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
54	0.006418	0.3902	b0946	zapC	-14.33	0.010402	184 -- 201	47 -- 63	FtsZ stabilizer	_____________183________________202\n_____________\|__________________\|\n5'-AUU...UUAUA_________AG_______UGCGA...GUU-3'\n______________GGGUAGGGG__AGGCAGA\n______________:::\|\|\|\|\|\|__\|::\|\|\|\|\n______________UUUAUCCCC__UUUGUCU\n3'-UUU...CCAAC_________A________GUAAG...UCG-5'\n_____________\|__________________\|\n_____________64_________________46\n	195 -- 201	47 -- 53	-19.5846 kcal/mol	3.17109 kcal/mol	2.08245 kcal/mol	183 202@LB@ \| \|@LB@5'-AUU...UUAUA AG UGCGA...GUU-3'@LB@ GGGUAGGGG AGGCAGA@LB@ :::\|\|\|\|\|\| \|::\|\|\|\|@LB@ UUUAUCCCC UUUGUCU@LB@3'-UUU...CCAAC A GUAAG...UCG-5'@LB@ \| \|@LB@ 64 46@LB@@LB@@LB@Energy -14.33 kcal/mol@LB@Hybridization Energy -19.5846 kcal/mol@LB@Unfolding Energy - mRNA 3.17109 kcal/mol@LB@Unfolding Energy - sRNA 2.08245 kcal/mol@LB@@LB@Position - mRNA 184 -- 201@LB@Position - sRNA 47 -- 63@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 47 -- 53@LB@
173	0.02817	0.531	b0952	pqiC	-7.60	0.267291	63 -- 71	1 -- 9	DUF330 family putative lipoprotein	_____________62________72\n_____________\|_________\|\n5'-ACG...AACAA_________GGAUA...GCG-3'\n______________GAUGGUGGC\n______________\|\|\|\|:\|:\|\|\n______________CUACUAUCG\n3'-UUU...AAUUA_________-5'\n_____________\|________\|\n_____________10_______1\n	65 -- 71	1 -- 7	-13.4268 kcal/mol	5.80912 kcal/mol	0.0200155 kcal/mol	62 72@LB@ \| \|@LB@5'-ACG...AACAA GGAUA...GCG-3'@LB@ GAUGGUGGC@LB@ \|\|\|\|:\|:\|\|@LB@ CUACUAUCG@LB@3'-UUU...AAUUA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -7.60 kcal/mol@LB@Hybridization Energy -13.4268 kcal/mol@LB@Unfolding Energy - mRNA 5.80912 kcal/mol@LB@Unfolding Energy - sRNA 0.0200155 kcal/mol@LB@@LB@Position - mRNA 63 -- 71@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 1 -- 7@LB@
183	0.03025	0.5427	b0999	cbpM	-7.72	0.255487	289 -- 296	53 -- 60	modulator of CbpA co-chaperone	_____________288______297\n_____________\|________\|\n5'-AUC...CGGUU________GUUG-3'\n______________UGGGGGUG\n______________\|:\|\|\|\|\|:\n______________AUCCCCAU\n3'-UUU...ACUUU________UUGUC...UCG-5'\n_____________\|________\|\n_____________61_______52\n	290 -- 296	53 -- 59	-12.779 kcal/mol	4.99203 kcal/mol	0.0710089 kcal/mol	288 297@LB@ \| \|@LB@5'-AUC...CGGUU GUUG-3'@LB@ UGGGGGUG@LB@ \|:\|\|\|\|\|:@LB@ AUCCCCAU@LB@3'-UUU...ACUUU UUGUC...UCG-5'@LB@ \| \|@LB@ 61 52@LB@@LB@@LB@Energy -7.72 kcal/mol@LB@Hybridization Energy -12.779 kcal/mol@LB@Unfolding Energy - mRNA 4.99203 kcal/mol@LB@Unfolding Energy - sRNA 0.0710089 kcal/mol@LB@@LB@Position - mRNA 289 -- 296@LB@Position - sRNA 53 -- 60@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 53 -- 59@LB@
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@
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@
