGA___ACG_UAAUAAAU___AGGUUGA\n______________\|\|\|\|\|_\|\|\|:\|\|\|________:\|\|\|\|___\|\|\|_\|\|\|\|\|\|\|\|___\|:\|\|\|:\|\n______________UCCCC_UUUGUCU________UUACU___UGC_AUUAUUUA___UUCAAUU\n3'-UUU...CUUUA_____A_______GUAAGUCU_____UAC___C________U_________ACUAC...UCG-5'\n_____________\|___________________________________________________\|\n_____________60__________________________________________________10\n	223 -- 229	11 -- 17	-28.8643 kcal/mol	6.31236 kcal/mol	6.33314 kcal/mol	187 230@LB@ \| \|@LB@5'-UUC...CUGUA CAC A UGC AGCUA...UCA-3'@LB@ AGGGG AAAUAGA GAUGA ACG UAAUAAAU AGGUUGA@LB@ \|\|\|\|\| \|\|\|:\|\|\| :\|\|\|\| \|\|\| \|\|\|\|\|\|\|\| \|:\|\|\|:\|@LB@ UCCCC UUUGUCU UUACU UGC AUUAUUUA UUCAAUU@LB@3'-UUU...CUUUA A GUAAGUCU UAC C U ACUAC...UCG-5'@LB@ \| \|@LB@ 60 10@LB@@LB@@LB@Energy -16.22 kcal/mol@LB@Hybridization Energy -28.8643 kcal/mol@LB@Unfolding Energy - mRNA 6.31236 kcal/mol@LB@Unfolding Energy - sRNA 6.33314 kcal/mol@LB@@LB@Position - mRNA 188 -- 229@LB@Position - sRNA 11 -- 59@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 11 -- 17@LB@
38	0.003831	0.3287	b3739	atpI	-13.67	0.015109	253 -- 271	1 -- 16	ATP synthase membrane-bound accessory factor	_____________252_________________272\n_____________\|___________________\|\n5'-GAA...CGUUC_____CUG___________AAGUG...ACC-3'\n______________AGUUA___GUGGUGAUAGC\n______________\|\|\|\|\|___:\|\|:\|\|\|\|\|\|\|\n______________UCAAU___UACUACUAUCG\n3'-UUU...UUAUU___________________-5'\n_____________\|__________________\|\n_____________17_________________1\n	265 -- 271	1 -- 7	-18.239 kcal/mol	4.52285 kcal/mol	0.0492804 kcal/mol	252 272@LB@ \| \|@LB@5'-GAA...CGUUC CUG AAGUG...ACC-3'@LB@ AGUUA GUGGUGAUAGC@LB@ \|\|\|\|\| :\|\|:\|\|\|\|\|\|\|@LB@ UCAAU UACUACUAUCG@LB@3'-UUU...UUAUU -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -13.67 kcal/mol@LB@Hybridization Energy -18.239 kcal/mol@LB@Unfolding Energy - mRNA 4.52285 kcal/mol@LB@Unfolding Energy - sRNA 0.0492804 kcal/mol@LB@@LB@Position - mRNA 253 -- 271@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 1 -- 7@LB@
51	0.006039	0.3887	b3822	recQ	-9.34	0.130811	192 -- 200	50 -- 58	ATP-dependent DNA helicase	_____________191_______201\n_____________\|_________\|\n5'-CGC...CAAUC_________GUGGC...UUA-3'\n______________GGGGUGAAU\n______________\|\|\|\|\|:\|\|:\n______________CCCCAUUUG\n3'-UUU...UUUAU_________UCUGU...UCG-5'\n_____________\|_________\|\n_____________59________49\n	194 -- 200	50 -- 56	-13.8974 kcal/mol	3.8337 kcal/mol	0.72763 kcal/mol	191 201@LB@ \| \|@LB@5'-CGC...CAAUC GUGGC...UUA-3'@LB@ GGGGUGAAU@LB@ \|\|\|\|\|:\|\|:@LB@ CCCCAUUUG@LB@3'-UUU...UUUAU UCUGU...UCG-5'@LB@ \| \|@LB@ 59 49@LB@@LB@@LB@Energy -9.34 kcal/mol@LB@Hybridization Energy -13.8974 kcal/mol@LB@Unfolding Energy - mRNA 3.8337 kcal/mol@LB@Unfolding Energy - sRNA 0.72763 kcal/mol@LB@@LB@Position - mRNA 192 -- 200@LB@Position - sRNA 50 -- 58@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 50 -- 56@LB@
