Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
51	0.0006491	0.04477	b3224	nanT	-16.25	0.000177	140 -- 151	1 -- 12	sialic acid transporter	b4279	_____________139__________152\n_____________\|____________\|\n5'-CGC...ACGCA____________AAUUU...GUU-3'\n______________UCUGUACCCUAC\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________AGACAUGGGAUG\n3'-AUU...AAUGG____________-5'\n_____________\|___________\|\n_____________13__________1\n	145 -- 151	1 -- 7	-21.6524 kcal/mol	1.93745 kcal/mol	3.49051 kcal/mol	139 152@LB@ \| \|@LB@5'-CGC...ACGCA AAUUU...GUU-3'@LB@ UCUGUACCCUAC@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ AGACAUGGGAUG@LB@3'-AUU...AAUGG -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -16.25 kcal/mol@LB@Hybridization Energy -21.6524 kcal/mol@LB@Unfolding Energy - mRNA 1.93745 kcal/mol@LB@Unfolding Energy - sRNA 3.49051 kcal/mol@LB@@LB@Position - mRNA 140 -- 151@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 1 -- 7@LB@
52	0.0006736	0.04557	b3964	yijD	-9.23	0.074829	177 -- 192	43 -- 57	DUF1422 family inner membrane protein		_____________176______________193\n_____________\|________________\|\n5'-ACU...AUUAU_____GAA________GACGA...UGC-3'\n______________UCCGG___AUGUGAAG\n______________\|\|\|\|:___\|:\|\|\|\|\|\|\n______________AGGCU___UGCACUUC\n3'-AUU...GGUUU_____AA_________AUUUU...AUG-5'\n_____________\|________________\|\n_____________58_______________42\n	186 -- 192	43 -- 49	-16.7307 kcal/mol	4.24116 kcal/mol	3.27382 kcal/mol	176 193@LB@ \| \|@LB@5'-ACU...AUUAU GAA GACGA...UGC-3'@LB@ UCCGG AUGUGAAG@LB@ \|\|\|\|: \|:\|\|\|\|\|\|@LB@ AGGCU UGCACUUC@LB@3'-AUU...GGUUU AA AUUUU...AUG-5'@LB@ \| \|@LB@ 58 42@LB@@LB@@LB@Energy -9.23 kcal/mol@LB@Hybridization Energy -16.7307 kcal/mol@LB@Unfolding Energy - mRNA 4.24116 kcal/mol@LB@Unfolding Energy - sRNA 3.27382 kcal/mol@LB@@LB@Position - mRNA 177 -- 192@LB@Position - sRNA 43 -- 57@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 43 -- 49@LB@
53	0.0007581	0.04961	b1302	puuE	-16.93	0.000076	166 -- 207	20 -- 57	4-aminobutyrate aminotransferase PLP-dependent	b2662	_____________165_________________________________________208\n_____________\|___________________________________________\|\n5'-AGC...UAAUU________AC_______AGUC_______G_____C________ACAAU...CGC-3'\n______________UCCGAUUA__CGUGAAG____AAAAGGU_UGAAA_AU_GAGCA\n______________\|\|\|\|\|\|\|\|__\|\|\|\|\|\|\|____\|\|\|\|\|\|\|_\|\|\|\|\|_\|\|_\|\|:\|\|\n______________AGGCUAAU__GCACUUC____UUUUCCA_ACUUU_UA_CUUGU\n3'-AUU...GGUUU_________________A__________G_____C__U_____AGAAU...AUG-5'\n_____________\|___________________________________________\|\n_____________58__________________________________________19\n	176 -- 182	43 -- 49	-36.956 kcal/mol	7.85943 kcal/mol	12.1551 kcal/mol	165 208@LB@ \| \|@LB@5'-AGC...UAAUU AC AGUC G C ACAAU...CGC-3'@LB@ UCCGAUUA CGUGAAG