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	Additional homologs
56	0.001982	0.1223	b2304	yfcH	-16.49	0.008143	193 -- 225	40 -- 77	putative NAD-dependent nucleotide-sugar epimerase		_____________192_________________________________________226\n_____________\|___________________________________________\|\n5'-AAA...AUCGG________AUGA__________________________A____CAGGA...ACC-3'\n______________GAGGCUGC____ACAUAGUGA_________UCAC_CGG_GGGA\n______________:\|\|:\|\|:\|____\|\|\|:\|\|::\|_________\|\|\|\|_\|:\|_\|\|\|\|\n______________UUCUGAUG____UGUGUCGUU_________AGUG_GUC_CCCU\n3'-UUU...CCCGU_____________________AAGCAACAA____A________AAAGG...GCA-5'\n_____________\|___________________________________________\|\n_____________78__________________________________________39\n	206 -- 212	62 -- 68	-29.217 kcal/mol	7.9505 kcal/mol	4.77871 kcal/mol	192 226@LB@ \| \|@LB@5'-AAA...AUCGG AUGA A CAGGA...ACC-3'@LB@ GAGGCUGC ACAUAGUGA UCAC CGG GGGA@LB@ :\|\|:\|\|:\| \|\|\|:\|\|::\| \|\|\|\| \|:\| \|\|\|\|@LB@ UUCUGAUG UGUGUCGUU AGUG GUC CCCU@LB@3'-UUU...CCCGU AAGCAACAA A AAAGG...GCA-5'@LB@ \| \|@LB@ 78 39@LB@@LB@@LB@Energy -16.49 kcal/mol@LB@Hybridization Energy -29.217 kcal/mol@LB@Unfolding Energy - mRNA 7.9505 kcal/mol@LB@Unfolding Energy - sRNA 4.77871 kcal/mol@LB@@LB@Position - mRNA 193 -- 225@LB@Position - sRNA 40 -- 77@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 62 -- 68@LB@
90	0.004009	0.1538	b3152	yraR	-13.99	0.037452	47 -- 72	45 -- 75	putative nucleoside-diphosphate-sugar epimerase		_____________46______________________________73\n_____________\|_______________________________\|\n5'-ACU...UCAGU_____AA___________UC___________UGCUU...CGA-3'\n______________GAUUA___ACGGCAAUUU______UUACUCA\n______________\|\|:\|\|___\|\|:\|\|\|\|\|\|:______\|:\|\|\|\|\|\n______________CUGAU___UGUCGUUAAG______AGUGAGU\n3'-UUU...CGUUU_____GUG__________CAACAA_______CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	66 -- 72	45 -- 51	-19.6514 kcal/mol	1.92306 kcal/mol	3.74078 kcal/mol	46 73@LB@ \| \|@LB@5'-ACU...UCAGU AA UC UGCUU...CGA-3'@LB@ GAUUA ACGGCAAUUU UUACUCA@LB@ \|\|:\|\| \|\|:\|\|\|\|\|\|: \|:\|\|\|\|\|@LB@ CUGAU UGUCGUUAAG AGUGAGU@LB@3'-UUU...CGUUU GUG CAACAA CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -13.99 kcal/mol@LB@Hybridization Energy -19.6514 kcal/mol@LB@Unfolding Energy - mRNA 1.92306 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 47 -- 72@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 66 -- 72@LB@Position Seed - sRNA 45 -- 51@LB@
