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
81	0.003429	0.1462	b0413	nrdR	-16.32	0.009130	136 -- 177	33 -- 64	Nrd regulon repressor	_____________135_________________________________________178\n_____________\|___________________________________________\|\n5'-AGG...GUUGC__C_________A___UCAG_______UAAAAUA_________UAACC...UGU-3'\n______________GC__UUUGUUGU_UCG____UUCAGGG_______GAUUUCCGU\n______________\|\|__\|\|:\|\|\|\|\|_\|\|:____:\|\|\|\|\|\|_______\|\|\|\|\|\|\|:\|\n______________CG__AAGCAACA_AGU____GAGUCCC_______CUAAAGGUA\n3'-UUU...UGUGU__UU________A______________________________CGAAU...GCA-5'\n_____________\|___________________________________________\|\n_____________65__________________________________________32\n	171 -- 177	33 -- 39	-28.4719 kcal/mol	7.3911 kcal/mol	4.76435 kcal/mol	135 178@LB@ \| \|@LB@5'-AGG...GUUGC C A UCAG UAAAAUA UAACC...UGU-3'@LB@ GC UUUGUUGU UCG UUCAGGG GAUUUCCGU@LB@ \|\| \|\|:\|\|\|\|\| \|\|: :\|\|\|\|\|\| \|\|\|\|\|\|\|:\|@LB@ CG AAGCAACA AGU GAGUCCC CUAAAGGUA@LB@3'-UUU...UGUGU UU A CGAAU...GCA-5'@LB@ \| \|@LB@ 65 32@LB@@LB@@LB@Energy -16.32 kcal/mol@LB@Hybridization Energy -28.4719 kcal/mol@LB@Unfolding Energy - mRNA 7.3911 kcal/mol@LB@Unfolding Energy - sRNA 4.76435 kcal/mol@LB@@LB@Position - mRNA 136 -- 177@LB@Position - sRNA 33 -- 64@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 33 -- 39@LB@
82	0.00343	0.1462	b4043	lexA	-10.80	0.176998	163 -- 196	40 -- 72	transcriptional repressor of SOS regulon	_____________162________________________________197\n_____________\|__________________________________\|\n5'-CGC...GUAUA___U_______UAAC___AUAUA___C_______CGGAA...AGC-3'\n______________UAC_CACAGCA____UGU_____CAC_CAGGGGG\n______________\|\|\|_\|\|\|\|\|\|\|____:\|\|_____\|\|\|_\|\|\|\|\|\|:\n______________AUG_GUGUCGU____GCA_____GUG_GUCCCCU\n3'-UUU...UUCUG___U_______UAA____ACAAA___A_______AAAGG...GCA-5'\n_____________\|__________________________________\|\n_____________73_________________________________39\n	190 -- 196	40 -- 46	-30.123 kcal/mol	14.5591 kcal/mol	4.76217 kcal/mol	162 197@LB@ \| \|@LB@5'-CGC...GUAUA U UAAC AUAUA C CGGAA...AGC-3'@LB@ UAC CACAGCA UGU CAC CAGGGGG@LB@ \|\|\| \|\|\|\|\|\|\| :\|\| \|\|\| \|\|\|\|\|\|:@LB@ AUG GUGUCGU GCA GUG GUCCCCU@LB@3'-UUU...UUCUG U UAA ACAAA A AAAGG...GCA-5'@LB@ \| \|@LB@ 73 39@LB@@LB@@LB@Energy -10.80 kcal/mol@LB@Hybridization Energy -30.123 kcal/mol@LB@Unfolding Energy - mRNA 14.5591 kcal/mol@LB@Unfolding Energy - sRNA 4.76217 kcal/mol@LB@@LB@Position - mRNA 163 -- 196@LB@Position - sRNA 40 -- 72@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@
84	0.003656	0.1509	b0827	moeA	-7.84	0.503176	157 -- 203	32 -- 75	molybdopterin molybdenumtransferase; molybdopterin biosynthesis protein	_____________156_______________________________________________204\n_____________\|_________________________________________________\|\n5'-AUU...UUUCU_______AUA___A______AUU___CC____G____A_U_________GAAUU...UAC-3'\n______________GAC_AUA___GGC_AAUUCG___UUG__UC_C_CAGG_G_GUUUUCAUG\n______________\|\|\|_\|:\|___:\|\|_\|\|\|\|\|\|___\|\|\|__\|\|_\|_\|\|\|\|_\|_:\|\|\|:\|\|\|\|\n______________CUG_UGU___UCG_UUAAGC___AAC__AG_G_GUCC_C_UAAAGGUAC\n3'-UUU...CGUUU___A___GUG________________AA__U_A______C_________GAAUA...GCA-5'\n_____________\|_________________________________________________\|\n_____________76________________________________________________31\n	