AAAAGGU UGAAA AU GAGCA@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\| \|\| \|\|:\|\|@LB@ AGGCUAAU GCACUUC UUUUCCA ACUUU UA CUUGU@LB@3'-AUU...GGUUU A G C U AGAAU...AUG-5'@LB@ \| \|@LB@ 58 19@LB@@LB@@LB@Energy -16.93 kcal/mol@LB@Hybridization Energy -36.956 kcal/mol@LB@Unfolding Energy - mRNA 7.85943 kcal/mol@LB@Unfolding Energy - sRNA 12.1551 kcal/mol@LB@@LB@Position - mRNA 166 -- 207@LB@Position - sRNA 20 -- 57@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 43 -- 49@LB@
54	0.0007615	0.04961	b0313	betI	-7.44	0.209816	47 -- 68	32 -- 57	choline-inducible betIBA-betT divergent operon transcriptional repressor		_____________46_________________________69\n_____________\|__________________________\|\n5'-CAG...CCUUU___C________U_____________UCAUC...CGC-3'\n______________UCC___UGC_UG__GUGAAAGGUCUG\n______________\|\|\|___\|:\|_\|\|__\|\|:\|\|\|\|\|\|\|\|\|\n______________AGG___AUG_AC__CAUUUUCCAGAC\n3'-AUU...GGUUU___CUA___C__UU____________UUUCU...AUG-5'\n_____________\|__________________________\|\n_____________58_________________________31\n	62 -- 68	32 -- 38	-22.1015 kcal/mol	6.64828 kcal/mol	7.92091 kcal/mol	46 69@LB@ \| \|@LB@5'-CAG...CCUUU C U UCAUC...CGC-3'@LB@ UCC UGC UG GUGAAAGGUCUG@LB@ \|\|\| \|:\| \|\| \|\|:\|\|\|\|\|\|\|\|\|@LB@ AGG AUG AC CAUUUUCCAGAC@LB@3'-AUU...GGUUU CUA C UU UUUCU...AUG-5'@LB@ \| \|@LB@ 58 31@LB@@LB@@LB@Energy -7.44 kcal/mol@LB@Hybridization Energy -22.1015 kcal/mol@LB@Unfolding Energy - mRNA 6.64828 kcal/mol@LB@Unfolding Energy - sRNA 7.92091 kcal/mol@LB@@LB@Position - mRNA 47 -- 68@LB@Position - sRNA 32 -- 57@LB@Position Seed - mRNA 62 -- 68@LB@Position Seed - sRNA 32 -- 38@LB@
55	0.0008105	0.05184	b3262	yhdJ	-10.49	0.032282	53 -- 83	1 -- 34	DNA adenine methyltransferase SAM-dependent		_____________52_________________________________84\n_____________\|__________________________________\|\n5'-CCU...CUGCG____U____________A____GUG____G____GUAAA...GUG-3'\n______________CUGA__GAU_GGGCAUC__ACC___GUAC_CUGC\n______________\|\|\|\|__\|\|\|_\|::\|\|\|\|__\|\|\|___\|\|\|\|_\|\|:\|\n______________GACU__CUA_CUUGUAG__UGG___CAUG_GAUG\n3'-AUU...UUCCA____UU___U_______AA___AGA____G____-5'\n_____________\|_________________________________\|\n_____________35________________________________1\n	61 -- 67	18 -- 24	-29.8286 kcal/mol	10.2122 kcal/mol	9.14469 kcal/mol	52 84@LB@ \| \|@LB@5'-CCU...CUGCG U A GUG G GUAAA...GUG-3'@LB@ CUGA GAU GGGCAUC ACC GUAC CUGC@LB@ \|\|\|\| \|\|\| \|::\|\|\|\| \|\|\| \|\|\|\| \|\|:\|@LB@ GACU CUA CUUGUAG UGG CAUG GAUG@LB@3'-AUU...UUCCA UU U AA AGA G -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -10.49 kcal/mol@LB@Hybridization Energy -29.8286 kcal/mol@LB@Unfolding Energy - mRNA 10.2122 kcal/mol@LB@Unfolding Energy - sRNA 9.14469 kcal/mol@LB@@LB@Position - mRNA 53 -- 83@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 61 -- 67@LB@Position Seed - sRNA 18 -- 24@LB@