64	0.002655	0.1417	b0876	ybjD	-10.33	0.215429	171 -- 200	39 -- 78	putative OLD family ATP-dependent endonuclease; DUF2813 family protein		_____________170________________________________________201\n_____________\|__________________________________________\|\n5'-CGU...GCGUA______AAGU_____________________UGG________AUGAU...GGG-3'\n______________AAGGAU____CACAUA___________UUUC____AGGGGAU\n______________\|\|:\|\|:____\|\|\|\|:\|___________\|\|\|\|____\|\|\|\|\|\|\|\n______________UUUCUG____GUGUGU___________AAAG____UCCCCUA\n3'-UUU...ACCCG______AU________CGUUAAGCAAC____UGAG_______AAGGU...GCA-5'\n_____________\|__________________________________________\|\n_____________79_________________________________________38\n	194 -- 200	39 -- 45	-20.0974 kcal/mol	4.99339 kcal/mol	4.77966 kcal/mol	170 201@LB@ \| \|@LB@5'-CGU...GCGUA AAGU UGG AUGAU...GGG-3'@LB@ AAGGAU CACAUA UUUC AGGGGAU@LB@ \|\|:\|\|: \|\|\|\|:\| \|\|\|\| \|\|\|\|\|\|\|@LB@ UUUCUG GUGUGU AAAG UCCCCUA@LB@3'-UUU...ACCCG AU CGUUAAGCAAC UGAG AAGGU...GCA-5'@LB@ \| \|@LB@ 79 38@LB@@LB@@LB@Energy -10.33 kcal/mol@LB@Hybridization Energy -20.0974 kcal/mol@LB@Unfolding Energy - mRNA 4.99339 kcal/mol@LB@Unfolding Energy - sRNA 4.77966 kcal/mol@LB@@LB@Position - mRNA 171 -- 200@LB@Position - sRNA 39 -- 78@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 39 -- 45@LB@
167	0.008121	0.1711	b2603	yfiR	-9.52	0.293133	262 -- 278	35 -- 51	putative periplasmic inhibitor of YfiN activity		_____________261_______________279\n_____________\|_________________\|\n5'-GUA...AAUAC_________A_CC____GACGU...GUA-3'\n______________UCGCUCAGG_G__UUCU\n______________\|\|:\|\|\|\|\|\|_\|__\|\|\|:\n______________AGUGAGUCC_C__AAGG\n3'-UUU...AACAA_________C_UA____UACGA...GCA-5'\n_____________\|_________________\|\n_____________52________________34\n	264 -- 270	43 -- 49	-18.1931 kcal/mol	6.80204 kcal/mol	1.87111 kcal/mol	261 279@LB@ \| \|@LB@5'-GUA...AAUAC A CC GACGU...GUA-3'@LB@ UCGCUCAGG G UUCU@LB@ \|\|:\|\|\|\|\|\| \| \|\|\|:@LB@ AGUGAGUCC C AAGG@LB@3'-UUU...AACAA C UA UACGA...GCA-5'@LB@ \| \|@LB@ 52 34@LB@@LB@@LB@Energy -9.52 kcal/mol@LB@Hybridization Energy -18.1931 kcal/mol@LB@Unfolding Energy - mRNA 6.80204 kcal/mol@LB@Unfolding Energy - sRNA 1.87111 kcal/mol@LB@@LB@Position - mRNA 262 -- 278@LB@Position - sRNA 35 -- 51@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 43 -- 49@LB@
51	0.001671	0.1153	b3527	yhjJ	-13.34	0.053290	153 -- 204	31 -- 75	putative periplasmic M16 family chaperone		_____________152_____________________________________________________205\n_____________\|_______________________________________________________\|\n5'-CUC...UGACC___A___G_____UU___UAUUACCAGGAUA___GA____________CA_____AGGGC...GGC-3'\n______________GAC_ACG_GCAGU__UUU_____________GUU____UCAGGGG_UU__CAUGC\n______________\|\|\|_\|\|:_:\|\|\|:__\|\|:_____________\|\|\|____\|\|\|\|\|\|\|_\|\|__\|\|\|\|\|\n______________CUG_UGU_UGUCG__AAG_____________CAA____AGUCCCC_AA__GUACG\n3'-UUU...CGUUU___A___G_____UU___CAA_____________AGUG_______U__AG_____AAUAU...GCA-5'\n_____________\|_______________________________________________________\|\n_____________76______________________________________________________30\n	189 -- 195	41 -- 47	-32.6504 kcal/mol	12.0549 kcal/mol	7.26183 kcal/mol	