197 -- 203	32 -- 38	-28.9008 kcal/mol	13.8106 kcal/mol	7.24967 kcal/mol	156 204@LB@ \| \|@LB@5'-AUU...UUUCU AUA A AUU CC G A U GAAUU...UAC-3'@LB@ GAC AUA GGC AAUUCG UUG UC C CAGG G GUUUUCAUG@LB@ \|\|\| \|:\| :\|\| \|\|\|\|\|\| \|\|\| \|\| \| \|\|\|\| \| :\|\|\|:\|\|\|\|@LB@ CUG UGU UCG UUAAGC AAC AG G GUCC C UAAAGGUAC@LB@3'-UUU...CGUUU A GUG AA U A C GAAUA...GCA-5'@LB@ \| \|@LB@ 76 31@LB@@LB@@LB@Energy -7.84 kcal/mol@LB@Hybridization Energy -28.9008 kcal/mol@LB@Unfolding Energy - mRNA 13.8106 kcal/mol@LB@Unfolding Energy - sRNA 7.24967 kcal/mol@LB@@LB@Position - mRNA 157 -- 203@LB@Position - sRNA 32 -- 75@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 32 -- 38@LB@
85	0.003677	0.1509	b0813	rhtA	-9.71	0.273689	106 -- 123	34 -- 46	threonine and homoserine efflux system	_____________105________________124\n_____________\|__________________\|\n5'-CAG...CAAAA_______AAAUU______ACAAA...CAC-3'\n______________CGGGGGA_____UUUUCA\n______________\|:\|\|\|\|\|_____\|\|\|:\|\|\n______________GUCCCCU_____AAAGGU\n3'-UUU...AGUGA__________________ACGAA...GCA-5'\n_____________\|__________________\|\n_____________47_________________33\n	106 -- 112	40 -- 46	-14.6812 kcal/mol	3.4305 kcal/mol	1.54427 kcal/mol	105 124@LB@ \| \|@LB@5'-CAG...CAAAA AAAUU ACAAA...CAC-3'@LB@ CGGGGGA UUUUCA@LB@ \|:\|\|\|\|\| \|\|\|:\|\|@LB@ GUCCCCU AAAGGU@LB@3'-UUU...AGUGA ACGAA...GCA-5'@LB@ \| \|@LB@ 47 33@LB@@LB@@LB@Energy -9.71 kcal/mol@LB@Hybridization Energy -14.6812 kcal/mol@LB@Unfolding Energy - mRNA 3.4305 kcal/mol@LB@Unfolding Energy - sRNA 1.54427 kcal/mol@LB@@LB@Position - mRNA 106 -- 123@LB@Position - sRNA 34 -- 46@LB@Position Seed - mRNA 106 -- 112@LB@Position Seed - sRNA 40 -- 46@LB@
86	0.003687	0.1509	b0774	bioA	-10.95	0.166636	92 -- 152	44 -- 98	7 8-diaminopelargonic acid synthase PLP-dependent	_____________91_____________________________________________________________153\n_____________\|______________________________________________________________\|\n5'-ACG...ACAAU_____G______C____A__CAU______UCUCCAAA___U__UU_________A_______UGUAG...AAG-3'\n______________GUCCA_CGUGGG_GGUG_GC___GGGGCU________ACG_GU__UUUGUUGUU__AUUCGG\n______________\|:\|\|\|_\|\|\|\|\|\|_\|:\|\|_\|\|___::\|:\|\|________\|\|:_\|:__\|\|:\|\|\|\|\|\|__\|:\|\|:\|\n______________CGGGU_GCACCC_CUAC_CG___UUCUGA________UGU_CG__AAGCAACAA__UGAGUC\n____3'-UUUUUUU_____A______U____C__U________UGUG__________UU_________AG______CCCUA...GCA-5'\n_____________\|______________________________________________________________\|\n_____________99_____________________________________________________________43\n	139 -- 145	52 -- 58	-48.0349 kcal/mol	20.1482 kcal/mol	16.9429 kcal/mol	91 153@LB@ \| \|@LB@5'-ACG...ACAAU G C A CAU UCUCCAAA U UU A UGUAG...AAG-3'@LB@ GUCCA CGUGGG GGUG GC GGGGCU ACG GU UUUGUUGUU AUUCGG@LB@ \|:\|\|\| \|\|\|\|\|\| \|:\|\| \|\| ::\|:\|\| \|\|: \|: \|\|:\|\|\|\|\|\| \|:\|\|:\|@LB@ CGGGU GCACCC CUAC CG UUCUGA UGU CG AAGCAACAA UGAGUC@LB@ 3'-UUUUUUU A U C U UGUG UU AG CCCUA...GCA-5'@LB@ \| \|@LB@ 99 43@LB@@LB@@LB@Energy -10.95 kcal/mol@LB@Hybridization Energy -48.0349 kcal/mol@LB@Unfolding Energy - mRNA 20.1482 kcal/mol@LB@Unfolding Energy - sRNA 16.9429 kcal/mol@LB@@LB@Position - mRNA 92 -- 152@LB@Position - sRNA 44 -- 98@LB@Position Seed - mRNA 139 -- 145@LB@Position Seed - sRNA 52 -- 58@LB@