56	0.0008344	0.05242	b3651	trmH	-7.19	0.238334	68 -- 84	17 -- 32	tRNA mG18-2'-O-methyltransferase SAM-dependent		_____________67________________85\n_____________\|_________________\|\n5'-CGC...GAAGA_________UC______ACAGC...UUU-3'\n______________GAAAGAUGG__GCGUCU\n______________\|\|\|\|\|\|\|:\|__:\|:\|\|\|\n______________CUUUCUAUC__UGUAGA\n3'-AUU...CCAGA_________U_______AUGGA...AUG-5'\n_____________\|_________________\|\n_____________33________________16\n	70 -- 76	24 -- 30	-18.3937 kcal/mol	6.9506 kcal/mol	4.26839 kcal/mol	67 85@LB@ \| \|@LB@5'-CGC...GAAGA UC ACAGC...UUU-3'@LB@ GAAAGAUGG GCGUCU@LB@ \|\|\|\|\|\|\|:\| :\|:\|\|\|@LB@ CUUUCUAUC UGUAGA@LB@3'-AUU...CCAGA U AUGGA...AUG-5'@LB@ \| \|@LB@ 33 16@LB@@LB@@LB@Energy -7.19 kcal/mol@LB@Hybridization Energy -18.3937 kcal/mol@LB@Unfolding Energy - mRNA 6.9506 kcal/mol@LB@Unfolding Energy - sRNA 4.26839 kcal/mol@LB@@LB@Position - mRNA 68 -- 84@LB@Position - sRNA 17 -- 32@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 24 -- 30@LB@
57	0.0008523	0.0526	b3281	aroE	-7.63	0.189523	225 -- 232	52 -- 59	dehydroshikimate reductase NAD(P)-binding		_____________224______233\n_____________\|________\|\n5'-UUU...UUGGU________AGCCC...AUG-3'\n______________AAUCCGAU\n______________\|\|\|\|\|\|\|\|\n______________UUAGGCUA\n3'-AUU...UCGGU________AUGCA...AUG-5'\n_____________\|________\|\n_____________60_______51\n	226 -- 232	52 -- 58	-9.52512 kcal/mol	1.61129 kcal/mol	0.296943 kcal/mol	224 233@LB@ \| \|@LB@5'-UUU...UUGGU AGCCC...AUG-3'@LB@ AAUCCGAU@LB@ \|\|\|\|\|\|\|\|@LB@ UUAGGCUA@LB@3'-AUU...UCGGU AUGCA...AUG-5'@LB@ \| \|@LB@ 60 51@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -9.52512 kcal/mol@LB@Unfolding Energy - mRNA 1.61129 kcal/mol@LB@Unfolding Energy - sRNA 0.296943 kcal/mol@LB@@LB@Position - mRNA 225 -- 232@LB@Position - sRNA 52 -- 59@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 52 -- 58@LB@
58	0.000878	0.0531	b2150	mglB	-10.24	0.038484	153 -- 179	1 -- 24	methyl-galactoside transporter subunit		_____________152__________________________180\n_____________\|____________________________\|\n5'-GUA...CCGCC______________AAGCAC________AUAAG...AUA-3'\n______________GAGCAUU_UAUCUC______UACCCUGC\n______________\|\|:\|\|\|:_\|\|:\|\|\|______\|\|\|\|\|\|:\|\n______________CUUGUAG_AUGGAG______AUGGGAUG\n3'-AUU...UCUAU_______A______AC____________-5'\n_____________\|___________________________\|\n_____________25__________________________1\n	173 -- 179	1 -- 7	-24.5136 kcal/mol	6.27388 kcal/mol	8.02158 kcal/mol	152 180@LB@ \| \|@LB@5'-GUA...CCGCC AAGCAC AUAAG...AUA-3'@LB@ GAGCAUU UAUCUC UACCCUGC@LB@ \|\|:\|\|\|: \|\|:\|\|\| \|\|\|\|\|\|:\|@LB@ CUUGUAG AUGGAG AUGGGAUG@LB@3'-AUU...UCUAU A AC -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -24.5136 kcal/mol@LB@Unfolding Energy - mRNA 6.27388 kcal/mol@LB@Unfolding Energy - sRNA 8.02158 kcal/mol@LB@@LB@Position - mRNA 153 -- 179@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 1 -- 7@LB@