152 205@LB@ \| \|@LB@5'-CUC...UGACC A G UU UAUUACCAGGAUA GA CA AGGGC...GGC-3'@LB@ GAC ACG GCAGU UUU GUU UCAGGGG UU CAUGC@LB@ \|\|\| \|\|: :\|\|\|: \|\|: \|\|\| \|\|\|\|\|\|\| \|\| \|\|\|\|\|@LB@ CUG UGU UGUCG AAG CAA AGUCCCC AA GUACG@LB@3'-UUU...CGUUU A G UU CAA AGUG U AG AAUAU...GCA-5'@LB@ \| \|@LB@ 76 30@LB@@LB@@LB@Energy -13.34 kcal/mol@LB@Hybridization Energy -32.6504 kcal/mol@LB@Unfolding Energy - mRNA 12.0549 kcal/mol@LB@Unfolding Energy - sRNA 7.26183 kcal/mol@LB@@LB@Position - mRNA 153 -- 204@LB@Position - sRNA 31 -- 75@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 41 -- 47@LB@
122	0.005462	0.1553	b3143	yraI	-10.36	0.212908	69 -- 81	40 -- 51	putative periplasmic pilin chaperone	b0939 b4316 b0531	_____________68____________82\n_____________\|_____________\|\n5'-GGA...AGAAA____CC_______AGCAG...UGA-3'\n______________UCAC__CAGGGGA\n______________\|\|\|\|__\|\|\|\|\|\|\|\n______________AGUG__GUCCCCU\n3'-UUU...AACAA____A________AAAGG...GCA-5'\n_____________\|_____________\|\n_____________52____________39\n	75 -- 81	40 -- 46	-16.6795 kcal/mol	4.56539 kcal/mol	1.76028 kcal/mol	68 82@LB@ \| \|@LB@5'-GGA...AGAAA CC AGCAG...UGA-3'@LB@ UCAC CAGGGGA@LB@ \|\|\|\| \|\|\|\|\|\|\|@LB@ AGUG GUCCCCU@LB@3'-UUU...AACAA A AAAGG...GCA-5'@LB@ \| \|@LB@ 52 39@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -16.6795 kcal/mol@LB@Unfolding Energy - mRNA 4.56539 kcal/mol@LB@Unfolding Energy - sRNA 1.76028 kcal/mol@LB@@LB@Position - mRNA 69 -- 81@LB@Position - sRNA 40 -- 51@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 40 -- 46@LB@
165	0.007934	0.1692	b3355	prkB	-7.13	0.603515	287 -- 294	63 -- 70	putative phosphoribulokinase		_____________286______295\n_____________\|________\|\n5'-GGC...AUAUU________UAAAUC-3'\n______________CGCGCAGU\n______________\|:\|:\|\|\|:\n______________GUGUGUCG\n3'-UUU...CUGAU________UUAAG...GCA-5'\n_____________\|________\|\n_____________71_______62\n	288 -- 294	63 -- 69	-11.0055 kcal/mol	0.741841 kcal/mol	3.13161 kcal/mol	286 295@LB@ \| \|@LB@5'-GGC...AUAUU UAAAUC-3'@LB@ CGCGCAGU@LB@ \|:\|:\|\|\|:@LB@ GUGUGUCG@LB@3'-UUU...CUGAU UUAAG...GCA-5'@LB@ \| \|@LB@ 71 62@LB@@LB@@LB@Energy -7.13 kcal/mol@LB@Hybridization Energy -11.0055 kcal/mol@LB@Unfolding Energy - mRNA 0.741841 kcal/mol@LB@Unfolding Energy - sRNA 3.13161 kcal/mol@LB@@LB@Position - mRNA 287 -- 294@LB@Position - sRNA 63 -- 70@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 63 -- 69@LB@
158	0.007677	0.1668	b1267	yciO	-9.92	0.252655	228 -- 242	61 -- 75	putative RNA binding protein		_____________227_____________243\n_____________\|_______________\|\n5'-GCG...AUCCU___A__C________CGUCU...CAA-3'\n______________GAU_AC_CACAGCAA\n______________\|\|:_\|\|_\|\|\|\|\|\|\|\|\n______________CUG_UG_GUGUCGUU\n3'-UUU...CGUUU___A__U________AAGCA...GCA-5'\n_____________\|_______________\|\n_____________76______________60\n	236 -- 242	61 -- 67	