184	0.03077	0.549	b1101	ptsG	-13.95	0.012872	39 -- 58	1 -- 19	fused glucose-specific PTS enzymes: IIB component/IIC component	_____________38___________________59\n_____________\|____________________\|\n5'-CAU...UGAUC_________AAC________CGUCA...GUU-3'\n______________UGAAGUUGA___GUGAUAGC\n______________\|:\|\|\|\|\|:\|___:\|\|\|\|\|\|\|\n______________AUUUCAAUU___UACUAUCG\n3'-UUU...UAUUU_________AC_________-5'\n_____________\|___________________\|\n_____________20__________________1\n	52 -- 58	1 -- 7	-17.415 kcal/mol	3.39679 kcal/mol	0.0638423 kcal/mol	38 59@LB@ \| \|@LB@5'-CAU...UGAUC AAC CGUCA...GUU-3'@LB@ UGAAGUUGA GUGAUAGC@LB@ \|:\|\|\|\|\|:\| :\|\|\|\|\|\|\|@LB@ AUUUCAAUU UACUAUCG@LB@3'-UUU...UAUUU AC -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -13.95 kcal/mol@LB@Hybridization Energy -17.415 kcal/mol@LB@Unfolding Energy - mRNA 3.39679 kcal/mol@LB@Unfolding Energy - sRNA 0.0638423 kcal/mol@LB@@LB@Position - mRNA 39 -- 58@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 52 -- 58@LB@Position Seed - sRNA 1 -- 7@LB@
133	0.02154	0.526	b1105	lpoB	-10.17	0.089721	187 -- 196	50 -- 59	OM lipoprotein stimulator of MrcB transpeptidase	_____________186________197\n_____________\|__________\|\n5'-UUA...UUGUA__________CUUGA...AAC-3'\n______________AGGGGUGAAU\n______________\|\|\|\|\|\|:\|\|:\n______________UCCCCAUUUG\n3'-UUU...CUUUA__________UCUGU...UCG-5'\n_____________\|__________\|\n_____________60_________49\n	190 -- 196	50 -- 56	-15.1396 kcal/mol	4.24097 kcal/mol	0.728772 kcal/mol	186 197@LB@ \| \|@LB@5'-UUA...UUGUA CUUGA...AAC-3'@LB@ AGGGGUGAAU@LB@ \|\|\|\|\|\|:\|\|:@LB@ UCCCCAUUUG@LB@3'-UUU...CUUUA UCUGU...UCG-5'@LB@ \| \|@LB@ 60 49@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -15.1396 kcal/mol@LB@Unfolding Energy - mRNA 4.24097 kcal/mol@LB@Unfolding Energy - sRNA 0.728772 kcal/mol@LB@@LB@Position - mRNA 187 -- 196@LB@Position - sRNA 50 -- 59@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 50 -- 56@LB@
31	0.00291	0.3081	b1205	ychH	-11.03	0.059536	152 -- 163	53 -- 64	DUF2583 family putative inner membrane protein	_____________151__________164\n_____________\|____________\|\n5'-CAA...CAUAA____G_______UUCCC...UAC-3'\n______________GGAA_AGGGGUA\n______________\|:\|\|_\|\|\|\|\|\|\|\n______________CUUU_UCCCCAU\n3'-UUU...GCCAA____A_______UUGUC...UCG-5'\n_____________\|____________\|\n_____________65___________52\n	157 -- 163	53 -- 59	-13.5677 kcal/mol	2.46117 kcal/mol	0.0747267 kcal/mol	151 164@LB@ \| \|@LB@5'-CAA...CAUAA G UUCCC...UAC-3'@LB@ GGAA AGGGGUA@LB@ \|:\|\| \|\|\|\|\|\|\|@LB@ CUUU UCCCCAU@LB@3'-UUU...GCCAA A UUGUC...UCG-5'@LB@ \| \|@LB@ 65 52@LB@@LB@@LB@Energy -11.03 kcal/mol@LB@Hybridization Energy -13.5677 kcal/mol@LB@Unfolding Energy - mRNA 2.46117 kcal/mol@LB@Unfolding Energy - sRNA 0.0747267 kcal/mol@LB@@LB@Position - mRNA 152 -- 163@LB@Position - sRNA 53 -- 64@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 53 -- 59@LB@