87	0.003844	0.1538	b3124	garK	-12.12	0.097757	2 -- 34	58 -- 88	glycerate kinase I	_____________1_________________________________35\n_____________\|_________________________________\|\n__________5'-U_______AU_____C______A____A______AGGAA...AUG-3'\n______________GGAGAUG__GCAGG_ACUGCG_GCAG_UGGUUU\n______________\|\|\|\|\|\|\|__\|\|\|::_\|\|\|:\|:_:\|\|\|_:::\|\|:\n______________CCUCUAC__CGUUU_UGAUGU_UGUC_GUUAAG\n3'-UUU...AGCAC_______C______C______G___________CAACA...GCA-5'\n_____________\|_________________________________\|\n_____________89________________________________57\n	2 -- 8	82 -- 88	-28.4892 kcal/mol	6.08629 kcal/mol	10.2803 kcal/mol	1 35@LB@ \| \|@LB@ 5'-U AU C A A AGGAA...AUG-3'@LB@ GGAGAUG GCAGG ACUGCG GCAG UGGUUU@LB@ \|\|\|\|\|\|\| \|\|\|:: \|\|\|:\|: :\|\|\| :::\|\|:@LB@ CCUCUAC CGUUU UGAUGU UGUC GUUAAG@LB@3'-UUU...AGCAC C C G CAACA...GCA-5'@LB@ \| \|@LB@ 89 57@LB@@LB@@LB@Energy -12.12 kcal/mol@LB@Hybridization Energy -28.4892 kcal/mol@LB@Unfolding Energy - mRNA 6.08629 kcal/mol@LB@Unfolding Energy - sRNA 10.2803 kcal/mol@LB@@LB@Position - mRNA 2 -- 34@LB@Position - sRNA 58 -- 88@LB@Position Seed - mRNA 2 -- 8@LB@Position Seed - sRNA 82 -- 88@LB@
88	0.003962	0.1538	b3084	rlmG	-11.78	0.115170	185 -- 197	40 -- 51	23S rRNA m(2)G1835 methyltransferase SAM-dependent	_____________184___________198\n_____________\|_____________\|\n5'-UGU...UUUUA_________A___CCGAU...AAU-3'\n______________UCAUUCAGG_GGG\n______________\|\|\|:\|\|\|\|\|_\|\|:\n______________AGUGAGUCC_CCU\n3'-UUU...AACAA_____________AAAGG...GCA-5'\n_____________\|_____________\|\n_____________52____________39\n	187 -- 193	43 -- 49	-16.9089 kcal/mol	3.37488 kcal/mol	1.76028 kcal/mol	184 198@LB@ \| \|@LB@5'-UGU...UUUUA A CCGAU...AAU-3'@LB@ UCAUUCAGG GGG@LB@ \|\|\|:\|\|\|\|\| \|\|:@LB@ AGUGAGUCC CCU@LB@3'-UUU...AACAA AAAGG...GCA-5'@LB@ \| \|@LB@ 52 39@LB@@LB@@LB@Energy -11.78 kcal/mol@LB@Hybridization Energy -16.9089 kcal/mol@LB@Unfolding Energy - mRNA 3.37488 kcal/mol@LB@Unfolding Energy - sRNA 1.76028 kcal/mol@LB@@LB@Position - mRNA 185 -- 197@LB@Position - sRNA 40 -- 51@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 43 -- 49@LB@
89	0.003963	0.1538	b1252	tonB	-10.58	0.194225	25 -- 43	64 -- 82	membrane spanning protein in TonB-ExbB-ExbD transport complex	_____________24___________________44\n_____________\|____________________\|\n5'-AGU...UGAAA_________U__________AAAGA...AUC-3'\n______________GGGCGAAGA_CUGCA_ACGG\n______________\|\|\|\|:\|\|\|\|_\|\|:\|\|_\|\|:\|\n______________CCCGUUUCU_GAUGU_UGUC\n3'-UUU...CUCUA_______________G____GUUAA...GCA-5'\n_____________\|____________________\|\n_____________83___________________63\n	25 -- 31	76 -- 82	-25.6168 kcal/mol	4.83236 kcal/mol	10.2054 kcal/mol	24 44@LB@ \| \|@LB@5'-AGU...UGAAA U AAAGA...AUC-3'@LB@ GGGCGAAGA CUGCA ACGG@LB@ \|\|\|\|:\|\|\|\| \|\|:\|\| \|\|:\|@LB@ CCCGUUUCU GAUGU UGUC@LB@3'-UUU...CUCUA G GUUAA...GCA-5'@LB@ \| \|@LB@ 83 63@LB@@LB@@LB@Energy -10.58 kcal/mol@LB@Hybridization Energy -25.6168 kcal/mol@LB@Unfolding Energy - mRNA 4.83236 kcal/mol@LB@Unfolding Energy - sRNA 10.2054 kcal/mol@LB@@LB@Position - mRNA 25 -- 43@LB@Position - sRNA 64 -- 82@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 76 -- 82@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@

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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