-14.6343 kcal/mol	1.46218 kcal/mol	3.25399 kcal/mol	227 243@LB@ \| \|@LB@5'-GCG...AUCCU A C CGUCU...CAA-3'@LB@ GAU AC CACAGCAA@LB@ \|\|: \|\| \|\|\|\|\|\|\|\|@LB@ CUG UG GUGUCGUU@LB@3'-UUU...CGUUU A U AAGCA...GCA-5'@LB@ \| \|@LB@ 76 60@LB@@LB@@LB@Energy -9.92 kcal/mol@LB@Hybridization Energy -14.6343 kcal/mol@LB@Unfolding Energy - mRNA 1.46218 kcal/mol@LB@Unfolding Energy - sRNA 3.25399 kcal/mol@LB@@LB@Position - mRNA 228 -- 242@LB@Position - sRNA 61 -- 75@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 61 -- 67@LB@
171	0.008374	0.1723	b4485	ytfR	-15.31	0.017344	177 -- 203	32 -- 71	putative sugar ABC transporter ATPase		_____________176_______________________________________204\n_____________\|_________________________________________\|\n5'-CCU...UGGGA_____________________A___________AA______ACGAC...GCC-3'\n______________GCACGC____________UUU_CAC_CGGGGGA___CCAUG\n______________:\|\|\|:\|____________\|\|\|_\|\|\|_\|:\|\|\|\|\|___\|\|\|\|\|\n______________UGUGUG____________AAA_GUG_GUCCCCU___GGUAC\n3'-UUU...UCUGA______UCGUUAAGCAAC_______A_______AAA_____GAAUA...GCA-5'\n_____________\|_________________________________________\|\n_____________72________________________________________31\n	190 -- 196	40 -- 46	-27.8319 kcal/mol	5.2959 kcal/mol	7.22604 kcal/mol	176 204@LB@ \| \|@LB@5'-CCU...UGGGA A AA ACGAC...GCC-3'@LB@ GCACGC UUU CAC CGGGGGA CCAUG@LB@ :\|\|\|:\| \|\|\| \|\|\| \|:\|\|\|\|\| \|\|\|\|\|@LB@ UGUGUG AAA GUG GUCCCCU GGUAC@LB@3'-UUU...UCUGA UCGUUAAGCAAC A AAA GAAUA...GCA-5'@LB@ \| \|@LB@ 72 31@LB@@LB@@LB@Energy -15.31 kcal/mol@LB@Hybridization Energy -27.8319 kcal/mol@LB@Unfolding Energy - mRNA 5.2959 kcal/mol@LB@Unfolding Energy - sRNA 7.22604 kcal/mol@LB@@LB@Position - mRNA 177 -- 203@LB@Position - sRNA 32 -- 71@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 40 -- 46@LB@
83	0.003448	0.1462	b4231	yjfF	-16.06	0.010834	60 -- 72	39 -- 51	putative sugar ABC transporter permease		_____________59____________73\n_____________\|_____________\|\n5'-CGG...GCUGA_____________GAACA...GAG-3'\n______________UUAUUCAGGGGAU\n______________\|:\|:\|\|\|\|\|\|\|\|\|\n______________AGUGAGUCCCCUA\n3'-UUU...AACAA_____________AAGGU...GCA-5'\n_____________\|_____________\|\n_____________52____________38\n	66 -- 72	39 -- 45	-20.8743 kcal/mol	3.02031 kcal/mol	1.79807 kcal/mol	59 73@LB@ \| \|@LB@5'-CGG...GCUGA GAACA...GAG-3'@LB@ UUAUUCAGGGGAU@LB@ \|:\|:\|\|\|\|\|\|\|\|\|@LB@ AGUGAGUCCCCUA@LB@3'-UUU...AACAA AAGGU...GCA-5'@LB@ \| \|@LB@ 52 38@LB@@LB@@LB@Energy -16.06 kcal/mol@LB@Hybridization Energy -20.8743 kcal/mol@LB@Unfolding Energy - mRNA 3.02031 kcal/mol@LB@Unfolding Energy - sRNA 1.79807 kcal/mol@LB@@LB@Position - mRNA 60 -- 72@LB@Position - sRNA 39 -- 51@LB@Position Seed - mRNA 66 -- 72@LB@Position Seed - sRNA 39 -- 45@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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