56	0.007094	0.4159	b1242	ychE	-10.14	0.091024	67 -- 90	1 -- 23	UPF0056 family inner membrane protein	_____________66_______________________91\n_____________\|________________________\|\n5'-CAU...ACAAC_______CAA___C_A________AAUUU...GCA-3'\n______________UAGAUAA___UAA_G_AUGAUAGC\n______________\|\|:\|\|\|\|___\|\|\|_\|_\|\|\|\|\|\|\|\|\n______________AUUUAUU___AUU_C_UACUAUCG\n3'-UUU...CCAUU_______UCA___A__________-5'\n_____________\|_______________________\|\n_____________24______________________1\n	84 -- 90	1 -- 7	-13.9916 kcal/mol	3.74778 kcal/mol	0.105066 kcal/mol	66 91@LB@ \| \|@LB@5'-CAU...ACAAC CAA C A AAUUU...GCA-3'@LB@ UAGAUAA UAA G AUGAUAGC@LB@ \|\|:\|\|\|\| \|\|\| \| \|\|\|\|\|\|\|\|@LB@ AUUUAUU AUU C UACUAUCG@LB@3'-UUU...CCAUU UCA A -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -10.14 kcal/mol@LB@Hybridization Energy -13.9916 kcal/mol@LB@Unfolding Energy - mRNA 3.74778 kcal/mol@LB@Unfolding Energy - sRNA 0.105066 kcal/mol@LB@@LB@Position - mRNA 67 -- 90@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 84 -- 90@LB@Position Seed - sRNA 1 -- 7@LB@
2	1.932e-06	0.003171	b1243	oppA	-16.40	0.003005	12 -- 82	1 -- 59	oligopeptide ABC transporter periplasmic binding protein	_____________11__________________________________________________________________________83\n_____________\|___________________________________________________________________________\|\n5'-UGU...UCGAC___________CAGUACGAAUC_____AA__U__UCGUC_____C__CAG____________C____________AAUAC...UCA-3'\n______________AGGGG_AGACA___________GACAU__GG_GA_____UGAAU_AC___AAUAAAUAAAGU____GGUGAUAGU\n______________\|\|\|\|\|_\|:\|\|\|___________\|\|\|\|\|__:\|_:\|_____\|\|\|\|\|_\|\|___\|\|\|\|\|\|\|\|\|\|\|\|____\|:\|\|\|\|\|\|:\n______________UCCCC_UUUGU___________CUGUA__UC_UU_____ACUUA_UG___UUAUUUAUUUCA____CUACUAUCG\n3'-UUU...CUUUA_____A_____________________AG__U____________C__CCA____________AUUA_________-5'\n_____________\|__________________________________________________________________________\|\n_____________60_________________________________________________________________________1\n	76 -- 82	1 -- 7	-40.1642 kcal/mol	17.4223 kcal/mol	6.33764 kcal/mol	11 83@LB@ \| \|@LB@5'-UGU...UCGAC CAGUACGAAUC AA U UCGUC C CAG C AAUAC...UCA-3'@LB@ AGGGG AGACA GACAU GG GA UGAAU AC AAUAAAUAAAGU GGUGAUAGU@LB@ \|\|\|\|\| \|:\|\|\| \|\|\|\|\| :\| :\| \|\|\|\|\| \|\| \|\|\|\|\|\|\|\|\|\|\|\| \|:\|\|\|\|\|\|:@LB@ UCCCC UUUGU CUGUA UC UU ACUUA UG UUAUUUAUUUCA CUACUAUCG@LB@3'-UUU...CUUUA A AG U C CCA AUUA -5'@LB@ \| \|@LB@ 60 1@LB@@LB@@LB@Energy -16.40 kcal/mol@LB@Hybridization Energy -40.1642 kcal/mol@LB@Unfolding Energy - mRNA 17.4223 kcal/mol@LB@Unfolding Energy - sRNA 6.33764 kcal/mol@LB@@LB@Position - mRNA 12 -- 82@LB@Position - sRNA 1 -- 59@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 1 -- 7@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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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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