59	0.0008996	0.0531	b1310	ycjN	-10.87	0.024752	113 -- 129	42 -- 59	putative ABC sugar transporter periplasmic binding protein		_____________112________________130\n_____________\|__________________\|\n5'-UUC...GUCGG__________________UGAUA...UUA-3'\n______________GAUCUGAUUA_GUGAAGU\n______________:\|\|\|:\|\|\|\|\|_\|\|\|\|\|\|\|\n______________UUAGGCUAAU_CACUUCA\n3'-AUU...UCGGU__________G_______UUUUC...AUG-5'\n_____________\|__________________\|\n_____________60_________________41\n	123 -- 129	42 -- 48	-20.0101 kcal/mol	5.87569 kcal/mol	3.27976 kcal/mol	112 130@LB@ \| \|@LB@5'-UUC...GUCGG UGAUA...UUA-3'@LB@ GAUCUGAUUA GUGAAGU@LB@ :\|\|\|:\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UUAGGCUAAU CACUUCA@LB@3'-AUU...UCGGU G UUUUC...AUG-5'@LB@ \| \|@LB@ 60 41@LB@@LB@@LB@Energy -10.87 kcal/mol@LB@Hybridization Energy -20.0101 kcal/mol@LB@Unfolding Energy - mRNA 5.87569 kcal/mol@LB@Unfolding Energy - sRNA 3.27976 kcal/mol@LB@@LB@Position - mRNA 113 -- 129@LB@Position - sRNA 42 -- 59@LB@Position Seed - mRNA 123 -- 129@LB@Position Seed - sRNA 42 -- 48@LB@
60	0.0009057	0.0531	b2740	ygbN	-7.72	0.181404	16 -- 72	3 -- 58	putative transporter		_____________15__________________________________________________________73\n_____________\|___________________________________________________________\|\n5'-GUG...CGCCU_______G_G_____A__UC___G_____UC___UGU______AA__________G___CACCG...UCC-3'\n______________GUUCGAU_A_GUGGG_UA__AGG_CUGGA__GGU___GAAUAU___ACCUC_GUG_CCU\n______________:\|:\|\|\|\|_\|_\|\|\|::_\|\|__\|\|\|_\|\|\|:\|__\|:\|___\|\|\|:\|\|___\|\|\|\|\|_\|\|:_\|\|\|\n______________UAGGCUA_U_CACUU_AU__UCC_GACUU__CUA___CUUGUA___UGGAG_CAU_GGA\n3'-AUU...CGGUU_______A_G_____C__UU___A_____U____U________GAA_____A___G___UG-5'\n_____________\|___________________________________________________________\|\n_____________59__________________________________________________________2\n	16 -- 22	52 -- 58	-40.891 kcal/mol	20.495 kcal/mol	12.7026 kcal/mol	15 73@LB@ \| \|@LB@5'-GUG...CGCCU G G A UC G UC UGU AA G CACCG...UCC-3'@LB@ GUUCGAU A GUGGG UA AGG CUGGA GGU GAAUAU ACCUC GUG CCU@LB@ :\|:\|\|\|\| \| \|\|\|:: \|\| \|\|\| \|\|\|:\| \|:\| \|\|\|:\|\| \|\|\|\|\| \|\|: \|\|\|@LB@ UAGGCUA U CACUU AU UCC GACUU CUA CUUGUA UGGAG CAU GGA@LB@3'-AUU...CGGUU A G C UU A U U GAA A G UG-5'@LB@ \| \|@LB@ 59 2@LB@@LB@@LB@Energy -7.72 kcal/mol@LB@Hybridization Energy -40.891 kcal/mol@LB@Unfolding Energy - mRNA 20.495 kcal/mol@LB@Unfolding Energy - sRNA 12.7026 kcal/mol@LB@@LB@Position - mRNA 16 -- 72@LB@Position - sRNA 3 -- 58@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 52 -- 58@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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