98	0.01586	0.5059	b1860	ruvB	-8.95	0.154425	184 -- 211	1 -- 30	ATP-dependent DNA helicase component of RuvABC resolvasome	_____________183_____________________________212\n_____________\|_______________________________\|\n5'-ACG...GCGCC___U__UG_______________U_______AGACC...GUC-3'\n______________GCG_UA__AGGUAAAG__GAUGA_UGA_AGC\n______________:\|\|_\|\|__\|::\|\|\|\|\|__:\|\|\|\|_\|\|\|_\|\|\|\n______________UGC_AU__UUUAUUUC__UUACU_ACU_UCG\n3'-UUU...CUUAC___C__UA________AA_________A___-5'\n_____________\|______________________________\|\n_____________31_____________________________1\n	193 -- 199	15 -- 21	-17.0174 kcal/mol	5.93551 kcal/mol	2.12822 kcal/mol	183 212@LB@ \| \|@LB@5'-ACG...GCGCC U UG U AGACC...GUC-3'@LB@ GCG UA AGGUAAAG GAUGA UGA AGC@LB@ :\|\| \|\| \|::\|\|\|\|\| :\|\|\|\| \|\|\| \|\|\|@LB@ UGC AU UUUAUUUC UUACU ACU UCG@LB@3'-UUU...CUUAC C UA AA A -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -8.95 kcal/mol@LB@Hybridization Energy -17.0174 kcal/mol@LB@Unfolding Energy - mRNA 5.93551 kcal/mol@LB@Unfolding Energy - sRNA 2.12822 kcal/mol@LB@@LB@Position - mRNA 184 -- 211@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 15 -- 21@LB@
17	0.000872	0.1482	b3940	metL	-12.03	0.036099	191 -- 199	51 -- 59	Bifunctional aspartokinase/homoserine dehydrogenase 2	_____________190_______200\n_____________\|_________\|\n5'-ACG...AAACA_________AAUGA...GCA-3'\n______________AGGGGUAAA\n______________\|\|\|\|\|\|\|\|\|\n______________UCCCCAUUU\n3'-UUU...CUUUA_________GUCUG...UCG-5'\n_____________\|_________\|\n_____________60________50\n	193 -- 199	51 -- 57	-13.5839 kcal/mol	1.01846 kcal/mol	0.532875 kcal/mol	190 200@LB@ \| \|@LB@5'-ACG...AAACA AAUGA...GCA-3'@LB@ AGGGGUAAA@LB@ \|\|\|\|\|\|\|\|\|@LB@ UCCCCAUUU@LB@3'-UUU...CUUUA GUCUG...UCG-5'@LB@ \| \|@LB@ 60 50@LB@@LB@@LB@Energy -12.03 kcal/mol@LB@Hybridization Energy -13.5839 kcal/mol@LB@Unfolding Energy - mRNA 1.01846 kcal/mol@LB@Unfolding Energy - sRNA 0.532875 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 51 -- 59@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 51 -- 57@LB@
130	0.02079	0.5217	b3455	livG	-10.98	0.060940	96 -- 122	4 -- 29	branched-chain amino acid ABC transporter ATPase	_____________95__________________________123\n_____________\|___________________________\|\n5'-AUG...AUGCU_______UU_____U_C__________CUGGC...UCG-3'\n______________CGGUGGU__GAUGG_G_UGAUGAUGAU\n______________\|\|\|\|::\|__:\|\|::_\|_\|:\|\|\|\|\|\|\|\|\n______________GCCAUUA__UUAUU_C_AUUACUACUA\n3'-UUU...UUACU_______U______U_A__________UCG-5'\n_____________\|___________________________\|\n_____________30__________________________3\n	116 -- 122	4 -- 10	-20.0623 kcal/mol	6.95142 kcal/mol	2.12698 kcal/mol	95 123@LB@ \| \|@LB@5'-AUG...AUGCU UU U C CUGGC...UCG-3'@LB@ CGGUGGU GAUGG G UGAUGAUGAU@LB@ \|\|\|\|::\| :\|\|:: \| \|:\|\|\|\|\|\|\|\|@LB@ GCCAUUA UUAUU C AUUACUACUA@LB@3'-UUU...UUACU U U A UCG-5'@LB@ \| \|@LB@ 30 3@LB@@LB@@LB@Energy -10.98 kcal/mol@LB@Hybridization Energy -20.0623 kcal/mol@LB@Unfolding Energy - mRNA 6.95142 kcal/mol@LB@Unfolding Energy - sRNA 2.12698 kcal/mol@LB@@LB@Position - mRNA 96 -- 122@LB@Position - sRNA 4 -- 29@LB@Position Seed - mRNA 116 -- 122@LB@Position Seed - sRNA 4 -- 10@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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